A5029473701- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Probiotics and Fermented Foods
- Oral microbiology and periodontitis research
- Bacteriophages and microbial interactions
- Clostridium difficile and Clostridium perfringens research
- Mycobacterium research and diagnosis
- Alcohol Consumption and Health Effects
- Machine Learning in Bioinformatics
- Biochemical Analysis and Sensing Techniques
- Regulation of Appetite and Obesity
- Neuropeptides and Animal Physiology
- Infant Nutrition and Health
- Digestive system and related health
- Plant Pathogens and Fungal Diseases
- Bacterial Genetics and Biotechnology
- Colorectal Cancer Screening and Detection
- Diphtheria, Corynebacterium, and Tetanus
- Gastrointestinal motility and disorders
- Microbial Metabolites in Food Biotechnology
- Oral Health Pathology and Treatment
- Protist diversity and phylogeny
- Diet and metabolism studies
- Advanced Proteomics Techniques and Applications
- Legume Nitrogen Fixing Symbiosis
BGI Research
2023-2025
BGI Group (China)
2021-2025
Botswana Geoscience Institute
2021-2025
State Key Laboratory of Diagnosis and Treatment of Infectious Diseases
2018
Zhejiang University
2018
Abstract The Lachnospiraceae family holds promise as a source of next‐generation probiotics, yet comprehensive delineation its diversity is lacking, hampering the identification suitable strains for future applications. To address this knowledge gap, we conducted an in‐depth genomic and functional analysis 1868 high‐quality genomes, combining data from public databases with our new isolates. This set represented 387 colonization‐selective species‐level clusters, which eight genera...
Culture-independent metagenomic studies have revolutionized our understanding of the gut microbiota. However, lack full genomes from cultured species is still a limitation for in-depth Here we present substantially expanded version Cultivated Genome Reference (CGR), termed CGR2, providing 3324 high-quality draft isolates selected large-scale cultivation bacterial fecal samples healthy Chinese individuals. The CGR2 classifies 527 (179 previously unidentified species) 8 phyla, and uncovers...
Abstract The oral cavity harbors highly diverse communities of microorganisms. However, the number isolated species and high-quality genomes is limited. Here we present a Cultivated Oral Bacteria Genome Reference (COGR), comprising 1089 based on large-scale aerobic anaerobic cultivation human bacteria from dental plaques, tongue, saliva. COGR covers five phyla contains 195 species-level clusters which 95 include 315 representing with no taxonomic annotation. microbiota differs markedly...
Abstract The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays may provide an alternative sequencing of genomes. To explore impact platforms on assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared assemblies based cultured species using 2000 BGISEQ-500 platforms. In addition, simulated reads were to evaluate insert size assembly. Genome...
Numerous studies have confirmed that gut microbiota is a key driver in the occurrence and progression of inflammatory bowel disease (IBD). Based on bacterial collection constructed our previous studies, we founded Bifidobacterium adolescentis AF91-08b2A has potential beneficial function. We designed cohort genomic animal experiments to further explore probiotic function its therapeutic effect IBD. The depletion B. individuals with IBD suggested significance for intestinal health. Genomic...
A Gram-staining-negative, non-spore-forming, short, straight rod, non-motile, and obligate anaerobic bacterial strain, AF73-05CM02 T , was isolated from a fecal sample of 30 years old healthy male living in Shenzhen, China. Colonies were approximately 0.2 mm diameter, beige, circular after 4 days incubation on PYG agar under conditions at 37°C. Strain grew temperature range between 42°C pH 6.0 to 8.5, with optimum growth 37–42°C 7.0. 16S rRNA gene sequence analysis demonstrated that strain...
The genus Bifidobacterium widely exists in human gut and has been increasingly used as the adjuvant probiotics for prevention treatment of diseases. However, functional differences genomes from different regions world remain unclear. We here describe an extensive study on genomic characteristics function annotations 1512 (clustered to 849 non-redundant genomes) cultured gut. distribution some carbohydrate-active enzymes varied among species continents. More than 36% B. pseudocatenulatum...
Introduction Faecalibacterium is one of the most abundant bacteria in gut microbiota healthy adults, highly regarded as a next-generation probiotic. However, functions genomes from cultured strains and distribution different species populations may differ among sources. Methods We here performed an extensive analysis pan-genomes, functions, safety evaluation 136 collected 10 countries. Results The are clustered into 11 clusters, with only five them were characterized validly nomenclated....
The microbiota hosted in the pig gastrointestinal tract are important to health of this biomedical model. However, individual species and functional repertoires that make up gut microbiome remain largely undefined. Here we comprehensively investigated genomes functions piglet using culture-based metagenomics approaches. A collection included 266 cultured 482 metagenome-assembled (MAGs) were clustered 428 across 10 phyla was established. Among these species, 333 represent potential new...
Abstract Aims Lactobacillus acidophilus has been extensively applied in plentiful probiotic products. Although several studies have performed to investigate the beneficial characteristics and genome function of L. acidophilus, comparative genomic analysis remains scarce. In this study, we collected 74 genomes from our gut bacterial collection public database conducted a comprehensive analysis. Methods results This study revealed potential correlation diversity niche adaptation different...
Abstract Background Current microbial sequencing relies on short-read platforms like Illumina and DNBSEQ, favored for their low cost high accuracy. However, these methods often produce fragmented draft genomes, hindering comprehensive bacterial function analysis. CycloneSEQ, a novel long-read platform developed by BGI-Research, its performance assembly improvements has been evaluated. Findings Using CycloneSEQ sequencing, the type strain produced long reads with an average length of 11.6 kbp...
Metaproteomics offers a profound understanding of the functional dynamics gut microbiome, which is crucial for personalized healthcare strategies. The selection an appropriate database critical step identification peptides and proteins, as well provision accurate taxonomic annotations. matched metagenomic-derived considered to be best, but its limitations include low-abundance organisms resolution. Herein, we constructed protein (DBCGR2) based on Cultivated Genome Reference 2 (CGR2)...
The episymbiotic Candidatus Saccharibacteria is the most studied lineage of candidate phyla radiation. Living an epiparasitic lifestyle, might be associated with human mucosal diseases by modulating structure oral microbiome through interactions host bacteria. However, knowledge Saccharibacterial genomic diversity and potential underlying their adaptation to a wide range habitats remains limited. Here, we construct high-quality genome collection from multiple sources, providing 2041 genomes...
<h3>Background</h3> Ulcerative colitis (UC) is a chronic immune-mediated disorder primarily characterized by gastrointestinal tract inflammation. Probiotics are an adjunct to traditional drug therapy for UC. In this study, Bifidobacterium adolescentis AF91-08b2A was isolated and screened, the beneficial effect of B. on mice induced sodium dextran sulfate (DSS) evaluated. Our data show that alleviates IBD symptoms protecting against intestinal barrier damage modulating immune response....
Alcohol intake causes many diseases including neuropsychiatric symptoms, nutritional deficiency, progressive pancreatitis, liver cirrhosis, and ischemic heart disease. The gut microbiota changes significantly after alcohol exposure. consumption tends to increase in underage young people, but the feature of puberty remains largely unexplored. In this study, we conducted alcohol-exposed pubertal adult mice model investigate intestinal damage change. Interestingly, responses exposure were...
An important risk factor for cardiovascular disease is dyslipidemia, especially abnormal cholesterol levels. The relation between probiotics and cholesterol-lowering capability has been extensively studied. Lactobacillus acidophilus plays a significant role in affecting host health, produces multitudinous metabolites, which have prohibitory functions against pathogenic microorganisms. In this study, we identified strain AM13-1, isolated from fecal sample obtained healthy adult male,...
Abstract Lactobacillus acidophilus has been extensively applied in plentiful probiotic products and is mostly found the gastrointestinal tract, vagina, oral cavity of human animal, fermented foods. Although several studies have performed to investigate beneficial characteristics genome function L. , comparative genomic analysis remains scarce. In this study, we collected 74 genomes from our gut bacterial collection public database conducted a comprehensive analysis. The average nucleotide...
ABSTRACT Lactobacillus acidophilus has been extensively applied in plentiful probiotic products and is mostly found the gastrointestinal tract, vagina, oral cavity of human animal, fermented foods. Although several studies have performed to investigate beneficial characteristics genome function L. , comparative genomic analysis remains scarce. In this study, we collected 74 genomes from our gut bacterial collection public database conducted a comprehensive analysis. The average nucleotide...
Abstract Background: The microbiota hosted in the pig gastrointestinal tract are important to health of this biomedical model. However, individual species and functional repertoires that make up gut microbiome remain largely undefined. Results: Here we comprehensively investigated genomes functions piglet using culture-based metagenomics approaches. A collection included 266 cultured 482 metagenome-assembled (MAGs) were clustered 428 across 10 phyla was established. Among these species, 333...