Journal Description
Bacteria
Bacteria
is an international, peer-reviewed, open access journal on bacteriology published quarterly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus and other databases.
- Journal Rank: CiteScore - Q2 (Immunology and Microbiology (miscellaneous))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 25.4 days after submission; acceptance to publication is undertaken in 8.8 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
- Bacteria is a companion journal of Pathogens and Microorganisms.
Latest Articles
Community Surveillance of MRSA and Staphylococcus aureus in Rural Portugal: The BI-STAPH Project—Phase 1: Sertã
Bacteria 2025, 4(4), 54; https://doi.org/10.3390/bacteria4040054 - 13 Oct 2025
Abstract
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.
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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.
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Open AccessCommunication
Survival of Pathogenic Escherichia coli Strains in Sand Subjected to Desiccation
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Rocío de la Cuesta, Mariana S. Sanin, Florencia Battaglia, Sandra L. Vasquez Pinochet, Cecilia C. Cundon, Adriana B. Bentancor, María P. Bonino and Ximena Blanco Crivelli
Bacteria 2025, 4(4), 53; https://doi.org/10.3390/bacteria4040053 - 2 Oct 2025
Abstract
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.
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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.
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Open AccessArticle
Shiga Toxin Genes Detected in Fecal Samples of Illinois Finisher Pigs
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Kathryn L. Lauder, Shafiullah M. Parvej, Yiyang Shen, Chongyang Zhang, Jehadi Osei-Bonsu, James F. Lowe and Weiping Zhang
Bacteria 2025, 4(4), 52; https://doi.org/10.3390/bacteria4040052 - 2 Oct 2025
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(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
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(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.
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Open AccessArticle
Antitumor Potential of Bioactive Crude Extracts Derived from Actinomycetes
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Hassan K. Dhaini, Bahaa Fahed Hassanieh, Rana El Hajj and Mahmoud I. Khalil
Bacteria 2025, 4(4), 51; https://doi.org/10.3390/bacteria4040051 - 1 Oct 2025
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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
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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.
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Open AccessReview
Beyond Genes: Non-Canonical Mechanisms Driving Antimicrobial Resistance in Bacteria
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Leonard Koolman, Chijioke Emenike, Debasis Mitra and Sourav Chattaraj
Bacteria 2025, 4(4), 50; https://doi.org/10.3390/bacteria4040050 - 1 Oct 2025
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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
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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.
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Open AccessReview
Bacterial Biosurfactants as Bioactive Ingredients: Surfactin’s Role in Food Preservation, Functional Foods, and Human Health
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Zainab Hussain Abdul Wahab and Shayma Thyab Gddoa Al-Sahlany
Bacteria 2025, 4(4), 49; https://doi.org/10.3390/bacteria4040049 - 25 Sep 2025
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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
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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.
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Open AccessArticle
Characterization and Biological Activity of Magnesium Nanoparticles Synthesized from Escherichia coli Metabolites Against Multidrug-Resistant Bacteria
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Malak Mezher, Salma Khazaal, Mahmoud I. Khalil, Dalia El Badan and Taymour A. Hamdalla
Bacteria 2025, 4(3), 48; https://doi.org/10.3390/bacteria4030048 - 10 Sep 2025
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(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
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(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.
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Open AccessArticle
Humoral Immune Activation Against Mycobacterium avium subsp. paratuberculosis Through Oral Immunization with Engineered Salmonella
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Azar Motamedi Boroojeni, Nikoo Veiskarami, Elena Rita Simula, Leonardo Antonio Sechi and Abdollah Derakhshandeh
Bacteria 2025, 4(3), 47; https://doi.org/10.3390/bacteria4030047 - 8 Sep 2025
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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
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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.
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Open AccessSystematic Review
Biotechnological Innovations to Combat Antimicrobial Resistance and Advance Global Health Equity
by
Sima Rugarabamu and Gaspary Mwanyika
Bacteria 2025, 4(3), 46; https://doi.org/10.3390/bacteria4030046 - 5 Sep 2025
Cited by 1
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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
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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.
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Open AccessFeature PaperArticle
Machine Learning-Powered ATR-FTIR Spectroscopic Clinical Evaluation for Rapid Typing of Salmonella enterica O-Serogroups and Salmonella Typhi
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Cesira Giordano, Francesca Del Conte, Maira Napoleoni and Simona Barnini
Bacteria 2025, 4(3), 45; https://doi.org/10.3390/bacteria4030045 - 2 Sep 2025
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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
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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.
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Open AccessReview
Biodegradation of Petrochemical Plastics by Microorganisms: Toward Sustainable Solutions for Plastic Pollution
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Luis Getino, José Antonio Revilla-Gómez, Luisa María Ariza-Carmona, Sofie Thijs, Claude Didierjean and Alejandro Chamizo-Ampudia
Bacteria 2025, 4(3), 44; https://doi.org/10.3390/bacteria4030044 - 1 Sep 2025
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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,
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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.
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Open AccessArticle
Genetic Characterization of Salmonella and Analysis of Ciprofloxacin Resistance Using Sanger Technique in Romania, 2024
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Elena Roxana Buzilă, Raluca Gatej, Cristina Trifan, Teodora Vremera, Mihaela Leustean, Adina David, Daniela Cosmina Bosogea, Georgiana Barbu, Adina Gatea, Ciprian Ilie and Luminița Smaranda Iancu
Bacteria 2025, 4(3), 43; https://doi.org/10.3390/bacteria4030043 - 1 Sep 2025
Abstract
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
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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.
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Open AccessHypothesis
POLETicians in the Mud: Preprokaryotic Organismal Lifeforms Existing Today (POLET) Hypothesis
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Douglas M. Ruden and Glen Ray Hood
Bacteria 2025, 4(3), 42; https://doi.org/10.3390/bacteria4030042 - 29 Aug 2025
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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
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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.
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Open AccessArticle
Prevalence, Antimicrobial Resistance Profiles, and Risk Factors Analysis of Campylobacter spp. from Dogs in Kelantan, Malaysia
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Chinedu Amaeze Frank, Mohammed Dauda Goni, Nor Fadhilah Kamaruzzaman, Hafeez A. Afolabi, Mohammed S. Gaddafi, Aliyu Yakubu and Shamsaldeen Ibrahim Saeed
Bacteria 2025, 4(3), 41; https://doi.org/10.3390/bacteria4030041 - 8 Aug 2025
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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,
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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.
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Open AccessArticle
Molecular Detection and Antibiogram of Bacteria and Fungi in Table Eggs Under Different Storage Durations with Organoleptic Properties
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Md Shahab Uddin, Md Ahosanul Haque Shahid, Saiduzzaman, Marzia Rahman and K. H. M. Nazmul Hussain Nazir
Bacteria 2025, 4(3), 40; https://doi.org/10.3390/bacteria4030040 - 4 Aug 2025
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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
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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.
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Open AccessArticle
Harnessing Extremophile Bacillus spp. for Biocontrol of Fusarium solani in Phaseolus vulgaris L. Agroecosystems
by
Tofick B. Wekesa, Justus M. Onguso, Damaris Barminga and Ndinda Kavesu
Bacteria 2025, 4(3), 39; https://doi.org/10.3390/bacteria4030039 - 1 Aug 2025
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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
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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.
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Open AccessArticle
Biostimulatory Effects of Bacillus subtilis and Pseudomonas corrugata on Phytochemical and Antioxidant Properties of In Vitro-Propagated Plants of Nardostachys jatamansi (D. Don) DC
by
Janhvi Mishra Rawat, Mrinalini Agarwal, Shivani Negi, Jigisha Anand, Prabhakar Semwal, Balwant Rawat, Rajneesh Bhardwaj and Debasis Mitra
Bacteria 2025, 4(3), 38; https://doi.org/10.3390/bacteria4030038 - 1 Aug 2025
Abstract
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
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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.
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(This article belongs to the Special Issue Harnessing of Soil Microbiome for Sustainable Agriculture)
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Open AccessArticle
Taxonomic and Functional Profiling of Bacterial Communities in Leather Biodegradation: Insights into Metabolic Pathways and Diversity
by
Manuela Bonilla-Espadas, Marcelo Bertazzo, Irene Lifante-Martinez, Mónica Camacho, Elena Orgilés-Calpena, Francisca Arán-Aís and María-José Bonete
Bacteria 2025, 4(3), 37; https://doi.org/10.3390/bacteria4030037 - 1 Aug 2025
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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
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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.
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Open AccessReview
Unveiling the Molecular Mechanism of Azospirillum in Plant Growth Promotion
by
Bikash Ranjan Giri, Sourav Chattaraj, Subhashree Rath, Mousumi Madhusmita Pattnaik, Debasis Mitra and Hrudayanath Thatoi
Bacteria 2025, 4(3), 36; https://doi.org/10.3390/bacteria4030036 - 18 Jul 2025
Cited by 1
Abstract
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,
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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.
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(This article belongs to the Special Issue New Insights into Microbial Biocontrol: Strategies for Sustainable Aquaculture and Agriculture)
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Open AccessArticle
Avian and Human Turicibacter Isolates Possess Bile Salt Hydrolases with Activity Against Tauro-Conjugated Bile Acids
by
Joel J. Maki, Lucas Showman and Torey Looft
Bacteria 2025, 4(3), 35; https://doi.org/10.3390/bacteria4030035 - 18 Jul 2025
Abstract
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
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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.
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(This article belongs to the Special Issue Bacterial Molecular Biology: Stress Responses and Adaptation)
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