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Gut Pathog. 2014 Jun 14;6:22. doi: 10.1186/1757-4749-6-22. eCollection 2014.

Characterization of bacterial community shift in human Ulcerative Colitis patients revealed by Illumina based 16S rRNA gene amplicon sequencing.

Author information

1
National Centre for Cell Science, Sai Trinity Complex, Sutarwadi Road, Pashan Gaon, Pashan, 411021 Pune, Maharashtra, India ; Department of Medical Microbiology, B.J. Govt Medical College, Pune, Maharashtra, India.
2
National Centre for Cell Science, Sai Trinity Complex, Sutarwadi Road, Pashan Gaon, Pashan, 411021 Pune, Maharashtra, India.
3
Department of Gastroenterology, Dr. ParimalLawate Gastroenterology Clinic, Pune, Maharashtra, India.
4
Department of Medical Microbiology, B.J. Govt Medical College, Pune, Maharashtra, India.

Abstract

BACKGROUND:

The healthy human intestine is represented by the presence of bacterial communities predominantly belonging to obligate anaerobes; however disparity and dysanaerobiosis in intestinal microflora may lead to the progression of ulcerative colitis (UC). The foremost aim of this study is to consider and compare the gut microbiota composition in patients suffering from different stages of UC.

METHODS:

This study represents data from the biopsy samples of six individuals suffering from UC. The samples were collected by colonoscopy and were processed immediately for isolation of DNA. Mucosal microbiota was analyzed by means of 16S rRNA gene-based Illumina high throughput sequencing. Quantitative real-time PCR (qPCR) was performed to determine total bacterial abundances.

RESULTS:

Analysis of 23,927 OTUs demonstrated a significant reduction of bacterial diversity consistently from phylum to species level (p < 0.05) for individuals suffering from severe stage of UC. Significant increase in abundance of unusual aerobes and facultative anaerobes, including members from the phylum Proteobacteria (p- = 0.031) was also observed. A 10 fold increase in the total bacterial count was detected in patients suffering from severe inflammatory stage (2.98 +/-0.49 E + 09/ml) when compared with patients with moderate (1.03+/-0.29 E + 08/ml) and mild (1.76 +/-0.34 E + 08/ml) stages of inflammation.

CONCLUSION:

The reduction of bacterial diversity with an increase in the total bacterial count indicates a shift of bacterial communities which signifies dysbiosis and dysanaerobiosis at the mucosal level for patients suffering from UC.

KEYWORDS:

16S rRNA gene; Bacterial community shift; High through-put sequencing; Inflammatory disease; QIIME analysis

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