Correlation Analysis of the Transcriptome and Gut Microbiota in Salmo trutta Resistance to Aeromonas salmonicida. - Related Documents




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846001.0000Correlation 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.202439458292
844510.9980A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for columnaris disease resistance. BACKGROUND: Columnaris causes severe mortalities among many different wild and cultured freshwater fish species, but understanding of host resistance is lacking. Catfish, the primary aquaculture species in the United States, serves as a great model for the analysis of host resistance against columnaris disease. Channel catfish in general is highly resistant to the disease while blue catfish is highly susceptible. F2 generation of hybrids can be produced where phenotypes and genotypes are segregating, providing a useful system for QTL analysis. To identify genes associated with columnaris resistance, we performed a genome-wide association study (GWAS) using the catfish 250 K SNP array with 340 backcross progenies derived from crossing female channel catfish (Ictalurus punctatus) with male F1 hybrid catfish (female channel catfish I. punctatus × male blue catfish I. furcatus). RESULTS: A genomic region on linkage group 7 was found to be significantly associated with columnaris resistance. Within this region, five have known functions in immunity, including pik3r3b, cyld-like, adcyap1r1, adcyap1r1-like, and mast2. In addition, 3 additional suggestively associated QTL regions were identified on linkage groups 7, 12, and 14. The resistant genotypes on the QTLs of linkage groups 7 and 12 were found to be homozygous with both alleles being derived from channel catfish. The paralogs of the candidate genes in the suggestively associated QTL of linkage group 12 were found on the QTLs of linkage group 7. Many candidate genes on the four associated regions are involved in PI3K pathway that is known to be required by many bacteria for efficient entry into the host. CONCLUSION: The GWAS revealed four QTLs associated with columnaris resistance in catfish. Strikingly, the candidate genes may be arranged as functional hubs; the candidate genes within the associated QTLs on linkage groups 7 and 12 are not only co-localized, but also functionally related, with many of them being involved in the PI3K signal transduction pathway, suggesting its importance for columnaris resistance.201525888203
841320.9980Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing. BACKGROUND: Salmon Rickettsial Syndrome (SRS), caused by Piscirickettsia salmonis, is one of the primary causes of morbidity and mortality in Atlantic salmon aquaculture, particularly in Chile. Host resistance is a heritable trait, and functional genomic studies have highlighted genes and pathways important in the response of salmon to the bacteria. However, the functional mechanisms underpinning genetic resistance are not yet well understood. In the current study, a large population of salmon pre-smolts were challenged with P. salmonis, with mortality levels recorded and samples taken for genotyping. In parallel, head kidney and liver samples were taken from animals of the same population with high and low genomic breeding values for resistance, and used for RNA-Sequencing to compare their transcriptome profile both pre and post infection. RESULTS: A significant and moderate heritability (h(2) = 0.43) was shown for the trait of binary survival. Genome-wide association analyses using 38 K imputed SNP genotypes across 2265 animals highlighted that resistance is a polygenic trait. Several thousand genes were identified as differentially expressed between controls and infected samples, and enriched pathways related to the host immune response were highlighted. In addition, several networks with significant correlation with SRS resistance breeding values were identified, suggesting their involvement in mediating genetic resistance. These included apoptosis, cytoskeletal organisation, and the inflammasome. CONCLUSIONS: While resistance to SRS is a polygenic trait, this study has highlighted several relevant networks and genes that are likely to play a role in mediating genetic resistance. These genes may be future targets for functional studies, including genome editing, to further elucidate their role underpinning genetic variation in host resistance.202133676414
471030.9980Gene Co-Expression Network Analysis Reveals the Hub Genes and Key Pathways Associated with Resistance to Salmonella Enteritidis Colonization in Chicken. Salmonella negatively impacts the poultry industry and threatens animals' and humans' health. The gastrointestinal microbiota and its metabolites can modulate the host's physiology and immune system. Recent research demonstrated the role of commensal bacteria and short-chain fatty acids (SCFAs) in developing resistance to Salmonella infection and colonization. However, the complex interactions among chicken, Salmonella, host-microbiome, and microbial metabolites remain unelucidated. Therefore, this study aimed to explore these complex interactions by identifying the driver and hub genes highly correlated with factors that confer resistance to Salmonella. Differential gene expression (DEGs) and dynamic developmental genes (DDGs) analyses and weighted gene co-expression network analysis (WGCNA) were performed using transcriptome data from the cecum of Salmonella Enteritidis-infected chicken at 7 and 21 days after infection. Furthermore, we identified the driver and hub genes associated with important traits such as the heterophil/lymphocyte (H/L) ratio, body weight post-infection, bacterial load, propionate and valerate cecal contents, and Firmicutes, Bacteroidetes, and Proteobacteria cecal relative abundance. Among the multiple genes detected in this study, EXFABP, S100A9/12, CEMIP, FKBP5, MAVS, FAM168B, HESX1, EMC6, and others were found as potential candidate gene and transcript (co-) factors for resistance to Salmonella infection. In addition, we found that the PPAR and oxidative phosphorylation (OXPHOS) metabolic pathways were also involved in the host's immune response/defense against Salmonella colonization at the earlier and later stage post-infection, respectively. This study provides a valuable resource of transcriptome profiles from chicken cecum at the earlier and later stage post-infection and mechanistic understanding of the complex interactions among chicken, Salmonella, host-microbiome, and associated metabolites.202336902251
603740.9980The Complete Genome of Probiotic Lactobacillus sakei Derived from Plateau Yak Feces. Probiotic bacteria are receiving increased attention due to the potential benefits to their hosts. Plateau yaks have resistance against diseases and stress, which is potentially related to their inner probiotics. To uncover the potential functional genes of yak probiotics, we sequenced the whole genome of Lactobacillus sakei (L. sakei). The results showed that the genome length of L. sakei was 1.99 Mbp, with 1943 protein coding genes (21 rRNA, 65 tRNA, and 1 tmRNA). There were three plasmids found in this bacteria, with 88 protein coding genes. EggNOG annotation uncovered that the L. sakei genes were found to belong to J (translation, ribosomal structure, and biogenesis), L (replication, recombination, and repair), G (carbohydrate transport and metabolism), and K (transcription). GO annotation showed that most of the L. sakei genes were related to cellular processes, metabolic processes, biological regulation, localization, response to stimulus, and organization or biogenesis of cellular components. CAZy annotation found that there were 123 CAZys in the L. sakei genome, with glycosyl transferases and glycoside hydrolases. Our results revealed the genome characteristics of L. sakei, which may give insight into the future employment of this probiotic bacterium for its functional benefits.202033371298
514950.9979Complete genome sequence and comparative genomic analysis of Enterococcus faecalis EF-2001, a probiotic bacterium. Enterococcus faecalis is a common human gut commensal bacterium. While some E. faecalis strains are probiotic, others are known to cause opportunistic infections, and clear distinction between these strains is difficult using traditional taxonomic approaches. In this study, we completed the genome sequencing of EF-2001, a probiotic strain, using our in-house hybrid assembly approach. Comparative analysis showed that EF-2001 was devoid of cytolysins, major factors associated with pathogenesis, and was phylogenetically distant from pathogenic E. faecalis V583. Genomic analysis of strains with a publicly available complete genome sequence predicted that drug-resistance genes- dfrE, efrA, efrB, emeA, and lsaA were present in all strains, and EF-2001 lacked additional drug-resistance genes. Core- and pan-genome analyses revealed a higher degree of genomic fluidity. We found 49 genes specific to EF-2001, further characterization of which may provide insights into its diverse biological activities. Our comparative genomic analysis approach could help predict the pathogenic or probiotic potential of E. faecalis leading to an early distinction based on genome sequences.202133771633
436060.9979Comparative Genomics Reveals Novel Species and Insights into the Biotechnological Potential, Virulence, and Resistance of Alcaligenes. Alcaligenes is a cosmopolitan bacterial genus that exhibits diverse properties which are beneficial to plants. However, the genomic versatility of Alcaligenes has also been associated with the ability to cause opportunistic infections in humans, raising concerns about the safety of these microorganisms in biotechnological applications. Here, we report an in-depth comparative analysis of Alcaligenes species using all publicly available genomes to investigate genes associated with species, biotechnological potential, virulence, and resistance to multiple antibiotics. Phylogenomic analysis revealed that Alcaligenes consists of at least seven species, including three novel species. Pan-GWAS analysis uncovered 389 species-associated genes, including cold shock proteins (e.g., cspA) and aquaporins (e.g., aqpZ) found exclusively in the water-isolated species, Alcaligenes aquatilis. Functional annotation of plant-growth-promoting traits revealed enrichment of genes for auxin biosynthesis, siderophores, and organic acids. Genes involved in xenobiotic degradation and toxic metal tolerance were also identified. Virulome and resistome profiles provide insights into selective pressures exerted in clinical settings. Taken together, the results presented here provide the grounds for more detailed clinical and ecological studies of the genus Alcaligenes.202337761923
435870.9979Genomic profiling of pediococcus acidilactici BCB1H and identification of its key features for Biotechnological innovation, food technology and medicine. Lactic acid bacteria has been extensively used in food industry because of widespread properties and Pediococcus is among one of them. This study aims to conduct a comprehensive genomic analysis of Pediococcus acidilactici strain BCB1H to elucidate its genetic composition, functional elements, and potential biotechnological applications. The objectives include identifying key genomic features such as coding sequences, tRNA and rRNA genes, antibiotic resistance genes, and secondary metabolite biosynthetic gene clusters, which will highlight the adaptability and potential of P. acidilactici strain BCB1H for use in a variety of industrial and therapeutic applications. P. acidilactici strain BCB1H was analyzed using whole-genome sequencing, which used advanced sequencing technologies to obtain comprehensive genomic data. Key genomic features, such as coding sequences, tRNA and rRNA genes, antibiotic resistance genes, and secondary metabolite biosynthetic gene clusters, were identified through bioinformatics analyses. The genomic analysis of P. acidilactici strain BCB1H revealed a genome size of approximately 1.92 million base pairs with a GC content of 42.4%. The annotation identified 1,895 genes across 192 subsystems, highlighting the metabolic pathways and functional categories. Notably, specialty genes associated with carbohydrate metabolism, stress response, pathogenicity, and amino acid synthesis were identified, underscoring the versatility and potential applications in food technology and medicine. These findings shed light on the genetic makeup and functional potential of P. acidilactici strain BCB1H, highlighting its flexibility and industrial importance. The genetic traits discovered suggest its prospective use in probiotics, food preservation, and biotechnological advancements.202539971970
435780.9979Comparative genomic analysis of 255 Oenococcus oeni isolates from China: unveiling strain diversity and genotype-phenotype associations of acid resistance. Oenococcus oeni, the only species of lactic acid bacteria capable of fully completing malolactic fermentation under challenging wine conditions, continues to intrigue researchers owing to its remarkable adaptability, particularly in combating acid stress. However, the mechanism underlying its superior adaptation to wine stresses still remains elusive due to the lack of viable genetic manipulation tools for this species. In this study, we conducted genomic sequencing and acid resistance phenotype analysis of 255 O. oeni isolates derived from diverse wine regions across China, aiming to elucidate their strain diversity and genotype-phenotype associations of acid resistance through comparative genomics. A significant correlation between phenotypes and evolutionary relationships was observed. Notably, phylogroup B predominantly consisted of acid-resistant isolates, primarily originating from Shandong and Shaanxi wine regions. Furthermore, we uncovered a noteworthy linkage between prophage genomic islands and acid resistance phenotype. Using genome-wide association studies, we identified key genes correlated with acid resistance, primarily involved in carbohydrates and amino acid metabolism processes. This study offers profound insights into the genetic diversity and genetic basis underlying adaptation mechanisms to acid stress in O. oeni.IMPORTANCEThis study provides valuable insights into the genetic basis of acid resistance in Oenococcus oeni, a key lactic acid bacterium in winemaking. By analyzing 255 isolates from diverse wine regions in China, we identified significant correlations between strain diversity, genomic islands, and acid resistance phenotypes. Our findings reveal that certain prophage-related genomic islands and specific genes are closely linked to acid resistance, offering a deeper understanding of how O. oeni adapts to acidic environments. These discoveries not only advance our knowledge of microbial stress responses but also pave the way for selecting and engineering acid-resistant strains, enhancing malolactic fermentation efficiency and wine quality. This research underscores the importance of genomics in improving winemaking practices and addressing challenges posed by high-acidity wines.202540261018
612590.9979Complete Genome Sequence Analysis of Brevibacillus laterosporus Bl-zj Reflects its Potential Algicidal Response. We analyzed the complete genome of the bacteria Brevibacillus laterosporus Bl-zj. Its genome has a total length of 5,202,546 bp with 4594 annotated genes. The functional groups included transporters, pathogen-host interaction factors, antibiotic resistance genes, virulence factor, and secreted proteins were predicted, and carbon and nitrogen metabolism and transporters were mapped. A total of 34 genes possibly involved in algae-lysing processes were further screened, including 8 virulence factors, 18 secreted proteases, and 8 antibiotic-resistant genes, which could be playing important roles in host identification, invasion, and the destruction of algal cells. This study will provide a theoretical framework for the algicidal mechanism of algae-lysing bacteria and possible application to algal control.202133649996
5165100.9978Transcription profiling of resistance to Bti toxins in the mosquito Aedes aegypti using next-generation sequencing. The control of mosquitoes transmitting infectious diseases relies mainly on the use of chemical insecticides. However, resistance to most chemical insecticides threatens mosquito control programs. In this context, the spraying of toxins produced by the bacteria Bacillus thuringiensis subsp. israelensis (Bti) in larval habitats represents an alternative to chemical insecticides and is now widely used for mosquito control. Recent studies suggest that resistance of mosquitoes to Bti toxin may occur locally but mechanisms have not been characterized so far. In the present study, we investigated gene transcription level variations associated with Bti toxin resistance in the mosquito Aedes aegypti using a next-generation sequencing approach. More than 6 million short cDNA tags were sequenced from larvae of two strains sharing the same genetic background: a Bti toxins-resistant strain and a susceptible strain. These cDNA tags were mapped with a high coverage (308 reads per position in average) to more than 6000 genes of Ae. aegypti genome and used to quantify and compare the transcription level of these genes between the two mosquito strains. Among them, 86 genes were significantly differentially transcribed more than 4-fold in the Bti toxins resistant strain comparatively to the susceptible strain. These included gene families previously associated with Bti toxins resistance such as serine proteases, alkaline phosphatase and alpha-amylase. These results are discussed in regards of potential Bti toxins resistance mechanisms in mosquitoes.201222115744
4617110.9978A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state. BACKGROUND: The serovars Enteritidis and Typhimurium of the Gram-negative bacterium Salmonella enterica are significant causes of human food poisoning. Fowl carrying these bacteria often show no clinical disease, with detection only established post-mortem. Increased resistance to the carrier state in commercial poultry could be a way to improve food safety by reducing the spread of these bacteria in poultry flocks. Previous studies identified QTLs for both resistance to carrier state and resistance to Salmonella colonization in the same White Leghorn inbred lines. Until now, none of the QTLs identified was common to the two types of resistance. All these analyses were performed using the F2 inbred or backcross option of the QTLExpress software based on linear regression. In the present study, QTL analysis was achieved using Maximum Likelihood with QTLMap software, in order to test the effect of the QTL analysis method on QTL detection. We analyzed the same phenotypic and genotypic data as those used in previous studies, which were collected on 378 animals genotyped with 480 genome-wide SNP markers. To enrich these data, we added eleven SNP markers located within QTLs controlling resistance to colonization and we looked for potential candidate genes co-localizing with QTLs. RESULTS: In our case the QTL analysis method had an important impact on QTL detection. We were able to identify new genomic regions controlling resistance to carrier-state, in particular by testing the existence of two segregating QTLs. But some of the previously identified QTLs were not confirmed. Interestingly, two QTLs were detected on chromosomes 2 and 3, close to the locations of the major QTLs controlling resistance to colonization and to candidate genes involved in the immune response identified in other, independent studies. CONCLUSIONS: Due to the lack of stability of the QTLs detected, we suggest that interesting regions for further studies are those that were identified in several independent studies, which is the case of the QTL regions on chromosomes 2 and 3, involved in resistance to both Salmonella colonization and carrier state. These observations provide evidence of common genes controlling S. Typhimurium colonization and S. Enteritidis carrier-state in chickens.201222613937
7716120.9978Metagenomic analysis fecal microbiota of dysentery-like diarrhoea in a pig farm using next-generation sequencing. Porcine enteric diseases including swine dysentery involves a wide range of possible aetiologies and seriously damages the intestine of pigs of all ages. Metagenomic next-generation sequencing is commonly used in research for detecting and analyzing pathogens. In this study, the feces of pigs from a commercial swine farm with dysentery-like diarrhea was collected and used for microbiota analysis by next-generation sequencing. While Brachyspira spp. was not detected in diarrheal pig fecal samples, indicating that the disease was not swine dysentery. The quantity of microbial population was extremely lowered, and the bacterial composition was altered with a reduction in the relative abundance of the probiotics organisms, Firmicutes and Bacteroidetes, with an increase in pathogens like Fusobacterium and Proteobacteria, in which the specific bacteria were identified at species-level. Viral pathogens, porcine circovirus type 2, porcine lymphotropic herpesviruses 1, and porcine mastadenovirus A were also detected at pretty low levels. Carbohydrate-active enzymes (CAZy) analysis indicated that the constitute of Firmicutes and Bacteroidete were also changed. Further, the Kyoto Encyclopedia of Genes and Genomes (KEGG) alignment analysis indicated that the microbiota of diarrheal pigs had a lower ability in utilizing energy sources but were enriched in multi-drug resistance pathways. Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factors of Pathogenic Bacteria (VFDB) analysis indicated that genes for elfamycin and sulfonamide resistance and the iron uptake system were enriched in diarrheal pigs. This revealed potential bacterial infection and can guide antibiotic selection for treating dysentery. Overall, our data suggested that alterations in both the population and functional attributes of microbiota in diarrheal pigs with decreased probiotic and increased pathogenic microorganisms. These results will help elucidate the mechanism of dysentery-like diarrhea and the development of approaches to control the disease.202337915946
4615130.9978Effect of conditioned media from Aeromonas caviae on the transcriptomic changes of the porcine isolates of Pasteurella multocida. BACKGROUND: Pasteurella multocida is an opportunistic pathogen causing porcine respiratory diseases by co-infections with other bacterial and viral pathogens. Various bacterial genera isolated from porcine respiratory tracts were shown to inhibit the growth of the porcine isolates of P. multocida. However, molecular mechanisms during the interaction between P. multocida and these commensal bacteria had not been examined.  METHODS: This study aimed to investigate the interaction between two porcine isolates of P. multocida (PM2 for type D and PM7 for type A) with Aeromonas caviae selected from the previously published work by co-culturing P. multocida in the conditioned media prepared from A. caviae growth and examining transcriptomic changes using RNA sequencing and bioinformatics analysis.  RESULTS: In total, 629 differentially expressed genes were observed in the isolate with capsular type D, while 110 genes were significantly shown in type A. High expression of genes required for energy metabolisms, nutrient uptakes, and quorum sensing were keys to the growth and adaptation to the conditioned media, together with the decreased expression of those in the unurgent pathways, including translation and antibacterial resistance. CONCLUSION: This transcriptomic analysis also displayed the distinct capability of the two isolates of P. multocida and the preference of the capsular type A isolate in response to the tough environment of the A. caviae conditioned media. Therefore, controlling the environmental sensing and nutrient acquisition mechanisms of P. multocida would possibly prevent the overpopulation of these bacteria and reduce the chance of becoming opportunistic pathogens.202236368971
6727140.9978Differences in the intestinal microbiota between insecticide-resistant and -sensitive Aedes albopictus based on full-length 16S rRNA sequencing. The intestinal symbiotic bacteria of Aedes albopictus play a potential role in host resistance to insecticides. In this study, we sequenced the full-length of 16S rRNA and analyzed the differences in the intestinal microbiota between deltamethrin-resistant and -sensitive Ae. albopictus. Symbiotic bacteria were cultured and analyzed using six types of culture media in aerobic and anaerobic environments. We found significant differences in the diversity and abundance of the intestinal microbiota of the two strains of Ae. albopictus. The symbiotic bacteria cultured in vitro were found to be mainly facultative anaerobes. The cultured bacteria such as Serratia oryzae and Acinetobacter junii may function to promote the development of insecticide resistance. This work indicates that intestinal bacteria may contribute to the enhancement of insecticide resistance of Ae. albopictus It also highlights the analytical advantage of full-length 16S rRNA sequencing to study the intestinal microbiota of mosquitoes.202133970535
5163150.9978Multi-omics data elucidate parasite-host-microbiota interactions and resistance to Haemonchus contortus in sheep. BACKGROUND: The integration of molecular data from hosts, parasites, and microbiota can enhance our understanding of the complex biological interactions underlying the resistance of hosts to parasites. Haemonchus contortus, the predominant sheep gastrointestinal parasite species in the tropics, causes significant production and economic losses, which are further compounded by the diminishing efficiency of chemical control owing to anthelmintic resistance. Knowledge of how the host responds to infection and how the parasite, in combination with microbiota, modulates host immunity can guide selection decisions to breed animals with improved parasite resistance. This understanding will help refine management practices and advance the development of new therapeutics for long-term helminth control. METHODS: Eggs per gram (EPG) of feces were obtained from Morada Nova sheep subjected to two artificial infections with H. contortus and used as a proxy to select animals with high resistance or susceptibility for transcriptome sequencing (RNA-seq) of the abomasum and 50 K single-nucleotide genotyping. Additionally, RNA-seq data for H. contortus were generated, and amplicon sequence variants (ASV) were obtained using polymerase chain reaction amplification and sequencing of bacterial and archaeal 16S ribosomal RNA genes from sheep feces and rumen content. RESULTS: The heritability estimate for EPG was 0.12. GAST, GNLY, IL13, MGRN1, FGF14, and RORC genes and transcripts were differentially expressed between resistant and susceptible animals. A genome-wide association study identified regions on chromosomes 2 and 11 that harbor candidate genes for resistance, immune response, body weight, and adaptation. Trans-expression quantitative trait loci were found between significant variants and differentially expressed transcripts. Functional co-expression modules based on sheep genes and ASVs correlated with resistance to H. contortus, showing enrichment in pathways of response to bacteria, immune and inflammatory responses, and hub features of the Christensenellaceae, Bacteroides, and Methanobrevibacter genera; Prevotellaceae family; and Verrucomicrobiota phylum. In H. contortus, some mitochondrial, collagen-, and cuticle-related genes were expressed only in parasites isolated from susceptible sheep. CONCLUSIONS: The present study identified chromosome regions, genes, transcripts, and pathways involved in the elaborate interactions between the sheep host, its gastrointestinal microbiota, and the H. contortus parasite. These findings will assist in the development of animal selection strategies for parasite resistance and interdisciplinary approaches to control H. contortus infection in sheep.202438429820
6036160.9978Comprehensive Phenotypic Characterization and Genomic Analysis Unveil the Probiotic Potential of Bacillus velezensis K12. Bacillus spp. have emerged as pivotal sources of probiotic preparations, garnering considerable attention in recent years owing to their vigorous bacteriostatic activity and antimicrobial resistance. This study aimed to investigate these probiotic characteristics in depth and verify the safety of Bacillus velezensis K12, a strain isolated from broiler intestine. The K12 strain was identified as Bacillus velezensis based on its morphology and 16S rDNA sequence homology analysis. Subsequently, B. velezensis K12 was evaluated for acid resistance, bile salt resistance, gastrointestinal tolerance, drug sensitivity, and antimicrobial activity. Additionally, whole-genome sequencing technology was employed to dissect its genomic components further, aiming to explore its potential applications as a probiotic strain. B. velezensis K12 was sensitive to six antibiotics and had acid tolerance. Furthermore, it showed potent antimicrobial activity against a wide range of pathogenic bacteria, including Escherichia coli (E. coli), Staphylococcus aureus, Salmonella, Clostridium perfringens, Bacillus cereus, and Vibrio parahaemolyticus. The complete genome sequencing of B. velezensis K12 revealed a genomic length of 3,973,105 base pairs containing 4123 coding genes, among which 3973 genes were functionally annotated. The genomic analysis identified genes associated with acid and bile tolerance, adhesion, antioxidants, and secondary metabolite production, whereas no functional genes related to enterotoxins or transferable antibiotic resistance were detected, thereby confirming the probiotic properties of B. velezensis K12. B. velezensis K12 exhibits broad-spectrum bacteriostatic activity and in vitro safety, positioning it as a potential candidate strain for developing probiotic Bacillus preparations.202540150327
4683170.9978Characterization of Bacteroides fragilis from the vagina of a giant panda (Ailuropoda melanoleuca) with vaginitis. BACKGROUND: Bacteroides fragilis is a prevalent anaerobic bacterium typically resides in the human vagina. It is known to potentially induce infections under specific conditions. Interestingly, there have been no previous reports of B. fragilis being isolated from the vagina of giant pandas. CASE PRESENTATION: A novel strain of anaerobic bacteria was isolated from the vaginal tract of a giant panda exhibiting symptoms of vaginitis. This strain, designated as GPBF01, was identified as Bacteroides fragilis, a species commonly found in the vaginal microbiome of humans and other animals. After purifying of the single colony, a series of evaluations were conducted including morphological examination, physiological and biochemical identification, antibiotic resistance analysis, resistance genes detection, 16S rRNA sequence, and phylogenetic tree sequence analysis to investigate its biological characteristics. The findings indicated the presence of a predominant anaerobic bacterium, which was identified as B. fragilis and temporarily named GPBF01 with unique biological traits not previously. CONCLUSIONS: This study is the first to report B. fragilis in the vaginal tract of giant pandas. The analysis of antibiotic resistance patterns among anaerobic bacteria, as conducted in this research, is critical for informing the selection of appropriate antimicrobial agents in the clinical treatment of vaginitis in this species. The findings of this report substantially enhance the scientific basis needed to understand the etiology and refine therapeutic approaches for vaginitis in giant pandas.202439605068
4642180.9978Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection. BACKGROUND: The abundance and diversity of antibiotic resistance genes (ARGs) in the human respiratory microbiome remain poorly characterized. In the context of influenza virus infection, interactions between the virus, the host, and resident bacteria with pathogenic potential are known to complicate and worsen disease, resulting in coinfection and increased morbidity and mortality of infected individuals. When pathogenic bacteria acquire antibiotic resistance, they are more difficult to treat and of global health concern. Characterization of ARG expression in the upper respiratory tract could help better understand the role antibiotic resistance plays in the pathogenesis of influenza-associated bacterial secondary infection. RESULTS: Thirty-seven individuals participating in the Household Influenza Transmission Study (HITS) in Managua, Nicaragua, were selected for this study. We performed metatranscriptomics and 16S rRNA gene sequencing analyses on nasal and throat swab samples, and host transcriptome profiling on blood samples. Individuals clustered into two groups based on their microbial gene expression profiles, with several microbial pathways enriched with genes differentially expressed between groups. We also analyzed antibiotic resistance gene expression and determined that approximately 25% of the sequence reads that corresponded to antibiotic resistance genes mapped to Streptococcus pneumoniae and Staphylococcus aureus. Following construction of an integrated network of ARG expression with host gene co-expression, we identified several host key regulators involved in the host response to influenza virus and bacterial infections, and host gene pathways associated with specific antibiotic resistance genes. CONCLUSIONS: This study indicates the host response to influenza infection could indirectly affect antibiotic resistance gene expression in the respiratory tract by impacting the microbial community structure and overall microbial gene expression. Interactions between the host systemic responses to influenza infection and antibiotic resistance gene expression highlight the importance of viral-bacterial co-infection in acute respiratory infections like influenza. Video abstract.202032178738
5148190.9978Unveiling the whole genomic features and potential probiotic characteristics of novel Lactiplantibacillus plantarum HMX2. This study investigates the genomic features and probiotic potential of Lactiplantibacillus plantarum HMX2, isolated from Chinese Sauerkraut, using whole-genome sequencing (WGS) and bioinformatics for the first time. This study also aims to find genetic diversity, antibiotic resistance genes, and functional capabilities to help us better understand its food safety applications and potential as a probiotic. L. plantarum HMX2 was cultured, and DNA was extracted for WGS. Genomic analysis comprised average nucleotide identity (ANI) prediction, genome annotation, pangenome, and synteny analysis. Bioinformatics techniques were used to identify CoDing Sequences (CDSs), transfer RNA (tRNA) and ribosomal RNA (rRNA) genes, and antibiotic resistance genes, as well as to conduct phylogenetic analysis to establish genetic diversity and evolution. The study found a significant genetic similarity (99.17% ANI) between L. plantarum HMX2 and the reference strain. Genome annotation revealed 3,242 coding sequences, 65 tRNA genes, and 16 rRNA genes. Significant genetic variety was found, including 25 antibiotic resistance genes. A phylogenetic study placed L. plantarum HMX2 among closely related bacteria, emphasizing its potential for probiotic and food safety applications. The genomic investigation of L. plantarum showed essential genes, including plnJK and plnEF, which contribute to antibacterial action against foodborne pathogens. Furthermore, genes such as MurA, Alr, and MprF improve food safety and probiotic potential by promoting bacterial survival under stress conditions in food and the gastrointestinal tract. This study introduces the new genomic features of L. plantarum HMX2 about specific genetics and its possibility of relevant uses in food security and technologies. These findings of specific genes involved in antimicrobial activity provide fresh possibilities for exploiting this strain in forming probiotic preparations and food preservation methods. The future research should focus on the experimental validation of antibiotic resistance genes, comparative genomics to investigate functional diversity, and the development of novel antimicrobial therapies that take advantage of L. plantarum's capabilities.202439611087