GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purposes are to increase the reusability and accessibility of human gut metagenomic data, and enable cross-project and phenotype comparisons. To achieve these goals, we pe...
The genome sequences of many species of the human gut microbiome remain unknown, largely owing to challenges in cultivating microorganisms under laboratory conditions. Here we address this problem by reconstructing 60,664 draft prokaryotic genomes from 3
we performed sequence similarity network (SSN) analysis40of all GH18 family members contained in the CAZy database (more than 53 thousand sequences)41. We found that the GH18 family of ENGases (EC 3.2.1.96) from the prevalent human gut bacteriumB. thetaiotaomicron...
Universal biochemical reaction database We start from AGORA 1.0311, which comprises manually curated metabolic models of 818 species of the human gut microbiome. In order to reduce the computation cost, we modeled the overall microbial community as a mixed-bag network strategy, where reactions from ...
Towards this goal, we leveraged the Unified Human Gastrointestinal Genome (UHGG) database of 286,997 genomes of Bacteria and Archaea from the gut microbiome43, which represents 4,644 prokaryotic species (Fig. 2). First, we extracted 1,846,441 CRISPR spacers from the UHGG genomes, and looked...
//genome.wustl.edu/pub/organism/Microbes/Human_Gut_Microbiome/), and sequenced by the MetaHIT project (17 genomes, version September 2009,http://www.sanger.ac.uk/pathogens/metahit/). The other gut metagenome data used in this project include: (1) human gut metagenomic data sequenced from ...
human gut microbiota. In this study, we propose a systematic workflow including three modules and the use of machine learning-based classifiers to collect, expand, and mine the QS-related entries. Furthermore, we develop the Quorum Sensing of Human Gut Microbes (QSHGM) database (http://www....
To address this gap, we present GutMetaNet ( https://gutmetanet.deepomics.org/ ), a first-of-its-kind database integrating extensive human gut microbiome data with comprehensive HGT and FR analyses. GutMetaNet contains 21567 human gut metagenome samples with whole-genome shotgun sequencing data...
The raw data of 16S rRNA gene sequencing were analyzed using QIIME2 platform (v2020.2). In briefly, DADA2 plugin was used to filter the sequencing reads and to construct ASVs feature table. The taxonomy information of ASVs were assigned against the Silva Database (https://www.arb-silva.de...
(Supplementary Fig.3b). These results underscore the contribution of the CGR to the existing database of gut bacterial whole genomes. Improvement in metagenomic and SNP analyses The existing reference genomes for metagenomic sequence mapping are far from saturated. For example, the genomes or draft ...