A5076136013- Gut microbiota and health
- Genomics and Phylogenetic Studies
- X-ray Diffraction in Crystallography
- Metabolomics and Mass Spectrometry Studies
- Crystallization and Solubility Studies
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Microbial Community Ecology and Physiology
- Diet and metabolism studies
- Probiotics and Fermented Foods
- RNA Research and Splicing
- Forensic Entomology and Diptera Studies
- Scientific Computing and Data Management
- Clostridium difficile and Clostridium perfringens research
- Machine Learning in Bioinformatics
- Bacteriophages and microbial interactions
- Oral microbiology and periodontitis research
- Plant tissue culture and regeneration
- Bioinformatics and Genomic Networks
- Molecular Biology Techniques and Applications
- Seed Germination and Physiology
- Aquaculture disease management and microbiota
- Tea Polyphenols and Effects
- Paleopathology and ancient diseases
- Inflammatory Bowel Disease
Nanchang University
2018-2025
State Key Laboratory of Food Science and Technology
2018-2025
Stomatology Hospital
2022-2025
Shanghai Changzheng Hospital
2025
Southern Medical University Shenzhen Hospital
2022-2025
United States Department of the Navy
2025
South China Agricultural University
2014-2024
Shanghai University
2024
University of California, San Diego
2015-2023
Zhujiang Hospital
2022-2023
Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, the data contains many zeros. Although we are typically interested in comparing relative abundance taxa ecosystem two or more groups, can only measure taxon specimens obtained ecosystems. Because comparison specimen is not equivalent ecosystems, this presents a special challenge. Second, because (as...
High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding complex microbial communities, but the inherent noise in PCR and DNA limits differentiation closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain...
Abstract Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those traditional peoples. Here we examine the relationship between lifeways and microbiota through taxonomic functional potential characterization faecal samples hunter-gatherer agriculturalist communities in Peru an community US. We find addition to metabolic differences urban lifestyles, hunter-gatherers form a distinct sub-group among As observed previous studies, Treponema...
The move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a de novo tree the short sequences) can provide incorrect results in human gut metagenomic studies and show phylogenetic placement new sequences SEPP resolves this problem yielding other benefits over existing methods.
Abstract Background Alteration of the gut microbiota may contribute to development inflammatory bowel disease (IBD). Epigallocatechin-3-gallate (EGCG), a major bioactive constituent green tea, is known be beneficial in IBD alleviation. However, it unclear whether exerts an effect when EGCG attenuates IBD. Results We first explored oral or rectal delivery on DSS-induced murine colitis. Our results revealed that anti-inflammatory and colonic barrier integrity were enhanced by oral, but not...
Immediate freezing at -20°C or below has been considered the gold standard for microbiome preservation, yet this approach is not feasible many field studies, ranging from anthropology to wildlife conservation. Here we tested five methods preserving human and dog fecal specimens periods of up 8 weeks, including such types variation as freeze-thaw cycles high temperature fluctuations often encountered under conditions. We found that three methods-95% ethanol, FTA cards, OMNIgene Gut kit-can...
Vertebrate corpse decomposition provides an important stage in nutrient cycling most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing assembly during of mouse human corpses on different substrates. We find a suite bacterial fungal groups that contribute nitrogen reproducible network...
Abstract Antibiotic-induced microbiome depletion (AIMD) has been used frequently to study the role of gut in pathological conditions. However, unlike germ-free mice, effects AIMD on host metabolism remain incompletely understood. Here we show elucidate its homeostasis, luminal signaling, and metabolism. We demonstrate that AIMD, which decreases Firmicutes Bacteroidetes species, baseline serum glucose levels, reduces surge a tolerance test, improves insulin sensitivity without altering...
Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution individual genes. Here we build a reference phylogeny 10,575 evenly-sampled bacterial and archaeal genomes, based on comprehensive set 381 markers, using multiple strategies. Our trees indicate remarkably closer proximity between Archaea Bacteria than previous estimates that were limited to fewer "core" genes, such as ribosomal proteins. The...
Abstract The presence of cirrhosis in nonalcoholic-fatty-liver-disease (NAFLD) is the most important predictor liver-related mortality. Limited data exist concerning diagnostic accuracy gut-microbiome-derived signatures for detecting NAFLD-cirrhosis. Here we report 16S gut-microbiome compositions 203 uniquely well-characterized participants from a prospective twin and family cohort, including 98 probands encompassing entire spectrum NAFLD 105 their first-degree relatives, assessed by...
In the present report, we show that human fecal microbiota contains promising and universal biomarkers for noninvasive evaluation of inflammatory bowel disease severity IFX treatment efficacy, emphasizing potential ability to mine gut as a modality stratify IBD patients apply personalized therapy optimal outcomes.
Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated performance recently released state-of-the-art open-source software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST USEARCH) QIIME, hierarchical methods mothur, USEARCH's most recent algorithm,...
Abstract Microbial breakdown of organic matter is one the most important processes on Earth, yet controls decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during despite selection effects location, climate season. We generated metagenome-assembled genome library from cadaver-associated soils integrated it with metabolomics data to identify links between...
Ocean-derived, airborne microbes play important roles in Earth's climate system and human health, yet little is known about factors controlling their transfer from the ocean to atmosphere. Here, we study microbiomes of isolated sea spray aerosol (SSA) collected a unique ocean-atmosphere facility demonstrate taxon-specific aerosolization bacteria viruses. These trends are conserved within taxonomic orders classes, temporal variation similarly shared by related taxa. We observe enhanced into...
Abstract Although increasing atmospheric nitrous oxide (N 2 O) has been linked to nitrogen loading, predicting emissions remains difficult, in part due challenges disentangling diverse N O production pathways. As coastal ecosystems are especially impacted by elevated nitrogen, we investigated controls on mechanisms intertidal sediments using novel isotopic approaches and microsensors flow-through incubations. Here show that during incubations with nitrate, increased fluxes not mediated...