Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

29632427

DOI Digital object identifier for electronic documents.

10.3748/wjg.v24.i13.1464

URI

Authors

Ma HQ, Yu TT, Zhao XJ, Zhang Y, Zhang HJ

Journal

World journal of gastroenterology

Year

2018

Keywords:

16S ribosomal DNA, Chinese, Crohn’s disease, Microbial dysbiosis, Ulcerative colitis

AIM: To analyze the alterations of fecal microbiota in Chinese patients with inflammatory bowel disease (IBD). METHODS: Fecal samples from 15 patients with Crohn's disease (CD) (11 active CD, 4 inactive CD), 14 patients with active ulcerative colitis (UC) and 13 healthy individuals were collected and subjected to 16S ribosomal DNA (rDNA) gene sequencing. The V4 hypervariable regions of 16S rDNA gene were amplified from all samples and sequenced by the Illumina MiSeq platform. Quality control and operational taxonomic units classification of reads were calculated with QIIME software. Alpha diversity and beta diversity were displayed with R software. RESULTS: Community richness (chao) and microbial structure in both CD and UC were significantly different from those in normal controls. At the phyla level, analysis of the microbial compositions revealed a significantly greater abundance of Proteobacteria in IBD as compared to that in controls. At the genera level, 8 genera in CD and 23 genera in UC (in particular, the Escherichia genus) showed significantly greater abundance as compared to that in normal controls. The relative abundance of Bacteroidetes in the active CD group was markedly lower than that in the inactive CD group. The abundance of Proteobacteria in patients with active CD was nominally higher than that in patients with inactive CD; however, the difference was not statistically significant after correction. Furthermore, the relative abundance of Bacteroidetes showed a negative correlation with the CD activity index scores. CONCLUSION: Our study profiles specific characteristics and microbial dysbiosis in the gut of Chinese patients with IBD. Bacteroidetes may have a negative impact on inflammatory development.

Experiment 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1, LGeistlinger

Differences from previous experiment shown

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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: ulcerative colitis 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

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: Patients with ulcerative colitis

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with ulcerative colitis

Group 0 sample size Number of subjects in the control (unexposed) group: 29

Group 1 sample size Number of subjects in the case (exposed) group: 14

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months

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

Statistical test: Kruskall-Wallis

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)?: Yes

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: unchanged

Chao1 Abundance-based estimator of species richness: decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: decreased

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Source: Table 2

Description: Differential microbial abundance between ulcerative colitis patients and healthy controls

Abundance in Group 1: increased abundance in Patients with ulcerative colitis

NCBI	Quality Control	Links
Granulicatella
Peptostreptococcus
Schwartzia
Capnocytophaga
Pseudomonadota
Escherichia
Janthinobacterium
Campylobacter
Actinomyces
Eggerthella
Corynebacterium
Spirochaetota

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Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

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Source: Table 2

Description: Differential microbial abundance between ulcerative colitis patients and healthy controls

Abundance in Group 1: decreased abundance in Patients with ulcerative colitis

NCBI	Quality Control	Links
Alistipes
Butyricimonas
Desulfovibrio
Holdemania
Lachnobacterium
Lentisphaerota
Megamonas
Mitsuokella
Oxalobacter
Prevotella
Pyramidobacter
Synergistes
Victivallis
Prevotella sp.

Revision editor(s): Claregrieve1, Merit

Experiment 3

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Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1, LGeistlinger

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Patients with ulcerative colitis

Group 1 name Corresponds to the case (exposed) group for case-control studies: Patients with Crohn's disease

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with Crohn's disease