Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases

Study information

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

33718417

DOI Digital object identifier for electronic documents.

10.3389/fnut.2021.615064

URI Uniform resource identifier for web resources.

Authors

Zhou Y., He Y., Liu L., Zhou W., Wang P., Hu H., Nie Y., Chen Y.

Journal

Frontiers in nutrition

Year

2021

Keywords:

Crohn's disease, Fusobacterium, Gardnerella, disease location, gut microbiota, ulcerative colitis

We previously discovered that gut microbiota can serve as universal microbial biomarkers for diagnosis, disease activity assessment, and predicting the response to infliximab treatment for inflammatory bowel diseases (IBD). Much still remains unknown about the relationship between alterations in gut microbiota and IBD affected bowel region, in particular in the case of ulcerative colitis (UC) and colonic Crohn's disease (cCD) without endoscopic and biopsy data. In the current study gut microbiota from a population in China was found to be distinct from that of the Western world [Human Microbiome Project (HMP) data]. Furthermore, both gut microbiota greatly differed from microbiota of other anatomical locations (oral, skin, airway, and vagina), with higher alpha-diversity (Chinese gut > HMP gut > oral microbiome > airway microbiome > skin microbiome > vaginal microbiome), and marked differences in microbiome composition. In patients with IBD in China, UC was characterized by the presence of Gardnerella, while cCD was characterized by the presence of Fusobacterium. Moreover, gut microbiota, such as Gardnerella and Fusobacterium, may be potential biomarkers for identifying UC from cCD. Together, this study revealed crucial differences in microbial communities across anatomical locations, and demonstrated that there was an important association between IBD affected bowel region and gut microbiota.

Experiment 1

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2025/10/10

Curator: Reddicx

Revision editor(s): Reddicx

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: Inflammatory bowel disease , Ulcerative colitis , Crohn's colitis autoimmune bowel disorder,Bowel Diseases, Inflammatory,IBD,INFLAMM BOWEL DIS,inflammatory bowel disease,Inflammatory Bowel Diseases,Inflammatory bowel disease,colitis ulcerative,Colitis, Ulcerative,Left-sided ulcerative (chronic) colitis,Left-sided ulcerative colitis,left-sided ulcerative colitis,Other ulcerative colitis,Other ulcerative colitis (disorder),UC - ulcerative colitis,ulcerative colitis,ulcerative colitis (disease),ulcerative colitis (disorder),Ulcerative colitis, unspecified,ULCERATVE COLITIS UNSPCF,Ulcerative colitis,Crohn colitis,Crohn's colitis,crohn's colitis

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: patients with the condition

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with Inflammatory Bowel Disease specifically Ulcerative Colitis and colonic Crohn's disease (Crohn's Colitis).

Group 0 sample size Number of subjects in the control (unexposed) group: 73

Group 1 sample size Number of subjects in the case (exposed) group: 123

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 1 month

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

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: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 3.5

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged