Study of microbiome changes in patients with ulcerative colitis in the Central European part of Russia

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-12

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

33748490

DOI Digital object identifier for electronic documents.

10.1016/j.heliyon.2021.e06432

URI

Authors

Gryaznova MV, Solodskikh SA, Panevina AV, Syromyatnikov MY, Dvoretskaya YD, Sviridova TN, Popov ES, Popov VN

Journal

Heliyon

Year

2021

Keywords:

Inflammatory bowel disease, Intestinal microbiota, Russian population, Sequencing, Ulcerative colitis

Ulcerative colitis (UC) is an inflammatory disease that affects the colon and rectum. Recently, evidence has emerged about the influence of microbiota on the development of this disease. However, studies on the role of intestinal microbiota in the pathogenesis of UC have been incomplete. In addition, there are no comprehensive studies of the causes of ulcerative colitis and data on the microbiological composition of the intestines of patients with ulcerative colitis in Russia. We carried out a study of the microbiological composition of the intestines of patients with ulcerative colitis and healthy individuals. We found significant changes in the bacteria genera and species in patients with UC compared with the control group using sequencing on the IonTorrent PGM system and subsequent data analysis. In our study we observed a significant increase of the genus Haemophilus, Olsenella, Prevotella, Cedecea, Peptostreptococcus, Faecalibacterium, Lachnospira, Negativibacillus, Butyrivibrio, and the species Bacteroides coprocola, Phascolarctobacterium succinatutens, Dialister succinatiphilus, Sutterella wadsworthensis, Faecalibacterium prausnitzii in patients with ulcerative colitis. In addition, in patients with ulcerative colitis there was a significant decrease in the genus Fusicatenibacter, Butyricimonas, Lactococcus, Eisenbergiella, Coprobacter, Cutibacterium, Falsochrobactrum, Brevundimonas, Yersinia, Leuconostoc and in the species Fusicatenibacter saccharivorans. We found confirmation of our data with literary sources and studies of UC. In addition, we discovered a few taxa such as Negativibacillus spp. and Falsochrobactrum spp. that have not been previously found in human stool samples. Our data confirm that more research is needed to understand the role of microbiome changes in the development of UC in different people populations.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-12

Curated date: 2023/12/12

Curator: Yjung24

Revision editor(s): Yjung24, Peace Sandy

Subjects

Location of subjects: Russian Federation

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: 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,Ulcerative colitis

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: 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: 10

Group 1 sample size Number of subjects in the case (exposed) group: 10

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

Lab analysis

Sequencing type: PCR

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: Ion Torrent

Statistical Analysis

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

Statistical test: DESeq2

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

Signature 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-12

Curated date: 2023/12/12

Curator: Yjung24

Revision editor(s): Yjung24, Peace Sandy

Source: Figure 2 and Figure 3

Description: Quantitative changes in the bacteria generic composition of the intestinal microbiome in patients with ulcerative colitis relative to control group.

Changes in species composition of intestinal microbiome in patients with ulcerative colitis relative to control group (∗Pvalue≤0.05, ∗∗Pvalue≤0.01, ∗∗∗Pvalue≤0.001).

Abundance in Group 1: increased abundance in Ulcerative colitis

NCBI	Quality Control	Links
Butyrivibrio
Cedecea
Faecalibacterium
Haemophilus
Lachnospira
Lachnospiraceae bacterium NK4A136
Negativibacillus
Olsenella
Peptostreptococcus
Prevotella
Phocaeicola coprocola
Phascolarctobacterium succinatutens
Dialister succinatiphilus
Sutterella wadsworthensis
Faecalibacterium prausnitzii

Revision editor(s): Yjung24, Peace Sandy

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-12

Curated date: 2023/12/12

Curator: Yjung24

Revision editor(s): Yjung24, Peace Sandy

Source: Figure 2 and Figure 3

Description: Quantitative changes in the bacteria generic composition of the intestinal microbiome in patients with ulcerative colitis relative to control group.

Changes in species composition of intestinal microbiome in patients with ulcerative colitis relative to control group (∗Pvalue≤0.05, ∗∗Pvalue≤0.01, ∗∗∗Pvalue≤0.001).

Abundance in Group 1: decreased abundance in Ulcerative colitis

NCBI	Quality Control	Links
Brevundimonas
Butyricimonas
Coprobacter
Cutibacterium
Eisenbergiella
Falsochrobactrum
Fusicatenibacter
Lactococcus
Leuconostoc
Yersinia
unclassified Lachnospiraceae
Fusicatenibacter saccharivorans

Revision editor(s): Yjung24, Peace Sandy