Gut Metagenome as a Potential Diagnostic and Predictive Biomarker in Slow Transit Constipation

Study information

Reviewed Marked as Reviewed by Svetlana up on 2025-4-3

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

35211481

DOI Digital object identifier for electronic documents.

10.3389/fmed.2021.777961

URI

Authors

Tian H, Ye C, Yang B, Cui J, Zheng Z, Wu C, Zhou S, Lv X, Qin N, Qin H, Li N, Chen Q

Journal

Frontiers in medicine

Year

2021

Keywords:

biomarker, diagnostic, gut microbiome, metagenomic analysis, pathogenesis, slow transit constipation

Slow transit constipation (STC) is one of the most frequent gastrointestinal diagnoses. In this study, we conducted a quantitative metagenomics study in 118 Chinese individuals. These participants were divided into the discovery cohort of 50 patients with STC and 40 healthy controls as well as a validation cohort of 16 patients and 12 healthy controls. We found that the intestinal microbiome of patients with STC was significantly different from that of healthy individuals at the phylum, genus, and species level. Patients with STC had markedly higher levels of Alistipes and Eubacterium and lower abundance of multiple species belonging to the Roseburia genus. Patients with STC gene expression levels and the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology pathway (such as fatty acid biosynthesis, butanoate metabolism, and methane metabolism pathways) enrichment were also substantially different from those of healthy controls. These microbiome and metabolite differences may be valuable biomarkers for STC. Our findings suggest that alteration of the microbiome may lead to constipation by changing the levels of microbial-derived metabolites in the gut. Above findings may help us in the development of microbial drugs.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-3

Curated date: 2025/03/22

Curator: Tosin

Revision editor(s): Tosin

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Chronic constipation Chronic constipation,Infrequent bowel movements,chronic constipation

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: Slow transit constipation (STC) group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with slow transit constipation (STC)

Group 0 sample size Number of subjects in the control (unexposed) group: 52

Group 1 sample size Number of subjects in the case (exposed) group: 66

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: Mann-Whitney (Wilcoxon)

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.1

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Signature 1

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Source: Figure 1, Table S2, Table S3, Table S4, Table 3

Description: Differentially abundant taxa between slow transit constipation (STC) patients and healthy controls

Abundance in Group 1: increased abundance in Slow transit constipation (STC) group

NCBI	Quality Control	Links
Actinomycetota
Akkermansia
Akkermansia muciniphila
Alistipes
Anaerotruncus
Bacillota
Bifidobacterium
Clostridiales bacterium 1_7_47FAA
Clostridium
Eggerthella
Eggerthella lenta
Enterocloster asparagiformis
Enterocloster citroniae
Erysipelotrichaceae bacterium 21_3
Erysipelotrichaceae bacterium 2_2_44A
Flavonifractor
Gordonibacter
Gordonibacter pamelaeae
Holdemania
Hungatella hathewayi
Lachnospiraceae bacterium 3_1_57FAA_CT1
Lachnospiraceae bacterium 7_1_58FAA
Odoribacter
Oscillibacter
Parabacteroides
Parabacteroides goldsteinii
Parabacteroides merdae
Ruminococcus bromii
Subdoligranulum
Verrucomicrobiota
[Clostridium] leptum
[Clostridium] symbiosum
unclassified Eggerthella
unclassified Eubacteriales
unclassified Lachnospiraceae
unclassified Oscillibacter
unclassified Subdoligranulum

Revision editor(s): Tosin

Signature 2

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Curated date: 2025/03/22

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 1, Table S2, Table S3, Table S4, Table 3

Description: Differentially abundant taxa between slow transit constipation (STC) patients and healthy controls

Abundance in Group 1: decreased abundance in Slow transit constipation (STC) group

NCBI	Quality Control	Links
Bacteroidota
Enterobacter
Fusobacteriota
Lachnospiraceae bacterium 5_1_57FAA
Megamonas
Methanobacteriota
Oxalobacter
Roseburia intestinalis
Subdoligranulum sp. 4_3_54A2FAA
Synergistota
[Clostridium] scindens
unclassified Oscillospiraceae
Coprobacillus_sp_29_1Coprobacillus_sp_29_1

Revision editor(s): Tosin