2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21061381
SRA accession
spire_mag_01281653
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
missing: third party data
collection date
69.84
%
completeness score
checkm2 0.1.3
completeness software
3.27
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run ERR1999772 of study ERP019513.
description
stool
environmental medium
not provided
geographic location (country and/or sea)
missing: third party data
DD
geographic location (latitude)
missing: third party data
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
human gut metagenome
isolation_source
human gut
local environmental context
human gut metagenome
metagenomic source
Phocaeicola vulgatus
organism
Background: Bread is consumed by billions of people daily but evidence regarding the effect of different types of bread on clinical parameters is contradicting. In addition, the effect of bread consumption on the microbiome, an important effector of metabolic health, has not been extensively studied. Methods and Findings: We recruited 20 healthy human subjects and performed a 2x2 randomized crossover trial with baseline measurements of two one-week-long dietary interventions. In both interventions subjects consumed a single type of bread and refrained from consuming other wheat products. Consumed bread included industrial white bread made from refined wheat in one intervention, and sourdough leavened bread made with traditional methods from whole-grain wheat in the other. We found no significant differences in the effects of the different types of breads on multiple clinical parameters. In contrast, a one-week long dietary intervention of bread consumption, regardless of its type, resulted in numerous statistically significant changes, including an increase in LDH levels and a reduction of cholesterol, liver enzymes, creatinine, CRP, magnesium, and iron levels. Notably, despite its marked clinical phenotypic effect, bread consumption did not significantly alter the gut microbiome species composition, but it did induce several statistically significant and consistent changes in the abundance of genes from distinct microbial metabolic pathways. Metabolic pathways that increased following short-term bread consumption have elevated abundance in long-term bread consumers, suggesting that the effect of a short-term dietary change on the microbiome may persist in individuals that maintain the dietary change. Finally, using a statistically rigorous framework we found that our study subjects exhibited high interpersonal variability in their postprandial glycemic responses to the different bread types. Conclusions: We detected no difference between wholegrain sourdough and industrial white breads used in this study in their effects on multiple clinical parameters. Conversely, we showed that even a week long consumption of bread, irrespective of its type, induces changes to multiple clinical variables and risk factors. Our study shows that the microbiome species composition is resilient even to significant dietary interventions, but suggests that changes in microbial metabolic pathways induced by short-term interventions are retained in long-term bread consumers. The personalized postprandial glycemic responses to different bread types that we detected across subjects may partly explain the lack of differential effects between bread types and the contradicting evidence regarding the effects of different bread types in previous studies.
project name
SAMEA104112443
sample derived from
Phocaeicola vulgatus
scientific_name
NextSeq 500
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_01281653
title