# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 6081 | 0 | 0.8481 | In vitro probiotic characteristics and whole-genome sequence analysis of lactic acid bacteria isolated from monkey faeces. This study aimed to isolate lactic acid bacteria from monkey faeces and evaluate their safety and probiotic properties through a combination of in vitro assays and complete genomic sequencing. The results revealed that two Limosilactobacillus reuteri strains (LDHa and LSHe) exhibited promising probiotic attributes: no hemolytic activity, remarkable antibacterial activity against intestinal pathogens, high bile salt tolerance (77.46% survival rate for LDHa at 0.3% bile salt concentration), excellent gastrointestinal resistance (survival rate > 40%), and favorable surface characteristics (63.92-66.00% auto-aggregation; 91.33-93.80% hydrophobicity). The whole genome sequencing results revealed that strain LDHa has a total length of 2,031,794 bp with a GC content of 39.02% and contains (Strompfová et al. 2014) coding genes. The LSHe strain has a total length of 2,031,507 bp with a GC content of 39.02% and contains 1954 coding genes. Genomic analysis revealed that both strains possess four CRISPR sequences and one secondary metabolic gene cluster, with functional annotations from the EGGNOG, KEGG, and CAZy databases demonstrating genome stability; the absence of horizontally transferable antibiotic resistance genes; the enrichment of metabolic pathway-related genes, and probiotic-associated functional potential including antimicrobial, anti-inflammatory, immunomodulatory, and antitumor activities. This study demonstrated that L. reuteri LDHa and LSHe exhibit favorable safety profiles and probiotic potential at both physiological and genomic levels, positioning them as promising candidates for probiotic formulations in captive primate populations. | 2025 | 40852645 |
| 810 | 1 | 0.8466 | Draft genome sequencing and functional annotation and characterization of biofilm-producing bacterium Bacillus novalis PD1 isolated from rhizospheric soil. Biofilm forming bacterium Bacillus novalis PD1 was isolated from the rhizospheric soil of a paddy field. B. novalis PD1 is a Gram-positive, facultatively anaerobic, motile, slightly curved, round-ended, and spore-forming bacteria. The isolate B. novalis PD1 shares 98.45% similarity with B. novalis KB27B. B. vireti LMG21834 and B. drentensis NBRC 102,427 are the closest phylogenetic neighbours for B. novalis PD1. The draft genome RAST annotation showed a linear chromosome with 4,569,088 bp, encoding 6139 coding sequences, 70 transfer RNA (tRNA), and 11 ribosomal RNA (rRNA) genes. The genomic annotation of biofilm forming B. novalis PD1(> 3.6@OD(595nm)) showed the presence of exopolysaccharide-forming genes (ALG, PSL, and PEL) as well as other biofilm-related genes (comER, Spo0A, codY, sinR, TasA, sipW, degS, and degU). Antibiotic inactivation gene clusters (ANT (6)-I, APH (3')-I, CatA15/A16 family), efflux pumps conferring antibiotic resistance genes (BceA, BceB, MdtABC-OMF, MdtABC-TolC, and MexCD-OprJ), and secondary metabolites linked to phenazine, terpene, and beta lactone gene clusters are part of the genome. | 2021 | 34537868 |
| 104 | 2 | 0.8401 | Bile Salt Hydrolases with Extended Substrate Specificity Confer a High Level of Resistance to Bile Toxicity on Atopobiaceae Bacteria. The bile resistance of intestinal bacteria is among the key factors responsible for their successful colonization of and survival in the mammalian gastrointestinal tract. In this study, we demonstrated that lactate-producing Atopobiaceae bacteria (Leptogranulimonas caecicola TOC12(T) and Granulimonas faecalis OPF53(T)) isolated from mouse intestine showed high resistance to mammalian bile extracts, due to significant bile salt hydrolase (BSH) activity. We further succeeded in isolating BSH proteins (designated LcBSH and GfBSH) from L. caecicola TOC12(T) and G. faecalis OPF53(T), respectively, and characterized their enzymatic features. Interestingly, recombinant LcBSH and GfBSH proteins exhibited BSH activity against 12 conjugated bile salts, indicating that LcBSH and GfBSH have much broader substrate specificity than the previously identified BSHs from lactic acid bacteria, which are generally known to hydrolyze six bile salt isomers. Phylogenetic analysis showed that LcBSH and GfBSH had no affinities with any known BSH subgroup and constituted a new BSH subgroup in the phylogeny. In summary, we discovered functional BSHs with broad substrate specificity from Atopobiaceae bacteria and demonstrated that these BSH enzymes confer bile resistance to L. caecicola TOC12(T) and G. faecalis OPF53(T). | 2022 | 36142891 |
| 5213 | 3 | 0.8401 | Draft genome sequences of Limosilactobacillus fermentum IJAL 01 335, isolated from a traditional cereal fermented dough. Limosilactobacillus fermentum IJAL 01 335 was isolated from mawè, a spontaneously fermented cereal dough from Benin. The 1.83 Mb draft genome sequence (52.37% GC) comprises 154 contigs, 1,836 coding sequences, and 23 predicted antibiotic resistance genes, providing insights into its genetic features and potential application in food fermentation. | 2025 | 41170963 |
| 6015 | 4 | 0.8392 | Integrative genome analysis of bacteriocin-producing Lactiplantibacillus pentosus LNP1-39 and its synbiotic role in suppressing food-borne pathogens. Lactic acid bacteria were isolated from traditional Thai-fermented foods. Among these, the strain LNP1-39, closely related to Lactiplantibacillus pentosus, was selected for further study because of its non-pathogenic profile. The bacteriocins produced by L. pentosus LNP1-39 were proteinaceous substances that exhibited strong antimicrobial activity across a wide pH range (pH 2-11; 6400-2400 AU/mL) and thermal stability at 100 °C for 40 min (400 AU/mL). These bacteriocins showed a narrow antimicrobial spectrum, effectively targeting Gram-positive pathogens, such as Kocuria rhizophila MIII, Enterococcus faecalis JCM 5803( T), and Listeria monocytogenes ATCC 19115. Comprehensive safety assessments, including whole-genome analysis and in vitro tests, confirmed a low risk of antibiotic resistance and the absence of virulence factors. Strain LNP1-39 was confirmed to be closely related to L. pentosus DSM 20314( T) via digital DNA‒DNA hybridization (dDDH; 75.4%), with average nucleotide identity (ANI) at 96.56% ANIb and 97.22% ANIm values. Additionally, LNP1-39 produces pediocin with notable similarity (76.29% identity to pediocin) and presents low risks for antibiotic-resistance genes or transfer genes while providing antioxidant properties. Strain LNP1-39 survived harsh gastrointestinal tract conditions and exhibited a favorable prebiotic index and positive prebiotic activity score when paired with polydextrose or isomalto-oligosaccharide. These findings support L. pentosus LNP1-39 as potential bacteriocin-producing lactic acid bacteria for further application in food preservation and pathogen control or as a synbiotic. | 2025 | 40622670 |
| 811 | 5 | 0.8380 | Genomic analysis of five antibiotic-resistant bacteria isolated from the environment. Our study presents the whole-genome sequences and annotation of five bacteria isolates, each demonstrating distinct antibiotic resistance. These isolates include Bacillus paranthracis RIT 841, Atlantibacter hermanii RIT 842, Pantoea leporis RIT 844, Enterococcus casseliflavus RIT 845, and Pseudomonas alkylphenolica RIT 846, underscoring the importance of understanding antimicrobial resistance. | 2024 | 39189722 |
| 6082 | 6 | 0.8347 | 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 |
| 6026 | 7 | 0.8331 | Probiotic Characteristics and Whole Genome Analysis of Lactiplantibacillus plantarum PM8 from Giant Panda (Ailuropoda melanoleuca) Milk. Milk is a rich source of probiotics, particularly lactic acid bacteria (LAB), which have been shown to promote gut health, support the immune system, enhance digestion, and prevent pathogen colonization. This study aimed to isolate and identify LAB strains from giant panda (Ailuropoda melanoleuca) milk, evaluate their probiotic properties, and analyze the genomic characteristics of a promising strain. Thirteen LAB strains were isolated from 12 samples of giant panda milk. Among all LAB strains, Lactiplantibacillus plantarum PM8 (PM8) demonstrated probiotic properties and safety features. It exhibited strong growth performance, high antipathogenic activity against four pathogens, and strong survival rates under simulated gastrointestinal conditions. PM8 also showed excellent adhesion capabilities to Caco-2 cells. Additionally, safety assessment revealed no hemolysin production and minimal antibiotic resistance, making it a promising candidate for probiotic applications. The genome of PM8 consists of 3,227,035 bp with a GC content of 44.60% and contains 3171 coding sequences, including 113 carbohydrate-active enzyme genes and genes related to exopolysaccharides synthesis, vitamin B biosynthesis, adhesion, antioxidant activity, and bile salt hydrolysis. Notably, it contains genes involved in nonribosomally synthesized secondary metabolite and bacteriocin production. The genomic safety analysis confirmed that PM8 lacks the capacity to transmit bacterial antimicrobial resistance and is non-pathogenic to both humans and animals. These findings suggest that PM8 holds considerable potential for enhancing gut health and supporting the development of safe probiotic products. | 2025 | 39900880 |
| 6053 | 8 | 0.8320 | Probiotic properties of lactic acid bacteria isolated from water-buffalo mozzarella cheese. This study evaluated the probiotic properties (stability at different pH values and bile salt concentration, auto-aggregation and co-aggregation, survival in the presence of antibiotics and commercial drugs, study of β-galactosidase production, evaluation of the presence of genes encoding MapA and Mub adhesion proteins and EF-Tu elongation factor, and the presence of genes encoding virulence factor) of four LAB strains (Lactobacillus casei SJRP35, Leuconostoc citreum SJRP44, Lactobacillus delbrueckii subsp. bulgaricus SJRP57 and Leuconostoc mesenteroides subsp. mesenteroides SJRP58) which produced antimicrobial substances (antimicrobial peptides). The strains survived the simulated GIT modeled in MRS broth, whole and skim milk. In addition, auto-aggregation and the cell surface hydrophobicity of all strains were high, and various degrees of co-aggregation were observed with indicator strains. All strains presented low resistance to several antibiotics and survived in the presence of commercial drugs. Only the strain SJRP44 did not produce the β-galactosidase enzyme. Moreover, the strain SJRP57 did not show the presence of any genes encoding virulence factors; however, the strain SJRP35 presented vancomycin resistance and adhesion of collagen genes, the strain SJRP44 harbored the ornithine decarboxylase gene and the strain SJRP58 generated positive results for aggregation substance and histidine decarboxylase genes. In conclusion, the strain SJRP57 was considered the best candidate as probiotic cultures for further in vivo studies and functional food products development. | 2014 | 25117002 |
| 100 | 9 | 0.8318 | Pto3 and Pto4: novel genes from Lycopersicon hirsutum var. glabratum that confer resistance to Pseudomonas syringae pv tomato. Accessions of wild Lycopersicon germplasm were screened for resistance to Pseudomonas syringae pv tomato (P.s. tomato). Resistance to both race-0 and race-1 strains of P.s. tomato was identified in L. pimpinellifolium, L. peruvianum and L. hirsutum var. glabratum. Resistance to race-0 derived from L. hirsutum var. glabratum (Pto3) appeared to be inherited independently of Pto1 and Pto2. Filial and backcross generations derived from interspecific crosses between L. esculentum and L. hirsutum var. glabratum revealed that Pto3 resistance was inherited in a complex fashion and was incompletely dominant under conditions of high bacteria inocula. Resistance to P.s. tomato race-1 (Pto4) was also identified in L. hirsutum var. glabratum. Pto3 and Pto4 segregated independently of each other. | 1994 | 24178099 |
| 6077 | 10 | 0.8318 | 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 |
| 6027 | 11 | 0.8315 | Comprehensive Genomic Profiling and In Vitro Probiotic and Safety Assessments of Enterococcus faecium UFAS147 Isolated from Moroccan Goat Feces. Enterococci are beneficial commensal bacteria recognized for their probiotic effects and are commonly utilized as adjunct cultures in dairy product fermentation. However, their ability to acquire antibiotic resistance and contribute to infections raises significant safety concerns. In this study, both in vitro assays and genome sequencing were conducted to evaluate the safety, functionality, and probiotic potential of Enterococcus faecium UFAS147, isolated from Moroccan goat feces. The strain tolerated acidic conditions (96.79% survival at pH 1.5) and bile salt (1-4%), with notable autoaggregation (33.66%), coaggregation with Salmonella typhymurium ATCC14028 (72.78%), and Staphylococcus aureus B1 (65.55%). Safety assays confirmed the absence of hemolytic activity, mucin degradation, and biogenic amine production. Antibiotic susceptibility testing showed sensitivity to six antibiotics. PCR analysis further confirmed the absence of vanA and vanB genes associated with vancomycin resistance. Genome analysis revealed a length of 2,606,111 bp with a GC content of 38.11% and the absence of genes linked to acquired antimicrobial resistance, cytolysins, and biogenic amine production. Genes supporting probiotic traits, such as Enterocin A, Enterocin P, and Enterolysin A, acid and bile resistance, adhesion, and colonization were identified. These findings highlight E. faecium UFAS147 as a promising candidate for probiotic applications. | 2025 | 40608139 |
| 6080 | 12 | 0.8310 | Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia. Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries. | 2023 | 38276185 |
| 5381 | 13 | 0.8309 | Draft genome sequence of Staphylococcus urealyticus strain MUWRP0921, isolated from the urine of an adult female Ugandan. Staphylococcus urealyticus bacteria are pathogenic among immune-compromised individuals. A strain (MUWRP0921) of Staphylococcus urealyticus with a genome of 2,708,354 bp was isolated from Uganda and carries genes that are associated with antibiotic resistance, including resistance to macrolides (erm(C) and mph(C')), aminoglycosides (aac(6")-aph(2")), tetracyclines (tet(K)), and trimethoprim (dfrG). | 2024 | 38078696 |
| 6014 | 14 | 0.8301 | Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut. Coconut, cocoa and arecanut are commercial plantation crops that play a vital role in the Indian economy while sustaining the livelihood of more than 10 million Indians. According to 2012 Food and Agricultural organization's report, India is the third largest producer of coconut and it dominates the production of arecanut worldwide. In this study, three Plant Growth Promoting Rhizobacteria (PGPR) from coconut (CPCRI-1), cocoa (CPCRI-2) and arecanut (CPCRI-3) characterized for the PGP activities have been sequenced. The draft genome sizes were 4.7 Mb (56% GC), 5.9 Mb (63.6% GC) and 5.1 Mb (54.8% GB) for CPCRI-1, CPCRI-2, CPCRI-3, respectively. These genomes encoded 4056 (CPCRI-1), 4637 (CPCRI-2) and 4286 (CPCRI-3) protein-coding genes. Phylogenetic analysis revealed that both CPCRI-1 and CPCRI-3 belonged to Enterobacteriaceae family, while, CPCRI-2 was a Pseudomonadaceae family member. Functional annotation of the genes predicted that all three bacteria encoded genes needed for mineral phosphate solubilization, siderophores, acetoin, butanediol, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinase, phenazine, 4-hydroxybenzoate, trehalose and quorum sensing molecules supportive of the plant growth promoting traits observed in the course of their isolation and characterization. Additionally, in all the three CPCRI PGPRs, we identified genes involved in synthesis of hydrogen sulfide (H2S), which recently has been proposed to aid plant growth. The PGPRs also carried genes for central carbohydrate metabolism indicating that the bacteria can efficiently utilize the root exudates and other organic materials as energy source. Genes for production of peroxidases, catalases and superoxide dismutases that confer resistance to oxidative stresses in plants were identified. Besides these, genes for heat shock tolerance, cold shock tolerance and glycine-betaine production that enable bacteria to survive abiotic stress were also identified. | 2014 | 25162593 |
| 5215 | 15 | 0.8298 | Draft genome sequence of Bacillus safensis 2T-2, isolated from drinking water. Bacillus safensis 2T-2 was isolated from potable water at a municipal water treatment facility in the North West province of South Africa, representing the first report of this species in treated drinking water systems. Whole genome sequencing revealed a 3.78 Mb genome with 41.3 % GC content and 4000 coding sequences distributed across 126 contigs. Genome analysis identified six antibiotic resistance genes, including vancomycin resistance genes (vanT, vanY), fosfomycin resistance (fosBx1), chloramphenicol resistance (cat86), and two disinfectant resistance genes (qacG, qacJ). Despite the presence of resistance genes, PathogenFinder analysis confirmed low pathogenic potential (0.168 probability). The strain demonstrated significant biosynthetic capabilities with 12 secondary metabolite gene clusters, including antimicrobial compound production (plantazolicin), biosurfactants (lichenysin), siderophores (bacillibactin, schizokinen), and the lipopeptide fengycin. Five bacteriocin gene clusters were identified, containing three core peptide genes (UviB, plantazolicin, pumilarin) with associated modification and transport genes. Phylogenetic analysis positioned strain 2T-2 closest to B. safensis F0-36b, confirming species identification. These findings highlight the dual nature of environmental bacteria in water systems, possessing both concerning antibiotic resistance traits and beneficial biotechnological potential, emphasizing the need for enhanced water treatment strategies while revealing opportunities for bioactive compound discovery. | 2025 | 40727027 |
| 6005 | 16 | 0.8297 | Antimicrobial activity of Pediococcus pentosaceus strains against diarrheal pathogens isolated from pigs and effect on paracellular permeability of HT-29 cells. This study aimed to investigate lactic acid bacteria with antimicrobial activities against infectious diarrheal pathogens in pigs and their genetic characteristics. Acid-resistant lactic acid bacteria were examined for bile resistance, pancreatic enzyme resistance, gelatinase and urease activities, and antibiotic resistance. Subsequently, selected isolates were examined for antimicrobial activities against Campylobacter coli, Clostridium perfringens, Escherichia coli, and Salmonella Typhimurium, and their effects on paracellular permeability and the expression of tight junction protein-encoding genes in HT-29 cells were assessed. Whole genome sequencing was performed to identify the genes related to safety and antibacterial activity. Of the 51 isolates examined, 12 were resistant to bile and pancreatin and did not produce gelatinase and urease. Of these 12, isolates 19, 20, 30, 36, and 67 showed tetracycline resistance and isolates 15, 19, and 38W showed antimicrobial activity against infectious diarrheal bacteria. Treatment with isolate 38W significantly reduced the paracellular permeability induced by E. coli in HT-29 cells and alleviated the expression of tight junction protein-encoding genes (claudin-1, occludin, and ZO-1) induced by E. coli inoculation. Isolates 15, 19, and 38W were named as Pediococcus pentosaceus SMFM2016-NK1, SMFM2016-YK1, and SMFM2016-WK1, respectively. Bacteriocin-related genes were YheH, ytrF, BceA, BceB, and MccF in SMFM2016-NK1; YheH, ytrF, BceA, BceB, entK, lcnA, MccF, and skgD in SMFM2016-YK1; and YheH, ytrF, BceA, BceB, and MccF in SMFM2016-WK1. SMFM2016-YK1 harbored the tetM gene. These results indicate that P. pentosaceus SMFM2016-WK1 might control diarrheal pathogens isolated from pigs. However, a further study is necessary because the results were obtained only from in vitro experiment. | 2025 | 40873998 |
| 8460 | 17 | 0.8292 | Correlation Analysis of the Transcriptome and Gut Microbiota in Salmo trutta Resistance to Aeromonas salmonicida. Aeromonas salmonicida is a major pathogenic bacterium that poses a significant threat to salmonid fish. Yadong County, located in the Xizang Autonomous Region, is renowned for its characteristic industry of Salmo trutta aquaculture. In recent years, the outbreak of Bacterial Gill Disease (BGD) has led to substantial economic losses for S. trutta farmers. Our prior research identified A. salmonicida as one of the primary culprits behind BGD. To mitigate the impact of A. salmonicida on S. trutta, we conducted a comprehensive study aimed at identifying genes associated with resistance to A. salmonicida. This involved transcriptome sequencing and 16S rRNA sequencing of intestinal flora, providing valuable insights for the study of disease resistance in S. trutta. In this study, we identified 324 genera with 5171 ASVs in the susceptible group and 293 genera with 5669 ASVs in the resistant group. Notably, Methylobacterium and Sphingomonas were common bacteria present in the salmon's gut, and their proportions remained relatively stable before and after infection. Shewanella, with its antagonistic relationship with Aeromonas, may play a crucial role in the salmon's defense against A. salmonicida. Several related genes were identified, including angptl4, cipcb, grasp, ccr9a, sulf1, mtmr11, B3GNT3, mt2, PLXDC1, and ank1b. | 2024 | 39458292 |
| 6003 | 18 | 0.8292 | Contact Lens Wear Alters Transcriptional Responses to Pseudomonas aeruginosa in Both the Corneal Epithelium and the Bacteria. PURPOSE: Healthy corneas resist colonization by virtually all microbes yet contact lens wear can predispose the cornea to sight-threatening infection with Pseudomonas aeruginosa. Here, we explored how lens wear changes corneal epithelium transcriptional responses to P. aeruginosa and its impact on bacterial gene expression. METHODS: Male and female C57BL/6J mice were fitted with a contact lens on one eye for 24 h. After lens removal, corneas were immediately challenged for 4 h with P. aeruginosa. A separate group of naïve mice were similarly challenged with bacteria. Bacteria-challenged eyes were compared to uninoculated naive controls as was lens wear alone. Total RNA-sequencing determined corneal epithelium and bacterial gene expression. RESULTS: Prior lens wear profoundly altered the corneal response to P. aeruginosa, including: upregulated pattern-recognition receptors (tlr3, nod1), downregulated lectin pathway of complement activation (masp1), amplified upregulation of tcf7, gpr55, ifi205, wfdc2 (immune defense) and further suppression of efemp1 (corneal stromal integrity). Without lens wear, P. aeruginosa upregulated mitochondrial and ubiquinone metabolism genes. Lens wear alone upregulated axl, grn, tcf7, gpr55 (immune defense) and downregulated Ca2(+)-dependent genes necab1, snx31 and npr3. P. aeruginosa exposure to prior lens wearing vs. naïve corneas upregulated bacterial genes of virulence (popD), its regulation (rsmY, PA1226) and antimicrobial resistance (arnB, oprR). CONCLUSION: Prior lens wear impacts corneal epithelium gene expression altering its responses to P. aeruginosa and how P. aeruginosa responds to it favoring virulence, survival and adaptation. Impacted genes and associated networks provide avenues for research to better understand infection pathogenesis. | 2024 | 39677621 |
| 6004 | 19 | 0.8290 | Contact Lens Wear Alters Transcriptional Responses to Pseudomonas aeruginosa in Both the Corneal Epithelium and the Bacteria. PURPOSE: Healthy corneas resist colonization by virtually all microbes, yet contact lens wear can predispose the cornea to sight-threatening infection with Pseudomonas aeruginosa. Here, we explored how lens wear changes corneal epithelium transcriptional responses to P. aeruginosa and its impact on bacterial gene expression. METHODS: Male and female C57BL/6J mice were fitted with a contact lens on one eye for 24 hours. After lens removal, corneas were immediately challenged for 4 hours with P. aeruginosa. A separate group of naïve mice was similarly challenged with bacteria. Bacteria-challenged eyes were compared to uninoculated naïve controls, as was lens wear alone. Total RNA sequencing determined corneal epithelium and bacterial gene expression. RESULTS: Prior lens wear profoundly altered the corneal response to P. aeruginosa, including upregulated pattern recognition receptors (tlr3, nod1); downregulated lectin pathway of complement activation (masp1); amplified upregulation of tcf7, gpr55, ifi205, and wfdc2 (immune defense); and further suppression of efemp1 (corneal stromal integrity). Without lens wear, P. aeruginosa upregulated mitochondrial and ubiquinone metabolism genes. Lens wear alone upregulated axl, grn, tcf7, and gpr55 (immune defense) and downregulated Ca2+-dependent genes necab1, snx31, and npr3. P. aeruginosa exposure to prior lens wearing versus naïve corneas upregulated bacterial genes of virulence (popD), its regulation (rsmY, PA1226), and antimicrobial resistance (arnB, oprR). CONCLUSIONS: Prior lens wear impacts corneal epithelium gene expression, altering its responses to P. aeruginosa and how P. aeruginosa responds to it favoring virulence, survival, and adaptation. Impacted genes and associated networks provide avenues for research to better understand infection pathogenesis. | 2025 | 39932472 |