Modulation of faecal metagenome in Crohn's disease: Role of microRNAs as biomarkers

Study information

Reviewed Marked as Reviewed by Fatima on 2022/07/25

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

30581271

DOI Digital object identifier for electronic documents.

10.3748/wjg.v24.i46.5223

URI

Authors

Rojas-Feria M, Romero-García T, Fernández Caballero-Rico JÁ, Pastor Ramírez H, Avilés-Recio M, Castro-Fernandez M, Chueca Porcuna N, Romero-Gόmez M, García F, Grande L, Del Campo JA

Journal

World journal of gastroenterology

Year

2018

Keywords:

Bacteroidetes, Crohn’s disease, Dysbiosis, Firmicutes, microRNAs

BACKGROUND: The gut microbiota plays a key role in the maintenance of intestinal homeostasis and the development and activation of the host immune system. It has been shown that commensal bacterial species can regulate the expression of host genes. 16S rRNA gene sequencing has shown that the microbiota in inflammatory bowel disease (IBD) is abnormal and characterized by reduced diversity. MicroRNAs (miRNAs) have been explored as biomarkers and therapeutic targets, since they are able to regulate specific genes associated with Crohn's disease (CD). In this work, we aim to investigate the composition of gut microbiota of active treatment-naïve adult CD patients, with miRNA profile from gut microbiota. AIM: To investigate the composition of gut microbiota of active treatment-naïve adult CD patients, with miRNA profile from gut microbiota. METHODS: Patients attending the outpatient clinics at Valme University Hospital without relevant co-morbidities were matched according to age and gender. Faecal samples of new-onset CD patients, free of treatment, and healthy controls were collected. Faecal samples were homogenized, and DNA was amplified by PCR using primers directed to the 16S bacterial rRNA gene. Pyrosequencing was performed using GS-Junior platform. For sequence analysis, MG-RAST server with the database Ribosomal Project was used. MiRNA profile and their relative abundance were analyzed by quantitative PCR. RESULTS: Microbial community was characterized using 16S rRNA gene sequencing in 29 samples (n = 13 CD patients, and n = 16 healthy controls). The mean Shannon diversity was higher in the healthy control population compared to CD group (5.5 vs 3.7). A reduction in Firmicutes and an increase in Bacteroidetes were found. Clostridia class was also significantly reduced in CD. Principal components analysis showed a grouping pattern, identified in most of the subjects in both groups, showing a marked difference between control and CD groups. A functional metabolic study showed that a lower metabolism of carbohydrates (P = 0.000) was found in CD group, while the metabolism of lipids was increased. In CD patients, three miRNAs were induced in affected mucosa: mir-144 (6.2 ± 1.3 fold), mir-519 (21.8 ± 3.1) and mir-211 (2.3 ± 0.4). CONCLUSION: Changes in microbial function in active non-treated CD subjects and three miRNAs in affected vs non-affected mucosa have been found. miRNAs profile may serve as a biomarker.

Experiment 1

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Reviewed Marked as Reviewed by Fatima on 2022/07/25

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Fatima, WikiWorks

Subjects

Location of subjects: Spain

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 control
Group 1 name Corresponds to the case (exposed) group for case-control studies: crohn's disease
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: new-onset adult crohn's disease (CD) patients
Group 0 sample size Number of subjects in the control (unexposed) group: 16
Group 1 sample size Number of subjects in the case (exposed) group: 13
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 10 weeks

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

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

Statistical Analysis

Statistical test: Chi-Square

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
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: decreased

Signature 1

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Curated date: 2021/01/10

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Source: figure 2, 3, 4

Description: Significant difference between control group and crohn's disease

Abundance in Group 1: decreased abundance in crohn's disease

NCBI	Quality Control	Links
Clostridia
Oscillospiraceae
Lachnospiraceae
Eubacteriaceae
Rikenellaceae
Entomoplasmataceae
Desulfohalobiaceae
Corynebacteriaceae
Mycoplasmataceae
Faecalibacterium
Ruminococcus
Roseburia
Alistipes
Eubacterium
Mesoplasma
Desulfonauticus
Porphyromonas
Rikenella
Parabacteroides
Butyrivibrio

Revision editor(s): WikiWorks