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
Characterization and Biological Activity of Magnesium Nanoparticles Synthesized from Escherichia coli Metabolites Against Multidrug-Resistant Bacteria
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
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Sima Rugarabamu and Gaspary Mwanyika
Bacteria 2025, 4(3), 46; https://doi.org/10.3390/bacteria4030046 - 5 Sep 2025
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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,
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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
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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.
Full article
(This article belongs to the Special Issue Bacterial Molecular Biology: Stress Responses and Adaptation)
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Open AccessArticle
Isolation and Identification of Pathogenic Bacteria Aeromonas veronii in Ctenopharyngodon idella (Grass Carp) and Chinese Herbal Medicine Antibacterial Experiment
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Yanhua Zhao, Hui Xue, Guoxing Liu, Li Sun and Hucheng Jiang
Bacteria 2025, 4(3), 34; https://doi.org/10.3390/bacteria4030034 - 12 Jul 2025
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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
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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.
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Open AccessSystematic Review
Potential Risks Associated with the Growth of Nitrifying Bacteria in Drinking Water Distribution Lines and Storage Tanks: A Systematic Literature Review
by
Amandhi N. Ekanayake, Wasana Gunawardana and Rohan Weerasooriya
Bacteria 2025, 4(3), 33; https://doi.org/10.3390/bacteria4030033 - 12 Jul 2025
Abstract
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
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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.
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(This article belongs to the Collection Feature Papers in Bacteria)
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Open AccessCommunication
Helicobacter pylori Isolate from Endoscopy-Examined Patients in Bahir Dar, Northwest Ethiopia
by
Mulat Erkihun, Desalegn Nigatu Chanie and Yesuf Adem Siraj
Bacteria 2025, 4(3), 32; https://doi.org/10.3390/bacteria4030032 - 10 Jul 2025
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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
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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.
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Open AccessArticle
First Culturing of Potential Bacterial Endophytes from the African Sahelian Crop Fonio Grown Under Abiotic Stress Conditions
by
Roshan Pudasaini, Eman M. Khalaf, Dylan J. L. Brettingham and Manish N. Raizada
Bacteria 2025, 4(3), 31; https://doi.org/10.3390/bacteria4030031 - 30 Jun 2025
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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
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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.
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Open AccessReview
The Relationship Between Neuropsychiatric Disorders and the Oral Microbiome
by
Julia Kalinowski, Tasneem Ahsan, Mariam Ayed and Michelle Marie Esposito
Bacteria 2025, 4(3), 30; https://doi.org/10.3390/bacteria4030030 - 30 Jun 2025
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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
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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.
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Open AccessReview
Microbial Antagonists for the Control of Plant Diseases in Solanaceae Crops: Current Status, Challenges, and Global Perspectives
by
Takalani Whitney Maake and Phumzile Sibisi
Bacteria 2025, 4(3), 29; https://doi.org/10.3390/bacteria4030029 - 28 Jun 2025
Abstract
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
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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.
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(This article belongs to the Special Issue Harnessing of Soil Microbiome for Sustainable Agriculture)
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Multidrug Resistance Across Pathogens: Fungi, Bacteria, Parasites, and Viruses
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