Markers of dysbiosis in patients with ulcerative colitis and Crohn's disease

  • Authors: Danilova NA1, Abdulkhakov SR1,2, Grigoryeva TV1, Markelova MI1, Vasilyev IY.1, Boulygina EA1, Ardatskaya MD3, Pavlenko AV4, Tyakht AV5, Odintsova AK.6, Abdulkhakov RA2
  • Affiliations:
    1. Kazan Federal University
    2. Kazan State Medical University of the Ministry of Health of the Russian Federation
    3. Central State Medical Academy of Administrative Department of the President of the Russian Federation
    4. Federal Research and Clinical Centre of Physical-Chemical Medicine of the Federal Medical and Biological Agency
    5. Institute of Gene Biology of RAS
    6. Republican Clinical Hospital of the Ministry of Health of the Republic of Tatarstan
  • Issue: Vol 91, No 4 (2019)
  • Pages: 13-20
  • Section: Articles
  • URL:
  • DOI:
  • Cite item


The results of recent studies indicate a significant role of gut microbiota in the pathogenesis of inflammatory bowel diseases (IBD). The aim of the study was to study the taxonomic and functional composition of the gut microbiota in ulcerative colitis (UC) and Crohn's disease (CD) patients to identify key markers of dysbiosis in IBD. Materials and methods. Fecal samples obtained from 95 IBD patients (78 UC and 17 CD) as well as 96 healthy volunteers were used for whole-genome sequencing carried out on the SOLiD 5500 W platform. Taxonomic profiling was performed by aligning the reeds, not maped on hg19, on MetaPhlAn2 reference database. Reeds were mapped using the HUNAnN2 algorithm to the ChocoPhlAn database to assess the representation of microbial metabolic pathways. Short-chain fatty acids (SCFA) level were measured in fecal samples by gas-liquid chromatographic analysis. Results and discussion. Changes in IBD patients gut microbiota were characterized by an increase in the representation of Proteobacteria and Bacteroidetes phyla bacteria and decrease in the number of Firmicutes phylum bacteria and Euryarchaeota phylum archaea; a decrease in the alpha-diversity index, relative representation of butyrate-producing, hydrogen-utilizing bacteria, and Methanobrevibacter smithii; increase in the relative representation of Ruminococcus gnavus in UC and CD patients and Akkermansia muciniphila in CD patients. Reduction of Butyryl-CoA: acetate CoA transferase gene relative representation in CD patients, decrease of absolute content of SCFA total number as well as particular SCFAs and main SCFAs ratio in IBD patients may indicate inhibition of functional activity and number of anaerobic microflora and/or an change in SCFA utilization by colonocytes. Conclusion: the revealed changes can be considered as typical signs of dysbiosis in IBD patients and can be used as potential targets for IBD patients personalized treatment development.

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About the authors

N A Danilova

Kazan Federal University

Kazan, Russia

S R Abdulkhakov

Kazan Federal University; Kazan State Medical University of the Ministry of Health of the Russian Federation

Kazan, Russia

T V Grigoryeva

Kazan Federal University

Kazan, Russia

M I Markelova

Kazan Federal University

Kazan, Russia

I Yu Vasilyev

Kazan Federal University

Kazan, Russia

E A Boulygina

Kazan Federal University

Kazan, Russia

M D Ardatskaya

Central State Medical Academy of Administrative Department of the President of the Russian Federation

Moscow, Russia

A V Pavlenko

Federal Research and Clinical Centre of Physical-Chemical Medicine of the Federal Medical and Biological Agency

Moscow, Russia

A V Tyakht

Institute of Gene Biology of RAS

Moscow, Russia

A Kh Odintsova

Republican Clinical Hospital of the Ministry of Health of the Republic of Tatarstan

Kazan, Russia

R A Abdulkhakov

Kazan State Medical University of the Ministry of Health of the Russian Federation

Kazan, Russia


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