# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 6077 | 0 | 0.9881 | Brytella acorum gen. nov., sp. nov., a novel acetic acid bacterium from sour beverages. Polyphasic taxonomic and comparative genomic analyses revealed that a series of lambic beer isolates including strain LMG 32668(T) and the kombucha isolate LMG 32879 represent a novel species among the acetic acid bacteria, with Acidomonas methanolica as the nearest phylogenomic neighbor with a valid name. Overall genomic relatedness indices and phylogenomic and physiological analyses revealed that this novel species was best classified in a novel genus for which we propose the name Brytella acorum gen. nov., sp. nov., with LMG 32668(T) (=CECT 30723(T)) as the type strain. The B. acorum genomes encode a complete but modified tricarboxylic acid cycle, and complete pentose phosphate, pyruvate oxidation and gluconeogenesis pathways. The absence of 6-phosphofructokinase which rendered the glycolysis pathway non-functional, and an energy metabolism that included both aerobic respiration and oxidative fermentation are typical metabolic characteristics of acetic acid bacteria. Neither genome encodes nitrogen fixation or nitrate reduction genes, but both genomes encode genes for the biosynthesis of a broad range of amino acids. Antibiotic resistance genes or virulence factors are absent. | 2023 | 37429096 |
| 5214 | 1 | 0.9869 | Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula. The Psychrobacter genus is a cosmopolitan and diverse group of aerobic, cold-adapted, Gram-negative bacteria exhibiting biotechnological potential for low-temperature applications including bioremediation. Here, we present the draft genome sequence of a bacterium from the Psychrobacter genus isolated from a sediment sample from King George Island, Antarctica (3,490,622 bp; 18 scaffolds; G + C = 42.76%). Using phylogenetic analysis, biochemical properties and scanning electron microscopy the bacterium was identified as Psychrobacter glacincola BNF20, making it the first genome sequence reported for this species. P. glacincola BNF20 showed high tellurite (MIC 2.3 mM) and chromate (MIC 6.0 mM) resistance, respectively. Genome-wide nucleotide identity comparisons revealed that P. glacincola BNF20 is highly similar (>90%) to other uncharacterized Psychrobacter spp. such as JCM18903, JCM18902, and P11F6. Bayesian multi-locus phylogenetic analysis showed that P. glacincola BNF20 belongs to a polyphyletic clade with other bacteria isolated from polar regions. A high number of genes related to metal(loid) resistance were found, including tellurite resistance genetic determinants located in two contigs: Contig LIQB01000002.1 exhibited five ter genes, each showing putative promoter sequences (terACDEZ), whereas contig LIQB1000003.2 showed a variant of the terZ gene. Finally, investigating the presence and taxonomic distribution of ter genes in the NCBI's RefSeq bacterial database (5,398 genomes, as January 2017), revealed that 2,623 (48.59%) genomes showed at least one ter gene. At the family level, most (68.7%) genomes harbored one ter gene and 15.6% exhibited five (including P. glacincola BNF20). Overall, our results highlight the diverse nature (genetic and geographic diversity) of the Psychrobacter genus, provide insights into potential mechanisms of metal resistance, and exemplify the benefits of sampling remote locations for prospecting new molecular determinants. | 2018 | 29479501 |
| 8670 | 2 | 0.9866 | Complete Genome Analysis of Subtercola sp. PAMC28395: Genomic Insights into Its Potential Role for Cold Adaptation and Biotechnological Applications. This study reports the complete genome sequence of Subtercola sp. PAMC28395, a strain isolated from cryoconite in Uganda. This strain possesses several active carbohydrate-active enzyme (CAZyme) genes involved in glycogen and trehalose metabolism. Additionally, two specific genes associated with α-galactosidase (GH36) and bacterial alpha-1,2-mannosidase (GH92) were identified in this strain. The presence of these genes indicates the likelihood that they can be expressed, enabling the strain to break down specific polysaccharides derived from plants or the shells of nearby crabs. The authors performed a comparative analysis of CAZyme patterns and biosynthetic gene clusters (BGCs) in several Subtercola strains and provided annotations describing the unique characteristics of these strains. The comparative analysis of BGCs revealed that four strains, including PAMC28395, have oligosaccharide BGCs, and we confirmed that the pentose phosphate pathway was configured perfectly in the genome of PAMC28395, which may be associated with adaptation to low temperatures. Additionally, all strains contained antibiotic resistance genes, indicating a complex self-resistance system. These results suggest that PAMC28395 can adapt quickly to the cold environment and produce energy autonomously. This study provides valuable information on novel functional enzymes, particularly CAZymes, that operate at low temperatures and can be used for biotechnological applications and fundamental research purposes. | 2023 | 37374983 |
| 8470 | 3 | 0.9865 | Genomic Insights into Vaccinium spp. Endophytes B. halotolerans and B. velezensis and Their Antimicrobial Potential. Plant microbiota contributes to nutrient absorption, and the production of hormones and vitamins, and plays a crucial role in responding to environmental stress. We hypothesized that Vaccinium spp. harbour a unique microbiota that enables them to coexist in extreme environments such as saline, nutrient-poor, and waterlogged conditions. Upon examining Bacillus spp. endophytes isolated from blueberries, cranberries and lingonberries in vitro, we identified B. halotolerans (Bil-LT1_1, Bil-LT1_2) and B. velezensis (Cran-LT1_8, Ling-NOR4_15) strains that inhibit the growth of five pathogenic fungi and five foodborne bacteria. Whole-genome sequencing provided insights into genome organization and plasticity, helping identify mobile elements and genes potentially acquired through horizontal gene transfer. Functional annotation identified genes associated with plant colonization, stress tolerance, biocontrol activity, and plant growth promotion. Comparative genomic analyses revealed key biosynthetic gene clusters (BGCs) responsible for producing antifungal metabolites, including lipopeptides and polyketides. Genes supporting plant nutrition, growth, and environmental adaptation were present also in these strains. Notably, isolated endophytes exhibited particularly high levels of genomic plasticity, likely due to horizontal gene transfer involving gene ontology (GO) pathways related to survival in polymicrobial and foreign environments. | 2025 | 40724928 |
| 5189 | 4 | 0.9865 | Genomic analysis of halophilic bacterium, Lentibacillus sp. CBA3610, derived from human feces. BACKGROUND: Lentibacillus species are gram variable aerobic bacteria that live primarily in halophilic environments. Previous reports have shown that bacteria belonging to this species are primarily isolated from salty environments or food. We isolated a bacterial strain CBA3610, identified as a novel species of the genus Lentibacillus, from a human fecal sample. In this report, the whole genome sequence of Lentibacillus sp. CBA3610 is presented, and genomic analyses are performed. RESULTS: Complete genome sequence of strain CBA3610 was obtained through PacBio RSII and Illumina HiSeq platforms. The size of genome is 4,035,571 bp and genes estimated to be 4714 coding DNA sequences and 64 tRNA and 17 rRNA were identified. The phylogenetic analysis confirmed that it belongs to the genus Lentibacillus. In addition, there were genes related to antibiotic resistance and virulence, and genes predicted as CRISPR and prophage were also identified. Genes related to osmotic stress were found according to the characteristics of halophilic bacterium. Genomic differences from other Lentibacillus species were also confirmed through comparative genomic analysis. CONCLUSIONS: Strain CBA3610 is predicted to be a novel candidate species of Lentibacillus through phylogenetic analysis and comparative genomic analysis with other species in the same genus. This strain has antibiotic resistance gene and pathogenic genes. In future, the information derived from the results of several genomic analyses of this strain is thought to be helpful in identifying the relationship between halophilic bacteria and human gut microbiota. | 2021 | 34162403 |
| 6078 | 5 | 0.9864 | Genomic Insights into Cyanide Biodegradation in the Pseudomonas Genus. Molecular studies about cyanide biodegradation have been mainly focused on the hydrolytic pathways catalyzed by the cyanide dihydratase CynD or the nitrilase NitC. In some Pseudomonas strains, the assimilation of cyanide has been linked to NitC, such as the cyanotrophic model strain Pseudomonas pseudoalcaligenes CECT 5344, which has been recently reclassified as Pseudomonas oleovorans CECT 5344. In this work, a phylogenomic approach established a more precise taxonomic position of the strain CECT 5344 within the species P. oleovorans. Furthermore, a pan-genomic analysis of P. oleovorans and other species with cyanotrophic strains, such as P. fluorescens and P. monteilii, allowed for the comparison and identification of the cioAB and mqoAB genes involved in cyanide resistance, and the nitC and cynS genes required for the assimilation of cyanide or cyanate, respectively. While cyanide resistance genes presented a high frequency among the analyzed genomes, genes responsible for cyanide or cyanate assimilation were identified in a considerably lower proportion. According to the results obtained in this work, an in silico approach based on a comparative genomic approach can be considered as an agile strategy for the bioprospection of putative cyanotrophic bacteria and for the identification of new genes putatively involved in cyanide biodegradation. | 2024 | 38674043 |
| 8462 | 6 | 0.9863 | Comparative Genomics of Lactiplantibacillus plantarum: Insights Into Probiotic Markers in Strains Isolated From the Human Gastrointestinal Tract and Fermented Foods. Lactiplantibacillus (Lpb.) plantarum is a versatile species commonly found in a wide variety of ecological niches including dairy products and vegetables, while it may also occur as a natural inhabitant of the human gastrointestinal tract. Although Lpb. plantarum strains have been suggested to exert beneficial properties on their host, the precise mechanisms underlying these microbe-host interactions are still obscure. In this context, the genome-scale in silico analysis of putative probiotic bacteria represents a bottom-up approach to identify probiotic biomarkers, predict desirable functional properties, and identify potentially detrimental antibiotic resistance genes. In this study, we characterized the bacterial genomes of three Lpb. plantarum strains isolated from three distinct environments [strain IMC513 (from the human GIT), C904 (from table olives), and LT52 (from raw-milk cheese)]. A whole-genome sequencing was performed combining Illumina short reads with Oxford Nanopore long reads. The phylogenomic analyses suggested the highest relatedness between IMC513 and C904 strains which were both clade 4 strains, with LT52 positioned within clade 5 within the Lpb. plantarum species. The comparative genome analysis performed across several Lpb. plantarum representatives highlighted the genes involved in the key metabolic pathways as well as those encoding potential probiotic features in these new isolates. In particular, our strains varied significantly in genes encoding exopolysaccharide biosynthesis and in contrast to strains IMC513 and C904, the LT52 strain does not encode a Mannose-binding adhesion protein. The LT52 strain is also deficient in genes encoding complete pentose phosphate and the Embden-Meyerhof pathways. Finally, analyses using the CARD and ResFinder databases revealed that none of the strains encode known antibiotic resistance loci. Ultimately, the results provide better insights into the probiotic potential and safety of these three strains and indicate avenues for further mechanistic studies using these isolates. | 2022 | 35663852 |
| 8469 | 7 | 0.9857 | Probiogenomic analysis of Lactiplantibacillus plantarum SPS109: A potential GABA-producing and cholesterol-lowering probiotic strain. Lactiplantibacillus plantarum SPS109, an isolated strain of lactic acid bacteria (LAB) from fermented foods, showed remarkable potential as a probiotic with dual capabilities in γ-aminobutyric acid (GABA) production and cholesterol reduction. This study employs genomic and comparative analyses to search into the strain's genetic profile, safety features, and probiotic attributes. The safety assessment reveals the absence of virulence factors and antimicrobial resistance genes, while the genome uncovers bacteriocin-related elements, including sactipeptides and a cluster for putative plantaricins, strengthening its ability to combat diverse pathogens. Pangenome analysis revealed unique bacteriocin-related genes, specifically lcnD and bcrA, distinguishing SPS109 from four other L. plantarum strains producing GABA. In addition, genomic study emphasizes SPS109 strain distinctive features, two GABA-related genes responsible for GABA production and a bile tolerance gene (cbh) crucial for cholesterol reduction. Additionally, the analysis highlights several genes of potential probiotic properties, including stress tolerance, vitamin production, and antioxidant activity. In summary, L. plantarum SPS109 emerges as a promising probiotic candidate with versatile applications in the food and beverage industries, supported by its unique genomic features and safety profile. | 2024 | 39044985 |
| 6138 | 8 | 0.9857 | Draft genome of five Cupriavidus plantarum strains: agave, maize and sorghum plant-associated bacteria with resistance to metals. Five strains of Cupriavidus plantarum, a metal-resistant, plant-associated bacterium, were selected for genome sequencing through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) Phase IV project at the Joint Genome Institute (JGI) of the U.S. Department of Energy (DOE). The genome of the strains was in the size range of 6.2-6.4 Mbp and encoded 5605-5834 proteins; 16.9-23.7% of these genes could not be assigned to a COG-associated functional category. The G + C content was 65.83-65.99%, and the genomes encoded 59-67 stable RNAs. The strains were resistant in vitro to arsenite, arsenate, cobalt, chromium, copper, nickel and zinc, and their genomes possessed the resistance genes for these metals. The genomes also encoded the biosynthesis of potential antimicrobial compounds, such as terpenes, phosphonates, bacteriocins, betalactones, nonribosomal peptides, phenazine and siderophores, as well as the biosynthesis of cellulose and enzymes such as chitinase and trehalase. The average nucleotide identity (ANI) and DNA-DNA in silico hybridization of the genomes confirmed that C. plantarum is a single species. Moreover, the strains cluster within a single group upon multilocus sequence analyses with eight genes and a phylogenomic analyses. Noteworthy, the ability of the species to tolerate high concentrations of different metals might prove useful for bioremediation of naturally contaminated environments. | 2020 | 32405446 |
| 5141 | 9 | 0.9856 | Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica. Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023(T) and P7388(T) were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed. | 2021 | 34745033 |
| 6126 | 10 | 0.9856 | The draft genome of Andean Rhodopseudomonas sp. strain AZUL predicts genome plasticity and adaptation to chemical homeostasis. The genus Rhodopseudomonas comprises purple non-sulfur bacteria with extremely versatile metabolisms. Characterization of several strains revealed that each is a distinct ecotype highly adapted to its specific micro-habitat. Here we present the sequencing, genomic comparison and functional annotation of AZUL, a Rhodopseudomonas strain isolated from a high altitude Andean lagoon dominated by extreme conditions and fluctuating levels of chemicals. Average nucleotide identity (ANI) analysis of 39 strains of this genus showed that the genome of AZUL is 96.2% identical to that of strain AAP120, which suggests that they belong to the same species. ANI values also show clear separation at the species level with the rest of the strains, being more closely related to R. palustris. Pangenomic analyses revealed that the genus Rhodopseudomonas has an open pangenome and that its core genome represents roughly 5 to 12% of the total gene repertoire of the genus. Functional annotation showed that AZUL has genes that participate in conferring genome plasticity and that, in addition to sharing the basal metabolic complexity of the genus, it is also specialized in metal and multidrug resistance and in responding to nutrient limitation. Our results also indicate that AZUL might have evolved to use some of the mechanisms involved in resistance as redox reactions for bioenergetic purposes. Most of those features are shared with strain AAP120, and mainly involve the presence of additional orthologs responsible for the mentioned processes. Altogether, our results suggest that AZUL, one of the few bacteria from its habitat with a sequenced genome, is highly adapted to the extreme and changing conditions that constitute its niche. | 2022 | 36494611 |
| 6088 | 11 | 0.9854 | Complete Genome of Achromobacter xylosoxidans, a Nitrogen-Fixing Bacteria from the Rhizosphere of Cowpea (Vigna unguiculata [L.] Walp) Tolerant to Cucumber Mosaic Virus Infection. Achromobacter xylosoxidans is one of the nitrogen-fixing bacteria associated with cowpea rhizosphere across Africa. Although its role in improving soil fertility and inducing systemic resistance in plants against pathogens has been documented, there is limited information on its complete genomic characteristics from cowpea roots. Here, we report the complete genome sequence of A. xylosoxidans strain DDA01 isolated from the topsoil of a field where cowpea plants tolerant to cucumber mosaic virus (CMV) were grown in Ibadan, Nigeria. The genome of DDA01 was sequenced via Illumina MiSeq and contained 6,930,067 nucleotides with 67.55% G + C content, 73 RNAs, 59 tRNAs, and 6421 protein-coding genes, including those associated with nitrogen fixation, phosphate solubilization, Indole3-acetic acid production, and siderophore activity. Eleven genetic clusters for secondary metabolites, including alcaligin, were identified. The potential of DDA01 as a plant growth-promoting bacteria with genetic capabilities to enhance soil fertility for resilience against CMV infection in cowpea is discussed. To our knowledge, this is the first complete genome of diazotrophic bacteria obtained from cowpea rhizosphere in sub-Saharan Africa, with potential implications for improved soil fertility, plant disease resistance, and food security. | 2024 | 39278894 |
| 6139 | 12 | 0.9853 | Complete genome and two plasmids sequences of Lactiplantibacillus plantarum L55 for probiotic potentials. In this study, we report the complete genome sequence of Lactiplantibacillus plantarum L55, a probiotic strain of lactic acid bacteria isolated from kimchi. The genome consists of one circular chromosome (2,077,416 base pair [bp]) with a guanine cytosine (GC) content of 44.5%, and two circular plasmid sequences (54,267 and 19,592 bp, respectively). We also conducted a comprehensive analysis of the genome, which identified the presence of functional genes, genomic islands, and antibiotic-resistance genes. The genome sequence data presented in this study provide insights into the genetic basis of L. plantarum L55, which could be beneficial for the future development of probiotic applications. | 2023 | 38616876 |
| 6136 | 13 | 0.9852 | Complete genome sequences of Lacticaseibacillus paracasei INIA P272 (CECT 8315) and Lacticaseibacillus rhamnosus INIA P344 (CECT 8316) isolated from breast-fed infants reveal probiotic determinants. Lacticaseibacillus paracasei INIA P272 and Lacticaseibacillus rhamnosus INIA P344, isolated from breast-fed infants, are two promising bacterial strains for their use in functional foods according to their demonstrated probiotic and technological characteristics. To better understand their probiotic characteristics and evaluate their safety, here we report the draft genome sequences of both strains as well as the analysis of their genetical content. The draft genomes of L. paracasei INIA P272 and L. rhamnosus INIA P344 comprise 3.01 and 3.26 Mb, a total of 2994 and 3166 genes and a GC content of 46.27 % and 46.56 %, respectively. Genomic safety was assessed following the EFSA guidelines: the identification of both strains was confirmed through Average Nucleotide Identity, and the absence of virulence, pathogenic and antibiotic resistance genes was demonstrated. The genome stability analysis revealed the presence of plasmids and phage regions in both genomes, however, CRISPR sequences and other mechanisms to fight against phage infections were encoded. The probiotic abilities of both strains were supported by the presence of genes for the synthesis of SCFA, genes involved in resistance to acid and bile salts or a thiamine production cluster. Moreover, the encoded exopolysaccharide biosynthesis genes could provide additional protection against the deleterious gastrointestinal conditions, besides which, playing a key role in adherence and coaggregation of pathogenic bacteria together with the high number of adhesion proteins and domains encoded by both genomes. Additionally, the bacteriocin cluster genes found in both strains, could provide an advantageous ability to compete against pathogenic bacteria. This genomic study supports the probiotic characteristics described previously for these two strains and satisfies the safety requirements to be used in food products. | 2022 | 35868412 |
| 5140 | 14 | 0.9852 | -Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis. Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment. | 2017 | 28229018 |
| 6090 | 15 | 0.9850 | Draft genome sequence of Mesorhizobium alhagi CCNWXJ12-2T, a novel salt-resistant species isolated from the desert of northwestern China. Mesorhizobium alhagi strain CCNWXJ12-2(T) is a novel species of soil-dwelling, nitrogen-fixing bacteria that can form symbiotic root nodules with Alhagi sparsifolia. Moreover, the strain has high resistance to salt and alkali. Here we report the draft genome sequence of Mesorhizobium alhagi strain CCNWXJ12-2(T). A large number of osmotic regulation-related genes have been identified. | 2012 | 22328758 |
| 6082 | 16 | 0.9850 | Complete genome sequence of the probiotic candidate strain Lacticaseibacillus rhamnosus B3421 isolated from Panax ginseng C. A. Meyer in South Korea. OBJECTIVES: Lacticaseibacillus rhamnosus is a widely recognized probiotic bacteria with therapeutic applications in human and animal health. The L. rhamnosus B3421 strain, isolated from Panax ginseng, has been reported to be associated with antioxidant and anti-inflammatory properties, supporting its functional potential. We sequenced and analyzed the genome of L. rhamnosus B3421 to evaluate its probiotic potential for human healthcare and animal applications, focusing on genomic features related to safety and functionality. DATA DESCRIPTION: In this study, we isolated L. rhamnosus B3421 from Panax ginseng C. A. Meyer (Ginseng) and performed whole-genome sequencing. The genome of L. rhamnosus B3421 consists of 3,000,051 base pairs (bp) with a guanine + cytosine (G + C) content of 46.70%. It encodes 59 transfer RNAs, 15 ribosomal RNAs, and 2,807 coding sequences (CDSs). Of these CDSs, 99.13% (2,758 proteins) were assigned to functional categories in the Clusters of Orthologous Group (COGs) classification system, while 49 proteins remained uncharacterized. Our genome analysis identified no antibiotic resistance (ABR) or antimicrobial resistance (AMR) genes, indicating that L. rhamnosus B3421 is a safe probiotic bacterium with minimal risk of contributing to the horizontal transfer of antibiotic resistance within the gut microbiome. Additionally, the genome contains genes associated with the ggmotif (PF10439), Enterocin X chain beta, and Carnocin CP52, as identified through BAGEL4 analysis, along with 24 other genes related to reductase or peroxidase activities. These genes may confer competitive advantages against pathogenic bacteria and oxidative stress. Our findings highlight the probiotic potential of L. rhamnosus B3421 and its prospective applications in promoting human and animal health. | 2025 | 40877785 |
| 6137 | 17 | 0.9850 | Genomic and phenotypic analyses of Carnobacterium jeotgali strain MS3(T), a lactate-producing candidate biopreservative bacterium isolated from salt-fermented shrimp. Carnobacterium jeotgali strain MS3(T) was isolated from traditionally fermented Korean shrimp produced with bay salt. The bacterium belongs to the family Carnobacteriaceae, produces lactic acid and contains gene clusters involved in the production of lactate, butyrate, aromatic compounds and exopolysaccharides. Carnobacterium jeotgali strain MS3(T) was characterized through extensive comparison of the virulence potential, genomic relatedness and sequence similarities of its genome with the genomes of other Carnobacteria and lactic acid bacteria. In addition, links between predicted functions of genes and phenotypic characteristics, such as antibiotic resistance and lactate and butyrate production, were extensively evaluated. Genomic and phenotypic analyses of strain MS3(T) revealed promising features, including minimal virulence genes and lactate production, which make this bacterium a desirable candidate for exploitation by the fermented food industry. | 2015 | 25868912 |
| 5153 | 18 | 0.9850 | Single-Molecule Sequencing (PacBio) of the Staphylococcus capitis NRCS-A Clone Reveals the Basis of Multidrug Resistance and Adaptation to the Neonatal Intensive Care Unit Environment. The multi-resistant Staphylococcus capitis clone NRCS-A has recently been described as a major pathogen causing nosocomial, late-onset sepsis (LOS) in preterm neonates worldwide. NRCS-A representatives exhibit an atypical antibiotic resistance profile. Here, the complete closed genome (chromosomal and plasmid sequences) of NRCS-A prototype strain CR01 and the draft genomes of three other clinical NRCS-A strains from Australia, Belgium and the United Kingdom are annotated and compared to available non-NRCS-A S. capitis genomes. Our goal was to delineate the uniqueness of the NRCS-A clone with respect to antibiotic resistance, virulence factors and mobile genetic elements. We identified 6 antimicrobial resistance genes, all carried by mobile genetic elements. Previously described virulence genes present in the NRCS-A genomes are shared with the six non-NRCS-A S. capitis genomes. Overall, 63 genes are specific to the NRCS-A lineage, including 28 genes located in the methicillin-resistance cassette SCCmec. Among the 35 remaining genes, 25 are of unknown function, and 9 correspond to an additional type I restriction modification system (n = 3), a cytosine methylation operon (n = 2), and a cluster of genes related to the biosynthesis of teichoic acids (n = 4). Interestingly, a tenth gene corresponds to a resistance determinant for nisin (nsr gene), a bacteriocin secreted by potential NRCS-A strain niche competitors in the gut microbiota. The genomic characteristics presented here emphasize the contribution of mobile genetic elements to the emergence of multidrug resistance in the S. capitis NRCS-A clone. No NRCS-A-specific known virulence determinant was detected, which does not support a role for virulence as a driving force of NRCS-A emergence in NICUs worldwide. However, the presence of a nisin resistance determinant on the NRCS-A chromosome, but not in other S. capitis strains and most coagulase-negative representatives, might confer a competitive advantage to NRCS-A strains during the early steps of gut colonization in neonates. This suggests that the striking adaptation of NRCS-A to the NICU environment might be related to its specific antimicrobial resistance and also to a possible enhanced ability to challenge competing bacteria in its ecological niche. | 2016 | 28018320 |
| 5147 | 19 | 0.9849 | Multiscale comparative pathogenomic analysis of Vibrio anguillarum linking serotype diversity, genomic plasticity and pathogenicity. Vibrio anguillarum is a major marine fish pathogen causing high mortality and potential zoonotic risks. Understanding its genomic diversity, virulence factors, and antibiotic resistance is crucial for aquaculture disease management. In this study, a comparative pan-genomic analysis of 16 V. anguillarum strains was conducted to examine core and accessory genome diversity, virulence factors, and antibiotic resistance mechanisms. The phylogenetic analysis was conducted using six core genes and SNPs to evaluate evolutionary relationships and pathogenic traits. The core genome contained 2,038 unique ORFs, while the accessory genome had 5,197 cloud genes, confirming an open pangenome. This study identified 118 pathogenic genomic islands, antibiotic resistance genes (tetracycline, quinolone, and carbapenem), and virulence factors, including type VI secretion system (T6SS) components and RTX toxins (hcp-2, vipB/mglB, rtxC). Core genes such as ftsI uncovered substantial evolutionary divergence among species, identifying more than 150 distinct SNPs. Phylogenetic analysis showed serotype-specific clustering, with O1 strains displaying genetic homogeneity, whereas O2 and O3 exhibited divergence, suggesting distinct evolutionary adaptations influencing pathogenicity and ecological interactions. These findings provide primary insights for developing molecular markers and targeted treatments for aquaculture pathogens. | 2025 | 40854641 |