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PRJEB35769 ERP118881

Fermented milk probiotic trial in healthy adults, Germany

Gut microbiome response to a fermented milk product in healthy subjects

107 gut metagenome samples from healthy adult subjects in Germany, from a randomized, double-blind, controlled intervention trial testing daily doses of a multi-strain fermented milk (probiotic) product over 4 weeks. machine-written summary

107 samples · 107 runs · DE · Adult · 2020 · 8.86 Gbp / sample

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Sources
✓Sequence archive 535○Abstract / description✓Full text 428○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive535 sample values (collection date, country, latitude, location region, longitude)
○ Abstract / descriptionread; no usable statement
✓ Full text428 sample values (health condition, health condition detail, location locality, location site) · PMC7524715, PMC9348039
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention — arms not resolved

Antibiotic given as the study intervention (incl. eradication therapy Probiotic (live microorganisms; single strain or mixture) design randomized_controlled_trial · population healthy_control · Multi-strain fermented milk (L. paracasei CNCM I-1518/I-3689, L. rhamnosus CNCM I-3690 + yogurt strains) vs control, with H. pylori eradication

“daily ingestion for 4 weeks of two doses” — abstract:32994487 (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 sampling locations · 1 country
Age
adult107
Condition
healthy_control107
Country
DE107
Body site
primary107
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)all projects, 1–3 Gbp: 124,983 samples (22 %)all projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 71 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 36 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 8.86 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal — not resolved

Schedule stated by the source: “Stool collected at 4 visits: V2 (randomization, day 0), V3 (day 14), V4 (day 28), V5 (end-of-study, day 56)” (time origin: intervention_start); stated follow-up 56 d.

How longitudinal and relatedness information is derived

Community composition
Prevotella 8.1%Faecalibacterium 8.1%Roseburia 7.3%Blautia_A 6.6%Bacteroides 6.3%Phocaeicola 6.2%Bifidobacterium 3.6%Ruminococcoides 3.4%Anaerostipes 2.1%Alistipes 2.0%Gemmiger 2.0%Lachnospira 2.0%not assigned to a genus 5.1%other genera 37.3%

Genera, mean relative abundance over 97 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category107 100%
country107 100%107
health_condition107 100%107
subject_id0 0%
collection_date107 100%107
detailed_location107 100%
health_condition_detail107 100%107
latitude107 100%107
location_locality107 100%107
location_region107 100%107
location_site107 100%107
longitude107 100%107
Papers (2)
  • Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial. 2020 PMID 32994487 PMC7524715 own_data
  • Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains. 2022 PMID 35916669 PMC9348039 unsure
Details
Archive description

Although many clinical studies have been conducted to evaluate the effect of probiotics, there are limited studies that assessed the dose-response effects of probiotics on microbiota and host. In this context, a novel multi-strain fermented dairy product was developed (Test product), combining yogurt strains (Streptococcus thermophilus and Lactobacillus bulgaricus) and three candidate probiotic strains, Lactobacillus paracasei subsp. paracasei CNCM I-1518 and CNCM I-3689 and Lactobacillus rhamnosus CNCM I-3690 selected for their effects on gut barrier function and/or gut microbiota or immunity in various models. In the present study, we conducted a 4-week intervention, randomised, double-blind, controlled clinical trial to assess the tolerance of daily ingestion of one or three doses of the Test product in 96 healthy adults. We explored the structural and functional response of gut microbiota to intervention, and following discontinuation. Using shotgun metagenomic, we explored the KEGG orthologs that were carried by 3 probiotic candidate strains and their co-variation interactions with gut microbial species through metabolic sharing.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.

  • host run.scientific_name · “human gut metagenome”
  • body site study.title · “Gut microbiome response to a fermented milk”
  • life stage study.description · “96 healthy adults”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMEA6416059collection_date2010-05-08R10.90biosample.attribute:collection_date2010-05-08
SAMEA6416059countryDER10.90sample.attr.geographic_location_country_and_or_seaGermany
SAMEA6416059health_conditionhealthy_controlR30.70paper.fulltext.abstract96 healthy adults
SAMEA6416059health_condition_detailhealthy adultsR30.70paper.fulltext.abstract96 healthy adults
SAMEA6416059latitude48.1300R10.90biosample.attribute:geographic_location_latitude+geographic_location_longitude48,13 11,57
SAMEA6416059location_localityMunichR30.70paper.fulltext.methodsclinical unit (Harrison Clinical Research, Munich, Germany)
SAMEA6416059location_regionBavariaR10.60biosample.attribute:geographic_location_latitude+geographic_location_longitude48,13 11,57
SAMEA6416059location_siteHarrison Clinical ResearchR30.70paper.fulltext.methodsHarrison Clinical Research, Munich, Germany
SAMEA6416059longitude11.5700R10.90biosample.attribute:geographic_location_latitude+geographic_location_longitude48,13 11,57
Sequencing

107 runs over 107 samples · mean 8.95 Gbp per run (median 8.86 Gbp, total 958.08 Gbp; 107 runs with a base count) · layout PAIRED 107 · platform ILLUMINA 107 · models NextSeq 500 (107) · 91% of runs with a Sandpiper profile · first public 2020-09-27

Authors (17)

Alvarez AS first · Tap J · Chambaud I · Cools-Portier S · Quinquis L · Bourlioux P · Marteau P · Guillemard E · Schrezenmeir J · Derrien M last · FitzGerald J first · Patel S · Eckenberger J · Veiga P · Schäfer F · Walter J · Claesson MJ

Downloads

PRJEB35769.csv.gz (3.7 KB) · parquet (74.8 KB) — all 107 samples, every field with route and confidence · PRJEB35769_determinations.csv.gz (6.0 KB) — 963 evidence rows

Samples (107 · every field this project has values for · hover a cell for its source)
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