2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21074315
SRA accession
spire_mag_02751916
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
megahit 1.2.9
assembly software
default
binning parameters
metabat 2.12.1
binning software
human digestive system
broad-scale environmental context
EBI-EMG
broker name
2018
collection date
86.61
%
completeness score
checkm2 0.1.3
completeness software
2.59
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run ERR4467748 of study ERP119291.
description
stool
environmental medium
Norway
geographic location (country and/or sea)
69.68000000
DD
geographic location (latitude)
18.98000000
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
human gut metagenome
isolation_source
human gut
local environmental context
human gut metagenome
metagenomic source
Bacteroides uniformis
organism
Irritable bowel syndrome (IBS) is a common disorder of the lower gastrointestinal tract. The pathophysiology is far from settled, and components of micro-inflammation, neuro-immunological signaling and gut microbial dysbiosis are frequently emphasized as causative factors. Here, we present fecal metagenomic sequencing data from our earlier published randomized double-blind placebo-controlled clinical trial on fecal microbiota transplantation (FMT) for IBS – the REFIT trial. Only samples from participants who received active fecal microbiota transplants were included in the present data set 14 participants with effect of FMT (Effect) and 8 without (No effect) were chosen. Samples were collected at baseline before FMT, after 6 and 12 months. Also samples from the transplants (Donor) given to the participants were analyzed. In total 66 recipient samples and 17 donor samples were subjected to deep metagenomic sequencing (Illumina NextSeq550), generating on average 27.3 *106 reads. After in silico quality control, assembly and annotation, we generated taxonomic and functional profiles. Alpha diversity measures showed a significantly increased diversity and evenness in the IBS groups compared to the donors (P=0.0026 and 0.0046 for Effect and No effect groups by Simpson index, respectively). Taxonomic profiles showed higher relative abundance of phylum Firmicutes, and lower relative abundance of phylum Bacteroidetes, compared to donors at baseline. This profile was shifted towards the donor profile following FMT, and we derived, from the Effect group, a list of 170 species, differentially abundant, that were most prominent in this shift. Analysis of imputed growth rates showed that the resulting growth pattern was a conglomerate of donor and recipient activity. Thirty-four functional subclasses showed distinct differences between baseline samples and donors, most of which were shifted towards a donor-like profile after FMT. Functional systems involved in short chain fatty acid synthesis were detected, and also an increase in systems synthesizing growth factors like Menaquinone and scavenging metal ions like Zink and Manganese. We conclude that FMT induces long-term changes in gut microbiota, and these changes mirror the clinical effect of the treatment.
project name
SAMEA7082433
sample derived from
Bacteroides uniformis
scientific_name
NextSeq 550
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_02751916
title