PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data

Novel anti-herpes simplex activity of Chryseobacterium indologenes: Genomic and metabolomic insights

Herpes simplex virus (HSV) is a pathogenic virus responsible for various diseases, necessitating alternative antiviral strategies for HSV-1 treatment. Given the antiviral properties of lactic acid (LA), we screened rhizobacteria from the maize (Zea mays L.) rhizosphere for organic acid production. Among the isolates, SR50, SR126, and SR135 exhibited significant LA production, confirmed by High-Performance Liquid Chromatography (HPLC) analysis. Their antiviral efficacy against HSV-1 was evaluated by determining IC50 values and selectivity indices (SI = CC50/IC50), with SR50, SR126, and SR135 displaying SI values of 135.14, 10.74, and 2.17, respectively. SR50, identified via 16S rRNA sequencing as Chryseobacterium indologenes, was selected for further antiviral analysis. The cell-free supernatant (CFS) of SR50 demonstrated 73.3 % inhibition of viral adsorption, 60 % virucidal activity, and a 46.7 % reduction in viral replication. Metabolomic profiling using Gas Chromatography-Mass Spectrometry (GC-MS) identified short- and long-chain organic fatty acids. Whole Genome Sequencing (WGS) revealed a 4,581,372 bp genome encoding diverse biosynthetic pathways, including siderophores, plant hormones, terpenoids, polyketides, and other bacterial secondary metabolites. Additionally, genes encoding lactaldehyde dehydrogenase and pyruvate dehydrogenase confirmed the presence of lactic and acetic acid biosynthesis pathways. This study presents the first report of C. indologenes SR50 exhibiting anti-HSV-1 activity, highlighting its potential as a novel antiviral resource.

Draft genome sequence of Dolosicoccus paucivorans DSM 15742T isolated from a patient's blood in Cleveland, Ohio

This study describes the whole genome sequence of Dolosicoccus paucivorans 2991-95 (DSM 15742) isolated from human blood in Cleveland, Ohio. The genome length is approximately 1.8 Mbp with 107 contigs and a G + C content of 37.91%. Annotation identified 1,752 coding genes and multiple virulence factors.

Draft genome sequence of multidrug-resistant Bacillus subtilis strain Hakim RU_LJ isolated from lacchi juice in Bangladesh

This report details the draft genome sequence of the multidrug-resistant Bacillus subtilis strain Hakim RU_LJ derived from lacchi juice. The assembled genome spans 4.03 Mb, with 50.33× coverage and a GC content of 43.5%. Analysis revealed six CRISPR arrays, 19 prophages, 17 antibiotic resistance genes, and 10 virulence factor genes.

Draft genome sequence of Pseudomonas aeruginosa strain maqsudiensis isolated from cattle swab in Dhaka, Bangladesh

Here, we present the draft genome sequence of Pseudomonas aeruginosa strain maqsudiensis, isolated from cattle stool swab. The genome was sequenced using the Illumina MiSeq platform, yielding a 6.33 Mb assembly with 5,784 predicted coding sequences. The genome harbors multiple antibiotic-resistance genes and virulence factors, providing insights into P. aeruginosa colonization in livestock and potential implications for antimicrobial resistance dissemination through the food chain.

Genomic characterization of a novel Pseudomonas aeruginosa bacteriophage representing the newly proposed genus Angoravirus: in vitro antimicrobial and antibiofilm activity

Multi-drug-resistant (MDR) Pseudomonas aeruginosa is an important pathogen that poses a critical threat due to its metallo-beta-lactamase (MBL)-mediated carbapenem resistance and biofilm-forming ability, making bacterial treatment very complicated and requiring alternative strategies. Bacteriophages are promising alternatives; however, the discovery of novel phages targeting MDR strains remains urgent. In this study, Pseudomonas phage Baskent_P4_1, a novel virulent siphovirus that infects clinical MDR P. aeruginosa isolates, was isolated from wastewater and characterized comprehensively. Its efficacy was tested against biofilm-forming, MDR isolates with MBL activity by spot test and efficiency of plating (EOP). Biological characterization showed that phage Baskent_P4_1 is stable at pH 4-10 and temperatures up to 50 °C, while its stability decreases  >60 °C temperature. It has a short latent period of 10 min and a high burst size of 253 phages per cell. The phage lysed 40% of the MDR P. aeruginosa isolates tested, including strong biofilm producers. In vitro assays showed significant biofilm inhibition (48.8% reduction at 10⁹ PFU/mL) and degradation of pre-formed biofilms. Transmission electron microscopy (TEM) revealed an icosahedral head (70 nm) and a long non-contractile tail (150 nm). Whole genome sequencing by Illumina demonstrated a linear dsDNA genome of 41.947 bp (62.8% GC content) with 53 predicted coding sequences. No virulence factors, antibiotic resistance genes, or tRNAs were detected, thus ensuring therapeutic safety. Along with phylogenetic and vConTACT2 analysis, these results suggested that phage Baskent_P4_1 belongs to a new genus, which was proposed here as the genus Angoravirus with three other species. Genomic analysis identified hydrolases (ORF 13/14) and 7-deazaguanine modification enzymes (ORF 46/47) that may contribute to host lysis and evasion of bacterial defenses. These findings highlight Baskent_P4_1's potential as a therapeutic candidate against MDR P. aeruginosa infections. The study underscores the importance of expanding phage diversity libraries and provides a framework for characterizing novel phages to combat antimicrobial resistance.

Whole-genome sequence of Bacillus subtilis TP111, a potential fish probiotic that prevents motile Aeromonas septicemia in Nile tilapia (Oreochromis niloticus)

We report the genome of fish probiotic Bacillus subtilis TP111 strain isolated from the gut of a healthy Nile tilapia (Oreochromis niloticus) in Bangladesh. TP111 has a genome size of 4,174,638 bp, 43.48% guanine-cytosine, 243.0× genome coverage with 4,224 potential coding sequences, and 10 predicted secondary metabolite biosynthetic gene clusters.

Identifying potential novel widespread determinants of bacterial pathogenicity using phylogenetic-based orthology analysis

Introduction

The global rise in antibiotic resistance and emergence of new bacterial pathogens pose a significant threat to public health. Novel approaches to uncover potential novel diagnostic and therapeutic targets for these pathogens are needed.

Methods

In this study, we conducted a large-scale, phylogenetic-based orthology analysis (OA) to compare the proteomes of pathogenic to humans (HP) and non-pathogenic to humans (NHP) bacterial strains across 734 strains from 514 species and 91 families.

Results

Using a dedicated workflow, we identified 4,383 hierarchical orthologous groups (HOGs) significantly associated with the HP label, many of which are linked to critical factors such as stress tolerance, metabolic versatility, and antibiotic resistance. Both known virulence factors (VFs) and potential novel widespread pathogenicity determinants were uncovered, supported by both statistical testing and complementary protein domain analysis.

Discussion

By integrating curated strain-level pathogenicity annotations from BacSPaD with phylogeny-based OA, we introduce a novel approach and provide a novel resource for bacterial pathogenicity research.

Phenotypic and genomic analysis of Enterococcus avium MC09 pathogenicity isolated from Scylla spp. (mud crab) in a Thai market

Enterococcus avium is a Gram-positive pathogenic bacterium classified under the Enterococcaceae family. E. avium has been isolated from diverse environmental sources, raising concerns about its potential role in the spread of antibiotic resistance. E. avium MC09, isolated from a mud crab in a Thai market, was analyzed for its antibiotic resistance and pathogenic potential in this study. The isolation of E. avium from mud crab is significant as it highlights the potential role of seafood as a reservoir for antibiotic-resistant bacteria, which may pose risks to public health throughout the food chain. Antibiotic susceptibility testing using the Kirby-Bauer disk diffusion method revealed that E. avium MC09 is resistant to clindamycin, erythromycin, streptomycin, and tetracycline, and exhibits alpha hemolysis on blood agar, indicating its potential virulence. Genomic DNA was extracted and sequenced using the Oxford Nanopore Technologies (ONT) platform, revealing the presence of resistance genes for macrolides (ermB) and tetracyclines (tetL and tetM). Furthermore, several virulence-associated genes were detected, such as srtC, ecbA, efaA, dltA, cpsA/uppS, cpsB/cdsA, cylR2, icps4I, cpsY, epsE, vctC, mgtB, ndk, lisR, and lgt suggesting a pathogenic potential. Additionally, the study identified several insertion sequences (ISs), including (IS1216, IS1216E, IS1216V, IS6770, ISEfa7, ISEfa8, and ISS1W which are commonly found in pathogenic Enterococcus strains. The presence of these IS elements further emphasizes the strain's potential for virulence and genetic adaptability. This study provides comprehensive insights into both the phenotypic and genotypic characteristics of E. avium MC09, highlighting its antimicrobial resistance and pathogenic mechanisms, and underlines the importance of monitoring antibiotic resistance in seafood-associated bacteria.

Effect of Bacillus velezensis MT9 on Nile Tilapia (Oreochromis Niloticus) Intestinal Microbiota

In recent years, there has been a growing interest in the use of probiotics in aquaculture, due to their effectiveness on production, safety, and environmental friendliness. Probiotics, used as feed additives and as an alternative to antibiotics for disease prevention, have been shown to be active as growth promoters, improving survival and health of farmed fish. In this study, we have investigated the ability of the strain Bacillus velezensis MT9, as potential probiotic, to modulate the intestinal microbiota of the Nile tilapia (Oreochromis niloticus) fed with the Bacillus velezensis-supplemented feed in an experimental aquaculture plant. The analysis of the microbial community of the Nile tilapia by culture-based and 16S rRNA gene metabarcoding approaches demonstrated that B. velezensis MT9 reshapes the fish intestinal microbiota by reducing the amounts of opportunistic Gram-negative bacterial pathogens belonging to the phylum of Proteobacterium (Pseudomonadota) and increasing the amounts of beneficial bacteria belonging to the phyla Firmicutes (Bacillota) and Actinobacteria (Actinomycetota). Specifically, dietary supplementation of Nile tilapia with B. velezensis MT9 resulted in an increase in the relative abundance of bacteria of the genus Romboutsia, which has a well-documented probiotic activity, and a decrease in the relative abundance of Gammaproteobacteria of the genera Aeromonas and Vibrio, which include opportunistic pathogens for fish, and Escherichia/Shigella, which may pose a risk to consumers. The whole genome sequence of B. velezensis MT9 was then determined. Genome analysis revealed several peculiarities of B. velezensis MT9 compared to other B. velezensis reference strains including specific metabolic traits, differences in two-component and quorum sensing systems as well as the potential ability to produce a distinct array of secondary metabolites, which could explain the strong ability of this strain to modulate the intestinal microbiota of the Nile tilapia.

Draft genomic sequences of a rare environmental pathogen, Comamonas kerstersii, from immunocompromised patients with acute gastroenteritis

Comamonas kerstersii is a ubiquitous, aerobic, motile gram-negative bacteria considered commensal but has played a significant role as a potential pathogen causing clinical infections. Here, we report the genomic sequences of five C. kerstersii isolated from immunocompromised patients with acute gastroenteritis.

Probiogenomic insights into Bacillus velezensis MFSS1 for controlling aquaculture pathogens

Bacillus velezensis MFSS1 (previously known as B. subtilis FS6) was reported to have good probiotic criteria and antibacterial activity against Vibrio spp. and Aeromonas spp., through phenotypic analysis. However, whole genome sequencing is required for commercialising a new probiotic, especially due to reports on probiotics that can cause horizontal gene transfer towards the host microbiome. Therefore, this study aims to investigate the comprehensive genomic characteristics of B. velezensis MFSS1, focusing on its antimicrobial genes against aquaculture pathogens, its probiotic traits, and safety assessment. The bacterial genome was sequenced using Oxford Nanopore sequencing, resulting in 7 contigs with a total length of 3,914,361 base pairs and an average G + C content of 46.58 %. The analysis using ContEst16S and average nucleotide identity revealed that the bacterium previously reported as B. subtilis is actually B. velezensis. Additionally, secondary metabolites against pathogens were predicted using the antiSMASH website, which identified eight secondary metabolites: Bacillibactin, Bacilysin, Surfactin, Difficidin, Fengycin, Bacillaene, Macrolactin H, and Plantazolicin. Furthermore, several probiotic markers were detected, functioning in acid tolerance, bile salt tolerance, adhesion, osmotic stress, and intestinal persistence during the delivery of the bacteria to the host. Interestingly, the in silico safety assessment of the bacterium revealed a lack of 96 antibiotic resistance genes and confirmed it as non-pathogenic to humans, compared with genomic bacteria from ATCC. The study indicates that B. velezensis MFSS1 is a good probiotic through genomic analysis and can be commercialised to control aquaculture pathogens and reduce reliance on antibiotics.

Pan-genome analysis of the Enterobacter hormaechei complex highlights its genomic flexibility and pertinence as a multidrug resistant pathogen

BACKGROUND

Enterobacter hormaechei is of increasing concern as both an opportunistic and nosocomial pathogen, exacerbated by its evolving multidrug resistance. However, its taxonomy remains contentious, and little is known about its pathogenesis and the broader context of its resistome. In this study, a comprehensive comparative genomic analysis was undertaken to address these issues.

RESULTS

Phylogenomic analysis revealed that E. hormaechei represents a complex, comprising three predicted species, E. hormaechei, E. hoffmannii and E. xiangfangensis, with the latter putatively comprising three distinct subspecies, namely oharae, steigerwaltii and xiangfangensis. The species and subspecies all display open and distinct pan-genomes, with diversification driven by an array of mobile genetic elements including numerous plasmid replicons and prophages, integrative conjugative elements (ICE) and transposable elements. These elements have given rise to a broad, relatively conserved set of pathogenicity determinants, but also a variable set of secretion systems. The E. hormaechei complex displays a highly mutable resistome, with most taxa being multidrug resistant.

CONCLUSIONS

This study addressed key issues pertaining to the taxonomy of the E. hormaechei complex, which may contribute towards more accurate identification of strains belonging to this species complex in the clinical setting. The pathogenicity determinants identified in this study could serve as a basis for a deeper understanding of E. hormaechei complex pathogenesis and virulence. The extensive nature of multidrug resistance among E. hormaechei complex strains highlights the need for responsible antibiotic stewardship to ensure effective treatment of these emerging pathogens.

Microbacterium chionoecetis sp. nov. and Agrococcus chionoecetis sp. nov.: Novel Gut Bacteria from Red Snow Crab

Two yellow-coloured, Gram-stain-positive, oxidase-negative, aerobic, non-motile, and rod-shaped strains, labelled as ProA8T and ProA11T, were isolated from digestive tract of red snow crab (Chionoecetes japonicus). Strain ProA8T grow at temperature range of 15-35°C, while strain ProA11T grow at temperature range of 15-40°C. Phylogenetic and 16S rRNA gene sequence analysis revealed that strains ProA8T and ProA11T belonged to the genera Microbacterium and Agrococcus, respectively. Strain ProA8T was closely affiliated with Microbacterium yannicii JCM 18959T (98.8%) and strain ProA11T was most closely related to Agrococcus baldri IAM 15147T (98.9%). The genome sizes of ProA8T and ProA11T were 4,373,776 bp and 2,665,899 bp, with DNA G+C contents of 70.5% and 70.1%, respectively. The genomic relatedness values of ProA8T and ProA11T with their respective reference strains were <32.0% (for digital DNA-DNA hybridization) and <87.0% (for average nucleotide identity). Biosynthetic gene analysis showed the presence of genes for resorcinol production in ProA8T and ectoine biosynthesis in ProA11T, indicating ecological and biotechnological significance. Virulence analyses determined that strains ProA8T and ProA11T were non-pathogenic to humans, highlighting their safe application in biotechnological field. The major cellular fatty acids reported in ProA8T and ProA11T were anteiso-C15:0, iso-C16:0, and anteiso-C17:0. Overall, the polyphasic taxonomic data suggest that both strains ProA8T and ProA11T represent two novel species within the genera Microbacterium and Agrococcus, respectively. Accordingly, we propose the names Microbacterium chionoecetis sp. nov., with the type strain ProA8T (= KCTC 49861T = JCM 37392T) and Agrococcus chionoecetis sp. nov., with the type strain ProA11T (= KCTC 49958T = JCM 37393T).

Genomic Characterization of Serratia fonticola (EBS19) as a Biocontrol Agent against Botrytis cinerea

Botrytis cinerea (Bc), a plant pathogenic fungus, is the causative agent of gray mold disease, which rapidly develops resistance to fungicides in cultivation areas. This study explores the biocontrol potential of various bacterial isolates collected from the rhizosphere of tomato plants (Solanum lycopersicum). Bacterial isolates were purified and neutralized through phenol vaporization for 2 days. Colonies that inhibited pathogen spore growth were confirmed via antibiosis effect using in vitro bioassays. Bacterial colonies demonstrated up to 84% inhibition of pathogen growth at 7-day post-inoculation (dpi) with a one-layer agar diffusion test and up to 70% inhibition with a double-layer agar diffusion test, compared to control plates. Both bacterial suspension and filtrate significantly suppressed pathogen mycelium growth at 11 and 14 dpi. The isolate used in further studies was identified as Serratia fonticola (EBS19) through whole-genome sequencing. Annotated genome data revealed the presence of genes encoding enzymes crucial for pathogen inhibition. Carbon preference analyses identified specific carbon sources unique to the bacterial strain. These findings are advantageous for developing effective biopreparations that ensure bacterial strain stability in practical applications. In addition, the primary focus was on the interaction between the pathogen's major stress regulator protein (BAG1) and the bacterial glycoside hydrolase. Protein-protein docking analyses elucidated strong interaction between BAG1 and bacterial glycoside hydrolase. In conclusion, this study provides a knowledge for further research using recombinant DNA and gene cloning techniques on the bacterium's mapped genome.

Antimicrobial resistance in coagulase negative staphylococci: Genome analysis and role of horizontal gene transfer

Coagulase-negative staphylococci (CNS) are emerging as significant contributors to antimicrobial resistance, yet their genomic characteristics remain incompletely understood. This study presents a whole-genome analysis of 12 multidrug-resistant CNS strains (Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis) isolated from blood cultures, focusing on antimicrobial resistance genes, mobile genetic elements (MGEs), and horizontal gene transfer (HGT) mechanisms. We identified 22 resistance genes conferring resistance to 11 antimicrobial classes, many of which were plasmid-associated. Notably, we report the first detection of the ISSha1 insertion sequence in S. hominis, along with novel resistance plasmids, including pGO1 and VRSAp in S. haemolyticus and pAMα1 in S. hominis. The identification of bacteriophage-derived sequences in S. haemolyticus and S. hominis suggests a role for phages in genetic exchange. CRISPR sequences and a Cas gene were detected in S. hominis, suggesting a potential but unconfirmed role in restricting gene transfer. Additionally, pGO1 was identified as a conjugative plasmid, while pAMα1 and VRSAp were determined to be mobilizable, reinforcing the role of CNS in resistance dissemination. These results highlight CNS as reservoirs of antimicrobial resistance genes and emphasize the importance of species-specific genomic surveillance. Proactive monitoring of CNS is crucial for controlling antimicrobial resistance in clinical settings.

Unlocking Nature's Microbial Defenders: Genetic Mechanisms and Potential Against Monilinia spp. Pathogens

Monilinia spp., which causes brown rot, is one of the most damaging pathogens in stone fruits. Researchers are exploring epiphytic and endophytic microorganisms with the potential to suppress pathogens, control pathogenic microorganisms, and/or promote plant growth. In this study, microorganisms with antagonistic activity against three Monilinia species were isolated from plum orchard soil and plum fruits. Antagonism tests in vitro showed strong antagonistic properties of six strains of bacteria and two yeast-like fungi against M. fructigena, M. fructicola, and M. laxa, with growth inhibition from 45.5 to 84.6%. The antagonists were identified and characterized at the genetic level using whole genome sequencing (WGS). Genes involved in antibiotic resistance, virulence, secondary metabolite synthesis, and plant growth promotion were identified and characterized through genome mapping, gene prediction, and annotation. None of the microorganisms studied were predicted to be pathogenic to humans. The results of this study indicate that the bacteria Bacillus pumilus, B. velezensis, two strains of Lysinibacillus agricola, Pseudomonas chlororaphis isolated from stone fruit orchard soil, and the yeast-like fungus Aureobasidium pullulans, isolated from plums, are promising candidates for the biological control of Monilinia spp.

Evaluating the safety and efficacy of Lacticaseibacillus paracasei TISTR 2593 as a therapeutic probiotic for obesity prevention

Several recent studies have reported the potential of probiotics in reducing body weight and fat mass and improving glucose and lipid metabolism. Therefore, probiotic administration is considered an alternative approach for treating obesity. The objective of this study was to evaluate the probiotic properties and antiadipogenic potential of the strain TISTR 2593. Through whole-genome sequence analysis, the strain TISTR 2593 was identified as Lacticaseibacillus paracasei. L. paracasei TISTR 2593 exhibited γ-hemolytic activity (nonhemolysis) and demonstrated susceptibility to antibiotics, indicating that it is generally safe for consumption. Additionally, this strain displayed desirable probiotic properties, including tolerance to artificial gastric juice and bile salts, adhesion to Caco-2 cells, and the ability to inhibit pathogens. Furthermore, L. paracasei TISTR 2593 exhibited cholesterol-reducing capability and demonstrated antiadipogenic activity. In 3T3-L1 adipocytes, treatment with 10% (w/v) heated L. paracasei TISTR 2593 cells resulted in an approximately 50% reduction in lipid accumulation, similar to the positive control (quercetin). Moreover, L. paracasei TISTR 2593 heat-killed cells dose-dependently decreased the expression levels of CCAAT/enhancer-binding protein-α and peroxisome proliferator-activated receptor-γ, two vital transcription factors involved in the early stage of adipocyte differentiation. These findings suggest that L. paracasei TISTR 2593 possesses probiotic and functional properties, including antiadipogenic activity, supporting its potential as a therapeutic probiotic supplement for preventing obesity. Overall, the results of this study indicate that L. paracasei TISTR 2593 exhibits promising probiotic characteristics and beneficial effects on adipogenesis modulation, reinforcing its potential as a therapeutic option in obesity prevention.

Complete genome sequence of psychrobacter sp. KFRI-CH2-11: A psychrotolerant bacterium with probiotic, biofortification, and antimicrobial potential for the dairy and meat industries

This dataset provides the complete genome sequence of Psychrobacter sp. KFRI-CH2-11, isolated from Korean fermented anchovy, Myeolchi-jeotgal. Genomic analysis identified genes involved in Vitamin B12 biosynthesis, carbohydrate metabolism, CRISPR-Cas defense systems, and antioxidant activity, underscoring the strain's potential for use in food biotechnology. Additional genes linked to antibiotic resistance and bioremediation suggest adaptability in diverse environments, particularly cold-chain storage in the dairy and meat industry. PathogenFinder analysis confirmed the absence of pathogenicity-associated genes, validating the strain's suitability as a probiotic and biofortifying agent in food products.

Insights Into the Role of Leuconostoc Mesenteroides SB1075 Fermentation in Enhancing the Shelf-Life of Soy Yogurt

Fermented foods with extended shelf life, free from synthetic preservatives, offer significant commercial and health advantages. With increasing consumer demand for plant-based alternatives, soy yogurt has gained substantial market interest. However, improving its shelf-life at ambient temperature without compromising quality remains challenging. This study investigates the application of Leuconostoc mesenteroides SB1075, a promising probiotic strain isolated from yellow-cultivar soybean seeds of Manipur (India), as a biopreservative starter culture for soy yogurt fermentation. Unlike conventional dairy-origin lactic acid bacteria, L. mesenteroides SB1075 demonstrated superior adaptability to soy fermentation. The resulting soy yogurt exhibited an impressive shelf-life of 40 days at room temperature (25°C), significantly outperforming the control (spontaneous fermentation without starter, <5 days) while maintaining its organoleptic and nutritional qualities. Sensory evaluation with a hedonic scale of 10 indicated that flavor, aroma, and taste consistently received a score >6, while color, firmness, consistency, syneresis, and overall acceptance were rated >7. Microscopic analysis, including atomic force and scanning electron microscopy, revealed that the flocculation behavior of L. mesenteroides SB1075 effectively inhibited spoilage microbes, thereby extending product stability. Genomic analysis highlighted its heterofermentative and biopreservative potential, while time-course metabolomics identified bioactive compounds, such as monobactam, organic acids, and neomycin, from the 5th day of storage. This study provides key insights into biopreservation strategies for plant-based fermented foods, offering a valuable alternative to chemical preservatives. The findings support the commercial development of naturally preserved soy yogurt, enhancing the sustainability and market expansion of plant-based dairy alternatives. PRACTICAL APPLICATION: Our research addresses a critical need in the food industry: prolonging the shelf life of soy yogurt without relying on preservatives, which is achieved using a plant-derived probiotic bacterium L. mesenteroides SB1075. The findings outlined in this manuscript propose an innovative and sustainable approach to improving the quality and shelf life of soy yogurt, meeting the increasing demand for vegan, healthier, and preservative-free food choices.

Exploring the occurrence of Pseudomonas aeruginosa and comprehensive whole genome analysis of the bcsir_p4_s20 strain from municipal wastewater in Chattogram

Various studies reported the existence of multidrug-resistant (MDR) Pseudomonas aeruginosa in environmental samples, including hospital wastewater, municipal wastewater, and surface water. In this study, we investigated the impact of untreated municipal wastewater transmitting antibiotic-resistant P. aeruginosa strains in wastewater networks of Chattogram City, Bangladesh, through antibiotic susceptibility profiles and whole-genome sequencing (WGS) of the MDR P. aeruginosa bcsir_p4_s20. Forty-two P. aeruginosa isolates were identified from eight locations using polymerase chain reaction (PCR), targeting the oprI and oprL genes, and antibiotic susceptibility was determined against 11 antibiotics by the disc diffusion method. Resistant isolates were identified at all locations, with the highest resistance frequency displayed towards meropenem, cefepime, and colistin. The WGS of bcsir_p4_s20 was performed using the NextSeq 2000 platform. Several bioinformatics tools, like FastQC, Trimmomatic, SPAdes, and Prokka, were used for quality evaluation, low-quality read and adapter filtration, de novo assembly, and functional annotation. Comprehensive Antibiotic Resistance Database (CARD), AMRFinderPlus, and virulence factor database (VFDB) were employed to determine resistance genes and virulence factors. The strain belongs to the O7 serogroup and sequence type ST357. The analysis identified antibiotic resistance genes (blaPDC-11, sul1, and others) that cause resistance through efflux pump and inactivation mechanisms, and virulent genes responsible for adherence (flagella, type IV pili), enzyme (phospholipase C), iron uptake (pyoverdine), secretion system (exoT, exoU), and toxin (toxA) secretion. Therefore, municipal wastewater is a potential reservoir for MDR P. aeruginosa, and establishing wastewater treatment plants (WWTPs) at the primary source points before discharging it to the wastewater network is suggested to mitigate the risk of outbreaks.

Revolutionizing the probiotic functionality, biochemical activity, antibiotic resistance and specialty genes of Pediococcus acidilactici BCB1H via in-vitro and in-silico approaches

This study presents a comprehensive genomic exploration, biochemical characterization, and the identification of antibiotic resistance and specialty genes of Pediococcus acidilactici BCB1H strain. The functional characterization, genetic makeup, biological activities, and other considerable parameters have been investigated in this study with a prime focus on antibiotic resistance and specialty gene profiles. The results of this study revealed the unique susceptibility patterns for antibiotic resistance and specialty genes. BCB1H had good in vitro probiotic properties, which survived well in simulated artificial gastrointestinal fluid, and exhibited acid and bile salt resistance. BCB1H didn't produce hemolysis and had certain antibiotic sensitivity, making it a relatively safe LAB strain. Simultaneously, it had good self-coagulation characteristics and antioxidant activity. The EPS produced by BCB1H also had certain antioxidant activity and hypoglycemic function. Moreover, the genome with a 42.4 % GC content and a size of roughly 1.92 million base pairs was analyzed in the genomic investigations. The genome annotation identified 192 subsystems and 1,895 genes, offering light on the metabolic pathways and functional categories found in BCB1H. The identification of specialty genes linked to the metabolism of carbohydrates, stress response, pathogenicity, and amino acids highlighted the strain's versatility and possible uses. This study establishes the groundwork for future investigations by highlighting the significance of using multiple strains to investigate genetic diversity and experimental validation of predicted genes. The results provide a roadmap for utilizing P. acidilactici BCB1H's genetic traits for industrial and medical applications, opening the door to real-world uses in industries including food technology and medicine.

Complete genome sequence, metabolic profiling and functional studies reveal Ligilactobacillus salivarius LS-ARS2 is a promising biofilm-forming probiotic with significant antioxidant, antibacterial, and antibiofilm potential

Background

Probiotics restore microbial balance and prevent gut-inflammation. Therefore, finding out novel probiotic strains is a demand. As gut-microbe, benefits of Ligilactobacillus salivarius (LS) are established. However, strain-specific detailed studies are limited. Here, we illustrate probiotic attributes of novel LS-ARS2 for its potential application as food-supplement and/or therapeutic to improve gut-health.

Methods

Whole genome sequencing (WGS) and phylogenetic analysis confirm the strain as LS. To establish probiotic properties, acid-bile tolerance, auto-aggregation, cell-surface-hydrophobicity, biofilm-formation, and adhesion-assays are performed. To ensure safety attributes, antibiotic-susceptibility, hemolytic, DNase, trypan-blue, and MTT assays are done. ABTS, DPPH, superoxide, hydroxyl free radical scavenging assays are used to determine anti-oxidant potential. Antibacterial assays, including co-culture assay with pathogen and pathogenic biofilm-inhibition assays, are performed to explore antibacterial efficacy. To characterize metabolic-profile of LS-ARS2-derived cell-free-supernatant (CFS), HRMS analysis are carried out. Consequently, WGS-analyses predict potential molecular associations related to functional outcomes.

Results

We find LS-ARS2 a remarkable fast-growing strain that shows acid and bile tolerance (>60% survival rate), indicating promising gut-sustainability. High auto-aggregation capacity (>80%), robust cell-surface hydrophobicity (>85%), and adhesion efficacy to Caco-2 cells illustrate significant potential of LS-ARS2 for gut colonization. Fascinatingly, LS-ARS2 is able to form biofilm within 24 h (p < 0.0001), rare among LS strains, indicating the potential of the strain for efficient stay in the gut. The strain ensures safety attributes. LS-ARS2-WGS analysis recognizes probiotic-specific determinants, predicts genomic stability, identifies orthologous-clusters for diverse functions, and predicts metabolites and bacteriocins. HRMS-studies with LS-ARS2-CFS further validate the presence of diverse beneficial metabolites with antimicrobial and immunomodulatory potential. LS-ARS2 shows significant antioxidant properties in ABTS (>60%), DPPH (>10 U/mL), superoxide (>70%), and hydroxyl free radical scavenging assays (>70%). Further, LS-ARS2 shows antimicrobial activities against Gram-positive Methicillin-resistant Staphylococcus aureus (MRSA) and Gram-negative multidrug-resistant clinical strains enterotoxigenic Escherichia coli, Vibrio cholerae, and Shigella flexneri. Anti-Salmonella effect of LS-ARS2 is prominent (p < 0.0001). Most interestingly, LS-ARS2-CFS inhibits MRSA-biofilm (p < 0.0001), again rare among LS strains.

Conclusion

LS-ARS2 is a novel, fast-growing, biofilm-forming probiotic with significant antioxidant, antibacterial, and anti-biofilm potentials, suggesting the promising applications of LS-ARS2 for combating pathogenic biofilms and improving gut-health. However, further in vivo studies would facilitate their potential applications.

In Vitro and In Silico Assessment of the Probiotic and Technological Potential of Lacticaseibacillus rhamnosus MW019593 Isolated from Algerian Cow's Milk

This study evaluated the in vitro and in silico probiotic potential and technological characteristics of Lacticaseibacillus rhamnosus MW019593 isolated from Algerian cow's milk. Safety was verified by the absence of hemolytic activity, biogenic amine production, and antibiotic sensitivity. Functional probiotic properties of L. rhamnosus MW019593 included moderate inhibition of gastrointestinal pathogens such as Salmonella, Listeria, Clostridioides, and Escherichia coli, tolerance to pH 2-3 and up to 1% bile salts, 46.4% hydrophobicity, 42.4% autoaggregation, and 12.9% adhesion to Caco-2/TC7 cells without cytotoxicity. The ability to form biofilms with a thickness of 23.7 µm, comparable to L. rhamnosus ATCC 53103, was observed using confocal microscopy. Technologically, L. rhamnosus MW019593 and ATCC 53103 showed similar growth profiles and biomass yields, reaching approximately 5 × 109 CFU/mL with a 63% yield after lyophilization. No significant difference in strain viability was noted at 4 °C and - 20 °C, which are suitable temperatures to maintain their viability for 3 months. Whole genome sequencing (WGS) was conducted on L. rhamnosus MW019593, followed by comprehensive in silico genomic analysis. Taxonomic validation using average nucleotide identity (ANI) and genome-to-genome distance hybridization (GGDH) confirmed the strain's affiliation to this species. Gene screening revealed the absence of virulence and antibiotic resistance genes, while beneficial genes, including those for bacteriocin production, were identified. These findings, supported by the demonstrated safety, functional, and technological properties of the strain, highlight its promising potential for food and therapeutic applications, pending in vivo validation.

Draft genome sequencing of a multidrug-resistant and virulent Escherichia coli strain isolated from milk of a cow with clinical mastitis

We present the draft genome of Escherichia coli strain MBBL3, a virulent and antimicrobial-resistant pathogen isolated from the milk of a cow suffering from clinical mastitis. The assembled genome spans 4,713,190 base pairs, organized into 115 contigs, and harbors 52 antimicrobial resistance genes (ARGs) alongside 25 virulence factor genes (VFGs).

Draft genome sequencing of a multidrug-resistant Klebsiella pneumoniae strain MBBL2 isolated from mastitic cow milk

Milk from cows with mastitis is a primary source of bacteria harboring antibiotic resistance genes (ARGs), including Klebsiella pneumoniae. We present the genome sequence of K. pneumoniae strain MBBL2 isolated from mastitic cow milk, which contains numerous ARGs and virulence-associated genes potentially pathogenic to humans.

Genome sequencing of a metallo-beta-lactamase-producing Escherichia coli Ne7 strain isolated from a patient with urinary tract infection in Ahvaz-Iran

We report the draft genome sequence of an extensively drug-resistant and metallo-beta-lactamase-producing Escherichia coli Ne7 strain isolated from a urinary tract infection patient. Under the O8:H9 serotype and F phylogenetic group, this strain had a sequence type of ST648, five replicon plasmids, 16 virulence genes, and 21 antibiotic resistance genes.

Draft genome sequencing of multidrug-resistant Escherichia coli strains isolated from mastitic cow milk

Escherichia coli is an important antibiotic-resistant pathogen in mastitis, with broader public health implications. We report the genomes of two E. coli strains, MBBL4 and MBBL5, isolated from mastitic cow milk. The draft genomes, covering 4.6 Mbp each, revealed 57.5% GC content and 100× sequencing depth.

A review of neural networks for metagenomic binning

One of the main goals of metagenomic studies is to describe the taxonomic diversity of microbial communities. A crucial step in metagenomic analysis is metagenomic binning, which involves the (supervised) classification or (unsupervised) clustering of metagenomic sequences. Various machine learning models have been applied to address this task. In this review, the contributions of artificial neural networks (ANN) in the context of metagenomic binning are detailed, addressing both supervised, unsupervised, and semi-supervised approaches. 34 ANN-based binning tools are systematically compared, detailing their architectures, input features, datasets, advantages, disadvantages, and other relevant aspects. The findings reveal that deep learning approaches, such as convolutional neural networks and autoencoders, achieve higher accuracy and scalability than traditional methods. Gaps in benchmarking practices are highlighted, and future directions are proposed, including standardized datasets and optimization of architectures, for third-generation sequencing. This review provides support to researchers in identifying trends and selecting suitable tools for the metagenomic binning problem.

Mycobacterium servetii sp. nov., a novel rapid-growing nontuberculous mycobacterial species recovered from a human patient in Zaragoza, Spain

In this study, we describe a novel rapid-growing Mycobacterium species isolated from a clinical specimen obtained from the lower respiratory tract of a patient with ciliary dysfunction, bronchiectasis and exacerbated respiratory symptoms. A comprehensive phenotypic characterization was conducted, including the establishment of a MALDI-TOF MS profile. Additionally, whole-genome sequencing was performed to assess overall genomic relatedness indices and conduct phylogenetic comparative analyses. These findings allowed us to characterize a previously unrecognized rapid-growing Mycobacterium species, for which we propose the name Mycobacterium servetii (=DSM 118141; =CECT 31091).

Genomic characterization of multidrug-resistant Escherichia albertii of fish origin-first isolation and insights into a potential food safety threat

Introduction

Escherichia albertii is an emerging food-borne pathogen with zoonotic potential which is often under-reported due to misidentifications.

Materials and methods

The current study identified E. albertii from retail fish sold in market which was confirmed by phenotypic (colorless colonies on Xylose-Rhamnose-Melibiose MacConkey Agar), genotypic (dual target uniplex PCR-based detection) and genomic methods (CheckM analysis). In this paper we report the phenotypic characters of the isolate and genomic features such as resistome, virulome and mobilome followed by in silico O and H antigen based typing and comparative phylogenomics using various tools (RAST, RGI v6.0.0, ABRicate v1.0.1, PathogenFinder v1.1, PlasmidFinder v2.0, BacAnt v3.3.1, Phigaro v2.4.0, MAFFT v7.490, FigTree v1.4.4).

Results and discussion

Multidrug resistance was identified with reduced susceptibility to gentamicin, azithromycin, ceftazidime and cefotaxime with a Multiple Antibiotic Resistance (MAR) index of 0.33. Clinically important virulence genes such as eae, cdt, east1 formed a part of the virulome and the probability of being pathogenic to humans was found to be 0.883. The genome was found to harbor mobile genetic elements such as plasmids [IncFIA, IncFIB(pB171), IncFII(pSE11)], transposons (Tn3411, Tn6292) and prophages (Siphoviridae, Myoviridae, Podoviridae). Various typing methods such as biotyping, multilocus sequence typing and in silico O and H antigen typing classified the isolate into biotype 3, multi locus sequence type 4596, O-genotype 4 and H-genotype 1. Phylogenomically, the isolate was placed close to isolate from neighboring country of China. Identification of virulent multidrug-resistant E. albertii from new food source such as fishes increases the risk for fish eating population and necessitates the requirement of further elucidation and development of appropriate control strategies.

Comprehensive genomic insights into a highly pathogenic clone ST656 of mcr8.1 containing multidrug-resistant Klebsiella pneumoniae from Bangladesh

Antimicrobial resistance (AMR) is a pressing global health issue, intensified by the spread of resistant pathogens like Klebsiella pneumoniae (K. pneumoniae), which frequently causes hospital-acquired infections. This study focuses on a multidrug-resistant K. pneumoniae sequence type (ST) 656 strain, isolated from canal water in Bangladesh. Whole-genome sequencing and comparative genomic analysis revealed extensive resistance mechanisms and genetic elements underlying its adaptability. The strain exhibited resistance to colistin and multiple β-lactam antibiotics, containing key resistance genes such as mcr8.1, blaLAP-2, blaTEM-1, blaSHV-11 and blaOXA-1, alongside genes for copper, zinc, and silver resistance, indicating survival capability in metal-rich environments. Virulence factor analysis identified genes supporting adhesion, biofilm formation, and immune evasion, amplifying its pathogenic potential. Plasmid and phage analyses revealed mobile genetic elements, highlighting the role of horizontal gene transfer in AMR dissemination. The study included a pangenome analysis using a dataset of 32 publicly available K. pneumoniae sequence type (ST) 656 genomes, demonstrating evidence of an expanding pangenome for K. pneumoniae ST656. This study emphasized the role of environmental sources in AMR spread and the importance of continued surveillance, particularly in settings with intensive antibiotic usage, to mitigate the spread of high-risk, multidrug-resistant clones like K. pneumoniae ST656.

Additive Effects of Natural Plant Extracts/Essential Oils and Probiotics as an Antipathogenic Topical Skin Patch Solution for Acne and Eczema

This work leverages the additive antipathogenic effects of natural extracts/essential oils (EOs) and probiotics for the treatment of acne vulgaris associated with Cutibacterium acnes (C. acnes) and eczema complicated by secondary infections with Staphylococcus aureus (S. aureus). Six probiotic strains and various extracts/EOs were evaluated in a large screening to evaluate their potential against both pathogens. Lacticaseibacillus paracasei PCB003 was able to inhibit the growth of both pathogens. For extracts/EOs, Oregano EO had the best antipathogenic effects on both pathogens and did not show any adverse impact on the growth of probiotics, making it suitable for simultaneous use. Using Lactiplantibacillus plantarum PCB011 as a probiotic model, five material formulations were assessed for their suitability to protect probiotic cells within freeze-dried topical patches. Alginate and trehalose (ALG+TRE) and thermoplastic starch (TPS) had the highest probiotic survivability, with ALG+TRE chosen as the final patch material as it was more robust. PCB003 and PCB011 were individually incorporated into the ALG+TRE freeze-dried matrix to form a 6 mm patch; both ALG+TRE (PCB003) and ALG+TRE (PCB011) patches, when used individually, successfully inhibited C. acnes growth by 4.7 and 6.0 mm, respectively, surpassing the performance of commercially available acne patches. The additive effect with 30% Oregano EO further improved pathogen inhibition. For S. aureus, the incorporation of 30% Oregano EO to ALG+TRE (PCB003) increased the size of the inhibition zone more than 10-fold. For C. acnes, the ALG+TRE (PCB003) patch with 30% Oregano EO demonstrated an inhibition zone of 16.3 mm, and the ALG+TRE (PCB011) patch with 30% Oregano EO achieved a 14.3 mm inhibition zone. Genomic analysis confirmed that PCB003 and PCB011 lack antimicrobial resistance determinants, ensuring safety. This study successfully combined probiotics and natural agents to create effective dermatological antipathogenic patches.

Unraveling the Resistome, Virulome, and Pathogenicity of Escherichia Coli O157:H7 From Cattle Feces

Antimicrobial-resistant Escherichia coli, especially those belonging to the serotype O157, are increasingly linked to foodborne diseases with significant fatality rates worldwide. The food and medical industries have focused on E. coli O157:H7 due to its ability to produce toxins coupled with its low infectious dose. The aim of this study was to assess the virulome, resistome, and pathogenicity of E. coli O157:H7 using whole genome sequencing. Three previously isolated E. coli O157:H7 strains from cattle feces were subjected to whole genome sequencing. The genome sizes of all three E. coli O157:H7 strains were 5,117,276 bp, 5,039,443 bp, and 5,034,351 bp. The C + G contents were 50.22%, 50.53%, and 50.54%, while the number of contigs was 110, 43, and 42, respectively, for E. coli O157:H7 strains J32, J57, and J69. Several virulence determinants (hemorrhagic E. coli pilus (HCP), eaeA, hemolysin, etc.) were found in the genomes of these isolates. In addition, antibiotic resistance genes conferring resistance to aminoglycosides, tetracyclines, macrolides, fluoroquinolones, penams, carbapenems, cephalosporins, cephamycin, rifamycin, phenicols, monobactams, and nitroimidazole were found in the genomes. Interestingly, the genomes of these isolates also harbored determinants encoding resistance to disinfectants and antiseptics, indicating their concern in the food production and medical sectors. This highlights the public health concerns of these isolates, indicating the need for constant surveillance.

A novel Enterococcus faecalis bacteriophage Ef212: biological and genomic features

This study aimed to isolate and characterize biological and genomic features of a phage infecting Enterococcus faecalis. The phage was isolated from environmental water and temperature and pH stability, one-step growth curve, and multiplicity of infection (MOI) were determined. Whole genome sequencing (WGS) and structural and functional annotations were performed. Its antibiofilm activity was also evaluated. The optimal MOI was 0.01, the latency period was 5 min, and the burst size was 202 plaque forming unit (PFU). High phage survival rates were observed at between pH 4-10 and temperatures between 4-50 °C. WGS and Transmission electron microscopy (TEM) showed that it was an Efquatrovirus representing siphovirus morphotype respectively. It was named as Enterococcus phage Ef212 and has a linear 40,690 bp double-stranded DNA with 45.3% G + C content (GenBank accession number: OR052631). BACPHLIP tool demonstrated that Enterococcus phage Ef212 is a lytic phage (88%). A total of 80 open reading frames (ORFs) were found and there were no antibiotic resistance genes, pathogenicity, virulence genes, or tRNAs in the phage genome. It was diverged from the most similar phages (identity, 88.35%; coverage, 89%) by phylogenetic analysis. Phage Ef212 shared a large part of its genome (60/80) with several other phages, yet some unique parts were found in their genomes. Host range analysis showed that phage Ef212 showed lytic activity against vancomycin-resistant and vancomycin-susceptible E. faecalis clinical isolates. This novel phage Ef212 showed the ability to inhibit and reduce the biofilm formation by around 42% and 38%, respectively. The biological and genomic features indicate that having an effective antibacterial activity, phage Ef212 seemed a promising therapeutic and biocontrol agent.

Design and regulation of engineered bacteria for environmental release

Emerging products of biotechnology involve the release of living genetically modified microbes (GMMs) into the environment. However, regulatory challenges limit their use. So far, GMMs have mainly been tested in agriculture and environmental cleanup, with few approved for commercial purposes. Current government regulations do not sufficiently address modern genetic engineering and limit the potential of new applications, including living therapeutics, engineered living materials, self-healing infrastructure, anticorrosion coatings and consumer products. Here, based on 47 global studies on soil-released GMMs and laboratory microcosm experiments, we discuss the environmental behaviour of released bacteria and offer engineering strategies to help improve performance, control persistence and reduce risk. Furthermore, advanced technologies that improve GMM function and control, but lead to increases in regulatory scrutiny, are reviewed. Finally, we propose a new regulatory framework informed by recent data to maximize the benefits of GMMs and address risks.

Brucella ceti in Common Dolphins (Delphinus delphis) in Portugal-Characterization of First Isolates

This study investigates Brucella ceti infection in marine mammals stranded along the Lisbon and Tagus Valley coast between 2022 and mid-2024, marking the first report of Brucella presence in Portuguese waters. Out of 59 examined marine mammals, B. ceti was isolated in three common dolphins (5.1%), a prevalence rate consistent with previous studies from other coastlines. PCR-based detection indicated a higher infection rate (23.7%), suggesting an underestimation of the prevalence of B. ceti infection in this population. Multi-locus Sequence Typing (MLST) and Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA) revealed distinct genetic profiles and close relationships to B. ceti strains from the Atlantic, supporting the hypothesis of specific host-adapted lineages in dolphins. Virulence genes, including those for host interaction (bspE, btpB) and intracellular survival (virB7, vceA), were consistent across isolates, highlighting the pathogenic potential. Additionally, antimicrobial resistance (AMR) genes, such as mprF and efflux proteins (bepC-G), were also identified. These findings underscore the need for further research and surveillance to understand B. ceti transmission, host range, and impacts on Atlantic cetaceans, as well as to develop effective diagnostic and management strategies to mitigate infection risks in marine environments.

Functional genomic insights into Floricoccus penangensis ML061-4 isolated from leaf surface of Assam tea

Floricoccus penangensis ML061-4 was originally isolated from the leaf surface of an Assam tea plant (Camellia sinensis var. assamica) from Northern Thailand. To assess the functions encoded by the F. penangensis ML061-4 genome, gene identification and annotation were undertaken by in silico analysis. The complete genome of F. penangensis ML061-4 consists of single chromosome of 2,159,127 base pairs, containing a GC content of 33.2% and encompassing 2049 predicted protein-encoding genes. A total of 1195 genes (58.0%) in the F. penangensis ML061-4 genome have assignable functions based on BlastKOALA analysis. Furthermore, 1235 genes (59.9%) were classified into six KEGG functional categories with 187 associated pathways, while 1419 genes (68.8%) were assigned a putative function by the Clusters of Orthologous Groups (COGs) database. The ML061-4 genome was evaluated for genes associated with complex carbohydrate metabolism, bacterial adhesion, virulence factors, pathogenicity, bacteriophages, antiviral defence systems as well as toxin- and antibiotic-resistance associated genes, and genes involved in toxin production, secondary metabolite biosynthesis and xenobiotics biodegradation. The obtained results support the notion of F. penangensis ML061-4 being safe for biotechnological and food industry purposes. This is the first report outlining functional genomic insights regarding a member of the genus Floricoccus.

Pseudocitrobacter cyperus, a novel bacterial species recovered from Cyperus alternifolius in Egypt

BACKGROUND

Strain Cyp38ST was isolated as an endophyte from the plant Cyperus alternifolius, collected along the banks of the River Nile in 2019. Preliminary analysis tentatively identified Cyp38ST as belonging to the genus Pseudocitrobacter.

METHODS

The preliminary identification of Cyp38ST was performed using the VITEK®2 identification system, MALDI-TOF-MS, and 16S rRNA gene sequencing. To confirm its taxonomic classification, the draft genome of Cyp38ST was generated using DNBseq, and the genome-based taxonomic evaluation was conducted by calculating the overall genome-relatedness indices (OGRIs) such as Average Nucleotide Identity (ANI), digital DNA-DNA hybridization (dDDH), and the tetra-nucleotide signatures (Tetra). Additionally, the biochemical features, antimicrobial susceptibility profiles, and fatty acid methyl ester content of Cyp38ST were characterized.

RESULTS

VITEK®2 misidentified Cyp38ST as Citrobacter werkmanii, MALDI-TOF-MS identified it as Pseudocitrobacter faecalis. While the 16S rRNA gene showed more than 99.0% similarity to other Pseudocitrobacter species, the calculated OGRIs were lower than the thresholds recommended for species assignment to all currently known Pseudocitrobacter species. Furthermore, the phylogenomic analysis revealed that Cyp38ST forms a distinct species cluster within the genus Pseudocitrobacter. Cyp38ST was predicted as a potential human pathogen and carried a unique ß-lactamase-coding gene.

CONCLUSION

Here we present Cyp38ST (= CCASU-2024-73T) as the type strain of a novel species within the genus Pseudocitrobacter to which we propose the name Pseudocitrobacter cyperus sp. nov. We provide a full description of the novel species and present its genome sequence and annotation. The discovery of this novel species highlights the potential of endophytic bacteria associated with unique plant hosts to harbor previously uncharacterized microbial diversity.

A comprehensive review on probiotics and their use in aquaculture: Biological control, efficacy, and safety through the genomics and wet methods

Probiotics, defined as viable microorganisms that enhance host health when consumed through the diet, exert their effects through mechanisms such as strengthening the immune system, enhancing resistance to infectious diseases, and improving tolerance to stressful conditions. Driven by a growing market, research on probiotics in aquaculture is a burgeoning field. However, the identification of new probiotics presents a complex challenge, necessitating careful consideration of both the safety and efficacy of the microorganisms employed. This review aims to delineate the most utilized and effective methods for identifying probiotics. The most effective approach currently combines in silico analysis of genomic sequences with in vitro and in vivo experiments. Two main categories of genetic traits are analyzed using bioinformatic tools: those that could harm the host or humans (e.g., toxin production, antibiotic resistance) and those that offer benefits (e.g., production of helpful compounds, and enzymes). Similarly, in vitro experiments allow us to examine the safety of a probiotic but also its effectiveness (e.g., ability to adhere to epithelia). Finally, in vivo experiments allow us to study the effect of probiotics on fish growth and health, including the ability of the probiotic to manipulate the host's microbiota and the ability to mitigate the infections. This review comprehensively analyzes these diverse aspects, with a particular focus on the potential of studying the interaction between bacterial pathogens and probiotics through these integrated methods.

Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India

Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.

Arvimicrobium flavum gen. nov., sp. nov., A Novel Genus in the Family Phyllobacteriaceae Isolated From Forest Soil

During the study of microbial diversity of forest soil in the Republic of Korea, a yellow pigment-producing, Gram-stain-negative, rod-shaped, motile bacterium was isolated and designated as strain 1W2T. This strain grew at temperature of 10-37 °C, at pH of 5.0-9.0, and at NaCl concentration of 0-3.0% (w/v). The 16S rRNA gene sequencing and genome sequencing revealed that strain 1W2T is a member of the family Phyllobacteriaceae but exhibits low similarity with known genera, suggesting that this strain is a new genus within the family. This strain showed the closest similarity to the genera Mesorhizobium (96.6-96.9%), Aminobacter (96.4 -96.6%), Aquamicrobium (96.5-96.7%), and Pseudaminobacter (96.6-96.7%). The nearest relative of 1W2T was Mesorhizobium shangrilense CCBAU 65327 T with the 16S rRNA gene sequence similarity of 96.9%. The genome size was 5,545,526 bp with DNA G + C content of 64.7%. The values of overall genomic relatedness indices between strain 1W2T and the reference members were 20.4-21.3% for digital DNA-DNA hybridization, 74.0-76.6% for average nucleotide identity, and 68.1-61.2% for amino acids identity. Chemotaxonomic profiling revealed that Q-10 was the sole ubiquinone; summed feature 8 (C18:1ω7c and/or C18:1ω6c), iso-C13:0, and C19:0 cyclo ω8c were the predominant fatty acids; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, and phosphatidylethanolamine were the major polar lipids. Based on these data, strain 1W2T represents a novel species of a new genus in the family Phyllobacteriaceae. Accordingly, we proposed the name Arvimicrobium flavum gen. nov., sp. nov., with the type strain 1W2T (= KCTC 92441 T = NBRC 116019 T).

Genomic insights into the probiotic potential and genes linked to gallic acid metabolism in Pediococcus pentosaceus MBBL6 isolated from healthy cow milk

Pediococcus pentosaceus is well known for its probiotic properties, including roles in improving health, antimicrobial production, and enhancing fermented food quality. This study aimed to comprehensively analyze the whole genome of P. pentosaceus MBBL6, isolated from healthy cow milk, to assess its probiotic and antimicrobial potentials. P. pentosaceus MBBL6, isolated from a healthy cow milk at BSMRAU dairy farm, Gazipur, Bangladesh, underwent comprehensive genomic analysis, including whole genome sequencing, assembly, annotation, phylogenetic comparison, and assessment of metabolic pathways and secondary metabolites. Antimicrobial efficacy was evaluated through in-vitro and in-vivo studies, alongside in-silico exploration for potential mastitis therapy. We predicted 1,906 genes and 204 SEED sub-systems involved in carbohydrate metabolism and vitamin B complex biosynthesis, with a focus on lactose metabolism in MMBL6. Notably, 43 putative carbohydrate-active enzyme genes, including lysozymes, suggest the ability of MBBL6 for carbohydrate biotransformation and antimicrobial activity. The genome also revealed primary metabolic pathways for arginine and gallic acid metabolism and secondary metabolite gene clusters, including T3PKS and RiPP-like regions. Importantly, two bacteriocin biosynthesis gene clusters namely bovicin_255_variant and penocin_A, were identified in MBBL6. The safety assessment of MBBL6 genome revealed no virulence genes and a low pathogenicity score (0.196 out of 1.0). Several genes related to survival in gastrointestinal tract and colonization were also identified. Furthermore, MBBL6 exhibited susceptibility to a wide range of antibiotics in-vitro, and effectively suppressed mastitis pathogens in an in-vivo mouse mastitis model trial. The observed bacteriocin, particularly bovicin, demonstrated the ability to disrupt the function of an essential protein, Rho factor of mastitis pathogens by blocking transcription termination process. Taken together, our in-depth genomic analysis underscores the metabolic versatility, safety profile, and antimicrobial potential of P. pentosaceus MBBL6, suggesting its promise for applications in therapeutics, bioremediation, and biopreservation.

Draft genome sequences of six multidrug-resistant Escherichia coli isolates from pigeons in Bangladesh

Household pigeons are a potential source of multidrug-resistant (Escherichia coli (E. coli) and act as a transmission vehicle of this bacterium to humans. Here, we characterized the antimicrobial resistance profile and molecular properties of the whole genome sequences of six E. coli strains from household pigeons.

Decoding the whole-genome sequence of multidrug-resistant Escherichia coli strain Hakim RU_BHWS isolated from wastewater in Bangladesh

This report presents the draft genome sequence of the multidrug-resistant Escherichia coli strain Hakim RU_BHWS isolated from wastewater. The genome assembly is 4.6 Mb, with 32.16× coverage and a GC content of 50.7%. It includes five CRISPR arrays, 16 prophages, 56 antibiotic resistance genes, and 35 virulence factor genes.

Marine Pediococcus pentosaceus E3 Probiotic Properties, Whole-Genome Sequence Analysis, and Safety Assessment

Probiotics play a significant role in enhancing health, and they are well known for bacteriocins production. Evaluating probiotics' whole-genome sequence provides insights into their consumption outcomes. Thus, genomic studies have a significant role in assessing the safety of probiotics more in-depth and offer valuable information regarding probiotics' functional diversity, metabolic pathways, and health-promoting mechanisms. Marine Pediococcus pentosaceus E3, isolated from shrimp gut, exhibited beneficial properties, indicating its potential as a probiotic candidate. Phenotypically, E3 strain was susceptible to most antibiotics assessed, tolerant to low pH and high bile salt conditions, and revealed no hemolysin activity. Interestingly, E3-neutralized CFS revealed significant antibacterial activity against pathogens under investigation. Therefore, the concentrated CFS was prepared and evaluated as a natural biopreservative and showed outstanding antimicrobial activity. Furthermore, integrated-based genome assessment has provided insight into probiotic characteristics at the genomic level. Whole-genome sequencing analysis revealed that the E3 genome possesses 1805 protein-coding genes, and the genome size was about 1.8 Mb with a G + C content of 37.28%. Moreover, the genome revealed the absence of virulence factors and clinically related antibiotic genes. Moreover, several genes consistent with probiotic microorganisms' features were estimated in the genome, including stress response, carbohydrate metabolism, and vitamin biosynthesis. In addition, several genes associated with survival and colonization within the gastrointestinal tract were also detected across the E3 genome. Therefore, the findings suggest that insights into the genetic characteristics of E3 guarantee the safety of the strain and facilitate future development of E3 isolate as a health-promoting probiotic and source of biopreservative.

Whole genome sequencing reveals circulation of potentially virulent Listeria innocua strains with novel genomic features in cattle farm environments in Dhaka, Bangladesh

Through the last decade, Listeria spp. has been detected in food and environmental samples in Bangladesh. However, the genomic information of this bacterium that prevails in the country remains scarce. This study analyzed the complete genome sequences of two Listeria spp. isolates obtained from cow dung and their drinking water collected from a cattle farm in Dhaka, Bangladesh. Both the isolates were identified as Listeria innocua, which shared almost identical genomic features. The genome sequences demonstrated the presence of 13 virulence genes associated with invasion (iap/cwhA, gtcA, and lpeA), surface protein anchoring (lspA), adherence (fbpA, and lap), intracellular survival (lplA1, and prsA2), peptidoglycan modification (oatA, and pdgA), and heat stress (clpC, clpE, and clpP). Additionally, the gene fosX, conferring resistance to fosfomycin, and two copper resistance-associated genes, copC and csoR, were identified in both. The genome sequences also revealed two plasmid replicons, rep25 and rep32, along with three insertion sequences [ISLmo3 (CP022021), ISLmo7 (CP006611), ISS1N (M37395)]. Notably, a composite transposon [CN_8789_ISS1N (M37395)], was detected in both L. innocua isolates, representing the first documented occurrence of this particular composite transposon in any reported Listeria species. Furthermore, the genomes contained four prophage regions [Listeria phage LP-030-2 (NC_021539), Listeria phage vB_LmoS_188 (NC_028871), Listeria phage A118 (NC_003216) and Escherichia phage RCS47 (NC_042128)]. Two CRISPR arrays were also identified, one belonging to the family type II-A. Multilocus Sequence Typing (MLST) analysis classified the L. innocua isolates of the same sequence type, ST-637. Single nucleotide polymorphism (SNP) analysis uncovered the presence of 231-340 SNPs between the L. innocua isolates and their closely related global lineage. In contrast, only 42 SNPs were identified between the two isolates, suggesting a potential transmission of L. innocua between cow dung and cattle farm water. The presence of L. innocua isolates harboring virulence genes associated with ruminant infection in the cattle farm environment of Bangladesh raises significant concerns about the potential presence of other human and animal pathogens. This poses a serious threat to the cattle farming industry. Additionally, the genomic analysis of the L. innocua isolates enhances our understanding of the evolutionary dynamics of Listeria species.

Genomic insights of Lactiplantibacillus plantarum CNPC024: a potential probiotic strain producing immune-boosting tryptophan-derived metabolites

Probiogenomics can provide important insights bout probiotic candidate bacteria. This study aimed to perform an in-depth genomic characterization of the probiotic candidate Lactiplantibacillus plantarum CNPC024 to investigate its probiosis mechanisms, identify metabolic pathways that might benefit the host, and improve the safety assessment for this strain to be effectively used as a probiotic. After whole-genome sequencing in Illumina MiSeq platform, the de novo genome assembly resulted in a 3.2 Mb draft genome. According to the Average Nucleotide Identity (ANI) analysis with 46 randomly validated probiotic LAB belonging to the Lactobacillaceae family, the strain showed a 99% nucleotide identity with other L. plantarum probiotic species. We identified a set of determinants conferring tolerance to bile salts and low pH conditions, as well as temperature, oxidative and osmotic stressors via the glutathione-glutaredoxin system (Grxs). As a β‑galactosidase‑producing strain, it has the potential to be used in fermented dairy products for lactose-intolerant individuals. There were no significant hits for transferable antibiotic-resistance genes. We also identified gene clusters associated with production of bacteriocins (plantaricins E, F and K). Lastly, we detected metabolic pathways associated with the production of tryptophan-derived metabolites that could potentially modulate the host's immune responses.

Effects of Lactiplantibacillus plantarum LM1215 on Candida albicans and Gardnerella vaginalis

PURPOSE

The aim of this study was to identify novel vaginal probiotics with the potential to prevent vulvovaginal candidiasis (VVC) and bacterial vaginosis (BV).

MATERIALS AND METHODS

Eighteen strains of Lactiplantibacillus plantarum were isolated from healthy Korean women, and their antimicrobial effects against Candida albicans and Gardnerella vaginalis were assessed. Three strains (L. plantarum LM1203, LM1209, and LM1215) were selected for further investigation, focusing on their growth inhibition, biofilm regulation, and cellular mechanisms against these vaginal pathogens. Additionally, electron microscopy revealed damage to G. vaginalis induced by L. plantarum LM1215, and genomic analysis was conducted on this strain.

RESULTS

L. plantarum LM1203, LM1209, and LM1215 showed approximately 1 and 2 Log CFU/mL growth reduction in C. albicans and G. vaginalis, respectively. These L. plantarum strains effectively inhibited biofilm formation and eliminated the mature biofilms formed by C. albicans. Furthermore, L. plantarum LM1215 decreased tricarboxylic acid cycle activity by 51.75 (p<0.001) and respiratory metabolic activity by 52.88% (p<0.001) in G. vaginalis. L. plantarum induced cellular membrane damage, inhibition of protein synthesis, and cell wall collapse in G. vaginalis. Genomic analysis confirmed L. plantarum LM1215 as a safe strain for vaginal probiotics.

CONCLUSION

The L. plantarum LM1215 is considered a safe probiotic agent suitable for the prevention of VVC and BV.

Genomic Insights into Stutzerimonas kunmingensis TFRC-KFRI-1 Isolated from Manila Clam (Ruditapes philippinarum): Functional and Phylogenetic Analysis

Stutzerimonas kunmingensis TFRC-KFRI-1, isolated from the gut of Manila Clam in the sediment of the West Sea of Korea, was investigated for its potential as a probiotic bacterium. This strain, belonging to the family Pseudomonadaceae, was previously classified as Pseudomonas kunmingensis but later reclassified to the genus Stutzerimonas, known for species with bioremediation and probiotic properties. To evaluate its genomic features and potential applications, we performed draft-genome sequencing and analysis. The genome of S. kunmingensis TFRC-KFRI-1 was assembled into a 4,756,396 bp sequence with a 62.8% GC content. Genomic analysis suggested potential genes for carbohydrate degradation and lactic acid production. The strain exhibited high average nucleotide identity (ANI) and 16S rRNA similarity with S. kunmingensis HL22-2T, further supporting its potential as a probiotic. This genome sequence provides valuable insights into the functional capabilities of S. kunmingensis TFRC-KFRI-1 and its potential applications in various industries, including aquaculture and food biotechnology. The genome sequence is available under GenBank accession number JBGJJB000000000.1, with related project information under BioProject PRJNA1147901 and Bio-Sample SAMN43173893.

Phylogenomics of novel clones of Aeromonas veronii recovered from a freshwater lake reveals unique biosynthetic gene clusters

Aquatic ecosystems serve as crucial reservoirs for pathogens and antimicrobial resistance genes, thus presenting a significant global health risk. Here, we investigated the phylogenomics of Aeromonas veronii from Lake Wilcox in Ontario. Among the 11 bacterial isolates, nine were identified as A. veronii. Notably, 67% of A. veronii isolates were potential human pathogens. Considerable genetic diversity was noted among the A. veronii isolates, suggesting the lake as a reservoir for multiple human pathogenic strains. Comparison of the A. veronii sequenced with global A. veronii genomes highlighted significant genetic diversity and suggests widespread dissemination of strains. All the isolates carried chromosomal genes encoding resistance to β-lactams. Although virulence gene content differed between human and non-human pathogenic strains, type III secretion systems was associated with human pathogenic isolates. The assessment of AMR genes in global isolates showed that β-lactam and tetracycline resistance genes were predominant. Although the machine learning-based pangenome-wide association approach performed did not yield any source-based genes, some genes were enriched in a few isolates from different sources. The mrkABCDF operon that mediates biofilm formation and genes encoding resistance to colistin, chloramphenicol, trimethoprim, and tetracycline were enriched in animal products, whereas macrolide resistance genes and Inc plasmid-types were linked to the aquatic environment. Novel biosynthetic gene clusters were identified, suggesting that A. veronii with varying pathogenic potential could produce unique secondary metabolites. There is a need for continuous tracking of pathogens in aquatic ecosystems to contribute to our understanding of their evolutionary dynamics and the ecological roles of their genetic elements.

IMPORTANCE

Lakes and other aquatic ecosystems can harbor harmful bacteria that can make people sick and resist antibiotics, posing a significant global health risk. In this study, we investigated Aeromonas veronii, a Gram-negative bacteria found in Lake Wilcox in Ontario. We used various techniques, including whole-genome sequencing (WGS), to analyze the bacteria and found that many of the isolates had the potential to cause human disease. We also discovered significant genetic diversity among the isolates, indicating that the lake may be a reservoir for multiple human pathogenic strains. All isolates carried genes that confer resistance to antibiotics, and some virulence genes were associated with human pathogenic isolates. This study highlights the importance of monitoring aquatic ecosystems for harmful bacteria to better understand their evolution, potential for human pathogenicity, and the ecological roles of their genetic elements. This knowledge can inform strategies for preventing the spread of antibiotic-resistant bacteria and protecting public health.