Bacteria doi: 10.3390/bacteria5020035

Authors: Jing Feng Dandan Liu Wei Xiao Peijie Fu Juanli Cheng Jinshui Lin

Pseudomonas aeruginosa, an opportunistic pathogen, is a major threat to hospital infection control and global public health due to its strong environmental adaptability, complex virulence systems, efficient biofilm formation capability, and widespread multidrug resistance. Traditional single-target antibiotics are often inadequate for clinical treatment. The research into Plant-Derived Bioactive Compounds for combating P. aeruginosa infections is reviewed, highlighting their advantages (many of which are extensively studied in Traditional Chinese Medicine) over conventional antibiotics. The antimicrobial mechanisms of these compounds include the inhibition of bacterial quorum sensing (QS) systems to suppress virulence factor expression rather than direct anti-bactericidal effects, delaying the development of resistance. The abundant natural medicinal plants and their diverse chemical structures provide ample material for active compound screening to identify unique chemical compositions with specific binding to pathogen targets. Plant-Derived Bioactive Compounds exhibit excellent safety profiles, targeting bacterial-specific pathways or host immune regulation, resulting in minimal off-target toxicity. Plant-Derived Bioactive Compounds exert anti-P. aeruginosa effects via inhibition of QS systems to reduce pathogenicity by disrupting intercellular signaling, suppressing biofilm formation/maturity to overcome biofilm-associated resistance, directly interacting with bacterial structure. Plant-Derived Bioactive Compounds are promising treatments for drug-resistant P. aeruginosa infections, providing lead compounds for novel anti-infective drug development.

Bacteria doi: 10.3390/bacteria5020034

Authors: Safoura Moradkasani Fahimeh Bagheri Amiri Saber Esmaeili

Background: The rapid rise in antimicrobial resistance (AMR) represents one of the most pressing global health challenges of the 21st century, threatening antibiotic effectiveness, compromising clinical outcomes, and undermining healthcare systems. Understanding how resistant pathogens emerge and spread across human, animal, and environmental sectors is essential for effective global response. Main body: This review evaluates traditional and advanced AMR detection methodologies, including phenotypic assays, molecular diagnostics, whole-genome sequencing (WGS), metagenomics, and biosensor-based technologies. It also highlights the role of bioinformatics tools, surveillance databases, and integrated platforms that support real-time analysis. Genomic surveillance provides unparalleled resolution for characterizing resistance mechanisms, transmission patterns, and evolutionary trajectories of multidrug-resistant organisms. Techniques such as WGS and metagenomics allow timely and precise identification of resistance genes, improving outbreak detection and strengthening antimicrobial stewardship. Despite these advantages, the adoption of genomic surveillance faces barriers in low- and middle-income countries, including high costs, limited infrastructure, insufficient technical expertise, and the lack of standardized data frameworks. Conclusions: Genomic surveillance is a transformative tool for combating AMR and strengthening global health systems. Effective implementation requires sustained investment, capacity-building, coordinated cross-sector collaboration, and commitment to the One Health approach to ensure equitable access and long-term global impact.

Bacteria doi: 10.3390/bacteria5020033

Authors: Rima Jaafar Nawal Al Hakawati Nathalie Hayeck Julnar Usta Jamilah Borjac

L. angustifolia is a perennial shrub native to the Mediterranean region with multiple medicinal properties. In this study, we report on the chemical composition of L. angustifolia essential oil (LEO), its antibacterial, antibiofilm, and antioxidant activities against ten clinical isolates. Chemical constituents of LEO were identified using Gas Chromatography-Mass Spectrometry (GC–MS). Its antibacterial activity was evaluated in vitro against Gram-positive and Gram-negative bacteria using disk diffusion and broth microdilution methods. A growth inhibition assay was performed to determine the bacterial growth spectrophotometrically. The antibiofilm activity was assessed using a Crystal Violet assay. Finally, the activities of oxidative stress indicators, including Superoxide dismutase (SOD) and Catalase (CAT), were evaluated. GC–MS findings of the essential oil revealed the predominance of Linalool as the major compound. Antimicrobial tests demonstrated activity against Acetobacter aceti, Acinetobacter baumannii, Enterococcus faecium, Escherichia coli, Methicillin-resistant Staphylococcus aureus, Proteus vulgaris, Klebsiella pneumonia, Staphylococcus aureus, Staphylococcus haemolyticus and Stenotrophomonas maltophilia. Furthermore, LEO modulated bacterial growth over time, inhibited biofilm formation and eradicated pre-formed ones. Additionally, LEO significantly decreased the activities of the antioxidant enzymes SOD and CAT. Our findings demonstrated the therapeutic potential of LEO against pathogenic strains and broad antibacterial efficacy.

Bacteria doi: 10.3390/bacteria5020032

Authors: Ahmed Nafis Brahim Oubaha Anas Raklami Emre Karakaya Aiman Slimani Elmostapha Outamamat Loubna El Fels Hayrettin Saygin

Saline ecosystems, including saline lakes, are indeed major hotbeds of microbial novelty, harboring diverse and largely unexplored microbes. The sebkha of Lake Naïla (Morocco), an ecologically protected area registered under the Ramsar Convention in 1998, remains largely unexplored. Isolation using three different selective media enabled seven phenotypically distinct actinobacterial isolates to be obtained. Molecular characterization, based on 16S RNA gene sequencing, was used to identify strains as members of the genera Streptomyces, Nocardiopsis, and Prauserella. Three strains showed antimicrobial potential against pathogenic microorganisms, with Streptomyces sp. strain 43 exhibiting the most potent effects. Additionally, all isolates displayed plant-growth-promoting (PGP) traits, including phosphate solubilization, auxin (IAA) synthesis, siderophore secretion, and ammonia production. Notably, Nocardiopsis sp. strain 42 produced the highest IAA levels (282 μg/mL), while Streptomyces sp. strain 39, Streptomyces sp. strain 43, and Streptomyces sp. strain 48 excelled in phosphate solubilization. GC-MS profiling of Streptomyces sp. strain 43 revealed a complex metabolite repertoire, including 1,2-propanediol and nonanal, highlighting the strain’s versatile secondary metabolism. These findings highlight that the sebkha of Lake Naïla represents a rich source of halophilic actinobacteria with promising dual potential for antimicrobial and biofertilizer applications. The findings provide a solid basis for new perspectives on biotechnology applications and sustainable agriculture.

Bacteria doi: 10.3390/bacteria5020031

Authors: Arjmand Fatima Muhammad Naeem

Shiga toxin-producing Escherichia coli (STEC) is a major zoonotic foodborne pathogen associated with severe human illnesses, including hemorrhagic colitis and hemolytic uremic syndrome. While ruminants are traditionally recognized as the primary reservoirs, increasing evidence suggests that poultry production systems may also contribute to the dissemination of pathogenic and antimicrobial-resistant E. coli through the food chain. However, the extent of this contribution and its relevance to human infection remain incompletely understood. This review provides a critical synthesis of the virulence mechanisms, epidemiology, and antimicrobial resistance (AMR) of E. coli, with particular emphasis on STEC in poultry production systems. Key virulence determinants, including Shiga toxins (Stx1 and Stx2), the locus of enterocyte effacement, and plasmid-encoded factors, are discussed in relation to their roles in host colonization and disease progression. Transmission pathways within poultry production and processing environments are examined, highlighting critical points of contamination from farm to consumer. The increasing prevalence of multidrug-resistant and extended-spectrum β-lactamase-producing E. coli in poultry underscores significant public health concerns. However, variability in epidemiological data and limitations in current surveillance systems complicate the interpretation of transmission dynamics. Current and emerging control strategies, including biosecurity measures, alternative antimicrobial interventions, and processing hygiene, are evaluated alongside their practical limitations under commercial conditions. Overall, this review identifies key knowledge gaps and emphasizes the need for integrated, evidence-based approaches within a One Health framework to better define zoonotic risks and develop sustainable control strategies.

Bacteria doi: 10.3390/bacteria5020030

Authors: Francisco Rodrigues Patrícia Coelho Sónia Mateus Hatem Eideh Miguel Castelo-Branco

Background: Urinary tract infections (UTIs) are among the most common bacterial infections worldwide and represent a significant public health concern due to their high prevalence and increasing antimicrobial resistance. This study aimed to systematically review the epidemiology, uropathogens, and resistance patterns of UTIs in Portugal over the last decade. Methods: A systematic review was conducted in accordance with PRISMA 2020 guidelines. A literature search was performed in April 2026. A total of 425 records were identified. After removal of duplicates and preliminary exclusions, 121 records were screened by title and abstract. Following application of eligibility criteria, 41 full-text articles were assessed, of which 13 met the criteria for detailed eligibility assessment. Six studies met the inclusion criteria and were included in the final qualitative synthesis. Results: The included studies consistently reported a higher prevalence of UTIs in females and, in some cases, in older populations. Escherichia coli was identified as the predominant uropathogen across all studies, followed by Klebsiella pneumoniae, Proteus spp., and Enterococcus spp. A consistently high prevalence of antimicrobial resistance was observed, particularly against commonly used antibiotics such as ampicillin and trimethoprim–sulfamethoxazole. The presence of extended-spectrum β-lactamase (ESBL)-producing strains was also reported, especially in healthcare-associated infections, which exhibited higher resistance profiles compared to community-acquired infections. Conclusions: The available evidence suggests that UTIs in Portugal are predominantly caused by enterobacteria, particularly Escherichia coli. However, the limited number and heterogeneity of studies highlight the need for cautious interpretation. Further multicenter and methodologically robust studies are required to better characterize national epidemiological patterns and antimicrobial resistance trends.

Bacteria doi: 10.3390/bacteria5020029

Authors: Debasis Mitra Marika Pellegrini Leonard Koolman

This Special Issue brings together a diverse collection of contributions that highlight the soil microbiome, including bacteria, fungi, and other microorganisms, which play a crucial role in enhancing crop productivity and nutrient absorption while minimizing dependence on synthetic chemicals [...]

Bacteria doi: 10.3390/bacteria5020028

Authors: Shaikha Alsayegh Zulfa Al Disi Nabil Zouari

Biosurfactant production by hydrocarbon-degrading bacteria is strongly influenced by the nature and concentration of available carbon substrates, which determine hydrocarbon bioavailability and microbial metabolic responses. In this study, five Bacillus subtilis strains isolated from weathered oil-contaminated sites in Qatar were evaluated for growth and biosurfactant activity using diesel fuel, fresh corn oil, and five-times-overheated corn oil as sole carbon sources. Cultures were grown in mineral salts medium under controlled conditions, and biosurfactant production was assessed through emulsification activity (EA), solubilization activity (SA), and colony-forming unit counts. All strains grew on the tested substrates but exhibited distinct strain-specific responses. Fresh corn oil supported the highest biomass production with values up to 3.3 × 107 CFU mL−1, whereas the strongest emulsification activity yield was observed in diesel cultures at low carbon loading (59 ± 2.3 EU g−1 carbon. Five-times-overheated corn oil maintained more stable emulsification activity across a broader concentration range, indicating tolerance to oxidized hydrocarbons and adaptation to chemically altered substrates. Increasing hydrocarbon concentrations led to progressive declines in EA and SA, indicating inhibitory effects at high substrate loads. Overall, biosurfactant production did not correlate directly with biomass, highlighting the importance of substrate properties in regulating functional output. These findings demonstrate that substrate composition and concentration are key determinants of biosurfactant performance in B. subtilis isolates and support the potential use of waste oils as low-cost feedstocks for biotechnological and bioremediation applications.

Bacteria doi: 10.3390/bacteria5020027

Authors: Reena Almutairi Rawan Alharbi Lamar Alfuraydi Yousef Alawi Nouralhoda Mourabya Hiba Shokry Ammar Ramli Idris Sula Hany Lotfy Mateq Ali Alreshidi

Background: Antibiotic misuse and prescribing errors are significant concerns in clinical practice, contributing to unnecessary antibiotic exposure, increased adverse effects, rising healthcare costs, and the escalation of antibiotic resistance. Understanding the prevalence, patterns, and risk factors of these prescription errors is essential for improving patient safety and healthcare efficiency in the future. Aim: Our aim was to evaluate the prevalence, patterns, and risk factors of antibiotic prescription errors in Saudi Arabia. Methods: A comprehensive search of three databases (PubMed, Scopus and ProQuest) was conducted to identify eligible cohort and cross-sectional studies in Saudi Arabia published up to January 2025. Studies that reported on error rates of antibiotic prescription errors and those that did not provide quantitative data were excluded. The primary outcome was the prevalence and patterns of inappropriate antibiotic use, while the secondary outcomes included the pooled prevalence of specific errors (i.e., selection, dose, duration, etc.). The quality of the studies was assessed using the Newcastle–Ottawa scale. This review was registered in PROSPERO (CRD42024611747). Results: Fourteen eligible cohort (n = 2) and cross-sectional (n = 12) studies conducted in Saudi Arabia were included in the review. Two studies reviewed medical records and orders of patients. Patient selection varied from emergency department to intensive care units and outpatients. The pooled prevalence of antibiotic prescription errors was 42.7% [95% CI: 37.5–47.8], with common errors including dosage (29.3%), duration (24.3%), selection (15%) and frequency (11.1%) errors. However, there was a high heterogeneity among the results. Overall, the quality assessment revealed a low risk of bias, except for one study with a high risk of bias. Conclusions: These findings highlight the high prevalence of antibiotic prescription errors. Future efforts should strengthen antibiotic stewardship, enhance clinician training, and ensure adherence to evidence-based guidelines to reduce prescription errors and combat antibiotic resistance.

Bacteria doi: 10.3390/bacteria5020026

Authors: María F. Cerioli Franco D. Fernández Melina V. Moliva Mishael Sánchez-Pérez Federico Serral Darío Fernandez Do Porto Elina B. Reinoso

Enterococcus lactis is increasingly recognized as an emerging mastitis pathogen, yet the functional basis of its virulence and associated health risks remain poorly defined. This study presents an integrated genomic and phenotypic characterization of E. lactis strain EL-A150 isolated from bovine subclinical mastitis. Whole-genome sequencing revealed a 2.49 Mb circular chromosome encoding multiple genes associated with adhesion (acm, bepA, fms, sagA), biofilm formation (empB, empC) and antimicrobial resistance, including determinants related to aminoglycosides and macrolides. Phenotypic assays demonstrated rapid growth, strong biofilm-forming capacity and high adhesion to bovine mammary epithelial cells, while internalization remained low and intracellular persistence was transient. Comparative genomic analyses confirmed the taxonomic placement of the strain within the E. lactis clade (ANI up to 99.5% against reference genomes) and revealed a limited resistome composed of chromosomally encoded genes, with no detectable plasmids or major mobile genetic elements. Collectively, these findings demonstrate that E. lactis EL-A150 possesses a coordinated set of traits conducive to intramammary colonization, supporting its classification as an opportunistic pathogen. The convergence of virulence potential and clinically relevant antimicrobial resistance within a single isolate underscores a One Health concern and highlights the need for surveillance frameworks that integrate functional validation with genomic risk assessment.

Bacteria doi: 10.3390/bacteria5020025

Authors: Kyung-A Hyun Ji-Hyun Kim Min Nyeong Ko Chang-Gu Hyun

Leuconostoc suionicum strain JNUCC 76 (=CH10) was isolated from cherry blossom flowers (Prunus yedoensis) collected on Jeju Island, Republic of Korea, representing a flower-associated strain of L. suionicum. To clarify its taxonomic position and genomic characteristics, whole-genome sequencing was performed using a hybrid PacBio–Illumina approach. The complete genome was assembled into a single circular chromosome of 2.20 Mb with a GC content of 36.8% and high sequencing depth, indicating a high-quality, closed genome assembly. Genome annotation revealed a compact gene repertoire dominated by functions related to carbohydrate transport and metabolism, amino acid utilization, and core cellular processes, consistent with adaptation to plant-derived, sugar-rich environments. Genome-based phylogenomic analyses using average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), and Genome BLAST Distance Phylogeny (GBDP) placed strain JNUCC 76 within the species L. suionicum. Genome-based metrics clearly exceeded the accepted species thresholds, supporting the assignment of the strain to L. suionicum. Secondary metabolite gene cluster analysis identified a limited number of low-complexity and precursor-oriented biosynthetic gene clusters, including RiPP-like, type III polyketide synthase, and terpene-precursor clusters, suggesting that the ecological fitness of the strain relies primarily on primary metabolism rather than extensive secondary metabolite production. Overall, this study expands current knowledge of flower-associated Leuconostoc lineages and provides a high-quality genomic framework for future comparative and functional studies. The genomic features of strain JNUCC 76 highlight floral environments as underexplored reservoirs of lactic acid bacteria diversity and support further evaluation of flower-derived Leuconostoc strains as potential postbiotic or fermentation-based resources for cosmetic and related biotechnological applications.

Bacteria doi: 10.3390/bacteria5020024

Authors: Nelson Elias Guevara-Pinedo Winston Franz Ríos-Ruiz José Carlos Rojas-García Roger Cabrera-Carranza

Iron (Fe) and zinc (Zn) are essential micronutrients for plant metabolism; however, their bioavailability in tropical soils is often limited by low solubility and complex mineral interactions. Root-associated bacteria may enhance micronutrient availability through siderophore production and the solubilisation of insoluble mineral forms. This study aimed to functionally characterise three bacterial isolates from rice roots—Bacillus siamensis TUR07-02b, Priestia aryabhattai SMNCH17-07, and Priestia megaterium SMBH14-02—under controlled in vitro conditions. Siderophore activity was evaluated qualitatively using Chrome Azurol S (CAS) agar, where percentages represent halo-based indices relative to colony diameter, and quantitatively using the CAS–shuttle assay, expressed as percent siderophore units relative to an uninoculated reference. Zinc solubilisation was assessed in solid media as halo-based indices and in liquid media as Zn-equivalent signals (mg L−1) obtained by spectrophotometry. All strains produced siderophores, with P. aryabhattai showing the highest qualitative index (167%), while P. aryabhattai and B. siamensis showed statistically similar activity in liquid medium (~23%). Zinc solubilisation was substrate-dependent: B. siamensis showed the broadest solubilisation spectrum in solid media, whereas P. aryabhattai achieved the highest Zn-equivalent signals for ZnCO3 and Zn3(PO4)2 after 20 days. These results demonstrate strain-specific functional differences and represent a preliminary screening method based on relative in vitro estimations.

Bacteria doi: 10.3390/bacteria5020023

Authors: Amiran Khabidovich Zanilov Zalim Islamovich Dudarov Milana Radievna Aznaeva Rustam Kharunovich Taov Dinara Gumarbievna Dudarova

The aim of the study was to evaluate the biotechnological potential of thermophilic microorganisms isolated from chernozem soil during composting of poultry manure. The efficiency of the strains was determined by their effect on organic matter degradation, humification intensity, and nitrogen accumulation. The correlation between the quality indicators of the composting process was assessed with the gross values, taking into account the proportion of compost fractions. The strains were identified as: Aeribacillus pallidus KCTC 3564T (cellulolytic), Neobacillus sedimentimangrovi FJAT-2464T, Aeribacillus composti N.8T, Caldifermentibacillus hisashii N-11T (nitrogen fixers), Acinetobacter pittii CIP 70.29T, and Pseudomonas plecoglossicida NBRC 103162T (nitrifies). It was found that all the bacteria increase the proportion of small fractions by 19.0–19.9%. The gross content of humic acids increases under the influence of nitrifiers (15.5%) and nitrogen fixers (5.5%). The total nitrogen content increases under cellulolytics (13.8%) and nitrogen fixers (20.2%). The smallest fraction (≤0.25 mm) in nitrogen fixers and nitrifying variants has the greatest bioreclamation properties, by 16.4% (p < 0.001) and 12.9% (p < 0.001). Targeted microbial strains provide the direction of the transformation processes during biocomposting. It can also be concluded that assessing the quality of composting based on the fraction distribution can be a promising element of the biofermentation process monitoring.

Bacteria doi: 10.3390/bacteria5020022

Authors: Hala M. Zaher

Acinetobacter baumannii remains a significant nosocomial infectious agent, with its ability to acquire antimicrobial resistance posing a global public health concern. Over time, substantial knowledge has been amassed regarding A. baumannii in human clinical cases. Recently, research has shifted to non-human A. baumannii. Therefore, the current work aimed to investigate the occurrence of A. baumannii carrying carbapenem resistance genes in broiler chickens via molecular detection and its public health significance. Two hundred cloacal swabs were collected from broiler chickens and grouped into 40 pools. DNA extraction was conducted on these pools, followed by molecular detection of the A. baumannii blaOXA-51-like gene. Among the 40 pools, 31 (77.5%) tested positive for the blaOXA-51-like gene and were further screened for additional carbapenemase genes, including blaOXA-58, blaOXA-23, and blaOXA-24. The blaOXA-58 gene was identified in eight pools (25.8%), whereas blaOXA-23 and blaOXA-24 were not detected. Subsequently, partial DNA sequencing was performed on two PCR amplicons of the A. baumannii blaOXA-51-like gene derived from broiler chickens, followed by a phylogenetic analysis. The analysis revealed genetic similarity between the A. baumannii sequences obtained in this work and those retrieved from humans, birds, animals, and environmental sources. In conclusion, the occurrence of A. baumannii harboring genes coding for carbapenem resistance in broiler chickens highlights a potential new path of transmission, which may require further investigation to better understand the dynamics of transmission and to guide effective strategies for preventing and controlling A. baumannii infections.

Bacteria doi: 10.3390/bacteria5020021

Authors: Leticia Isabel Peñuelas-Castro Jesús Guadalupe Luna-Valdez Analila Luna-Valenzuela Imelda Noehmi Monroy-García Héctor Alejandro Leyva-Hernández Marlet Marchena-Peñuelas Guadalupe Arlene Mora-Romero Lelie Denise Castro-Ochoa

Bacteria adapted to elevated temperatures are commonly associated with geothermal environments and are recognized for their functional diversity. In this study, cultivable bacteria were isolated from a geothermal spring in northern Sinaloa, Mexico, and characterized through physicochemical analysis, molecular identification, growth kinetics, and functional screening. The isolates were identified as Bacillus licheniformis (strains J1, J3, and J8) and Brevibacillus borstelensis (strains J6 and J9). Growth analyses showed that, in nutrient broth at 45 °C, the evaluated strains exhibited specific growth rates ranging from 1.25 to 1.78 h−1 and short doubling times between 23 and 33 min, with B. borstelensis J6 displaying the highest rate. At 50 °C, μmax values ranged from 0.77 to 1.08 h−1, indicating sustained growth at elevated temperatures. Functional assays demonstrated extracellular proteolytic, amylolytic, and cellulolytic activities, mainly associated with B. licheniformis strains, in addition to tolerance to the pesticides fluazinam and benomyl. Antagonistic tests showed that B. licheniformis J8 inhibited the phytopathogenic fungi Sclerotinia sclerotiorum and Sclerotium rolfsii, while qualitative mineral solubilization assays indicated the ability of selected isolates to mobilize phosphate and potassium. These findings highlight geothermal ecosystems as valuable reservoirs of thermotolerant bacteria with enzymatic versatility and environmental relevance, supporting further molecular and process-optimization studies.

Bacteria doi: 10.3390/bacteria5020020

Authors: Babatunde Ibrahim Olowu Maryam Ebunoluwa Zakariya Nahimah Opeyemi Idris Abdulhakeem Opeyemi Azeez Temitope Ruqqayah Ogunmodede Al-Amin Adebare Olojede Abdulmuheez Abiola Abdulkareem Abdullah Adedeji Al-Awal Halima Idris Muhammad

Antimicrobial resistance [AMR] is a silent yet intensifying global threat, with particularly severe consequences in tropical and subtropical ecosystems, where high ecological connectivity, extensive antimicrobial use, and inadequate sanitation create ideal conditions for the persistence and spread of antimicrobial resistance genes [ARGs]. Within the One Health framework, migratory birds warrant special attention because they traverse tropical AMR hotspots, linking contaminated aquatic, agricultural, and peri-urban environments along established flyways. Evidence from tropical and subtropical regions indicates that migratory birds frequently carry clinically relevant AMR-associated pathogens, including extended-spectrum β-lactamase-producing Escherichia coli, multidrug-resistant Salmonella enterica, and fluoroquinolone- and macrolide-resistant Campylobacter spp. These findings suggest that migratory birds primarily function as ecological sentinels and geographic redistributors of antimicrobial resistance, reflecting environmental contamination and ecological connectivity between human-dominated and natural ecosystems, while evidence for long-term reservoir status remains context-dependent. Addressing the complex interface among AMR, migratory birds, and ARGs requires integrative surveillance strategies that explicitly incorporate wildlife into existing health systems. Genomic and metagenomic monitoring of migratory bird populations, combined with cross-sectoral data sharing, can provide early warning signals of emerging resistance patterns and inform evidence-based interventions. Understanding the ecological role of migratory birds in tropical ecosystems is therefore essential for designing effective One Health strategies to mitigate transboundary AMR risks and preserve the long-term efficacy of antimicrobial therapies.

Bacteria doi: 10.3390/bacteria5020019

Authors: Baljit Singh Kamna Ravi

In today’s environment, rapid, reliable, and accurate bacterial detection is essential for protecting public health while preserving and ensuring the safety of food, water, and agricultural and environmental systems. Over the years, electrochemical sensors have gained widespread attention as viable candidates due to their rapid response, high sensitivity and selectivity, adaptability and portability, and low manufacturing cost. This facilitates their integration into various sectors, including healthcare and diagnostic applications, food safety and agriculture, and water and environmental monitoring. While these achievements represent tremendous progress, some of the challenges that need to be overcome include stability, batch-to-batch reproducibility, manufacturability, performance reliability, and the lack of point-of-care (POC) implementation for the utilization of these sensors for real-sample bacterial analysis. However, in the future, it is expected that with continued efforts made towards improving durability, standardization, and manufacturability, electrochemical bacterial sensors will be pivotal to the advancement of efficient bacterial diagnostics across various fields. This review presents major developments in modern electrochemical sensing technologies, which include, but are not limited to: electrochemical sensor and biosensor surface modifications, nanomaterials, the integration of artificial intelligence (AI) and machine learning (ML), and the emergence of wearable systems, for bacterial detection and monitoring. Additionally, their utilization in the aforementioned sectors is discussed. The integration and sustained use of these advanced electrochemical sensors for bacterial detection and surveillance can significantly enhance global safety and public well-being.

Bacteria doi: 10.3390/bacteria5010018

Authors: Ella Brake Susanne Gastiger David Peter Lara Schober Laurin Stuhlfauth Andreas Burkovski

Corynebacterium lactis was isolated from the skin abscess of a companion dog and from raw milk of a cow with unspecific mastitis. As information about the species was scarce and a zoonotic potential could not be excluded, we started a basic characterization of C. lactis strain RW3-42 with respect to antibiotic susceptibility and the response of invertebrate animal model systems to infection. C. lactis showed a number of antimicrobial resistances and is able to colonize Caenorhabditis elegans. In contrast, Galleria mellonella larvae were not impaired by C. lactis. Genome analyses of strain RW2-5 revealed the absence of toxin-encoding genes, and only a rather small number of other virulence factors were found, i.e., SpaA- and SpaH-type pili and the non-fimbrial adhesins DIP0733, DIP1281, DIP1621 and EmbC in addition to a homologue of Salmonella RhuM involved in killing of C. elegans. The results obtained indicate a limited pathogenic potential of the species.

Bacteria doi: 10.3390/bacteria5010017

Authors: Sura Jasem Mohammed Breig Saja Mohsen Alardhi Khalid Jaber Kadhum Luti Ahmed Jasim Mohammed Al-Obaidy Aymen J Al-Obaidy Aparna Banerjee

Prodigiosin, a red pigment with diverse biotechnological applications, is produced as a secondary metabolite by Gram-negative bacilli Serratia marcescens. In this study, we implemented an AI-guided hybrid optimization framework combining Response Surface Methodology (RSM) using a Circumscribed Central Composite Design (CCCD) and Artificial Neural Network (ANN) modeling to enhance prodigiosin pigment production. Across 34 experimental runs, we optimized sucrose and peptone concentrations along with inoculum size. The RSM-derived model exhibited a strong correlation (R2 = 0.953), while the ANN, trained using a backpropagation algorithm, demonstrated superior predictive power (R2 = 0.998; MSE = 0.000414), underscoring the potential of artificial intelligence in modeling complex bioprocesses. Beyond statistical optimization, an induction strategy using 1% of various natural additives (vegetable oils and egg components) identified egg white, rich in albumin, as the most effective enhancer, tripling prodigiosin yield. Further investigation revealed that a 2% egg white concentration maximized production to 1070 mg L−1, a substantial increase compared to the optimized yield of 359.2 ± 12 mg L−1 and predicted value of 391.86 mg L−1. These results highlight the value of integrating machine learning with experimental design and protein-rich inducers to strengthen sustainable microbial pigment production in a cost-effective and scalable manner.

Bacteria doi: 10.3390/bacteria5010016

Authors: Leyla Miloudi-Agha Mohammed Kebdani

Modern agriculture is increasingly challenged by fungal diseases, with phytopathogens such as Fusarium species causing substantial yield and quality losses in major crops globally. Although synthetic fungicides remain widely used, their intensive application raises serious concerns regarding environmental safety, human health, and the rapid emergence of resistant pathogen populations in the environment. These limitations have accelerated the search for sustainable, biologically based alternatives. In this context, Bacillus species isolated from saline and hypersaline habitats have emerged as a distinctive and still underexplored group of microorganisms with dual functionality as biological control agents (BCAs) and plant growth–promoting rhizobacteria (PGPRs) in salt-affected agroecosystems. Their novelty lies in their combined ability to suppress phytopathogens, enhance plant growth, and tolerate or mitigate salinity stress. Owing to their exceptional metabolic adaptability, these bacteria remain active under osmotic stress and produce a wide range of bioactive compounds that collectively contribute to their antifungal activity and improved plant performance. This review critically synthesizes advances published over the last six years (2019–2025), providing a comprehensive overview of the current understanding of the mechanisms underlying the biocontrol potential of halophilic/halotolerant Bacillus species against Fusarium spp. and other fungal phytopathogens. Particular emphasis is placed on ecological adaptations, molecular mechanisms, and the dual roles of these bacteria as BCAs and PGPR. The exploration and exploitation of saline-adapted Bacillus strains offer promising, eco-friendly, and cost-effective strategies for managing Fusarium diseases, thereby contributing to resilient and sustainable agricultural systems under increasing environmental constraints in the future.

Bacteria doi: 10.3390/bacteria5010015

Authors: Tran Trong Khoi Nguyen Le Thi My Thu Vo Yen Ngoc Nguyen Duc Trong Le Thanh Quang Tran Loc Thuy Ly Ngoc Thanh Xuan Tran Chi Nhan Nguyen Quoc Khuong

The increasing reliance on chemical fertilizers has raised environmental concerns and highlighted the need for sustainable alternatives. This study aimed to (i) optimize the carrier-to-substrate ratios and moisture content during composting with potassium-solubilizing purple nonsulfur bacteria (K-PNSB) and (ii) evaluate the growth-promoting effect of the optimized biofertilizer on maize seedlings. Three K-PNSB strains (Cereibacter sphaeroides M-Sl-09, Rhodopseudomonas thermotolerans M-So-11, and Rhodopseudomonas palustris M-So-14) were used. Composting experiments were conducted using different carrier-to-substrate ratios and moisture levels with K-PNSB inoculation. Compost quality was assessed through nutrient dynamics, bacterial density, and physicochemical properties over four weeks. The results showed that the 1:1:3 substrate ratio combined with 50–60% moisture content consistently enhanced K solubilization, bacterial survival, and compost maturity indicators. Application of the optimized biofertilizer improved maize growth traits compared with the non-inoculated control. These findings demonstrate that controlling material ratios and moisture content improves compost quality and plant growth performance, providing a sustainable alternative to chemical fertilizers. This study provides a practical framework for developing sustainable K-solubilizing biofertilizers from agricultural residues.

Bacteria doi: 10.3390/bacteria5010014

Authors: Benjamín Abraham Ayil-Gutiérrez Erika Acosta-Cruz Juan Manuel Bello-López Yesseny Vásquez-Martínez Marcelo Cortez-San Martin Lorenzo Felipe Sánchez-Teyer Luis Carlos Rodríguez-Zapata Francisco Alberto Tamayo-Ordoñez Esmeralda Cázares-Sánchez Víctor Hugo Ramos-García Eric Sánchez-López Hernan de Jesús Villanueva-Alonzo Virgilio Bocanegra-García Humberto Martínez-Montoya Grethel Díaz-Palafox María José García-Castillo María Concepción Tamayo-Ordoñez Yahaira de Jesús Tamayo-Ordoñez

Antimicrobial resistance (AMR) poses a severe threat to global health by limiting treatment options and increasing clinical and economic burdens. This review synthesizes evidence showing that resistance evolution is strongly shaped by antibiotic pressure, leading to the accumulation of adaptive mutations, activation of efflux systems, and widespread dissemination of resistance determinants across clinical, animal, and environmental settings. We highlight recent genomic, metagenomic, and structural findings that elucidate the molecular basis of AMR, with particular emphasis on horizontal gene transfer mediated by mobile genetic elements such as plasmids, integrons, and transposons. Analyses across One Health interfaces reveal extensive sharing of antimicrobial resistance genes among humans, livestock, and environmental reservoirs, identifying Enterobacteriaceae and ESKAPE pathogens as key hubs of resistance dissemination. Special focus is placed on Acinetobacter baumannii, where phylogenetic and three-dimensional structural analyses of class D β-lactamases OXA-23 and OXA-24/40 demonstrate a conserved catalytic framework coupled with substantial sequence and conformational variability. These structural differences likely influence carbapenem specificity and resistance levels. Collectively, the findings underscore how genetic diversity, mobile elements, and structural adaptation converge to drive AMR, reinforcing the need for integrated genomic and structural approaches to guide surveillance and antimicrobial development.

Bacteria doi: 10.3390/bacteria5010013

Authors: Noor Zarina Abd Wahab Kamal Saifullah Kamal Rul Azrul Nur Ain Najwa Mohd Yuseri Ahmad Khalis Yahya Fong Si Wei Sayed Mohd Saufi Fahmi Sayed Abdul Kadir Mohd Hanif Abdullah

The increasing prevalence of antimicrobial resistance, especially in methicillin-resistant Staphylococcus aureus (MRSA), underscores the need for alternative therapies from natural sources. This study investigated the chemical composition, antibacterial activity, and gene expression modulation of Melaleuca cajuputi essential oils. Gas chromatography–mass spectrometry (GC-MS) identified 91 compounds, with naphthalene (23.90%), guaiol (12.92%), caryophyllene oxide (9.69%), D-limonene 98% (8.59%), and gamma terpinene (7.54%) among the most abundant. In Silico molecular docking against MRSA virulence proteins revealed that alloaromadendrene had the strongest binding to toxic shock syndrome toxin-1 (TSST-1) (−7.948 kcal/mol), suggesting high inhibitory potential, while cyclohexane showed weak binding with staphylococcal enterotoxin A (SEA) (−3.532 kcal/mol). Antibacterial assays demonstrated concentration-dependent inhibition, with the zones ranging from 6.33 ± 0.33 mm to 16.67 ± 0.88 mm. MIC and MBC values ranged from 1.56 to 12.5% and 3.13 to 25%, respectively, with most isolates showing bactericidal effects (MBC/MIC ≤ 2). Gene expression analysis of MRSA isolate 4 indicated that sea was moderately upregulated (FC = 1.44), while sec remained unchanged (FC = 1.02). In contrast, fnbA (FC = 0.72), seb (FC = 0.33), and mecA (FC = 0.23) genes were downregulated, and the tsst-1 gene (FC = 0.05) was nearly silent. These findings highlight M. cajuputi essential oils as a promising candidate with both antibacterial efficacy and regulatory effects on MRSA virulence genes.

Bacteria doi: 10.3390/bacteria5010012

Authors: I Nengah Wirajana Nilam Vaghamshi Ni Putu Ariantari Agustino Beatronaldo Sawur Ketut Ratnayani Komal Antaliya Smita Atara Anjana Ghelani Dushyant Dudhagara Pravin Dudhagara

Hot springs represent unique geothermal ecosystems where extreme physicochemical conditions intersect with remarkable microbial diversity and metabolic innovation. These natural laboratories harbor specialized communities of thermophilic and hyperthermophilic microorganisms that have evolved exceptional adaptations to elevated temperatures, extreme pH, and high salinity. This review synthesizes current understanding of hot spring systems as multifunctional natural resources, examining their roles in fundamental microbiology, biotechnology, and sustainable development. We explore the ecological principles governing microbial community assembly, the taxonomic and functional diversity of prokaryotic and eukaryotic microorganisms, and the genomic mechanisms underlying thermophilic adaptation. Hot springs yield enzymes revolutionizing molecular biology and industrial catalysis, bioactive metabolites with pharmaceutical potential, and novel bioremediation capabilities including plastic degradation. Beyond biological significance, these systems contain valuable minerals and rare earth elements, supporting an emerging bioeconomy integrating wellness tourism, bioprospecting, and sustainable resource extraction. However, critical knowledge gaps remain regarding viral ecology, horizontal gene transfer, eukaryotic diversity, and climate change impacts. We emphasize that hot springs merit renewed interdisciplinary attention as model systems for understanding extremophile physiology, early life evolution, and the development of nature-based biotechnological solutions. Realizing their full potential requires balanced management strategies that preserve ecosystem integrity while enabling responsible utilization of these irreplaceable geobiological resources.

Bacteria doi: 10.3390/bacteria5010011

Authors: Hadeel Mazin Akram Saif Sehaam Saliem

Sequencing technologies have reshaped the study of the subgingival microbiome, but selecting the appropriate method remains challenging because of differences in resolution, cost, host DNA contamination, and computational complexity. This review compares 16S rRNA sequencing, full-length 16S, shotgun metagenomics, and metatranscriptomics with respect to taxonomic resolution, functional output, sample requirements, and analytical limitations. Key practical issues, including low microbial biomass, contamination control, and the choice of appropriate bioinformatic tools, are emphasized to help researchers avoid common pitfalls. A decision-making framework is provided to link study goals to suitable sequencing methods while outlining realistic budget and sample-handling constraints. The review concludes with recommendations for integrating sequencing with complementary techniques to improve the accuracy, reproducibility, and clinical relevance of periodontal microbiome studies.

Bacteria doi: 10.3390/bacteria5010010

Authors: Arnon Chukamnerd Woralop Modleahman Pattamarat Rattanachuay Rattanaruji Pomwised Pharanai Sukhumungoon

(1) Background: Carbapenem-resistant Escherichia coli (CREC) is widespread and resistant to almost all available antimicrobial agents. In this study, we aimed to assess the phenotypic and molecular characteristics of CREC isolated from retail meats in Hat Yai, Songkhla, Thailand. (2) Methods: A total of 155 retail meat samples were randomly collected, and 412 presumptive carbapenem-non-susceptible isolates were screened via culturing on imipenem-containing eosin methylene blue (EMB) agar. Susceptibility to imipenem and meropenem was tested using the disk diffusion method, and carbapenemase and virulence genes in CREC isolates were detected using PCR. Phylogenetic groups and genetic relatedness of carbapenemase-positive CREC isolates were analyzed using gene markers and BOX-PCR, respectively. (3) Results: The results revealed a high prevalence of presumptive carbapenem-non-susceptible E. coli (CNSEC) isolates in beef samples. Over 89% of the CNSEC isolates from all meat types were identified as CREC. Of these, only 4.8% of the isolates from beef samples were positive for the blaNDM gene, and one was also positive for the blaVIM gene. These isolates carried only the fimH gene as a virulence factor. The blaNDM-positive CREC isolates were classified in phylogenetic Group D. (4) Conclusions: Identifying antimicrobial-resistant pathogens, particularly CREC, in food-producing animals is critical due to potential risks to public health.

Bacteria doi: 10.3390/bacteria5010009

Authors: Assefa Asnakew Abebe Alemayehu Godana Birhanu Tesfaye Sisay Tessema

Klebsiella pneumoniae is a prominent pathogen implicated in a wide range of infections, including pneumonia, urinary tract infections, and septicemia. Its ability to acquire and disseminate antibiotic resistance, coupled with the rising prevalence of hypervirulent strains, represents a significant public health threat. Understanding the molecular basis of drug resistance can guide the design and development of effective treatment strategies. Antimicrobial resistance (AMR) in these bacteria is a complicated process and cannot be attributed to a single resistance mechanism. K. pneumoniae develops resistance to antibiotics through a variety of mechanisms, ranging from single molecular mechanisms to complex interactions, where molecular synergy exacerbates resistance. This review summarizes the current understanding of the molecular mechanisms that contribute to the drug resistance and virulence of this pathogen. Key antibiotic resistance mechanisms include drug inactivation via B-lactamases and carbapenemases, membrane remodeling, efflux pump systems, such as AcrAB-TolC and OqxAB, and biofilm formation facilitated by quorum sensing. Additionally, the role of ribosomal changes in resistance is highlighted. This review also examines the mechanisms of virulence, emphasizing fimbriae, iron acquisition systems, and immune evasion strategies. Understanding these mechanisms of drug resistance and virulence is crucial for remodeling existing antibiotics and developing new therapeutic strategies.

Bacteria doi: 10.3390/bacteria5010008

Authors: Muhammad Adnan Patrícia Coelho Miguel Castelo-Branco Francisco José Barbas Rodrigues

Background: Multidrug-resistant (MDR) Gram-negative bacilli (GNBs) significantly compromise the effective management of urinary tract infections (UTIs) worldwide. As antimicrobial resistance varies across regions, locally tailored data are essential to guide empirical therapy. This study investigated the prevalence, determinants, and temporal dynamics of MDR GNBs in UTI patients from Central Portugal between 2018 and 2022. Methods: We conducted a retrospective observational study at a hospital center in Central Portugal, analyzing data from 2018 to 2022. Data from 5194 UTI patients with GNB-positive cultures were analyzed. Binary logistic regression was used to identify determinants of MDR GNBs, defined as resistance to ≥1 agent in ≥3 antibiotic classes. Results: The study population had a mean age of 64.5 ± 25.3 years, and females represented two-thirds of the sample (67.0%). The overall prevalence of MDR GNBs was 35.8%. Advanced age (≥75 years), male sex, and specific treatment contexts—particularly day treatment and laboratory-only cases—were independently associated with MDR. SBL-producing Enterobacterales and non-fermenting GNBs showed the highest risk levels. Conclusions: MDR GNBs are highly prevalent among UTI patients in Central Portugal, and their increasing trend—particularly in 2022—highlights an urgent need for strengthened surveillance and updated empirical treatment strategies. The observed temporal increase highlights the urgent need for strengthened regional surveillance and updated empirical treatment guidelines.

Bacteria doi: 10.3390/bacteria5010007

Authors: Stephen L. W. On Maria J. Figueras James G. Fox Kurt Houf Francis Mégraud William G. Miller John Stolz Ken Takai Peter Vandamme

The taxonomy of the genus Arcobacter has been subject to substantive turmoil in recent years following a proposal to subdivide the genus into six genera. This proposal has been challenged by a number of multidisciplinary studies employing phenotypic, genomic, and phylogenetic analyses. Following several discussions among members of the International Committee on Systematics of Prokaryotes (ICSP) subcommittee on the taxonomy of Campylobacter and related bacteria, this group now unanimously recommends the use of the genus term Arcobacter to refer to these species.

Bacteria doi: 10.3390/bacteria5010006

Authors: Melina Vanesa Moliva María Florencia Cerioli Ignacio Velzi María Alejandra Molina Carina Maricel Pereyra Ayelen Nigra Andrea Lorena Cristofolini Cecilia Inés Merkis Pablo Bogino Elina Beatriz Reinoso

Streptococcus uberis is a bovine mastitis pathogen with a demonstrated ability to form biofilms. However, the dynamics of this process remain poorly characterized. This study aimed to comprehensively characterize biofilm formation in four S. uberis strains that differed in their biofilm-forming capacity, from weak to strong producers, and in the presence of key virulence-associated genes, such as sua, hasA and hasC. To achieve this, we integrated structural, biochemical, physiological and transcriptional analyses using scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FT-IR), spectral flow cytometry and qRT-PCR. The multi-faceted analysis revealed a coordinated maturation peak at 48 h, characterized by a structured architecture with water channels, a distinct biochemical signature rich in polysaccharides and proteins, and a predominantly viable bacterial population. This peak coincided with a marked upregulation of key virulence-associated genes, with sua expression increasing 2.5-fold and hasA increasing 3-fold at 48 h. This mature biofilm conferred high tolerance to antibiotics, with eradication concentrations (>256 µg/mL) exceeding planktonic MICs, although tetracycline was notably effective. At 72 h, the biofilm entered a dispersion phase characterized by structural collapse and reduced viability. These findings establish S. uberis biofilm maturation as a highly coordinated process, providing new insights into the biofilm lifecycle of this important pathogen and identifying key temporal and molecular targets for future interventions.

Bacteria doi: 10.3390/bacteria5010005

Authors: Natalia Alija-Novo Paul Whyte Declan Bolton

Globally, large quantities of animal waste and human sewage sludge are generated annually. Their application as soil amendments can enhance soil quality and support a circular economy. However, these wastes may harbour pathogenic bacteria, posing contamination risks to soil and water and potential transmission to animals and humans. This study investigated the survival of five bacterial pathogens during six months of storage in five types of organic waste and following their subsequent application to soil. During storage, T90 values ranged as follows: Salmonella Typhimurium (2.3–17.7 days), Campylobacter jejuni (0 to 23.9 days), Escherichia coli O157:H7 (4.3 to 57.8 days), and Listeria monocytogenes (1.9 to 170.4 days). In soil, T90 values were S. Typhimurium (4.2 to 17.4 days), C. jejuni (4.8 to 26.8 days), E. coli O157:H7 (4.3 to 52.9 days), and L. monocytogenes (2 to 83.7 days). Clostridium sporogenes remained stable throughout both experiments, preventing T90 calculation. Contrary to our initial hypothesis that soil microbiota would accelerate pathogen decline, T90 values were higher during storage in 11 cases and higher in soil in nine scenarios. These findings highlight the need for pre-treatment strategies for animal waste and biosolids before land spreading to consistently mitigate risks of pathogen transmission and environmental contamination.

Bacteria doi: 10.3390/bacteria5010004

Authors: Oumaima Anachad Wafaa Taha Chaimaa Saadoune Houssam Assioui Imad Fenjar Imane Thaifa Faiza Bennis Fatima Chegdani

Perinatal depression (PND) is a severe mood disorder affecting mothers during pregnancy and postpartum, with implications for both maternal and neonatal health. Emerging evidence suggests that gut microbiota-derived metabolites play a critical role in neuroinflammation and neurotransmission. In this study, we employed an in silico approach to evaluate the pharmacokinetic and therapeutic potential of metabolites produced by Lactobacillus helveticus and Bifidobacterium longum in targeting key proteins implicated in PND, including BDNF, CCL2, TNF, IL17A, IL1B, CXCL8, IL6, IL10. The ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profiles of selected microbial metabolites, including acetate, lactate, formate, folic acid, riboflavin, kynurenic acid, γ-aminobutyric acid, and vitamin B12 were assessed using computational tools to predict their bioavailability and safety. Enrichment analysis was performed to identify biological pathways and molecular mechanisms modulated by these metabolites, with a focus on neuroinflammation, stress response, and neurogenesis. Additionally, molecular docking studies were conducted to evaluate the binding affinities of these metabolites toward the selected PND-associated targets, providing insights into their potential as neuroactive agents. Our findings suggest that specific microbial metabolites exhibit favorable ADMET properties and strong binding interactions with key proteins implicated in PND pathophysiology. These results highlight the therapeutic potential of gut microbiota-derived metabolites in modulating neuroinflammatory and neuroendocrine pathways, paving the way for novel microbiome-based interventions for perinatal depression. Further experimental validation is warranted to confirm these computational predictions and explore the clinical relevance of these findings.

Bacteria doi: 10.3390/bacteria5010003

Authors: Chang You Zhi-Wen Ding Ai-Qun Jia Kai-Zhong Xu

This study focuses on discovering novel quorum-sensing inhibitors (QSIs) from endophytes of Coelothrix irregularis, aiming to develop new strategies against drug-resistant bacterial infections. From the endophytic bacterial strain Bacillus strain W10-B1, isolated from C. irregularis, twelve compounds were isolated and structurally identified. Subsequent screening against Serratia marcescens NJ01 revealed that compound (12), 3,3′-dibromo-4,4′-biphenyldiol, exhibited significant inhibitory activity against the quorum-sensing system of S. marcescens NJ01. It effectively suppressed biofilm formation, swimming, and swarming motilities of the bacterium. This work is the first to demonstrate that endophytes from C. irregularis are a novel source of potent QSIs, providing both material and theoretical foundations for combating pathogen virulence, drug resistance, and pathogenicity.

Bacteria doi: 10.3390/bacteria5010002

Authors: Babatunde Ibrahim Olowu Maryam Ebunoluwa Zakariya Abdulhakeem Opeyemi Azeez Abdullah Adedeji Al-Awal Kehinde Samuel Adebayo Nahimah Opeyemi Idris Halima Idris Muhammad Blessing Chizaram Ukauwa Al-Amin Adebare Olojede

Migratory birds have been implicated in the spread of diverse emerging infectious pathogens, including West Nile virus, Usutu virus, Avian influenza viruses, Salmonella, Campylobacter, antimicrobial-resistant (AMR) bacteria, and antibiotic resistance genes (ARGs). Beyond their roles as vectors and reservoirs, migratory birds are also susceptible hosts whose own health may be compromised by these infections, reflecting their dual position in the ecology of pathogens. As facilitators of pathogen transmission during their long-distance migrations, often spanning thousands of kilometres and connecting ecosystems across continents, these birds can easily cross-national borders and circumvent traditional biosecurity measures, thereby acting as primary or secondary vectors in the transmission of cross-species diseases among wildlife, livestock, and humans. Africa occupies a pivotal position in global migratory bird networks, yet comprehensive data on pathogen carriage remain limited. Gaps in knowledge of pathogen diversity constrain current surveillance systems, resulting in insufficient genomic monitoring of pathogen evolution and a weak integration of avian ecology with veterinary and human health. These limitations hinder early detection of novel pathogens and reduce the continent’s preparedness to manage outbreaks. Therefore, this review provides a holistic assessment of these challenges by consolidating existing knowledge concerning the pathogens transmitted by migratory birds in Africa, while recognizing the adverse effect of pathogens, which potentiates population decline, extinction, and ecological imbalance. It further advocates for the adoption of a comprehensive One Health-omics approach that not only strengthens surveillance and technological capacity but also prioritizes the protection of avian health as an integral component of ecosystem and public health.

Bacteria doi: 10.3390/bacteria5010001

Authors: Tamer Abdel Fattah Gamal M. El-Sherbiny Mohamed H. Kalaba Mohamed H. Sharaf Ahmed A. Radwan

Extensively drug-resistant (XDR) bacteria pose a serious global public health threat due to their high levels of resistance to multiple classes of antibiotics. This study aimed to characterize bacterial isolates obtained from clinical samples, evaluate their antibiotic resistance patterns, and investigate the antimicrobial and anticancer potential of essential oils (EOs) and their nanoemulsions (NEs). A total of 175 bacterial isolates were collected from various clinical sources, identified, and subjected to antibiotic susceptibility testing using both conventional methods and the VITEK® 2 system. Among these, nine isolates were identified as extensively drug-resistant. Among the tested EOs, carvacrol exhibited the strongest antibacterial activity, with minimum inhibitory concentrations (MICs) ranging from 14 to 35 µg/mL, compared to 8 to 19 µg/mL for meropenem. To enhance its stability and efficacy, carvacrol nanoemulsions (CANE) were prepared via ultrasonication and characterized using zeta potential measurements, which indicated a positive surface charge of +14.2 mV, while dynamic light scattering (DLS) analysis revealed a narrow size distribution with a mean hydrodynamic diameter of 411.3 nm. High-resolution transmission electron microscopy (HR-TEM) showed spherical droplets ranging from 18 to 144 nm in size, with an average diameter of 69 ± 28 nm. The nanoemulsion formulation significantly enhanced antibacterial activity, with MICs reduced to 11 ± 0.0–23 ± 0.21 µg/mL, compared to 14 ± 0.13–35 ± 0.11 µg/mL for pure carvacrol oil. Gas chromatography–mass spectrometry (GC–MS) analysis identified major active constituents, including thymol, methoxyphenyl, estragole, and D-limonene, which are likely contributors to the observed antimicrobial and anticancer effects. In addition, carvacrol nanoemulsions demonstrated potent cytotoxicity against multiple human cancer cell lines (HepG2, MCF-7, PC-3, and Caco-2) while showing minimal toxicity toward normal cells. Confocal microscopy further confirmed apoptosis induction in treated cancer cells, suggesting a mitochondria-mediated apoptotic pathway. In conclusion, this study highlights the strong therapeutic potential of essential oils—particularly carvacrol and its nanoemulsion formulation—as dual-action agents exhibiting broad-spectrum antibacterial activity against XDR pathogens and selective cytotoxicity against cancer cells.

Bacteria doi: 10.3390/bacteria4040063

Authors: Tanvi Premchandani Milind Umekar Amol Tatode Jayshree Taksande Rahmuddin Khan Mohammad Faizan Mohammad Qutub

Extracellular vesicles, encompassing eukaryotic exosomes and bacterial outer membrane vesicles (OMVs), play multifaceted roles in mediating host–pathogen interactions. These nanoscale structures act as critical mediators of intercellular communication, transporting diverse bioactive cargo such as miRNAs, cytokines, proteins, and bacterial components. Exosomes contribute to host immunity by delivering antimicrobial agents and modulating inflammatory responses, but they can also be hijacked by pathogens to suppress defenses and promote persistent infection. OMVs, on the other hand, enable bacteria to disseminate virulence factors, deliver toxins directly into host cells, and modulate immune signaling. For example, exosomes from infected macrophages can stimulate dendritic cell activation and T-cell priming, whereas bacterial OMVs have been shown to suppress host immunity or trigger excessive inflammation depending on their molecular cargo. Importantly, OMVs facilitate horizontal gene transfer and nutrient exchange within microbial communities, thereby influencing microbiome composition and adaptation. Together, these complex dynamics position both exosomes and OMVs as central players in immunity and pathogenesis. This review synthesizes recent insights into how host- and pathogen-derived vesicles modulate infection biology and immune responses, while also exploring their potential as diagnostic biomarkers and therapeutic carriers, and discussing current limitations in their clinical translation.

Bacteria doi: 10.3390/bacteria4040062

Authors: Olga Muter

The aim of this paper is to provide an overview of the main trends and progress in the biostimulation approach, which represents a crucial component of the broader multi-factor bioremediation process. A comprehensive search was carried out in the Scopus database. The stimulating roles of individual and complex nutrient amendments are reviewed, with particular emphasis on plant extracts, molasses, and surfactants. Methodological approaches for optimising nutrient formulations and conditions to strengthen the biostimulation effect are analysed, taking into account microbial ecology and physiology. Aspects of interspecies microbial interactions, such as cross-feeding connections, are discussed. The roles of directed evolution, starvation, and statistical optimisation in enhancing microbial activity are also highlighted. Overall, substantial theoretical knowledge on this topic has been accumulated in the scientific literature. However, data from long-term field studies remain scarce. Looking forward, modern methodological approaches may bridge these knowledge gaps by enabling the prediction of microbial activity, interactions, and cross-feeding, supported by comprehensive monitoring. In particular, artificial intelligence tools for the statistical optimisation of biostimulation conditions are expected to significantly improve process performance. This review summarises recent scientific papers alongside findings from our own long-term studies.

Bacteria doi: 10.3390/bacteria4040061

Authors: Aayush Bahl Manasa Rajagopalan Roopshali Rakshit Sashi Kant Saurabh Pandey Deeksha Tripathi

Toxin–antitoxin (TA) modules represent sophisticated regulatory networks that have evolved from simple plasmid maintenance factors into multifunctional genetic modules orchestrating bacterial stress responses, pathogenesis, and ecological adaptation. This review highlights a compelling correlation between the abundance of toxin–antitoxin (TA) modules and bacterial pathogenicity, as exemplified by Mycobacterium tuberculosis (M.tb), which encodes 118 TA loci—significantly more than the fewer than 10 found in closely related saprophytic species. The clinical significance of TA modules extends beyond traditional stress response roles to encompass antimicrobial persistence, where systems like VapBC and MazEF facilitate dormant subpopulations that survive antibiotic therapy while maintaining chronic infections. Recent discoveries have revealed TA modules as sophisticated bacterial defense mechanisms against bacteriophage infection, with DarTG and ToxIN systems representing novel antiviral immunity components that complement CRISPR-Cas and restriction–modification systems. The immunomodulatory capacity of TA modules demonstrates their role in host–pathogen interactions, where systems such as VapC12 in M.tb promote macrophage polarization toward permissive M2 phenotypes while inducing anti-inflammatory cytokine production. Large-scale genomic analyses reveal that TA modules function as drivers of horizontal gene transfer networks, with their signatures enabling accurate prediction of plasmid community membership and serving as determinants of microbial community structure. The biotechnological applications of TA modules have expanded to include genetic circuit stabilization, biocontainment device construction, and multi-species microbial community engineering, while therapeutic strategies focus on developing multi-target inhibitors against conserved TA protein families as promising approaches for combating drug-resistant bacterial infections. The evolutionary conservation of TA modules across diverse bacterial lineages underscores their fundamental importance as central organizing principles in bacterial adaptation strategies, where their multifunctional nature reflects complex selective pressures operating across environmental niches and host-associated ecosystems. This review provides an integrated perspective on TA modules as dynamic regulatory elements that support bacterial persistence, immune evasion, and ecological versatility, establishing them as genetic elements with truly “many faces and functions” in prokaryotic biology.

Bacteria doi: 10.3390/bacteria4040060

Authors: Akihito Nakanishi Natsumi Omino Ren Owa Hayato Kinoshita Hiroaki Fukunishi

Escherichia coli LS5218 is an attractive host for producing polyhydroxybutyrate. The strain, however, strongly requires heterologous gene expressions like phaC for efficient production. For enhancing the production, the whole gene expressions relating to end product-producing flow should be optimized so that not only heterologous induced-genes but also other relating genes are comprehensively analyzed on the transcription levels, resulting in normally time-consuming mutant-creation. Additionally, the explanation for each transcriptional relationship is likely to follow the relationships on known metabolic pathway map to limit the consideration. This study aimed to infer gene regulatory networks within glycolysis, a central metabolic pathway in LS5218, using machine learning-based causal discovery methods. To construct a directed acyclic graph representing the gene regulatory network, we employed the NOTEARS algorithm (Non-combinatorial Optimization via Trace Exponential and Augmented lagRangian for Structure learning). Using transcription data of 264 time-resolved sampling points, we inferred the gene regulatory network and identified several distal regulatory relationships. Notably, gapA, a key enzyme controlling the transition between the preparatory and rewarding phases in glycolysis, was found to influence pgi, the enzyme at the pathway’s entry point. These findings suggest that inferring such nonlocal regulatory interactions can provide valuable insights for guiding genetic engineering strategies.

Bacteria doi: 10.3390/bacteria4040059

Authors: López Franyer García Macias Adrian Beltran Oscar González Janneth Pinzón Andrés

Parkinson’s disease (PD) is a neurodegenerative disorder characterized by motor symptoms like tremor, rigidity, and bradykinesia. The WHO estimates that 10 million people currently have PD, with its prevalence expected to double to 20 million by 2050. Key risk factors include age, male sex, environmental contaminants, and family history. Emerging evidence links gut microbiota dysbiosis to PD, suggesting it contributes to neuroinflammation and disease progression, though the role of dietary interventions remains unclear. This study used computational simulations with genome-scale metabolic models (GEMs) to analyze how diet impacts the gut microbiota in PD patients. Fecal microbiota from PD patients and healthy controls were compared across three diets: high-fiber, Mediterranean, and vegan. Simulations revealed increased pro-inflammatory bacteria (e.g., Escherichia coli O157) in PD patients, likely due to reduced bacterial competition, alongside the decreased production of beneficial metabolites like butyrate, phenylalanine, and cysteine. The Mediterranean diet showed higher short-chain fatty acid production, potentially benefiting PD patients. These findings underscore the importance of dietary interventions in modulating the gut microbiome and suggest that targeted diets may complement PD therapies, improving patient outcomes.

Bacteria doi: 10.3390/bacteria4040058

Authors: Abdulhusein Jawdhari Robert Wolff Bianca-Maria Tihăuan Irina-Tania Ghitoc Nicolae Crăciun

This report investigates the interaction between the metabolites of the highly virulent bacteria Salmonella enterica and RTGill-W1 cells, a cell line derived from rainbow trout gills. As a facultative intracellular pathogen, Salmonella enterica infects both animals and humans through many routes. Upon entering an organism it can cause severe infection and pathology, which is also influenced by the bacterial metabolites. Although no intracellular presence of the pathogen in the exposed cell line could be detected, a dose-dependent effect of the metabolites on the cell line was observed, as exposure to 5%, 10%, and 20% concentrations led to enhanced metabolic activity and increased cytoplasmic neutral lipid droplets accumulation, whereas the lower dosage of 2.5% induced a lower metabolic rate compared to control and no significant intracellular lipid accumulation. The combination of all of the metabolites might be speculated to have increased the metabolic rate and lipid droplet production at higher concentrations due to possessing a growth factor or an endocrine effect, or as a response to a toxin. This paper may be the first report investigating the effect of a complete bacterial metabolite mixture in cultured cells.

Bacteria doi: 10.3390/bacteria4040057

Authors: Dominic L. Palazzolo Andrea Jorratt Deneil Patel Makenna Hoover Debasis Mondal Maya Tabakha Cathy Tran Juliette R. Amram Giancarlo A. Cuadra

Background: Past studies have documented the antimicrobial effects of dimethyl sulfoxide (D.M.SO). However, the side effects and toxicity profiles of DMSO in vivo have been a significant deterrent for its wide-ranging clinical use. Dimethyl sulfone (DMSO-2), a natural metabolite of DMSO, is currently used as a safe dietary supplement due to its antioxidant properties and multimodal mechanisms of action. While DMSO displays antimicrobial activity, little is known concerning DMSO-2’s antimicrobial effect. Thus, this investigation compares the antimicrobial effects of DMSO and DMSO-2 on the growth and viability of the pathogenic anaerobic bacteria, Porphyromonas gingivalis, and their cytotoxic effect on human oral epithelial (OKF6/TERT-2) cells. Methods: P. gingivalis was grown in TSBY media in the presence of DMSO or DMSO-2 (0–4%) for planktonic growth and viability determinations. OKF6/TERT-2 cells were expanded in vitro and similarly exposed to DMSO or DMSO-2 for viability studies. Results: After 24 h exposure to DMSO or DMSO-2, growth of P. gingivalis is inhibited by 57% and 77%, respectively, while viability is inhibited by 55% and 62%. In contrast, 24 h exposure to similar concentrations of DMSO or DMSO-2 induces 5% and 2% cytotoxicity in OKF6/TERT-2 cells, respectively. Conclusions: Both DMSO and DMSO-2 inhibit the growth and viability of P. gingivalis but show minimal toxic effect on OKF6/TERT-2 cells. Therefore, the utility of these two natural compounds as antimicrobial agents against anaerobic pathogens should be further investigated.

Bacteria doi: 10.3390/bacteria4040056

Authors: Ibrahim Isse Ali Kubilay Kurtulus Bastas

Common bacterial blight (CBB) is a significant disease caused by the seed-borne pathogen Xanthomonas axonopodis pv. phaseoli (Xap), which devastates global bean production. This study evaluated the effects of Bacillus subtilis (Bst26), Lactobacillus plantarum (Lpkb10), their combination (Bst26 + Lpkb10), copper hydroxide (CH), and an untreated control on controlling CBB in three bean cultivars (Göynük, Saltan, and Tezgeldi). Disease incidence (CI), disease severity index (DSI), severity score (SC), area under disease progress curve (AUDPC), and disease control (DC), along with agronomic traits such as plant height, number of primary branches, root length, and fresh root weight, were recorded to assess both infection rates and plant health under each treatment. The findings revealed significant differences in DI, DSI, SC, AUDPC, and DC (p ≤ 0.01) among the bean cultivars for CBB. Among the cultivars, the Bst26 treatment and the combination of Bst26 and Lpkb10 showed the highest control effectiveness, with DI values of 33.11% and 33.46% in Saltan, 35.65% and 44.16% in Göynük, and 37.71% and 42.43% in Tezgeldi, respectively, at 21 days after inoculation (DAI). Bst26 alone and in combination with Lpkb10 effectively controlled CBB, with disease reduction of 56.80% and 46.49% in Göynük, 57.08% and 56.62% in Saltan, and 52.18% and 46.19% in Tezgeldi, respectively. Disease progression was highest in the untreated control, with DI ranging from 77.15% to 82.54% across Göynük, Saltan, and Tezgeldi cultivars. Significant differences (p ≤ 0.01) in plant height, root length, and root weight were observed among treatments and cultivars. Disease parameters were negatively correlated with plant growth traits, and multi-treatment analysis demonstrated that combining bacterial strains effectively reduced disease severity in susceptible cultivars, highlighting their potential for improved CBB management.

Bacteria doi: 10.3390/bacteria4040055

Authors: Vinicius Silva Castro Emmanuel W. Bumunang Kim Stanford Eduardo Eustáquio de Souza Figueiredo

Background: Diarrheagenic Escherichia coli (DEC) remains relevant to public health and agri-food chains. The context in Brazil, as a major food producer and exporter, reinforces the need for genomic surveillance. Objective: We aimed to characterize Brazilian diffusely adhering (DAEC), enteropathogenic (EPEC), and Shiga toxin-producing E. coli (STEC) sequences in silico across O-serogroups, in addition to sequence-type (ST), virulence, resistome, and phylogenomic relationships. Methodology: We retrieved 973 genomes assigned to Brazil from NCBI Pathogen Detection Database and performed virtual-PCR screening for key DEC-genes. We then typed O-serogroups (ABRicate/EcOH), Multi-Locus Sequencing Type (MLST), virulome (Ecoli_VF), resistome (ResFinder), and characterized stx genes. Results: DEC represented 18.7% of genomes, driven primarily by EPEC. In EPEC, the eae β-1 subtype was most common; we detected, for the first time in Brazilian sequences, ξ-eae subtype and ST583/ST301. Seventy-eight percent of DAEC isolates were multidrug-resistant (MDR), and two ST were newly reported in the country (ST2141/ST500). In STEC, O157 formed a largely susceptible clade with uniform eae γ-1, whereas 57% of non-O157 were MDR. New STs (ST32/ST1804) were observed, and three genomes were closely related to international isolates. Conclusions: Despite the low DEC representation in the dataset, new STs and eae subtypes were detected in Brazil. Also, MDR in DAEC and non-O157 STEC reinforces the need for antimicrobial-resistance genomic surveillance.

Bacteria doi: 10.3390/bacteria4040054

Authors: Ainhoa Cordero Francisco Ferreira Patrícia Coelho João Belo João Metello Carina Santos Sónia Mateus Miguel Castelo-Branco Francisco José Barbas Rodrigues

Introduction: Colonization by Staphylococcus aureus—including methicillin-resistant strains (MRSA)—represents a growing public health concern, particularly in community and rural settings. In Portugal, limited data are available regarding its prevalence in populations with agricultural or animal-related exposures. Objectives: To determine the prevalence of S. aureus and MRSA nasal colonization among adults residing in the municipality of Sertã, Portugal, and to explore potential sociodemographic and behavioral factors associated with colonization. Methods: A cross-sectional study was conducted with 292 adult participants from multiple parishes of Sertã. Nasal swabs were collected for microbiological identification of S. aureus and MRSA. Data on sociodemographic characteristics, occupational exposure, animal contact, and recent antibiotic use were collected via structured questionnaires. Descriptive statistics and inferential analyses (chi-square and Fisher’s exact tests) were performed, and odds ratios were estimated. Results: The overall prevalence of S. aureus colonization was 19.9% (58/292), with MRSA detected in 4.8% (14/292) of participants, representing 24.1% of all S. aureus carriers. Colonization by S. aureus was slightly more frequent among females (51.7%) and predominantly observed in individuals aged 35–59 years. MRSA was more frequent in participants aged ≥ 60 years and was equally distributed between sexes. 57% of MRSA cases reported recent antibiotic use and all MRSA cases reported daily contact with animals—primarily domestic species. No statistically significant associations were identified between colonization and the analyzed variables, although trends suggested increased risk among individuals with animal contact and moderate to high-risk occupations. Conclusions: This study revealed a notable prevalence of S. aureus and MRSA colonization in a rural Portuguese population. Although no statistically significant associations were found, with animal contact, occupational exposure, and recent antibiotic use emerged as relevant epidemiological factors. These findings highlight the need for strengthened surveillance and further investigation into zoonotic transmission and occupational risk in rural environments.

Bacteria doi: 10.3390/bacteria4040053

Authors: Rocío de la Cuesta Mariana S. Sanin Florencia Battaglia Sandra L. Vasquez Pinochet Cecilia C. Cundon Adriana B. Bentancor María P. Bonino Ximena Blanco Crivelli

Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are E. coli pathovars of particular relevance to infant health. While the intestinal tract of humans and animals constitutes their primary habitat, these bacteria can also persist in natural environments such as sand. The aim of this study was to evaluate the persistence of STEC and EPEC strains in sand microcosms under controlled conditions of heat and desiccation in order to estimate their viability in this matrix and provide evidence regarding the potential risks associated with the use of sandboxes in public spaces. The study included STEC strains belonging to clinically important serotypes (O26:H11, O103:H2, O111:H8, O121:H19, O145:NM, O157:H7 and O174:H28), animal-derived EPEC strains, and a non-pathogenic E. coli strain (NCTC 12900). The strains were inoculated into sterile sand microcosms and maintained at 37 °C. Death curves, persistence in the matrix, presence of virulence genes, and ability to produce biofilm were evaluated. The death and persistence curves varied by serotype; some strains remained viable in the viable but non-culturable state for extended periods. All strains retained their virulence-associated genetic markers throughout the assays. None of the STEC strains was classified as a biofilm producer under the experimental conditions, whereas the two EPEC strains were identified as weak and moderate biofilm producers. However, no association was found between biofilm formation and persistence in the matrix. The findings provide an initial approach and provide relevant evidence of the capacity of STEC and EPEC strains to survive in sand, which could represent a potential risk in recreational environments.

Bacteria doi: 10.3390/bacteria4040052

Authors: Kathryn L. Lauder Shafiullah M. Parvej Yiyang Shen Chongyang Zhang Jehadi Osei-Bonsu James F. Lowe Weiping Zhang

(1) Background: Pigs can be another host of Shiga toxin-producing E. coli (STEC), suggesting that pork products could be a potential risk to public health. A USDA National Animal Health Monitoring System (NAHMS) study revealed that Shiga toxin genes were detected in more than half of samples nationwide but only about a quarter of samples from the state of Illinois. To characterize the presence of STEC in Illinois pigs better and to explore the discrepancy between Illinois and other swine-producing states, we increased the sampling size and collected samples in different regions of the state and in different months to detect Shiga toxin genes in Illinois finisher pigs and subtyped the Shiga toxin genes further to assess any potential risk of STEC originating from Illinois pigs to human health. (2) Methods: Fecal samples were collected from 471 Illinois finisher pigs at different locations from October 2021 to September 2022. DNA samples were extracted from individual fecal samples and PCR-tested for Shiga toxin genes (stx1, stx2) and then toxin subtypes (stx2a, stx2c, stx2d, and stx2e). (3) Results: The data showed that the stx2 gene was detected in 61% of the fecal samples (285/471), whereas stx1 was detected only in 0.4% of the samples (2/471). The data also indicated a lower prevalence of stx genes in the samples collected in certain cold months (36% in October and 19% in March) compared to that in those from warm months (56% to 100% from April to September). Stx2d, a subtype associated with severe human illness, was detected in 2% of the samples (10/471); in contrast, stx2e, which is expressed by E. coli strains causing diarrhea and edema disease in pigs, was the most detected (49%; 229/471). (4) Conclusions: The high prevalence of Shiga toxin genes in the fecal samples from Illinois finisher pigs suggests that Stx-positive E. coli strains circulate in Illinois pig farms. However, the highly detected stx2e-positive STEC (or enterotoxigenic E. coli, ETEC) strains are associated with diarrhea and edema disease in pigs, indicating the need for disease prevention or control for pigs but unlikely a safety concern for Illinois pork products or a major risk of human illnesses.

Bacteria doi: 10.3390/bacteria4040051

Authors: Hassan K. Dhaini Bahaa Fahed Hassanieh Rana El Hajj Mahmoud I. Khalil

Marine actinomycetes constitute a vigorous source of bioactive compounds with potential anti-tumor activity. This study investigates the antitumor activity and classification of actinomycetes isolated from 32 marine soil samples collected across four seasons from Tyr City Beach, Lebanon. A total of 80 morphologically diverse isolates were recovered and characterized, with dominant genera including Streptomyces, Kocuria, and Micrococcus. Among these, three promising strains—Kocuria rosea, Micrococcus luteus, and Streptomyces longisporoflavus—were selected for further analysis. Crude extracts were tested against human colorectal adenocarcinoma (Caco-2) and human hepatocellular carcinoma (HepG-2) cancer cell lines using MTT and Western blot assays. At the highest concentration (8 µg/µL), the extracts reduced cell viability to 24–37% in Caco-2 and 12–25% in HepG-2. The IC50 values ranged from 1.72 to 3.53 µg/µL, depending on the extract and cell line. Western blot analysis showed dose-dependent increases in the Bax/Bcl-2 ratio, with fold changes reaching 4.35 (Kocuria), 11.39 (Micrococcus), and 14.25 (Streptomyces) in HepG-2 cells. The p53 protein expression also increased significantly, with fold changes up to 7.79 in Caco-2 and 3.0 in HepG-2 cells. These results indicate that marine actinomycetes from the Lebanese coastline hold strong potential as a source of antitumor agents targeting apoptosis pathways.

Bacteria doi: 10.3390/bacteria4040050

Authors: Leonard Koolman Chijioke Emenike Debasis Mitra Sourav Chattaraj

Antimicrobial resistance (AMR) is traditionally discussed in the context of horizontally acquired resistance genes and point mutations at target loci. However, this gene-centred model fails to account for a large number of clinically important modalities of resistance. There is now substantial evidence implicating bacteria in the ability to escape the effects of antibiotics in a variety of non-canonical ways, which are not considered in traditional diagnostic and surveillance pipelines. Among these factors, we can list those arising from global regulatory networks, phase variability, epigenetic tuning, small RNAs, genome structural variability, and phenotypic states like tolerance and persistence. This review will blend the current knowledge on these alternative pathways of resistance and underscore how they intersect with canonical genetic determinants. We will highlight cases where resistance emerges in the absence of known resistance genes, analyse the role of regulatory plasticity in efflux pump expression and membrane remodelling, and examine the contributions of bacterial stress responses and post-transcriptional control. Additionally, we will address methodological gaps in the detection of these mechanisms and their implications for clinical treatment failure, resistance surveillance, and drug development. By integrating insights from molecular microbiology, systems biology, and genomics, this review aims to offer a framework for understanding AMR as a multifaceted, context-dependent phenotype, not merely a genotype. We conclude by identifying knowledge gaps and suggesting priorities for research and diagnostic innovation in this evolving field.

Bacteria doi: 10.3390/bacteria4040049

Authors: Zainab Hussain Abdul Wahab Shayma Thyab Gddoa Al-Sahlany

Biosurfactants are amphiphilic compounds synthesized by microorganisms, providing environmentally sustainable alternatives to synthetic surfactants owing to their biodegradability and minimal toxicity. This review examines bacterial origins of biosurfactants, with a focus on surfactin derived from Bacillus species including B. subtilis, B. amyloliquefaciens, B. licheniformis, and B. pumilus. The cyclic lipopeptide structure of surfactin, which consists of a heptapeptide attached to a β-hydroxy fatty acid chain, imparts remarkable surface-active characteristics, such as a reduced surface tension of 27 mN/m and a low critical micelle concentration of 20 µM. In medical applications, surfactin demonstrates antimicrobial, antiviral, and anticancer properties through mechanisms such as apoptosis induction and metastasis inhibition, as well as promoting wound healing by enhancing angiogenesis and decreasing fibrosis. In the realm of food processing, it functions as a natural antimicrobial agent against pathogens such as Listeria and Salmonella, improves emulsion stability in products like mayonnaise, prolongs shelf life, and influences gut microbiota composition. The safety profiles correspond with the Generally Recognized as Safe (GRAS) status for compounds derived from Bacillus; however, it is essential to optimize dosing to reduce the risks associated with hemolysis. Challenges encompass production expenses, scalability issues, and regulatory obstacles, with genetic engineering suggested as a means to achieve improved yields. Surfactin demonstrates potential as a sustainable bioactive component within the food and health industries.

Bacteria doi: 10.3390/bacteria4030048

Authors: Malak Mezher Salma Khazaal Mahmoud I. Khalil Dalia El Badan Taymour A. Hamdalla

(1) Background: This study evaluated the efficacy of magnesium nanoparticles (MgNPs) synthesized through a green method utilizing bacterial metabolites (BMs) produced by Escherichia coli. (2) Methods: BMs were tested for total phenolic content by high-performance liquid chromatography. MgNPs were characterized by X-ray diffraction, transmission electron microscopy, Fourier transform infrared spectroscopy, photoluminescence, and ultraviolet–visible spectroscopy. MgNPs and BMs were tested for antibacterial and antibiofilm potentials against multidrug-resistant clinical isolates by agar well diffusion, minimum inhibitory and bactericidal concentration assays, time–kill test, and inhibition of biofilm formation and destruction of pre-formed biofilm assays. Furthermore, they were tested for antioxidant potential by 2,2-diphenyl-1-picryhydrazyl radical scavenging assay. (3) Results: BMs included carbohydrates, reducing sugars, and phenols (gallic acid and catechin) with a total phenolic content of 0.024 mg GAE/g. MgNPs showed a pure crystalline structure with a spherical shape, 17.8 nm in size, and a 4.19 eV energy gap. Bacteria included Streptococcus pneumonia, Enterococcus faecium, Klebsiella pneumonia, and Salmonella Typhimurium. The antibacterial results showed inhibition zones ranging between 7.2 and 10.4 mm, a bactericidal effect of MgNPs, a bacteriostatic effect of BMs, and growth inhibition after 3 h. The antibiofilm results demonstrated significant inhibition of biofilm formation (inhibition percentages of 64.931% for MgNPs and 71.407% for BMs). However, the assays revealed modest biofilm destruction (eradication percentages of 48.667% for MgNPs and 37.730% for BMs). Antioxidant capacity revealed notable scavenging activity of MgNPs (scavenging activity of 41.482%) and weak activity of BMs (scavenging activity of 16.460%). (4) Conclusions: These findings support the application of MgNPs in biomedical fields.

Bacteria doi: 10.3390/bacteria4030047

Authors: Azar Motamedi Boroojeni Nikoo Veiskarami Elena Rita Simula Leonardo Antonio Sechi Abdollah Derakhshandeh

Attenuated Salmonella strains offer an opportunity for delivering DNA vaccines to antigen-presenting cells. DNA vaccines trigger cellular immune responses, making them suitable for targeting intracellular pathogens, such as Mycobacterium avium subspecies paratuberculosis (MAP). Since whole organism MAP vaccines interfere with tuberculosis diagnosis, innovative vaccine technologies have been introduced to elicit an immune response targeting species-specific antigens. Fibronectin attachment protein (FAP), a MAP surface antigen that is species-specific, can induce cellular immune responses. The present study aims to explore the immunogenic potential of a mammalian expression plasmid encoding the fap-P gene of MAP within a mouse model, utilizing a Salmonella vector for oral immunization using a fluorescent assay and Western blot analysis. The results proved the ability of the constructed plasmid to stimulate the humoral immune response in mice. Moreover, fluorescence microscopy of splenocytes confirmed the successful delivery of the plasmid to the immune system at 24, 48, and 72 h following oral administration. It can be concluded that FAP-P could be considered a candidate for further investigation in the context of MAP vaccine development. Additionally, the use of Salmonella as a delivery system not only improves the efficacy of DNA vaccines but also helps in the preliminary evaluation of the antigens’ immunogenic properties.

Bacteria doi: 10.3390/bacteria4030046

Authors: Sima Rugarabamu Gaspary Mwanyika

Antimicrobial resistance (AMR) is a growing global health emergency that threatens the effectiveness of modern medicine, exacerbating healthcare costs, morbidity, and mortality, particularly in low- and middle-income countries (LMICs). Traditional approaches to antimicrobial development and stewardship have proven inadequate in curbing the rapid emergence and spread of resistant pathogens. This review explores cutting-edge biotechnological innovations as sustainable, precision-based solutions to combat AMR and promote global health equity. A comprehensive narrative review was conducted using literature published between 2018 and 2023 from PubMed, ScienceDirect, and Web of Science. Peer-reviewed studies focusing on novel antimicrobial strategies were thematically analyzed, with attention to efficacy, feasibility, and translational readiness. Key innovations identified include nanotechnology-enhanced antimicrobial delivery, bacteriophage therapy, CRISPR-Cas gene editing, immunotherapy, and personalized medicine. These strategies demonstrated substantial in vitro and in vivo efficacy, such as >90% MRSA biofilm reduction via silver nanoparticles and 95% carbapenem susceptibility restoration in E. coli using CRISPR-Cas9. When integrated with machine learning and rapid diagnostics, these approaches enable precision-targeted therapies and data-informed stewardship, offering scalable solutions adaptable to diverse healthcare systems. Antimicrobial resistance demands urgent, equitable innovation. Integrating biotechnologies like CRISPR, phage therapy, and nanomedicine with data-driven tools offers promising solutions. To ensure real-world impact, we recommend establishing regionally tailored translational research platforms and public–private partnerships as the most effective strategy to scale innovations and strengthen AMR response in low-resource settings.

Bacteria doi: 10.3390/bacteria4030045

Authors: Cesira Giordano Francesca Del Conte Maira Napoleoni Simona Barnini

Clinical manifestations of salmonellosis in humans typically include acute gastroenteritis, abdominal pain, diarrhea, nausea, and fever. Diarrhea and anorexia may persist for several days. In some cases, the organisms may invade the intestinal mucosa and cause septicemia, even in the absence of significant gastrointestinal symptoms. Most clinical signs are attributed to hematogenous dissemination of the pathogen. As with other microbial infections, disease severity is influenced by the serotype of the organism, bacterial load, and host susceptibility. Serotyping analysis of Salmonella spp. using the White–Kauffmann–Le Minor scheme remains the gold standard for strain typing. However, this method is expensive, time-consuming, and requires significant expertise and visual interpretation by trained personnel, which is why it is typically restricted to regional or national reference laboratories. In this study, we evaluated a spectroscopic technique coupled with chemometrics and multivariate machine learning algorithms for its ability to discriminate the main Salmonella spp. serogroups in a clinical routine setting. We analyzed 95 isolates of Salmonella that were randomly selected, including four strains of S. Typhi. The I-dOne Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR) system (Alifax S.r.l., Polverara, Italy) also shows promising potential for distinguishing Salmonella Typhi within the D serogroup. The I-dOne system enables simultaneous identification of both species and subspecies using the same workflow and instrumentation, thus streamlining the diagnostic process.

Bacteria doi: 10.3390/bacteria4030044

Authors: Luis Getino José Antonio Revilla-Gómez Luisa María Ariza-Carmona Sofie Thijs Claude Didierjean Alejandro Chamizo-Ampudia

Plastic pollution has emerged as a critical environmental challenge due to the widespread accumulation of petrochemical plastics in natural ecosystems. Conventional waste management strategies, including mechanical recycling and incineration, have demonstrated limited efficiency in addressing the persistence of plastics such as polyethylene, polypropylene, polyethylene terephthalate, and polyvinyl chloride. While incineration eliminates plastic material, it does not promote circularity and may generate toxic emissions. As a sustainable alternative, microbial biodegradation involves bacteria, fungi, and actinomycetes capable of degrading synthetic polymers through enzymatic processes. This review provides a comprehensive overview of microbial degradation of major plastics such as polyethylene, polypropylene, polyethylene terephthalate, and polyvinyl chloride, highlighting key strains, degradation rates, and enzymatic mechanisms. Importantly, biodegradation research also informs the development of in situ remediation technologies and supports new recycling strategies. Advances in protein engineering and synthetic biology are discussed for enhancing degradation efficiency. However, scaling biodegradation to environmental conditions remains challenging due to variable temperature, pH, microbial competition, and potentially toxic intermediates. Despite these limitations, microbial biodegradation represents a promising ecofriendly approach to address plastic waste and promote a biobased circular economy. Future work should integrate microbial processes into existing recycling infrastructure and design robust consortia guided by omics tools.

Bacteria doi: 10.3390/bacteria4030043

Authors: Elena Roxana Buzilă Raluca Gatej Cristina Trifan Teodora Vremera Mihaela Leustean Adina David Daniela Cosmina Bosogea Georgiana Barbu Adina Gatea Ciprian Ilie Luminița Smaranda Iancu

Salmonella is a major foodborne pathogen, representing a significant public health concern across the European Union (EU), accounting for 39% of foodborne illness-related hospitalizations in 2022, with the highest rates observed in Romania, Cyprus, Greece, and Lithuania. This pilot study aimed to enhance the surveillance and characterization of Salmonella by implementing both phenotypic and genotypic methods for strain typing, as well as for the detection and confirmation of resistance to ciprofloxacin. Materials and methods: A total of 109 Salmonella strains from acute diarrheal cases in North-Eastern Romania were collected (January–August 2024). From these, 19 representative isolates were selected for molecular characterization, including Multi-Locus Sequence Typing (MLST) and the detection of ciprofloxacin resistance determinants. Whole-Genome Sequencing (WGS) was subsequently performed to confirm serotype identity and resistance markers. Results: The 19 isolates underwent Multi-Locus Sequence Typing (MLST) and ciprofloxacin resistance profiling, with Whole-Genome Sequencing (WGS) for confirmation. MLST identified S. Enteritidis (42.1%) as the predominant serotype, followed by S. Typhimurium, S. Livingstone, and S. Infantis. WGS confirmed serotypes in 15 isolates; 2 showed discrepancies with phenotypic results. Phenotypic resistance to ciprofloxacin was detected in 12/19 (63.2%) of the isolates, 6/12 presenting gyrA mutations (S83Y, D87G), and 2/12 strains presenting the plasmid-mediated qnrB19 gene.

Bacteria doi: 10.3390/bacteria4030042

Authors: Douglas M. Ruden Glen Ray Hood

The discovery of Asgard archaea has reshaped our understanding of eukaryotic origins, supporting a two-domain tree of life in which eukaryotes emerged from Archaea. Building on this revised framework, we propose the Pre-prokaryotic Organismal Lifeforms Existing Today (POLET) hypothesis, which suggests that relic pre-prokaryotic life forms—termed POLETicians—may persist in deep, anoxic, energy-limited environments. These organisms could represent a living bridge to the RNA world and other origin-of-life models, utilizing racemic oligoribonucleotides and peptides, non-enzymatic catalysis, and mineral-assisted compartmentalization. POLETicians might instead rely on radical-based redox chemistry or radiolysis for energy and maintenance. These biomolecules may be racemic or noncanonical, eluding conventional detection. New detection methods are required to determine such life. We propose generalized nanopore sequencing of any linear polymer—including mirror RNAs, mirror DNAs, or any novel genetic material—as a potential strategy to overcome chirality bias in modern sequencing technologies. These approaches, combined with chiral mass spectrometry and stereoisomer-resolved analytics, may enable the detection of molecular signatures from non-phylogenetic primitive lineages. POLETicians challenge the assumption that all life must follow familiar biochemical constraints and offer a compelling extension to our search for both ancient and extant forms of life hidden within Earth’s most extreme environments.

Bacteria doi: 10.3390/bacteria4030041

Authors: Chinedu Amaeze Frank Mohammed Dauda Goni Nor Fadhilah Kamaruzzaman Hafeez A. Afolabi Mohammed S. Gaddafi Aliyu Yakubu Shamsaldeen Ibrahim Saeed

Background: Campylobacter represents a significant global public health threat, with rising prevalence and increasing concern over antimicrobial resistance (AMR). This study aims to assess the prevalence, evaluate the antimicrobial resistance profiles, and identify risk factors associated with infection in dogs from Kelantan, Malaysia. To the best of our knowledge, this is the first comprehensive investigation of Campylobacter spp. in dogs within this region. Methods: Campylobacter was isolated from rectal swabs of 50 dogs using modified charcoal cefoperazone deoxycholate agar (mCCDA) and confirmed biochemically, with Campylobacter identified via polymerase chain reaction (PCR). Antimicrobial resistance profile of the isolates was determined using the Kirby–Bauer disk diffusion method. Data on risk factors were assessed through a semi-structured questionnaire. Results: The results revealed an overall prevalence of Campylobacter spp. 28.0% (14/50) in dogs. C. helveticus was the predominant species in dogs (40.7%). The resistance rates of Campylobacter isolates showed notable resistance to ampicillin (85.71%), amoxicillin (71.43%), erythromycin (64.29%), tetracycline (57.14%), and sulfonamides (50%), respectively. Overall, multiple antimicrobial resistance (MAR) indices for all Campylobacter isolates were consistently above the 0.2 threshold, signifying multidrug resistance. Risk factors such as dogs that are semi-roamers and those fed homemade /raw feed were found to be associated with higher risk of Campylobacter (odds ratios: 1.180, p-value = 0.025 semi-roamers; odds ratio: 1.196, p-value = 0.019 fed homemade/raw feed). Conclusions: This study reveals significant prevalence and a remarkable antimicrobial resistance profile, thus advocating the need for improved pet management, responsible antimicrobial use, and targeted interventions to mitigate the spread of multidrug-resistant Campylobacter in companion animals.

Bacteria doi: 10.3390/bacteria4030040

Authors: Md Shahab Uddin Md Ahosanul Haque Shahid Saiduzzaman Marzia Rahman K. H. M. Nazmul Hussain Nazir

This study was undertaken to identify foodborne bacteria and fungi from different parts of eggs depending on their storage duration, organoleptic properties, total viable count, and antibiotic resistance profile. Thirty-two samples were randomly collected from commercial layer farms in Mymensingh. Following the protocol of sample preparation, outer-surface and inner-content samples were streaked onto various selective media. Isolation and identification were carried out by observing Gram staining and biochemical properties. Molecular detection was confirmed through a PCR assay using specific primers for Salmonella spp., E. coli, Staphylococcus spp., and fungus (Simplicillium spp. and Saccharomyces spp.). To determine the antibiotic resistance profile, the disk diffusion method was followed against nine antibiotic disks. The isolation rate of E. coli, Salmonella spp., and Staphylococcus spp. was 53.13%, 40.63%, and 40.63%, respectively, in the outer eggshell and 15.63%, 25%, and 15.63%, respectively, in the inner content of the eggs. Regarding the fungus content (yeast and mold), 100% was obtained in the outer eggshell, whereas there was an absence of fungus in the inner content. It was observed that all the isolates of E. coli, Salmonella spp., and Staphylococcus spp. were highly sensitive to either Ciprofloxacin or Levofloxacin and extremely resistant to Amoxicillin or Azithromycin drug disks or both. The data also shows that storage duration had a proportional relationship with TVC and an inversely proportional relationship with organoleptic properties. This study indicates that eggs harbor multidrug-resistant foodborne bacteria, which might constitute a public health hazard if these antibiotic-resistant bacteria are transferred to humans.

Bacteria doi: 10.3390/bacteria4030039

Authors: Tofick B. Wekesa Justus M. Onguso Damaris Barminga Ndinda Kavesu

Common bean (Phaseolus vulgaris L.) is a critical protein-rich legume supporting food and nutritional security globally. However, Fusarium wilt, caused by Fusarium solani, remains a major constraint to production, with yield losses reaching up to 84%. While biocontrol strategies have been explored, most microbial agents are sourced from mesophilic environments and show limited effectiveness under abiotic stress. Here, we report the isolation and characterization of extremophilic Bacillus spp. from the hypersaline Lake Bogoria, Kenya, and their biocontrol potential against F. solani. From 30 isolates obtained via serial dilution, 9 exhibited antagonistic activity in vitro, with mycelial inhibition ranging from 1.07–1.93 cm 16S rRNA sequencing revealed taxonomic diversity within the Bacillus genus, including unique extremotolerant strains. Molecular screening identified genes associated with the biosynthesis of antifungal metabolites such as 2,4-diacetylphloroglucinol, pyrrolnitrin, and hydrogen cyanide. Enzyme assays confirmed substantial production of chitinase (1.33–3160 U/mL) and chitosanase (10.62–28.33 mm), supporting a cell wall-targeted antagonism mechanism. In planta assays with the lead isolate (B7) significantly reduced disease incidence (8–35%) and wilt severity (1–5 affected plants), while enhancing root colonization under pathogen pressure. These findings demonstrate that extremophile-derived Bacillus spp. possess robust antifungal traits and highlight their potential as climate-resilient biocontrol agents for sustainable bean production in arid and semi-arid agroecosystems.

Bacteria doi: 10.3390/bacteria4030038

Authors: Janhvi Mishra Rawat Mrinalini Agarwal Shivani Negi Jigisha Anand Prabhakar Semwal Balwant Rawat Rajneesh Bhardwaj Debasis Mitra

Plant growth-promoting rhizobacteria (PGPRs) are well known for their capacity to enhance the growth and survival of in vitro-grown plants. However, their effect on Nardostachys jatamansi (D. Don) DC., a critically endangered medicinal plant in the Indian Himalayan Region, is still unknown. In this study, a simple, reproducible protocol for in vitro propagation of N. jatamansi was established using shoot tip explants, cultured on Murashige and Skoog (MS) medium supplemented with different plant growth regulators, including N6-benzylaminopurine, thidiazuron (TDZ), and naphthalene acetic acid (NAA). MS media supplemented with 2.0 μM TDZ and 0.5 µM NAA created a significant shoot induction with an average of 6.2 shoots per explant. These aseptically excised individual shoots produced roots on MS medium supplemented with Indole Butyric Acid or NAA within 14 days of the transfer. The PGPR, viz., Bacillus subtilis and Pseudomonas corrugata, inoculation resulted in improved growth, higher chlorophyll content, and survival of in vitro-rooted plants (94.6%) after transfer to the soil. Moreover, the PGPRs depicted a two-fold higher total phenolics (45.87 mg GAE/g DW) in plants. These results clearly demonstrate the beneficial effects of P. corrugata and B. subtilis on the growth, survival, and phytochemical content of N. jatamansi.

Bacteria doi: 10.3390/bacteria4030037

Authors: Manuela Bonilla-Espadas Marcelo Bertazzo Irene Lifante-Martinez Mónica Camacho Elena Orgilés-Calpena Francisca Arán-Aís María-José Bonete

Leather biodegradation is a complex microbial process with increasing relevance for sustainable waste management. In this study, we investigated bacterial communities responsible for the degradation of leather treated with different tanning agents (chrome, Zeolite, Biole®) using high-throughput 16S rRNA gene sequencing and metatranscriptomic analysis. Proteobacteria, Bacteroidetes, and Patescibacteria emerged as the dominant phyla, while genera such as Acinetobacter, Pseudomonas, and Sphingopyxis were identified as key contributors to enzymatic activity and potential metal resistance. A total of 1302 enzymes were expressed across all the conditions, including 46 proteases, with endopeptidase La, endopeptidase Clp, and methionyl aminopeptidase being the most abundant. Collagen samples exhibited the highest functional diversity and total enzyme expression, whereas chrome-treated samples showed elevated protease activity, indicating selective pressure from heavy metals. Differential enzyme expression patterns were linked to both the microbial identity and tanning chemistry, revealing genus- and treatment-specific enzymatic signatures. These findings deepen our understanding of how tanning agents modulate the microbial structure and function and identify proteases with potential applications in the bioremediation and eco-innovation of leather waste processing.

Bacteria doi: 10.3390/bacteria4030036

Authors: Bikash Ranjan Giri Sourav Chattaraj Subhashree Rath Mousumi Madhusmita Pattnaik Debasis Mitra Hrudayanath Thatoi

Azospirillum is a well-studied genus of plant growth-promoting rhizobacteria (PGPR) and one of the most extensively researched diazotrophs. This genus can colonize rhizosphere soil and enhance plant growth and productivity by supplying essential nutrients to the host. Azospirillum–plant interactions involve multiple mechanisms, including nitrogen fixation, the production of phytohormones (auxins, cytokinins, indole acetic acid (IAA), and gibberellins), plant growth regulators, siderophore production, phosphate solubilization, and the synthesis of various bioactive molecules, such as flavonoids, hydrogen cyanide (HCN), and catalase. Thus, Azospirillum is involved in plant growth and development. The genus Azospirillum also enhances membrane activity by modifying the composition of membrane phospholipids and fatty acids, thereby ensuring membrane fluidity under water deficiency. It promotes the development of adventitious root systems, increases mineral and water uptake, mitigates environmental stressors (both biotic and abiotic), and exhibits antipathogenic activity. Biological nitrogen fixation (BNF) is the primary mechanism of Azospirillum, which is governed by structural nif genes present in all diazotrophic species. Globally, Azospirillum spp. are widely used as inoculants for commercial crop production. It is considered a non-pathogenic bacterium that can be utilized as a biofertilizer for a variety of crops, particularly cereals and grasses such as rice and wheat, which are economically significant for agriculture. Furthermore, Azospirillum spp. influence gene expression pathways in plants, enhancing their resistance to biotic and abiotic stressors. Advances in genomics and transcriptomics have provided new insights into plant-microbe interactions. This review explored the molecular mechanisms underlying the role of Azospirillum spp. in plant growth. Additionally, BNF phytohormone synthesis, root architecture modification for nutrient uptake and stress tolerance, and immobilization for enhanced crop production are also important. A deeper understanding of the molecular basis of Azospirillum in biofertilizer and biostimulant development, as well as genetically engineered and immobilized strains for improved phosphate solubilization and nitrogen fixation, will contribute to sustainable agricultural practices and help to meet global food security demands.

Bacteria doi: 10.3390/bacteria4030035

Authors: Joel J. Maki Lucas Showman Torey Looft

The genus Turicibacter is a common inhabitant of the small intestine of numerous animal species, including chickens. However, little is known about the phenotypic and genetic diversity of the genus. Within the chicken small intestine, bile and its primary components, bile acids, are involved in nutrient absorption and modulating microbial community structure. Here, we compare T. sanguinis MOL361 (type strain of the genus), with three strains of the recently described species T. bilis, two from chicken and one from swine. Multiple bile salt hydrolase (BSH) genes, responsible for modification of host-derived bile acids, were identified in each strain and were compared to other Turicibacter BSH with known activities. The bile acid deconjugation ability of individual strains were assessed using chicken bile, as well as the primary bile acids taurochenodeoxycholic acid and taurocholic acid. Both chicken isolates, T. bilis MMM721 and T. bilis ISU324, as well as T. sanguinis MOL361, significantly reduced the concentrations of the tauro-conjugated bile acids. Overall, this work identifies the context-dependent nature of Turicibacter BSH activity.

Bacteria doi: 10.3390/bacteria4030034

Authors: Yanhua Zhao Hui Xue Guoxing Liu Li Sun Hucheng Jiang

Grass carp in aquaculture exhibited symptoms of bacterial infection leading to mortality. To investigate the cause of the disease and control grass carp infections, samples from diseased grass carp were collected, and a bacterial strain named XH-1 was isolated from the internal organs of the infected fish. Artificial infection experiments were conducted to determine whether the isolated strain XH-1 was the pathogenic bacterium. The biological characteristics of the isolated strain were studied through a 16S rRNA sequence analysis, physiological and biochemical identification, and phylogenetic tree construction. Extracts from 14 traditional Chinese herbs were tested to evaluate their bacteriostatic and bactericidal effects on the isolated strain. The regression infection experiment confirmed that the isolated strain XH-1 was the pathogenic bacterium causing the grass carp disease. Biological characterization studies identified the bacterium as Aeromonas veronii, which is clustered with A. veronii MW116767.1 on the phylogenetic tree. Among the 14 Chinese herbal extracts, Lignum sappa, Pericarpium granna, Artemisia argyi, Scutellaria baicalensis Georgi, Coptis chinensis, and Artemisiacapillaris thunb exhibited significant bacteriostatic effects on XH-1. Lignum sappa showed the highest sensitivity to A. veronii, with the largest inhibition zone diameter, and its minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were 7.813 mg/mL and 15.625 mg/mL, respectively. As the concentration of Lignum sappa extract increased, its bacteriostatic and bactericidal effects strengthened. When the concentration exceeded 14 mg/mL, it maintained strong bactericidal activity over 32 h. This study on A. veronii XH-1 provides theoretical insights for the prevention of grass carp aquaculture diseases and the use of traditional Chinese herbs for treatment.

Bacteria doi: 10.3390/bacteria4030033

Authors: Amandhi N. Ekanayake Wasana Gunawardana Rohan Weerasooriya

Nitrifying bacteria, including ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), are players in the nitrogen cycle but pose serious health risks when colonizing drinking water distribution networks (DWDNs). While the global impact of these bacteria is increasingly recognized, a significant research gap remains concerning their effects in tropical regions, particularly in developing countries. This study aims to bridge that gap by systematically reviewing the existing literature on nitrifying bacteria in DWDNs, their behavior in biofilms, and associated public health risks, particularly in systems reliant on surface water sources in tropical climates. Using the PRISMA guidelines for systematic reviews, 51 relevant studies were selected based on content validity and relevance to the research objective. The findings highlight the critical role of nitrifying bacteria in the formation of nitrogenous disinfection by-products (N-DBPs) and highlight specific challenges faced by developing countries, including insufficient monitoring and low public awareness regarding safe water storage practices. Additionally, this review identifies key surrogate indicators, such as ammonia, nitrite, and nitrate concentrations, that influence the formation of DBPs. Although health risks from nitrifying bacteria are reported in comparable studies, there is a lack of epidemiological data from tropical regions. This underscores the urgent need for localized research, systematic monitoring, and targeted interventions to mitigate the risks associated with nitrifying bacteria in DWDNs. Addressing these challenges is essential for enhancing water safety and supporting sustainable water management in tropical developing countries.

Bacteria doi: 10.3390/bacteria4030032

Authors: Mulat Erkihun Desalegn Nigatu Chanie Yesuf Adem Siraj

Background: Helicobacter pylori infection is widely prevalent across the globe and is a major etiological agent of various gastric pathologies. This bacterium colonizes the human stomach, where it induces a range of mucosal abnormalities observable upon clinical examination. Accordingly, the present study aimed to assess the prevalence and clinical implications of H. pylori infection among patients undergoing endoscopic evaluation. Method: A cross-sectional study was conducted from January to May 2019 at endoscopy service-providing health institutions. Sociodemographic and clinical data were collected. Gastric biopsies were collected during endoscopic procedures and immediately inoculated into brain–heart infusion broth and plated out. Then, phenotypic bacterial identification was done. The collected data have been analyzed using SPSS version 23. A logistic regression model was used for association determination. Result: Among the 135 individuals enrolled in the study, 59.3% are male, and 40.7% are female, with a mean age of 45 years. H. pylori is isolated in 17.8% of participants (24/135). Notably, the majority of these isolates 71% (17/24) are from male participants, while 29% (7/24) are from females. A statistically significant association is identified between H. pylori infection and both high salt intake [AOR = 3.3; 95% CI: 1.5–10.8; p = 0.04] and the presence of duodenal ulcers [AOR = 3.8; 95% CI: 1.2–11.9; p = 0.02]. The highest prevalence of H. pylori is observed among patients diagnosed with atrophic pangastritis. Conclusions: The prevalence of H. pylori among the study participants is comparatively low. However, a significant association was observed between H. pylori infection and both high dietary salt intake and the presence of duodenal ulcers.

Bacteria doi: 10.3390/bacteria4030031

Authors: Roshan Pudasaini Eman M. Khalaf Dylan J. L. Brettingham Manish N. Raizada

In the African Sahel, fonio (Digitaria sp.) is a cereal crop that alleviates mid-season hunger before other main crops are harvested. As fonio is valued for its ability to grow under low nutrient and drought conditions, it was hypothesized that it may contain endophytic bacteria that can tolerate such extreme stress. White fonio seeds were obtained from a dry environment (Mali) and a moderate rainfall environment (Guinea). Plants were grown indoors on field soil mixed with sand to mimic Sahelian soils, grown at 30 °C, and exposed to drought, optimal water, and low nitrogen stress conditions. In total, 73 cultured bacteria were classified using full-length 16S rRNA sequencing followed by searching three 16S reference databases. Selected strains were tested in vitro for tolerance to relevant abiotic stresses. Including nine isolates from seeds, the candidate root/shoot endophytes spanned 27 genera and 18–39 top-match species. Several well-known nitrogen-fixing bacteria were cultured, including Ensifer. Leaves were dominated by Bacilli (spore-formers known to withstand dry conditions). There were five root isolates of Variovorax. Leifsonia was isolated from the leaves and showed 100% sequence identity with seed isolates, suggestive of transmission from seed to shoot. In vitro experiments showed that seed isolates, including Leifsonia, survived diverse abiotic stresses relevant to the Sahel. Combined, these results suggest that white fonio hosts stress-tolerant microbiota, and points to Leifsonia as a candidate seed-to-plant transmitted endophyte, pending confirmation by future whole genome sequencing. This microbial collection serves as a starting point for long-term experiments to understand stress tolerance in this under-studied crop.

Bacteria doi: 10.3390/bacteria4030030

Authors: Julia Kalinowski Tasneem Ahsan Mariam Ayed Michelle Marie Esposito

The oral microbiome, a highly diverse and intricate ecosystem of microorganisms, plays a pivotal role in the maintenance of systemic health. With the oral cavity housing over 700 different bacterial species, the body’s second most diverse microbial community, periodontal pathogens often lead to the dysregulation of immune responses and consequently, neuropsychiatric disorders. Emerging evidence suggests a significant link between the dysbiosis of oral taxa and the progression of neurogenic disorders such as depression, schizophrenia, bipolar disorders, and more. In this paper, we show the relationship between mental health conditions and shifts in the oral microbiome by highlighting inflammatory responses and neuroactive pathways. The connection between the central nervous system and the oral cavity highlights its role as a modulator of mental health. Clinically, these findings have significant importance as dysbiosis could compromise quality of life. The weight of mental health is often compounded with treatment resistance, non-adherence, and relapse, causing a further need for treatment development. This review seeks to underscore the crucial role of the proposed oral–brain axis in hopes of increasing its presence in future intervention strategies and mental health therapies.

Bacteria doi: 10.3390/bacteria4030029

Authors: Takalani Whitney Maake Phumzile Sibisi

Postharvest losses of Solanaceae crops, which include potatoes (Solanum tuberosum), tomatoes (Solanum lycopersicum), bell peppers (Capsicum annuum), and others, are one of the major challenges in agriculture throughout the world, impacting food security and economic viability. Agrochemicals have been successfully employed to prevent postharvest losses in agriculture. However, the excessive use of agrochemicals may cause detrimental effects on consumer health, the emergence of pesticide-resistant pathogens, increased restrictions on existing pesticides, environmental harm, and the decline of beneficial microorganisms, such as natural antagonists to pests and pathogens. Hence, there is a need to search for a safer and more environmentally friendly alternative. Microbial antagonists have gained more attention in recent years as substitutes for the management of pests and pathogens because they minimize the excessive applications of toxic substances while providing a sustainable approach to plant health management. However, more research is required to make microbial agents more stable and effective and less toxic before they can be used in commercial settings. Therefore, research is being conducted to develop new biological control agents and obtain knowledge of the mechanisms of action that underlie biological disease control. To accomplish this objective, the review aims to investigate microbial antagonists’ modes of action, potential future applications for biological control agents, and difficulties encountered during the commercialization process. We also highlight earlier publications on the function of microbial biological control agents against postharvest crop diseases. Therefore, we can emphasize that the prospects for biological control are promising and that the use of biological control agents to control crop diseases can benefit the environment.

Bacteria doi: 10.3390/bacteria4030028

Authors: Rahul Kumar Beatrice Farda Amedeo Mignini Rihab Djebaili Leonard Koolman Alivia Paul Subhankar Mondal Joy M. Joel Aditi Pandit Periyasamy Panneerselvam Marika Pellegrini Debasis Mitra

Soil microbes are important for maintaining agricultural ecosystems by promoting nutrient cycling, plant growth, and soil resilience. Microbial-based inoculants, such as bio-inoculants and bioremediation agents, have been identified as suitable means to promote soil health, reduce environmental deterioration, and achieve sustainable agriculture. Bio-inoculants, such as biofertilizers and biopesticides, promote nutrient availability, plant growth, and chemical input dependency reduction. Diverse microbial populations, especially plant growth-promoting bacteria (PGPB), enhance resistance by promoting a symbiotic association with plants and inducing natural resistance against insects. Bioremediation, the second significant microbial intervention, is the use of microorganisms for detoxifying and rehabilitating polluted soils. Methods effectively degrade organic pollutants, immobilize heavy metals, and mitigate the toxic effects of industrial and agricultural pollutants. Recent advances in microbial ecology and biotechnology, such as metagenomics, have transformed the knowledge of microbial soil communities, and tailor-made microbial formulations and monitoring equipment may be developed to maximize their activity. Though promising, environmental heterogeneity, scalability, and lack of field-based evidence constrain their widespread application. Multidimensional applications of microbial solutions in agroecology are explored in this review, with a focus on their potential in maintaining soil health, crop production, and environmental sustainability. It also addresses the application of bioremediation and microbial inoculants in agroecosystems and technological innovations with future research objectives. Microbial innovation to shape the soil microbiome offers a valid tool for addressing global challenges in agriculture, food security, and ecological resilience in the context of climate change.

Bacteria doi: 10.3390/bacteria4020027

Authors: Nanami Sakata Yasuhiro Ishiga

Peach (Prunus persica) is a fruit crop of significant economic and cultural value, particularly in Japan, where it is cherished for its symbolism of summer and high quality. However, its production is threatened by bacterial spot caused by Xanthomonas arboricola pv. pruni (Xap), a pathogen that also affects other Prunus species such as nectarines, plums, apricots, and almonds. Xap thrives in warm, humid environments and causes symptoms such as water-soaked lesions, necrotic spots, premature defoliation, and fruit blemishes, leading to reduced yield and marketability. Traditional control methods, including copper-based bactericides and antibiotics, are increasingly ineffective due to resistance development and environmental concerns. This review focuses on the biology, epidemiology, and pathogenic mechanisms of Xap, with particular emphasis on its impact on peach production in Japan. We discuss various disease management strategies, such as integrated disease management, biostimulants, cellulose nanofibers, plant defense activators, and biological control agents, alongside novel molecular approaches targeting bacterial virulence factors. By incorporating these innovative and eco-friendly methods with traditional practices, this review offers insights into the potential for sustainable, environmentally friendly solutions to manage bacterial spot and mitigate its impact on peach production.

Bacteria doi: 10.3390/bacteria4020026

Authors: Adeoye J. Kayode Aboi Igwaran Folasade Banji-Onisile Nneka A. Akwu John O. Unuofin Ayodeji C. Osunla Samson O. Egbewale Hery Purnobasuki

Medicinal plants have long been a vital source of various natural products in the form of pure compounds or standardized extracts. The World Health Organization estimated that 80% of populations in Africa, Asia, and Latin America rely on traditional medicine for primary health care. In recent decades, endophytic microorganisms living within plants have gained attention for their ability to produce bioactive compounds with significant therapeutic potential. This review explores the diversity of medicinal plant endophytes, focusing on their pharmacological significance, including antimicrobial, anticancer, antidiabetic, and antioxidant properties. Additionally, we discuss the application of nanotechnology and computational tools in enhancing the potency and screening of endophyte-derived metabolites. Despite the promising potential, challenges such as scalability, safety, and commercial viability remain. Future research should prioritize optimizing production, elucidating biosynthetic pathways, and integrating advanced technologies to effectively harness these bioactive compounds for novel drug development.

Bacteria doi: 10.3390/bacteria4020025

Authors: Annabel Arhin Sydney Wiegand Isabella Foriska Kiersten Brown Kylee Crayne Kaitlyn Stroscio Rajinikanth Mohan

Curtobacterium species are increasingly recognized as plant pathogens and soil decomposers, but their prevalence and function as plant endophytes in aerial organs are less clear. In this study, we isolated six endophytic Curtobacterium species from the fruits, flower petals (previously unreported) and stem tissue of plants from diverse environments and examined their general characteristics. We found that all Curtobacterium endophytes belonging to three major Curtobacterium clusters—C. oceanosedimentum (a group not previously recognized as endophytic), C. luteum and C. flaccumfaciens—shared some common features. All or nearly all isolates tested were pigmented, displayed moderate salt tolerance and, surprisingly, were psychrotolerant, being able to grow at 6 °C. The exception was a fruit C. luteum isolate that appears to have evolved thermotolerance (up to 45 °C) instead as a likely adaptation to its environment. All isolates were able to metabolize starch and casein and solubilize inorganic phosphate, indicating conserved secreted hydrolase activity, but only isolates in the C. oceanosedimentum group were able to absorb and metabolize citrate. Finally, all endophytes tested were able to ferment the plant sugars sucrose and fructose, while they differed in their ability to use other sugars. Thus, this study documents common traits and adaptations in various Curtobacterium endophytes, and the presence of these isolates in floral and fruit organs implies the possible seed-borne inheritance of these isolates.

Bacteria doi: 10.3390/bacteria4020024

Authors: Diwan Mahmood Khan Venkatakrishna I. Rao M. S. Moosabba Davoodbasha MubarakAli Muhammed Manzoor

Diabetic foot infections (DFIs) are a severe complication of diabetes and are increasing in prevalence globally. The microbiology of DFIs exhibits significant regional variation, with Acinetobacter baumannii frequently emerging as the predominant pathogen. This study aimed to investigate the microbiological profile of A. baumannii in DFIs of different Wagner grades. Pus and tissue specimens from 480 diabetic patients treated for DFIs between September 2016 and August 2019 were collected, and antimicrobial susceptibility testing was performed. Multiplex PCR was conducted to amplify extended spectrum β-lactamase (ESBL) and metallo-β-lactamase (MBL) genes. A. baumannii had a prevalence of 14.58% in DFIs, with 100% resistance to cephalosporins. Among the 70 A. baumannii isolates, 19 (27.14%) were ESBL producers and 43 (61.43%) were MBL producers. blaTEM was the most prevalent gene (52.94%) in ESBL producers; blaNDM-1 was the most prevalent gene (52.94%) in MBL producers. Our findings highlight the need for regular antimicrobial susceptibility testing, molecular surveillance, and robust antimicrobial stewardship programmes to effectively manage A. baumannii DFIs and mitigate their resistance.

Bacteria doi: 10.3390/bacteria4020023

Authors: Lee Seong Wei Vui Kien Liew Albaris B. Tahiluddin Ramasamy Harikrishnan Md. Eilious Hosain Mohamad Nor Azra Wendy Wee

This study evaluated the effects of dietary dill weed (DW) on growth, hematological profile, digestive enzyme activities, antioxidative response, heat tolerance, gut microbiota composition, and disease resistance in African catfish (Clarias gariepinus). A control diet (basal diet) was compared to three DW diets (DW5, DW10, and DW15) with increasing DW levels (0.5, 1.0, and 1.5%, respectively). After eight weeks, fish fed DW diets exhibited significantly higher growth performance (p < 0.05) compared to the control group, as evidenced by increased final weight (FW), specific growth rate (SGR), and weight gain (WG). Conversely, the feed conversion ratio (FCR), hepatosomatic index (HSI), and visceral somatic index (VSI) were significantly lower (p < 0.05) in fish fed DW diets compared to the control. Dietary DW supplementation significantly enhanced (p < 0.05) hematological profiles, including red blood cell (RBC), white blood cell (WBC), hematocrit (HCT), and hemoglobin (HBG), compared to the control group. Similarly, antioxidant responses, including superoxide dismutase (SOD), glutathione peroxidase (GPx), and catalase (CAT) activity, significantly increased (p < 0.05) in fish fed DW diets before or after the heat tolerance assay. Fish fed DW diets displayed a higher relative abundance of beneficial gut microbiota, including Cetobacterium spp., Akkermansia muciniphila, Phocaeicola spp., and Niameybacter massiliensis. Furthermore, dietary DW supplementation stimulated disease resistance against Edwardsiella tarda infection in African catfish. Regression analysis indicated that the optimal DW inclusion level for promoting growth performance and health status in African catfish ranged from 0.229 to 0.433%.

Bacteria doi: 10.3390/bacteria4020022

Authors: Ali A. Dashti Mehrez M. Jadaon

Antibiotic resistance is a major problem worldwide, especially with the overuse and misuse of antibiotics. This makes it more challenging to treat patients infected with antibiotic-resistant bacteria, with more costs on the health system. This review article describes extended-spectrum β-lactam antibiotics as the most used antibacterial agents, and how bacteria developed beta-lactamases (ESBLs) to resist these antibiotics. The review focuses more on the problem of ESBLs in Kuwait to uncover which ESBLs are present and what ESBL gene mutations have been found in this country. The literature review, surprisingly, revealed a limited number of studies in Kuwait on ESBL gene mutations, published over the last 25 years. The results showed that Kuwait has an alarming number of bacterial strains with ESBL gene mutations. These studies reported different mutations in different bacterial strains isolated from different types of specimens, which were collected from different hospitals in Kuwait. The data from these studies were scattered and not linked or analysed together to highlight the big picture of the problem of ESBLs in Kuwait. This review article highlights that the amount of research on ESBLs in Kuwait is not up to the expectations of a country like Kuwait, which has high-standard research facilities. Bearing in mind that the geographic area of Kuwait is relatively small, the authors of this paper think that there might be more β-lactam bacteria spreading in Kuwait, which need to be explored, and that more research and more collaboration are needed among researchers in Kuwait to address this risky situation.

Bacteria doi: 10.3390/bacteria4020021

Authors: Mohammad Qutub Amol Tatode Ujban Md Hussain Tanvi Premchandani Jayshree Taksande Milind Umekar Deepak Thakre

Clostridioides difficile Infection (CDI) continues to be a major cause of antibiotic-associated diarrhea and pseudomembranous colitis, fueled in large measure by virulence factors TcdA and TcdB. These giant glucosyltransferase toxins interfere with host cytoskeletal integrity and inflammatory signaling by inhibiting Rho GTPase; however, the detailed structural dynamics, receptor selectivity, and subcellular trafficking mechanisms remain in part unspecified. This review integrates recent insights from cryo-electron microscopy (cryo-EM) and X-ray crystallography to describe the quaternary architecture of TcdA/B, emphasizing conformational changes key to pore formation and endosomal escape. We also examine the genomic heterogeneity of hypervirulent C. difficile strains (e.g., ribotype 027), correlating toxin gene polymorphisms (e.g., tcdC mutations) with increased toxin production and virulence. Mechanistic explanations of toxin-driven inflammasome activation and epithelial barrier dysfunction are situated within host immune evasion mechanisms, including microbiota-derived bile acid regulation of toxin stability. Subsequent innovative therapeutic strategies, encompassing the utilization of engineered neutralizing antibodies that specifically target the autoprocessing domain alongside structure-guided small-molecule inhibitors, are subjected to a rigorous evaluation. By integrating structural biology, systems-level omics, and clinical epidemiology, this review establishes a comprehensive framework for understanding C. difficile toxin pathogenesis and guiding next-generation precision antimicrobials.

Bacteria doi: 10.3390/bacteria4020020

Authors: Aline Sitowski Gladis Aver Ribeiro Emma J. Murphy Gustavo Waltzer Fehrenbach

Minimally processed foods (MPFs), often considered ready-to-eat, do not undergo cooking and therefore require proper handling and preparation to ensure safety. If not handled correctly, these foods can serve as a pathway for diseases caused by pathogenic bacteria, including Escherichia coli and Salmonella spp. The antibacterial activity of essential oils (EOs) has been increasingly studied as a tool for controlling microorganisms in the food sector. Therefore, we aimed to verify the contamination of MPF by E. coli and Salmonella and to test the sensitivity of these strains to Copaifera langsdorffii, Schinus terebinthifolius, Citrus reticulata, Eucalyptus citriodora, Elettaria cardamomum, Ocimum basilicum, and Eugenia caryophyllus EOs using the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) methods. From 25 MPF samples, one E. coli strain and one Salmonella spp. were isolated. C. langsdorffii and C. reticulata EOs did not show antibacterial activity, while S. terebinthifolius and E. citriodora inhibited the growth of both strains. The E. cardamomum, O. basilicum, and E. caryophyllus EOs presented inhibitory and bactericidal responses at concentrations 0.78, 0.39, and 0.19% (v/v), respectively, compared to the two isolated strains. The present study reinforces the antibacterial potential of EOs and suggests their application in the MPF production chain.

Bacteria doi: 10.3390/bacteria4020019

Authors: Habiba Lawal Shamsaldeen Ibrahim Saeed Nor Fadhilah Kamaruzzaman Zarizal Suhaili Gaddafi Mohammed Sani Mulu Lemlem Qiya Yang Erkihun Aklilu

Pathogenic Escherichia coli can cause a variety of intestinal and extra-intestinal infections in humans and animals. The availability and subsequent misuse of antimicrobials, especially in poultry production systems, has contributed immensely to the emergence and spread of multidrug-resistant E. coli. This study investigated the genotypic characterization of colistin-resistant E. coli and selected antimicrobial-resistance encoding genes along with their phenotypic resistant pattern and the multiple antimicrobial resistant (MAR) index from village chickens in Kelantan. Sixty E. coli isolates obtained from a previous study’s stock culture were enriched and analyzed using routine microbiological methods: Kirby–Bauer disc diffusion method, minimum inhibitory concentration (MIC), and PCR amplification of E. coli species-specific and multidrug-resistance mcr-positive E. coli. All the isolates were confirmed as E. coli and 16.6% (10/60) were positive for mcr. Five isolates were positive for mcr-1, three for mcr-4, and two for mcr-9. The mcr-positive isolates showed varying degrees of resistance to different antimicrobials. The isolates were resistant to gentamicin (100%), chloramphenicol (100%), and tetracycline (89.4%) and susceptible to ceftaxidime (2.26%) and imipenem (18%). Furthermore, 100%, 94.7%, and 89.4% of isolates from village chickens belonged to phylogroup C, B2, and E, while 21.0% and 42.1% of the isolates belonged to phylogroup A and B1, respectively. Sequence types (STs) of selected E. coli isolates were further analyzed using multi-locus sequence typing, and 10 different STs were identified. This study showed the emerging threats of multidrug-resistant mcr-positive E. coli gene in village chickens that are believed to be raised with minimal or no antibiotics.

Bacteria doi: 10.3390/bacteria4020018

Authors: Mike Nundwe Joseph Yamweka Chizimu John Mwaba Misheck Shawa Rodrick S. Katete Mable Mwale Mutengo Ruth Nakazwe Namwiinga R. Mulunda Cephas Sialubanje Mox Malama Kalumbi Yamba Kaunda Rapheal Chanda Herman Chambaro Harvey K. Kamboyi Thoko Kapalamula Steward Mudenda Freeman W. Chabala Bernard M. Hang’ombe Roma Chilengi Chie Nakajima Yasuhiko Suzuki

Background: Shigella species are the leading cause of human shigellosis. In Zambia, more than 30% of children experiencing diarrhea are infected with Shigella species. The increasing resistance of Shigella species to the recommended therapy is of great concern. Therefore, this study investigated the antibiotic resistance profiles and phenotypic and genotypic characteristics of Shigella isolates at the largest referral hospital in Zambia. Methodology: Of the forty-eight archived presumptive Shigella isolates, thirty-two were serologically confirmed and subjected to antimicrobial susceptibility testing using the Kirby Bauer disk diffusion method. Thereafter, polymerase chain reaction was performed to detect the bla genes. Results: Most isolates were Shigella flexneri (16/32, 50%) and Shigella sonnei (14/32, 44%), while Shigella boydii and Shigella dysenteriae were rare. High resistance rates were noted for sulfamethoxazole/trimethoprim (78%) and tetracycline (75%), while 15.6% of the isolates showed resistance to ciprofloxacin and/or azithromycin. The blaTEM gene encoding beta-lactamase was detected in 7/32 (22%) of isolates. Conclusions: In this study, a significant number of multidrug-resistant isolates were identified. Additionally, Shigella species resistant to the World Health Organization-recommended drugs call for strengthened laboratory diagnosis and close monitoring of these pathogens to guide the clinical management of shigellosis.

Bacteria doi: 10.3390/bacteria4020017

Authors: Antonietta Quigg Aurora Gaona-Hernández Mona S. Hochman Sammy M. Ray John R. Schwarz

Concerns about the health consequences of seafood-born human pathogens are ongoing given their occurrence, prevalence, and ability to cause infections, and sometimes death in humans as well as seafood-associated morbidity and mortality worldwide. An applied time-series (2000–2017) analysis of six reefs examined pathogen-specific annual trends and seasonal patterns in the eastern oyster, Crassostrea virginica, in Galveston Bay (Texas), a subtropical estuary in the Gulf of Mexico. Pearson correlation coefficients showed that temperature had a strong positive correlation with Vibrio vulnificus and V. parahaemolyticus (r = 0.66 and 0.51), but not the pathogenic thermostable direct hemolysin (tdh+) V. parahaemolyticus (r = 0.12). The correlations between Vibrio spp. and salinity showed the opposite trend. A cross-correlation factor analysis revealed the strongest positive correlations (r = 0.41 and r = 0.36, respectively) for high densities of V. vulnificus during high Perkinsus marinus infections with short lags (up to 1 month); this was not the case for total or tdh+ V. parahaemolyticus. These results reveal some of the complexity of interannual and long-term patterns of pathogens in oysters. Given climate change impacts and a growing aquaculture industry, examinations of oyster microbiomes in response to environmental and water quality variables are needed.

Bacteria doi: 10.3390/bacteria4010016

Authors: Natalie Naidoo Oliver T. Zishiri

Escherichia coli (E. coli) is a Gram-negative, commensal/pathogenic bacteria found in human intestines and the natural environment. Pathogenic E. coli is known as extra-intestinal pathogenic E. coli (ExPEC) or intestinal pathogenic E. coli (InPEC). InPEC E. coli strains are separated into six pathogenic groups, known as enteropathogenic (EPEC), enterotoxigenic (ETEC), enteroinvasive (EIEC), enteroaggregative (EAEC), enterohaemorrhagic (EHEC), and diffusely adherent (DAEC), that have various virulence factors that cause infection. Virulence factors refer to a combination of distinctive accessory traits that affect a broad range of cellular processes in pathogens. There are two important virulence factors that directly interact with cells to cause diarrhoeal diseases within the intestines: adhesion and colonization factors and exotoxins. Virulence factors are crucial for bacteria to overcome the host’s immune system and result in antibiotic resistance. Antibiotics are used to combat the symptoms and duration of infection by pathogenic E. coli. However, the misuse and overuse of antibiotics have led to the global concern of antibiotic resistance. Currently, the antibiotic colistin is the last-resort drug to fight infection caused by this bacterium. Antibiotic resistance can be achieved in two main ways: horizontal gene transfer and mutation in different genes. The genetic basis for developing antibiotic resistance in E. coli occurs through four mechanisms: limiting drug uptake, modification of the drug target, inactivation of the drug, and active efflux of the drug. These mechanisms use different processes to remove the antibiotic from the bacterial cell or prevent the antibiotic from entering the bacterial cell or binding to targets. This prevents drugs from working effectively, and bacteria can acquire antibiotic resistance. E. coli is classified into different phylogenetic groups (A, B1, B2, D1, D2, E, and clade I). It is a very versatile bacterium that can easily adapt to different environmental factors. The present review gathered information about the pathogenicity, antimicrobial resistance, and phylogenetics of E. coli. These aspects are interconnected; thus, it will provide information on tracking the spread of pathogenic strains and antibiotic resistance genes of different strains using phylogenetics and how antibiotic resistance genes evolve. Understanding genetic variation in E. coli will help in monitoring and controlling outbreaks and in developing novel antibiotics and treatment. The increasing rate of antibiotic resistance, and the ability of E. coli to evolve rapidly, suggest that in-depth research is needed in these areas.

Bacteria doi: 10.3390/bacteria4010015

Authors: Anjuman Ayub Atif Khurshid Wani Chirag Chopra Devinder Kumar Sharma Owais Amin Ab Waheed Wani Anjuvan Singh Subaya Manzoor Reena Singh

Textile dyes pose a major environmental threat due to their toxicity, persistence in water bodies, and resistance to conventional wastewater treatment. To address this, researchers have explored biological and physicochemical degradation methods, focusing on microbial, photolytic, and nanoparticle-mediated approaches, among others. Microbial degradation depends on fungi, bacteria, yeasts, and algae, utilizing enzymatic pathways involving oxidoreductases like laccases, peroxidases, and azoreductases to breakdown or modify complex dye molecules. Photolytic degradation employs hydroxyl radical generation and electron-hole pair formation, while nanoparticle-mediated degradation utilizes titanium dioxide (TiO2), zinc oxide (ZnO), and silver (Ag) nanoparticles to enhance dye removal. To improve efficiency, microbial consortia have been developed to enhance decolorization and mineralization, offering a cost-effective and eco-friendly alternative to physicochemical methods. Photocatalytic degradation, particularly using TiO2, harnesses light energy for dye breakdown. Research advancements focus on shifting TiO2 activation from UV to visible light through doping and composite materials, while optimizing surface area and mesoporosity for better adsorption. Nanoparticle-mediated approaches benefit from a high surface area and rapid adsorption, with ongoing improvements in synthesis, functionalization, and reusability, particularly through magnetic nanoparticle integration. These emerging technologies provide sustainable solutions for dye degradation. The primary aim of this review is to comprehensively evaluate and synthesize current research and advancements in the degradation of azo dyes through microbial methods, photolytic processes, and nanotechnology-based approaches. The review also provides detailed information on salient mechanistic aspects of these methods, efficiencies, advantages, challenges, and potential applications in industrial and environmental contexts.

Bacteria doi: 10.3390/bacteria4010014

Authors: Meryem Idrissi Yahyaoui Nour Eddine Bentouhami Sara Moumnassi Amine Elbouzidi Mohamed Taibi Doha Berraaouan Reda Bellaouchi Bassem Jaouadi Abdelkarim Abousalham Ennouamane Saalaoui Abdeslam Asehraou

This study aimed to characterize the fermentation of commercial xylooligosaccharide (XOS) using Lactiplantibacillus plantarum S61. XOS was utilized as the main carbon source in a modified MRS medium (MRSm) at concentrations of 1%, 2%, 4%, and 6% (w/v). The growth of L. plantarum S61 was tracked daily over a week and compared to a control MRS medium using glucose as the main carbon source. The pH, total free acidity, and biomass were analyzed during fermentation, and the resulting fermentation product was analyzed for its content of fatty acids, total polyphenols, and the production of antioxidant and antimicrobial metabolites. The findings revealed that L. plantarum S61 thrived in MRSm, particularly at a 6% XOS concentration, which was identified as the best condition among the four tested concentrations (1%, 2%, 4%, and 6%). The fermentation of XOS by L. plantarum S61 significantly increased the total phenolic content and antioxidant activity compared to glucose, with the highest phenolic content observed at 6% XOS (6.70 ± 0.01 mg GAE/g). The strains produced various organic acids including lactic, malic, and oxalic acids from glucose and XOS. Notably, the strains yielded a broader range of organic acids with higher contents in the presence of XOS, leading to enhanced antifungal and antibacterial activities compared to glucose. Significant antibacterial activity was observed against Gram-negative bacteria, particularly Salmonella enterica, with inhibition zones of 20.25 mm and 11.75 mm for XOS (5% and 6%) and glucose, respectively. For Gram-positive bacteria, S. aureus and M. luteus exhibited inhibition zones of 20.01 mm for XOS 6% and 10.25 mm for glucose. In terms of antifungal activity, the strongest inhibition was observed against Rhodotorula glutinis, with inhibition zones of 26.00 mm for XOS 6% and 20.04 mm for glucose. The fermentation product of XOS by L. plantarum S61 showed significant inhibitory effects against pathogenic bacteria and yeasts, suggesting its potential application in the manufacturing of preservatives with antifungal properties and pharmaceutical products targeting pathogenic and spoilage yeasts.

Bacteria doi: 10.3390/bacteria4010013

Authors: Sarayu Bhogoju Thyneice Taylor-Bowden Collins N. Khwatenge Samuel N. Nahashon

The continuous use of antibiotics is associated with many complications in the poultry industry. Probiotics have emerged as a viable alternative over the past few decades to counter the adverse effects of antibiotics. No candidate probiotic microorganisms have been fully evaluated in the poultry industry for their effectiveness as potential probiotics in guinea fowls (GFs) compared to chickens. Recently, a metagenome evaluation of GFs in our laboratory revealed a predominance of Lactobacillus reuteri (L. reuteri) and actinobacteria class of bacteria in their gastrointestinal tract. The aim of this study is to evaluate a well-known lactic acid probiotic bacterium (L. reuteri) and a unique probiotic (S. coelicolor) that has not been assessed in any guinea fowl species. In the current study, L. reuteri and Streptomyces coelicolor (S. coelicolor) were selected as probiotic bacteria, encapsulated, and added into French guinea fowl (FGF) feed individually at a concentration of 108 cfu/g or both microorganisms combined each at 104 cfu/g. In an 8-week study, 216-day-old guinea keets were randomly assigned to four dietary treatments as indicated: (1) L. reuteri (108 cfu/g); (2) S. coelicolor (108 cfu/g); (3) mixture of L. reuteri (104 cfu/g) and S. coelicolor (104 cfu/g); and (4) control treatment (no probiotics included). The L. reuteri, S. coelicolor, and L. reuteri + S. coelicolor were added into the feed using wheat middlings as a carrier at a final concentration of 108 cfu/g. The FGFs that were fed diets containing L. reuteri showed improved feed consumption at 3–8 weeks of age (WOA). The guineas fed L. reuteri and S. coelicolor showed a lower feed conversion ratio (FCR), which was significant at 2 and 8 WOA, and a numerically lower 8-week average FCR when compared with other dietary treatments. Differences in body weight gain among all dietary treatments were not significant. This research suggests that L. reuteri and S. coelicolor may have the potential for use as probiotics in FGFs when used in combination or separately.

Bacteria doi: 10.3390/bacteria4010012

Authors: Diksha Joshi Amit Kaushik Reetesh Kumar Aditi Arya Gustavo Santoyo Vipin Kumar Singh Nikhil Kashyap Manoj Kumar Solanki Madhuree Kumari Nikunaj Bhardwaj Ajay Kumar

In the recent past, microbiome manipulation has emerged as a promising approach to improve plant growth performance by exploring the deep insight of plant–microbe interactions. The exploration of a plant microbiome either present on an ectosphere or endosphere can provide a far better understanding about the potential application of plant-associated microbes for the improvement of plant growth, protection from pathogen invasion, and tolerance to environmental stresses of a diverse nature. In this context, next-generation sequencing methods, omics approaches, and synthetic biology have made significant progress in plant microbiome research and are being frequently used to explore the intriguing role of plant-associated microorganisms. Despite the successfulness of conventional approaches, the incorporation of CRISPR/Cas9, RNA interference technology, rhizosphere engineering, microbiome engineering, and other manipulation techniques appear to be a promising approach to enhancing plant performance, and tolerance against biotic and abiotic stress factors. The present review presents the significance of plant microbe interaction, vital functional aspects, collaborative action, potential constraints, and finally the latest developments in bioengineering approaches destined for microbiome modulation with an objective to improve the performance of a host plant challenged with environmental stressors.

Bacteria doi: 10.3390/bacteria4010011

Authors: Yolanda Yolisa Nokamatye Gabriel Tchuente Kamsu Eugene Jamot Ndebia

The microbiome plays a crucial role in cancer development, influencing fundamental processes such as cell proliferation, apoptosis, immune system regulation, and host metabolism. Recent studies have highlighted a possible relationship between esophageal cancer and the oral microbiota, making oral microflora a possible risk factor. The bacteria Prevotella intermedia, Tannerella forsythia, Streptococcus sanguinis, and Streptococcus mutans, implicated in various oral pathologies, were of interest in this study, which was initiated to examine their potential role in the etiology of esophageal squamous cell carcinoma (ESCC). To achieve this, a case-control design was used, with whole saliva samples collected from 24 healthy controls and 24 patients with esophageal squamous cell carcinoma. DNA was then extracted, and real-time PCR was performed to quantify the presence of the targeted bacteria in both groups. The results showed that all the bacteria studied were present in the saliva of both patients with ESCC and healthy controls. However, expression levels were significantly higher in patients with ESCC. Specifically, a marked increase in the presence of P. intermedia, T. forsythia, S. sanguinis, and S. mutans was observed in the patients with cancer compared to the healthy controls. In short, this study highlights a significant imbalance in the microbial flora, with an increased abundance of selected bacteria in patients with ESCC. The monitoring of these bacteria could thus be exploited to track patients who are at risk. Their integration into diagnostic and therapeutic strategies would offer new prospects for the early diagnosis and improved prognosis of patients at risk of ESCC.

Bacteria doi: 10.3390/bacteria4010010

Authors: Francisco Rodrigues Patrícia Coelho Sónia Mateus Hatem Eideh Teresa Gonçalves Armando Caseiro Miguel Castelo Branco

This study explores the prevalence and antibiotic resistance of urinary tract infections (UTIs) in pregnant women in central Portugal. A retrospective observational study was conducted on 201 positive urine cultures from pregnant women at a hospital center between January 2018 and December 2022. The data collected included age, hospital admission source, history of antibiotic therapy, catheterization status, identity of bacterial isolates, and their antibiotic profile. The most common bacterial strains were Escherichia coli (52.4%) and Streptococcus agalactiae (16.9%). In terms of antibiotic resistance, Escherichia coli demonstrated complete sensitivity to ertapenem, while Streptococcus agalactiae showed sensitivity to four antibiotics, including trimethoprim/sulfamethoxazole. Notably, most infections occurred in the third trimester, underscoring the need for continuous monitoring throughout pregnancy. This study emphasizes the importance of tailored treatment strategies to manage UTIs in pregnancy effectively, reducing the potential maternal and fetal complications. These findings contribute to regional data on UTI management in pregnant populations and aim to support improved healthcare practices. These regional data provide a solid foundation for optimizing healthcare practices in pregnant women, suggesting targeted approaches to combat antibiotic resistance and improve maternal–fetal safety during UTI treatment.

Bacteria doi: 10.3390/bacteria4010009

Authors: Elie Bou Sanayeh Hadi Itani Elie Moussa Allison Glaser

Background: Purple urine discoloration, known as purple urine bag syndrome (PUBS), has various etiologies ranging from benign to serious conditions. We present a case of cefiderocol-induced PUBS and review the literature. Methods: A 56-year-old bedridden patient developed purplish urine discoloration three days after initiating cefiderocol treatment for severe sepsis caused by carbapenem-resistant Acinetobacter baumannii/nosocomialis isolated from an infected sacral pressure ulcer. A comprehensive literature review of PubMed and Google Scholar was performed, with articles screened by two independent reviewers. Results: Our patient’s urine color cleared one day after cefiderocol discontinuation. Eight additional cases of cefiderocol-induced PUBS were identified in the literature. In all reported cases, urine discoloration resolved spontaneously within 1 to 3 days of cefiderocol cessation. Conclusions: Cefiderocol-induced PUBS is being increasingly recognized. While generally benign and self-limiting, it is crucial to exclude other potentially life-threatening diagnoses before attributing PUBS to cefiderocol.

Bacteria doi: 10.3390/bacteria4010008

Authors: Bert Ely Quill Thomas Tannaz Mohammadi

Members of the Dolichocephalovirinae subfamily are giant viruses with an elongated head and a flexible tail that is used to infect Caulobacter strains. In this paper, we describe the isolation and characterization of nine newly isolated phages and present evidence that seven of these phages represent a new Dolichocephalovirinae genus that has significant differences from the four previously described Dolichocephalovirinae genera. In addition, since these new phages were isolated from a single sampling site over the course of three years, a comparison of their genome sequences reveals a low level of within-population diversity resulting from both single-nucleotide polymorphisms and insertions or deletions. A comparison of the host ranges of these phages suggests that differences in host susceptibility may be an important factor in maintaining this diversity.

Bacteria doi: 10.3390/bacteria4010007

Authors: Agradip Bhattacharyya Goutam Banerjee Pritam Chattopadhyay

Background: Aeromonas hydrophila is a key pathogen affecting freshwater fish, including Labeo rohita (rohu), causing significant aquaculture losses. This study explores the role of intimin and invasin, known virulence factors, in A. hydrophila pathogenesis using in silico methods. Methods: We analyzed the distribution of invasin and intimin across 53 A. hydrophila genomes and examined their physicochemical properties, secondary structures, and 3D models. Since crystal structures were unavailable, homology-based modeling was employed to study the structure of rohu β-integrins. In silico docking was performed to explore the interactions between intimin/invasin and β-integrins. Results: Our findings revealed that intimin and invasin were present in only 6 out of the 53 A. hydrophila strains examined, which were designated as hypervirulent strains. The transmembrane regions of intimin and invasin were modeled as β-barrels, a common feature of porins. The in silico docking experiments indicated the significant binding affinity of invasin and intimin with all the β-integrins of rohu fish, suggesting a critical role in host attachment and cellular internalization. Conclusions: This in silico study highlights the pivotal role of invasin and intimin in host tissue’s binding efficacy, offering valuable insights into the binding potential of A. hydrophila across various organs in rohu fish.

Bacteria doi: 10.3390/bacteria4010006

Authors: José Weverton Almeida-Bezerra José Thyálisson da Costa Silva Saulo Almeida Menezes Gabriel Gonçalves Alencar Daiany Alves Ribeiro Bárbara Fernandes Melo João Pereira da Silva-Junior Francisca de Fátima Silva de Sousa Severino Denicio Gonçalves de Sousa Marcos Aurélio Figueirêdo dos Santos Dieferson Leandro de Souza Luiz Neldecílio Alves Vitor Ademar Maia Filho Murilo Felipe Felício Jacqueline Cosmo Andrade-Pinheiro Viviane Bezerra da Silva José Jailson Lima Bezerra Maria Flaviana Bezerra Morais-Braga Henrique Douglas Melo Coutinho

Biofilms, formed by microbial communities that increase resistance to antibiotics, are responsible for chronic infections, making their combat a therapeutic priority. Taking this into account, the fruit Caryocar coriaceum stands out for its potential in the treatment of infectious diseases. The different parts of this plant can be used, and the fixed oil extracted from its fruit, rich in fatty acids, is indicated as responsible for its biological activities. Thus, the objective of this study was to evaluate the chemical composition of the fixed oil extracted from the fruits of C. coriaceum (FOCC), in addition to analyzing its action in the inhibition and pre-formed biofilm disruption of bacteria. The fixed oil was extracted from the internal mesocarp through exhaustive extraction with n-hexane, resulting in a yield of 38.29%. For antibiofilm evaluation, multidrug-resistant bacterial strains were exposed to the oil, and the antibiofilm activity was verified through biofilm formation and pre-formed biofilm disruption assays. The chemical analysis of the fixed oil of C. coriaceum (FOCC) identified eight fatty acids, representing 98.2% of the total composition, with a predominance of oleic acid (60.1%) and palmitic acid (33.5%). FOCC demonstrated approximately 70% inhibition of Streptococcus mutans biofilm formation at a concentration of 10 mg/mL and approximately 60% inhibition against Staphylococcus aureus and Pseudomonas aeruginosa. In pre-formed biofilm disruption, FOCC showed low efficacy against S. mutans and P. aeruginosa but showed greater activity against Enterococcus faecalis and S. aureus. These results indicate that FOCC has the potential to prevent biofilms, but its pre-formed biofilm disruption capacity is still limited.

Bacteria doi: 10.3390/bacteria4010005

Authors: Vikash Kerketta Amrita Kumari Panda Aseem Kerketta Surajit De Mandal Satpal Singh Bisht

Phosphorus is a macronutrient crucially important for plant growth and development; its limited amount in soil and water poses bewildering concerns amongst agronomists. Externally applied phosphorus fertilizers can fulfil crops’ phosphorus needs throughout essential growth stages; however, the overapplication of phosphorus fertilizers leads to diminished phosphorus acquisition efficiency (PAE), disrupts the delicate balance of nutrients in soil and water, leads to deficiencies in other essential elements, poses significant environmental risks, and accelerates the loss of phosphorus mineral supplies. Moreover, much of the applied phosphorus may become fixed as insoluble phosphates by combining with calcium, iron, aluminum, manganese, etc., present in soil, making it unavailable for the plants. Phosphate solubilizing bacteria (PSB) can render insoluble phosphate accessible to plants by solubilization and mineralization, hence enhancing crop yields while ensuring environmental sustainability. Earthworms are vital soil invertebrates that interact continuously with soil and soil microorganisms and play an essential role in maintaining soil fertility. The present study aims to screen and identify potential phosphate solubilizing bacteria from the intestinal tract of the earthworm Aporrectodea rosea. The experimental results indicate that the strain PSEG-1 was effective in phosphate solubilization, with a solubilization index of 1.6 in Pikovskaya (PVK)’s medium. The strain produced organic acid in the National Botanical Research Institute (NBRIP)’s medium. Phenotypic and genotypic studies of the isolate showed that the strain PSEG-1 belongs to Klebsiella variicola. Our results suggest that the vermi-bacterial strain Klebsiella variicola PSEG-1 possesses intrinsic abilities to solubilize phosphate, which could be exploited for formulating potential microbial biofertilizers to enhance crop production.

Bacteria doi: 10.3390/bacteria4010004

Authors: Lanceï Kaba Audrey Giraud-Gatineau Philippe Colson Pierre-Edouard Fournier Hervé Chaudet

This study aimed at systematically exploring the seasonalities of bacterial identifications from 1 February 2014 to 31 January 2020 in hospitalized patients, considering the infectious site and the community-acquired or hospital-associated origin. Bacterial identifications were extracted from the data warehouse of the Institut Hospitalo-Universitaire Mediterranée Infection surveillance system, along with their epidemiological characteristics. Each species’ series was processed using a scientific workflow based on the TBATS time series model. Possible co-seasonalities were researched using seasonal peak clustering and series cross-correlations. In this study, only the 15 most frequent species were described in detail. The three most frequent species were Escherichia coli, Staphylococcus aureus, and Staphylococcus epidermidis, with median weekly incidences of 145, 74, and 39 cases, respectively. Samplings of S. aureus and E. coli follow the same seasonal dynamics. S. aureus hospital-associated infections exhibited a significant association with temperature, humidity, and pressure change, whereas community-acquired infections were only associated with precipitations. More seasonal peaks were observed during the winter season. Among the 15 peaks of this seasonal maximum, 6.7% came from blood (Klebsiellia oxytoca) and 13.3% from respiratory specimens (E. coli and S aureus). Our results showed significant associations of periodicity between pathogens, origin of infection, type of sampling, and weather drivers.

Bacteria doi: 10.3390/bacteria4010003

Authors: Nitesh Jaishwal Mamta Jayswal Deep Chand Gupta Bishnu Dhakal Santosh Koirala Ram Bahadur Khadka Hari Prasad Devkota Jitendra Pandey

This research is focused on assessing the antibacterial properties of Pogostemon benghalensis stem bark and inflorescence extracts, as well as their inhibitory effects on xanthine oxidase, antioxidant potential, overall phenolic content, and flavonoid concentration. The cold maceration technique was used to obtain extracts using water, methanol, and ethyl acetate solvents. The disk diffusion method demonstrated the significant antibacterial efficacy of the methanol stem bark extract against Staphylococcus epidermidis, with a zone of inhibition (ZOI) of 13 mm, and the inflorescence methanol extract against Klebsiella pneumonia (ZOI: 12.9 mm). Moreover, the methanol stem bark extract exhibited the minimum bactericidal concentration (MBC) at 1.56 mg/mL and the minimum inhibitory concentration (MIC) at 0.78 mg/mL against S. epidermidis. The ethyl acetate inflorescence extract displayed noteworthy xanthine oxidase inhibition (IC50: 29.1 µg/mL) comparable to allopurinol (IC50: 12.7 µg/mL). Furthermore, the methanol stem bark extract exhibited a remarkable DPPH free radical inhibitory effect, showing an IC50 value of 42.5 µg/mL. The total polyphenol content ranged from 29.9 μg to 161.3 µg GAE per mg of dried extract weight in the methanol inflorescence extract, while the total flavonoid content ranged from 38.4 μg to 96.8 μg QE per mg of dried extract weight within the water-derived extract. Overall, these findings demonstrate the potent antibacterial properties, xanthine oxidase inhibition, and antioxidant activity of P. benghalensis extracts.

Bacteria doi: 10.3390/bacteria4010002

Authors: Rittick Mondal Dipanjan Das Amit Kumar Mandal

To safeguard against microbial diseases and maintain optimal silk yields, the sericulture industry relies on antibiotics to promote the health, well-being, and vitality of silkworms (Bombyx mori). Antibiotics are commonly incorporated into synthetic diets for rearing silkworms or included as key components in bed disinfectant formulations. The silkworm-rearing industry’s reliance on antibiotics has led to concerns about the development of antibiotic-resistant bacteria. Previous research has uncovered a dual role for antibiotics: not only do they prevent disease, but they also promote silkworm growth by reshaping the gut microbiome and enhancing nutrient absorption, highlighting the need for judicious use. Therefore, there is a critical need for prudent management and further exploration of alternative growth-promoting strategies to minimize resistance risks. This study investigates the relationship between antibiotic administration and silkworm growth, shedding light on the mechanisms underlying antibiotic-induced effects and assessing the risk of antimicrobial resistance (AMR) emergence and dissemination.

Bacteria doi: 10.3390/bacteria4010001

Authors: Claire A. Shaw Maria Soltero-Rivera Rodrigo Profeta Bart C. Weimer

The cat oral microbiome plays an important role in maintaining host health, yet little is known about how to apply microbial data in a clinical setting. One such use of microbiome signatures is in cases of feline chronic gingivostomatitis (FCGS), a severe debilitating complex disease of the oral cavity. FCGS-afflicted cats have limited treatment options, and individual patient responses to treatment are needed. In this work, we used deep sequencing of total RNA of the oral microbiome to chronicle microbial changes that accompanied an FCGS-afflicted cat’s change from treatment-non-responsive to treatment-responsive within a 17-month span. The oral microbiome composition of the two treatment-non-responsive time points differed from that of the treatment-responsive point, with notable shifts in the abundance of Myscoplasmopsis, Aspergillus, and Capnocytophaga species. Intriguingly, the presence of the fungal groups Aspergillus and Candida primarily differentiated the two non-responsive microbiomes. Associated with responder status were multiple Capnocytophaga species, including Capnocytophaga sp. H2931, Capnocytophaga gingivalis, and Capnocytophaga canimorsus. The observation that the oral microbiome shifts in tandem by response to treatment in FCGS suggests a potential use for microbiome evaluations in a clinical setting. This work contributes to developing improved molecular diagnostics for enhanced efficacy of individualized treatment plans to improve oral disease.

Bacteria doi: 10.3390/bacteria3040033

Authors: Kanon Yamamoto Takashi Fujikawa Ayaka Uke Giyu Usuki Yasuhiro Ishiga Nanami Sakata

Pseudomonas cannabina pv. alisalensis (Pcal) causes bacterial blight on cabbage. In a previous study, we screened for reduced virulence using Tn5 transposon mutants and identified a LysR-type transcriptional regulator (LTTR) as a potential virulence factor in Pcal. However, the role of LTTR in Pcal virulence has not been thoroughly investigated. In this study, we demonstrated that the Pcal NN14 mutant (with Tn5 insertion in the LTTR-encoding gene) showed reduced disease symptoms and bacterial populations in cabbage, indicating that LTTR contributes to Pcal virulence. RNA-seq analysis identified 39 LTTR-dependent genes. Genes associated with 13 of the type three secretion system (T3SS), two of flagellar apparatus, ABC transporters, and transcription factors were expressed at lower levels in the NN14 mutant compared to the wild type. Conversely, tssH and hcp, type six secretion system (T6SS)-related genes, showed higher expression in NN14. Furthermore, these differences in gene expression were observed in minimal medium, but not in nutrient-rich medium, suggesting that LTTR acts as a global regulator responsive to nutrient conditions. Additionally, LTTR activated the expression of T3SS-related genes during Pcal infection. We also demonstrated that NN14 showed a reduced ability to induce hypersensitive reaction (HR) cell death in non-host plants. Collectively, these results suggest that LTTR contributes to Pcal virulence by regulating T3SS in response to environmental changes.

Bacteria doi: 10.3390/bacteria3040032

Authors: Michelle E. H. Thompson Anuja Shrestha Eman M. Khalaf Jeffrey Rinne Victor Limay-Rios Lana M. Reid Manish N. Raizada

The style is the female reproductive channel in flowers, receiving pollen and transmitting male gametes through elongating pollen tubes to the ovules during fertilization. In maize/corn, the styles are known as silks. Fertilization-stage silks contain diverse bacteria, possibly originating from pollen. Bacteria were cultured and individually sequenced from the tip and base portions of healthy, fertilization-stage silks of 14 North American maize genotypes, resulting in 350 isolates, spanning 48 genera and 221 OTUs. The objective of this study was to taxonomically analyze these bacteria in the context of the maize host tissue and genotype, taking advantage of long-read (V1–V9) 16S Sanger sequencing. The results suggest that the maize genotype and heterotic breeding group may impact the bacterial diversity of healthy, fertilization-stage silks. Some taxa were relatively conserved across maize genotypes and silk tip/base locations, including Pantoea, which may represent part of the core microbiome or form stable, symbiotic relationships with healthy, pollinated silks. We also observed similarities between the silk microbiomes of maize genotypes that were related by plant pedigree; these preliminary results suggest inheritance or the ability of related genotypes to recruit common bacterial taxa. Overall, this study demonstrates that healthy maize silks represent a valuable resource for learning about relationships between plant reproductive microbiomes.