binned metagenome: spire_mag_02750136
Bacteroides uniformis
ENA first public
2024-09-20
INSDC center name
EMBL Heidelberg
INSDC status
public
Submitter Id
spire_mag_02750136
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
megahit 1.2.9
binning parameters
default
binning software
metabat 2.12.1
broad-scale environmental context
human digestive system
broker name
EBI-EMG
collection date
2018
completeness score
75.45
completeness software
checkm2 0.1.3
contamination score
7.15
environmental medium
stool
geographic location (country and/or sea)
Norway
geographic location (latitude)
69.68000000
geographic location (longitude)
18.98000000
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
local environmental context
human gut
metagenomic source
human gut metagenome
project name
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.
sample derived from
SAMEA7082403
sample name
spire_mag_02750136
scientific_name
Bacteroides uniformis
sequencing method
NextSeq 550
taxonomic identity marker
multi-marker approach