Metagenome-assembled genome: ERR346580_bin.2_metawrap_v1.3_MAG
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR346580 of study ERP003648.
ENA-FIRST-PUBLIC
2022-12-15
ENA-LAST-UPDATE
2022-12-15
External Id
SAMEA112227831
INSDC center alias
EMG
INSDC center name
EMG
INSDC first public
2022-12-15T16:21:23Z
INSDC last update
2022-12-15T16:21:23Z
INSDC status
public
Submitter Id
ERR346580_bin.2_metawrap_v1.3_MAG
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaSPAdes v3.15.3
binning parameters
MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning software
metawrap v1.3
broad-scale environmental context
mouse digestive system
broker name
EMG broker account, EMBL-EBI
collection date
2010-01-01
completeness score
79.28
completeness software
CheckM
contamination score
2.65
environmental medium
feces
geographic location (country and/or sea)
USA
geographic location (latitude)
37.09024
geographic location (longitude)
-95.71289
investigation type
metagenome-assembled genome
isolation_source
mouse gut metagenome
local environmental context
digestive tube
metagenomic source
mouse gut metagenome
project name
The microbial diversity, interpersonal variation and dynamism of the human gut microbiota make the task of identifying the factors that define community configurations, both structural and functional, extremely challenging. Bacterial viruses (phage) are the most abundant biological group on Earth and are more genetically diverse than their bacterial prey/hosts. To characterize their role as agents shaping gut community structure, adult germ-free mice were colonized with a consortium of 15 sequenced human bacterial symbionts, 13 of which harbored one or more predicted prophage in their genomes. One member, Bacteroides cellulosilyticus WH2, was represented by a library of isogenic transposon mutants covering 90% of its genes. Once assembled, the community was subjected to a staged phage attack with a pool of live or heat-killed virus-like particles (VLPs) purified from the fecal microbiota of five healthy humans. Shotgun sequencing of DNA from the input pooled human VLP preparation plus shotgun sequencing of gut microbiota samples, and purified fecal VLPs, from the gnotobiotic mice revealed a reproducible non-simultaneous pattern of attack extending over a 25 day period and involving five phage, none described previously. This system allowed us to (i) correlate increases in abundances of specific phage present in the input VLP preparation with reductions in the representation of particular bacterial hosts, (ii) provide evidence that phage resistance occurred because of ecological or epigenetic factors, (ii) track the origin of each of the five phages among the five human donors plus the extent of their genome variation between and within recipient mice, and (iv) establish the dramatic in vivo fitness advantage that a locus within a B. cellulosilyticus prophage confers upon its host bacterium. Together, these results provide a defined community-wide view of phage-bacterial host dynamics in the gut ecosystem.
sample derived from
SAMEA2148723
sample name
ERR346580_bin.2_metawrap_v1.3_MAG
sequencing method
Illumina HiSeq 1000
taxonomic classification
The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides ovatus
taxonomic identity marker
multi-marker approach