A5110238057- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Probiotics and Fermented Foods
- Microbial Community Ecology and Physiology
- Clostridium difficile and Clostridium perfringens research
- SARS-CoV-2 and COVID-19 Research
- Bacteriophages and microbial interactions
- Bacterial Identification and Susceptibility Testing
- vaccines and immunoinformatics approaches
- Influenza Virus Research Studies
- Mycorrhizal Fungi and Plant Interactions
- Evolution and Genetic Dynamics
- Identification and Quantification in Food
- Plant Pathogens and Fungal Diseases
- Microbial Metabolism and Applications
- Microbial Natural Products and Biosynthesis
- Epigenetics and DNA Methylation
- Polar Research and Ecology
- CRISPR and Genetic Engineering
- Microbial infections and disease research
- Cryospheric studies and observations
- Animal Disease Management and Epidemiology
- Antibiotic Resistance in Bacteria
- RNA and protein synthesis mechanisms
- Mycobacterium research and diagnosis
Chinese Academy of Sciences
2015-2024
Microbiology Institute of Shaanxi
2018-2024
Institute of Microbiology
2015-2024
Czech Academy of Sciences, Institute of Microbiology
2019-2024
NOAA National Data Buoy Center
2024
State Key Laboratory of Microbial Resources
2023
Center for Excellence in Brain Science and Intelligence Technology
2022
Jiangnan University
2016
Computer Network Information Center
2014
Abstract Background In gut microbiome studies, the cultured microbial resource plays essential roles, such as helping to unravel functions and host-microbe interactions. Although several major studies have been performed elucidate human microbiota, up 70% of Unified Human Gastrointestinal Genome species not date. Large-scale isolation identification well availability public are imperative for further characterizing functions. Results this study, we constructed a Gut Microbial Biobank (hGMB;...
MycoBank, a registration system for fungi established in 2004 to capture all taxonomic novelties, acts as coordination hub between repositories such Index Fungorum and Fungal Names. Since January 2013, of fungal names is mandatory requirement valid publication under the International Code Nomenclature algae, plants (ICN). This review explains database innovations that have been implemented over past few years, discusses new features advanced queries, typification events (MBT numbers lecto,...
Abstract The human gastrointestinal (GI) tract harbors diverse microbes, and the family Lachnospiraceae is one of most abundant widely occurring bacterial groups in GI tract. Beneficial adverse effects on host health were reported, but diversities at species/strain levels as well their metabolites have been, so far, not documented. In present study, we report collection 77 h uman‐originated L a ch nospiraceae sp ecies (please refer hLchsp, https://hgmb.nmdc.cn/subject/lachnospiraceae ) vitro...
Pan-genomics is one of the most powerful means to study genomic variation and obtain a sketch genes within defined clade species. Though there are lot computational tools achieve this, an integrated framework evaluate their performance offer best choice users has never been achieved. To ease process large-scale prokaryotic genome analysis, we introduce Integrated Prokaryotes Genome pan-genome Analysis (IPGA), one-stop web service analyze, compare, visualize as well individual genomes, that...
Abstract Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data methods. As the depository Global Catalogue Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Type Strain (gcType) published 1049 genomes sequenced by GCM project which are preserved in global culture collections with a valid status. Additionally, information provided through gcType includes >12 000 publicly available genome sequences from GenBank incorporated...
Abstract Mice are widely used as experimental models for gut microbiome (GM) studies, yet the majority of mouse GM members remain uncharacterized. Here, we report construction a microbial biobank (mGMB) that contains 126 species, represented by 244 strains have been deposited in China General Microorganism Culture Collection. We sequence and phenotypically characterize 77 potential new species propose their nomenclatures. The mGMB includes 22 17 significantly enriched ob/ob wild-type...
Abstract Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly increasing in some countries. Exploring their receptor binding interspecies transmission risk urgently needed. Herein, we examine capacities of human other 28 animal ACE2 orthologs covering nine orders towards S proteins these sub-variants. The affinities between hACE2 sub-variants remain...
The World Federation of Culture Collections and the Data Center for Microorganisms (wdcm) initiated an international community-led project to sequence annotate newly described prokaryotic taxa. This sequencing aims cooperate with culture collections International Journal Systematic Evolutionary Microbiology contribute expansion whole genome databases type strains. It will provide global microbial taxonomists free standard annotation services. Taxonomists are encouraged contact wdcm...
Meta-omics approaches have been increasingly used to study the structure and function of microbial communities. A variety large-scale collaborative projects are being conducted encompass samples from diverse environments habitats. This change has resulted in enormous demands for long-term data maintenance capacity analysis. The Global Catalogue Metagenomics (gcMeta) is a part 'Chinese Academy Sciences Initiative Microbiome (CAS-CMI)', which focuses on studying human environmental microbiome,...
Abstract Fungal taxonomy is a complex and rapidly changing subject, which makes proper naming of fungi challenging for taxonomists. A registration platform with standardized information-integrated database powerful tool efficient research on fungal taxonomy. Names (FN, https://nmdc.cn/fungalnames/; launched in 2011) one the three official nomenclatural repositories authorized by International Nomenclature Committee Fungi (NCF). Currently, FN includes >567 000 taxon names from...
The Microbiome Protocols eBook (MPB) serves as a crucial bridge, filling gaps in microbiome protocols for both wet experiments and data analysis. first edition, launched 2020, featured 152 meticulously curated protocols, garnering widespread acclaim. We now extend sincere invitation to researchers participate the upcoming 2nd version of MPB, contributing their valuable advance research. is research area that focuses on studying omics microbe [1] with rapid development past few decades,...
The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of Federation Culture Collections (WFCC)-Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big technology microbial resource centers and microbiologists all over world. Here, we an overview including its services. Information Worldwide (CCINFO) provides metadata on 708 culture collections from 72 countries regions. Global Catalogue Microorganism (GCM)...
ABSTRACT Acetoin (3-hydroxy-2-butanone) formation in vinegar microbiota is crucial for the flavor quality of Zhenjiang aromatic vinegar, a traditional produced from cereals. However, specific microorganisms responsible acetoin this centuries-long repeated batch fermentation have not yet been clearly identified. Here, microbial distribution discrepancy diacetyl/acetoin metabolic pathway was revealed at species level by combination metagenomic sequencing and clone library analysis. The results...
Abstract Background Infections caused by linezolid-resistant enterococci (LRE) are clinically difficult to treat and threaten patient health. However, there is a lack of studies on long time-span LRE strains in China. For this reason, our study comprehensively revealed the resistance mechanisms collected Chinese tertiary care hospital from 2011 2022. Methods Enterococcal were screened verified after retrospective analysis microbial data. Subsequently, 65 (61 Enterococcus faecalis 4 faecium ,...
Klebsiella pneumoniae, a major clinical pathogen known for causing severe infections, is attracting heightened attention due to its escalating antibiotic resistance. Phages are emerging as promising alternative antibiotics; however, their specificity particular hosts often restricts use. In this study, collection of 114 phages obtained and subjected analysis against 238 K. pneumoniae strains, revealing spectrum lytic behaviors. A correlation between putative tail protein clusters lysis...
Throughout the long history of industrial and academic research, many microbes have been isolated, characterized preserved (whenever possible) in culture collections. With steady accumulation observational data biodiversity as well microbial sequencing data, bio-resource centers to function information repositories serve academia, industry, regulators on behalf for general public. Hence, World Data Centre Microorganisms (WDCM) started take its responsibility constructing an effective...
Genomic information is essential for taxonomic, phylogenetic, and functional studies to comprehensively decipher the characteristics of microorganisms, explore microbiomes through metagenomics, answer fundamental questions nature human life. However, large gaps remain in available genomic sequencing published bacterial archaeal species, are even larger fungal type strains. The Global Catalogue Microorganisms (GCM) leads an internationally coordinated effort sequence strains close maps...
Clostridium inhabiting pit mud (PM) is one of the important bacterial populations for synthesizing flavor compounds Chinese strong-flavor baijiu. The long-term cereal fermentation with sorghum as main raw material creates an environment rich in starch, ethanol, and organic acids (mainly lactic acid). However, genetic factors underpinning Clostridium's adaptation to PM remain poorly understood. Here, we performed comparative genomic analysis between 30 mud-associated (PMA) 100 non-pit (NPMA)...
The recent outbreak of novel coronavirus-infected pneumonia (NCIP) in China (1) has attracted much attention domestically and internationally.As the occurred, carried out emergency responses quickly, notified World Health Organization (WHO) a timely manner, shared viral gene sequence with international communities immediately after pathogenic identification.The release information on coronavirus (2019-nCoV), joint research relevant genome mutations, pathogenicity, transmission mechanisms,...
The genomic variations of SARS-CoV-2 continue to emerge and spread worldwide. Some mutant strains show increased transmissibility virulence, which may cause reduced protection provided by vaccines. Thus, it is necessary continuously monitor analyze the SARS-COV-2 genomes. We established an evaluation prewarning system, system (VarEPS), including known virtual mutations genomes achieve rapid risks posed strains. From perspective genomics structural biology, database comprehensively analyzes...
Abstract Here, we present the manually curated Global Catalogue of Pathogens (gcPathogen), an extensive genomic resource designed to facilitate rapid and accurate pathogen analysis, epidemiological exploration monitoring antibiotic resistance features virulence factors. The catalogue seamlessly integrates analyzes data associated metadata for human pathogens isolated from infected patients, animal hosts, food environment. list is supported by evidence medical or government pathogenic lists...
Since late 2019, COVID-19 has significantly impacted the world. Understanding evolution of SARS-CoV-2 is crucial for protecting against future infectious pathogens. In this study, we conducted a comprehensive chronological analysis by examining mutation prevalence from source countries VOCs: United Kingdom, India, Brazil, South Africa, plus two countries: States, Russia, utilizing genomic sequences GISAID. Our methodological approach involved large-scale sequence alignment using MAFFT,...