Bacteroides uniformis
ENA first public
2024-09-21
INSDC center name
EMBL Heidelberg
INSDC status
public
Submitter Id
spire_mag_01637776
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
missing: third party data
completeness score
79.27
completeness software
checkm2 0.1.3
contamination score
0.83
environmental medium
stool
geographic location (country and/or sea)
not provided
geographic location (latitude)
missing: third party data
geographic location (longitude)
missing: third party data
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
local environmental context
human gut
metagenomic source
human gut metagenome
project name
Abstract (1):Empiric probiotics are commonly consumed in healthy individuals as means of life quality improvement and disease prevention. However, evidence of probiotic gut mucosal colonization efficacy remains sparse and controversial. We metagenomically characterized the murine and human mucosal-associated gastrointestinal microbiome and found it to only partially correlate with stool microbiome. A sequential invasive multi-omics measurement at baseline and during consumption of an 11-strain probiotic combination or placebo, demonstrated that probiotics remain viable upon gastrointestinal passage. In colonized, but not germ-free mice, probiotics encountered a marked mucosal colonization resistance. In contrast, humans featured a person-, region- and microbial-specific mucosal colonization patterns, hallmarked by differential baseline host and microbiome features, but indistinguishable by probiotics presence in stool. Consequently, probiotics induced a transient, highly-individualized impact on mucosal community structure and gut transcriptome. Collectively, empiric probiotics supplementation may be limited in universally and persistently impacting the gut mucosa, meriting development of new personalized probiotic approaches.Abstract (2):Probiotics are widely prescribed for prevention of antibiotics-associated dysbiosis and related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut mucosal host-microbiome niche remains elusive. We invasively examined the effects of multi-strain probiotics or autologous fecal microbiome transplantation (aFMT) on post-antibiotic reconstitution of the murine and human mucosal microbiome niche. Contrary to homeostasis, antibiotic perturbation enhanced probiotics colonization in the human mucosa, but only mildly improved colonization in mice. Compared to spontaneous recovery, probiotics induced a markedly delayed and persistently-incomplete indigenous stool/mucosal microbiome reconstitution and gut transcriptome recovery to steady-state configuration, while aFMT induced a rapid and near-complete recovery within days of administration. In-vitro, Lactobacillus-secreted soluble factors contributed to probiotics-induced microbiome inhibition. Collectively, potential post-antibiotic probiotic benefits may be offset by a compromised microbiome and host recovery, highlighting a need of developing aFMT or personalized probiotic approaches achieving mucosal protection, without compromising microbiome recolonization in the antibiotics-perturbed host.
sample derived from
SAMEA4845775
sample name
spire_mag_01637776
scientific_name
Bacteroides uniformis
sequencing method
NextSeq 500
taxonomic identity marker
multi-marker approach