Gut microbiome in H. pylori infection vs controls, China
Shotgun metagenomics of fecal DNA from 132 stool samples (108 H. pylori-infected, 24 healthy controls) in a cross-sectional study of the digestive tract microbiome in China. machine-written summary
132 samples · 132 runs · CN · Age unknown · 2025 · 6.82 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 396 sample values (country, health condition, health condition detail) |
| ✓ Abstract / description | 264 sample values (location site, subject id) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 132 | 100% | 132 | |||
| health_condition | 132 | 100% | 132 | |||
| subject_id | 132 | 100% | 132 | |||
| detailed_location | 132 | 100% | ||||
| health_condition_detail | 132 | 100% | 132 | |||
| location_site | 132 | 100% | 132 |
- The Systemic Impact of Helicobacter pylori Infection on the Microbiome of Whole Digestive Tract Based on Mucosal, Gastric Juice, and Fecal Specimens. 2025 PMID 40426336 own_data
Archive description
<![CDATA[Background: Recent studies have found that in addition to directly impacting the gastric microbiome, Helicobacter pylori (H. pylori) infection may cause intestinal microbial dysbiosis. However, most existing studies on the influence of H. pylori infection on the intestinal microbiome used fecal specimens with inconsistent conclusions. Few studies have collected mucosal specimens to assess the impact of H. pylori infection on the microbiome of the whole digestive tract.</p><p>Materials and Methods: This single-center cross-sectional study collected mucosa of the esophagus, stomach, small intestine, and colon, as well as gastric juice and feces from 120 participants of the H. pylori-infected group (HIG) and 30 of the healthy control group (HCG). 16S rRNA sequencing was applied to analyze the bacterial composition and functional pathways, and metagenomics was adopted to assess the composition of viruses, eukaryotes, and archaea in the feces, as well as the antibiotic resistance gene (ARG) and virulence factors of bacteria (VF).</p><p>Results: Compared with the HCG, the alpha and beta diversity of bacteria in the mucosa of the whole digestive tract and the gastric juice of the HIG showed significant changes, with increased microbial dysbiosis index and significantly different compositions at the phylum and genus levels. Functional pathway analysis revealed that the metabolic characteristics of the flora changed in the HIG, with site-specific differences. Fecal specimens demonstrated no significant differences in the above indicators between the two groups. In addition, feces based metagenomic analysis revealed that only eukaryotes had higher diversity in the HIG, whereas viruses and archaea showed no significant changes; the Shannon index of ARG increased; and VF showed no significant change.</p><p>Conclusions: This study revealed that H. pylori infection significantly influenced the diversity and composition of bacteria in different parts of the digestive tract, the gastric juice, and the metabolic functional pathway. Moreover, feces-based studies on the intestinal microbiome had limitations.]]>
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by curator_audit with confidence 0.60. Assay shotgun_dna.
- host runs.scientific_name · “human gut metagenome (132)”
- host runs.sample_titles_examples · “HCG_STOOL | HIG_STOOL”
- body site runs.scientific_name · “human gut metagenome (132)”
- body site runs.sample_titles_examples · “HCG_STOOL | HIG_STOOL”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN45102808 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Beijing |
| SAMN45102808 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample.attribute:TITLE | TITLE: HIG_STOOL |
| SAMN45102808 | health_condition_detail | Helicobacter pylori infection (H. pylori-infected group, HIG) | R1 | 0.85 | biosample.attribute:TITLE | TITLE: HIG_STOOL |
| SAMN45102808 | location_site | single-center | R4 | 0.50 | paper.abstract | single-center cross-sectional study collected mucosa |
| SAMN45102808 | subject_id | SAMN45102808 | R4 | 0.65 | design.one_sample_per_subject:abstract | This single-center cross-sectional study collected mucosa of the esophagus, stomach, small intestine, and colon, as |
Sequencing
132 runs over 132 samples · mean 6.94 Gbp per run (median 6.82 Gbp, total 916.02 Gbp; 132 runs with a base count) · layout PAIRED 132 · platform ILLUMINA 132 · models Illumina NovaSeq X Plus (132) · 100% of runs with a Sandpiper profile · first public 2025-04-03 – 2025-04-27
Authors (0)
No author record.
Downloads
PRJNA1192252.csv.gz (4.3 KB) · parquet (75.4 KB) — all 132 samples, every field with route and confidence · PRJNA1192252_determinations.csv.gz (5.2 KB) — 660 evidence rows