A5082397869- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Diet and metabolism studies
- Probiotics and Fermented Foods
- Methane Hydrates and Related Phenomena
- Sinusitis and nasal conditions
- Environmental DNA in Biodiversity Studies
- Salivary Gland Tumors Diagnosis and Treatment
- Oropharyngeal Anatomy and Pathologies
- Oral microbiology and periodontitis research
- Dietary Effects on Health
- Tryptophan and brain disorders
- Circadian rhythm and melatonin
- DNA and Biological Computing
- Legume Nitrogen Fixing Symbiosis
- Photoreceptor and optogenetics research
- Microfluidic and Bio-sensing Technologies
- Atherosclerosis and Cardiovascular Diseases
- Indoor Air Quality and Microbial Exposure
- Epigenetics and DNA Methylation
- Marine Biology and Ecology Research
- Nicotinic Acetylcholine Receptors Study
- DNA and Nucleic Acid Chemistry
- Socioeconomic Development in Asia
University of Copenhagen
2019-2025
BGI Group (China)
2017-2025
BGI Research
2017-2025
China National GeneBank
2017-2024
China Pharmaceutical University
2024
State Key Laboratory of Natural Medicine
2024
Abstract Background More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation performance new high-throughput platform BGISEQ-500 for and compare its with that 2 Illumina platforms. Findings Using fecal samples from 20 healthy individuals, evaluated intra-platform reproducibility setup comprising 8 library replicates replicates. Cross-platform consistency was by...
The oral cavity of each person is home to hundreds bacterial species. While taxa for diseases have been studied using culture-based characterization as well amplicon sequencing, metagenomic and genomic information remains scarce compared the fecal microbiome. Here, shotgun data 3346 samples together with 808 published samples, we obtain 56,213 metagenome-assembled genomes (MAGs), more than 64% 3589 species-level genome bins (SGBs) contain no publicly available genomes. resulting collection...
Abstract Intermittent fasting (IF) is a promising paradigm for weight loss which has been shown to modulate the gut microbiota based on 16S rRNA gene amplicon sequencing. Here, 72 Chinese volunteers with wide range of body mass index (BMI) participated in three-week IF program during an average 3.67 kg accompanied improved clinical parameters was observed irrespective initial anthropometric and status. Fecal samples were collected before after intervention subjected shotgun metagenomic De...
Abstract The nasal cavity harbors diverse microbiota that contributes to human health and respiratory diseases. However, whether what extent the host genome shapes microbiome remains largely unknown. Here, by dissecting metagenome data from 1401 healthy individuals, we demonstrated top three genetic principal components strongly correlated with diversity composition. association analyses identified 63 genome-wide significant loci affecting microbial taxa functions, of which 2 reached...
Abstract Background Shotgun metagenomic sequencing has improved our understanding of the human gut microbiota. Various DNA extraction methods have been compared to find protocols that robustly and most accurately reflect original microbial community structures. However, these recommendations can be further refined by considering time cost demands in dealing with samples from very large cohorts. Additionally, fungal performance so far little investigated. Results We 6 protocols, MagPure Fast...
The number of large-scale studies on the gut microbiota in human cohorts is rapidly increasing. However, few and expensive options for storage fecal samples at room temperature have been an obstacle metagenomic development clinical/commercial personal sequencing. In this study, we systematically tested a novel N-octylpyridinium bromide-based sample preservation method compared it with other currently used methods. We found that enabled bacterial composition transported stored up to least 14...
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...
Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in Mariana Trench, Yap and Philippine Basin for Trench Environment Ecology Research (MEER) project. Metagenomic 16S rRNA gene amplicon sequencing generated 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike reported environments, neutral drift played a minimal role,...
Circadian rhythm disruption (CRD) has been associated with inflammation and immune disorders, but its role in SLE progression is unclear. We aimed to investigate the impact of circadian rhythms on function their contribution lupus nephritis (LN). This study retrospectively analysed clinical characteristics transcriptional profiles 373 samples using bioinformatics machine-learning methods. A flare risk score (FRS) was established predict overall disease for patients lupus. Mendelian...
Ototoxicity and nephrotoxicity are the most prevalent side effects of aminoglycoside antibiotics (gentamicin, amikacin, neomycin) platinum anti-tumor drugs (cisplatin, carboplatin). The inner ear kidney share similarities in drug deposition toxicity, but underlying pathophysiological mechanisms remain unclear. Investigating shared metabolic alterations these distinct organs will provide valuable insights for clinical therapy. A strong correlation has been identified between spatiotemporal...
High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing the mouse gut metagenome limits numbers identified genes in catalogs. We therefore established an expanded catalog (EMGC) containing >5.8 million by integrating 88 newly sequenced samples, 86 gut-related bacterial genomes, 3 EMGC increases number nonredundant more than 1 compared so-far most extensive catalog. More 60% were assigned...
Background: Exposure to environmental pollutants, including benzo[a]pyrene (BaP), has been implicated in allergic diseases and intestinal microbiota homeostasis, but the environment–microbiota–immunity triangular relationship what extent BaP-induced remodeling of gut contributes inflammation remain be established. Objectives: We investigated impact BaP on examined between this effect dysbiosis. explored potential ability bacteria degrade alleviate cytotoxicity as a detoxification strategy...
Metabarcoding is a widely used method for fast characterization of microbial communities in complex environmental samples. However, the selction sequencing platform can have noticeable effect on estimated community composition. Here, we evaluated metabarcoding performance DNBSEQ-G400 sequencer developed by MGI Tech using 16S and internal transcribed spacer (ITS) markers to investigate bacterial fungal mock communities, as well ITS2 marker 1144 soil samples, with additional technical...
Abstract Background Metagenomic sequencing protocols are increasingly employed in research on deep-sea microbial communities for the purpose of examining their taxonomic makeup and metabolic capabilities. Despite development testing various experimental techniques, commercial kits, analytical software mock stool samples, a noticeable gap remains systematic evaluation entire procedure across range diverse habitats. Moreover, growing scale studies raises need an efficient resource-friendly...
Sediment plays a pivotal role in deep-sea ecosystems by providing habitats for diverse range of microorganisms and facilitates the cycling processes carbon, sulfur nitrogen. Beyond normal seafloor (NS), distinctive geographical features such as cold seeps (CS) hydrothermal vent (HV) are recognized life oases harboring highly microbial communities. A global atlas can reveal notable association between geological colonization. However, comprehensive understanding systematic comparison...
The MGIEasy UDB Universal Library Prep Set(1000022803,MGI Tech) is specifically designed for creating WGS libraries the MGI high-throughput sequencing platform series. This library prep set optimized to convert 1-1000ng of fragmented DNA into a customized library. Unique Dual barcode supported double checked split method ensuring Homogeneity and accuracy.
This method presents an optimized protocol of SDS-based DNA extraction for sediment samples. The extracted can be used metagenomic research.
This method presents an optimized protocol for the automated extraction of sediment samples and filter membranes using magnetic beads. DNA was extracted purified MGIEasy Stool Microbiome Extraction Kit (940-000122-00, MGI Tech) on a compatible automation system (MGISP-NE384, .
The MGIEasy FS DNA Library Prep Set(1000006987,MGI Tech) is specifically designed for WGS libraries construction MGI high-throughput sequencing platform series. This library prep set optimized to convert 5-400 ng genomic into a customized library. uses advanced Adapter Ligation technology and High-fidelity PCR Enzymes significantly increase yield conversion rate. applicable samples from all common animals, plants, fungus, bacteria, etc., including human, mice, rice, Arabidopsis, yeast, E....
The MGIEasy Fast FS Library Prep Set(1000006987, MGI Tech) is designed to convert genomic DNA (gDNA) into a special library for DNBSEQTMsequencers and combines the fragmentation, end-repair add A one step, simplify preparation process significantly shorten duration of preparation, reducing prep time in 2 hours. This set provides be optimized low inputs, suitable microbial sequencing, metagenomics WGS.
Dietary constituents modulate development of obesity and type 2 diabetes. The metabolic impact from different food sources in western diets (WD) on is not fully elucidated. This study aims to identify dietary that differentially affect the processes involved.
ABSTRACT The oral cavity of each person is home for hundreds bacterial species. While taxa diseases have been well studied using culture-based as amplicon sequencing methods, metagenomic and genomic information remain scarce compared to the fecal microbiome. Here we provide shotgun data 3346 metagenomics samples, together with 808 published assemble 56,213 metagenome-assembled genomes (MAGs). 64% 3,589 species-level genome bins contained no publicly available genomes, others only a handful....
Abstract Intermittent fasting is a promising paradigm for weight loss which has been shown to modulate the gut microbiota in couple of populations, yet limited information at species level available. Here, 72 Chinese volunteers with wide range BMIs participated three-week IF program during an average 3.67 kg body accompanied improved clinical parameters was observed irrespective initial anthropometric and status. Fecal samples were collected before after intervention subjected shotgun...
Abstract High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing mouse gut metagenomes limits the size numbers identified genes in catalogs. We therefore established an expanded catalog (EMGC) containing >5.8 million by integrating 88 newly sequenced samples, 86 mouse-gut-related bacterial genomes 3 EMGC increases number on non-redundant more than one compared so far most extensive...