Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease

Study information

Reviewed Marked as Reviewed by Atrayees on 2023-6-9

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

26789999

DOI Digital object identifier for electronic documents.

https://doi.org/10.1159/000441768

URI

https://pubmed.ncbi.nlm.nih.gov/26789999/

Authors

Takahashi K, Nishida A, Fujimoto T, Fujii M, Shioya M, Imaeda H, Inatomi O, Bamba S, Sugimoto M, Andoh A

Journal

Digestion

Year

2016

BACKGROUND: The global alteration of the gut microbial community (dysbiosis) plays an important role in the pathogenesis of inflammatory bowel diseases (IBDs). However, bacterial species that characterize dysbiosis in IBD remain unclear. In this study, we assessed the alteration of the fecal microbiota profile in patients with Crohn's disease (CD) using 16S rRNA sequencing. SUMMARY: Fecal samples from 10 inactive CD patients and 10 healthy individuals were subjected to 16S rRNA sequencing. The V3-V4 hypervariable regions of 16S rRNA were sequenced by the Illumina MiSeq™II system. The average of 62,201 reads per CD sample was significantly lower than the average of 73,716 reads per control sample. The genera Bacteroides, Eubacterium, Faecalibacterium and Ruminococcus significantly decreased in CD patients as compared to healthy controls. In contrast, the genera Actinomyces and Bifidobacterium significantly increased in CD patients. At the species level, butyrate-producing bacterial species, such as Blautia faecis, Roseburia inulinivorans, Ruminococcus torques, Clostridium lavalense, Bacteroides uniformis and Faecalibacterium prausnitzii were significantly reduced in CD patients as compared to healthy individuals (p < 0.05). These results of 16S rRNA sequencing were confirmed in additional CD patients (n = 68) and in healthy controls (n = 46) using quantitative PCR. The abundance of Roseburia inulinivorans and Ruminococcus torques was significantly lower in C-reactive protein (CRP)-positive CD patients as compared to CRP-negative CD patients (p < 0.05). KEY MESSAGE: The dysbiosis of CD patients is characterized by reduced abundance of multiple butyrate-producing bacteria species.

Experiment 1

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Reviewed Marked as Reviewed by Atrayees on 2023-6-9

Curated date: 2023/06/09

Curator: Atrayees

Revision editor(s): Atrayees

Subjects

Location of subjects: Japan

Host species Species from which microbiome was sampled (if applicable): 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: 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: Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies: CD patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with Crohn's disease
Group 0 sample size Number of subjects in the control (unexposed) group: 46
Group 1 sample size Number of subjects in the case (exposed) group: 68

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-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

T-Test

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

Signature 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2023/06/09

Curator: Atrayees

Revision editor(s): Atrayees

Source: Table 2, Figure 2

Description: Relative abundance of bacteria between control and CD

Abundance in Group 1: increased abundance in CD patients

NCBI	Quality Control	Links
Actinomyces
Bifidobacterium

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Curated date: 2023/06/09

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Source: Figure 2, Table 2

Description: Relative abundance of bacteria between control and CD

Abundance in Group 1: decreased abundance in CD patients

NCBI	Quality Control	Links
Cellulosilyticum
Eubacterium
Holdemania
Parabacteroides
Roseburia
Pseudoflavonifractor
Subdoligranulum
Blautia faecis
Roseburia intestinalis
[Ruminococcus] torques
Enterocloster lavalensis

Revision editor(s): Atrayees