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Open Access Research

Metagenomic profile of gut microbiota in children during cholera and recovery

Shirajum Monira1, Shota Nakamura2, Kazuyoshi Gotoh2, Kaori Izutsu2, Haruo Watanabe3, Nur Haque Alam1, Takaaki Nakaya4, Toshihiro Horii2, Sk Imran Ali1, Tetsuya Iida2* and Munirul Alam1*

Author Affiliations

1 International Center for Diarrhoeal Disease Research, Bangladesh, 68 Shahid Tajjudin Ahmed, Sarani, Mohakhali, Dhaka 1212, Bangladesh

2 Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan

3 National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan

4 Department of Infectious Diseases, Kyoto Prefectural University of Medicine, 465 Kawaramachi-hirokoji, Kamigyo-ku, Kyoto, Japan

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Gut Pathogens 2013, 5:1  doi:10.1186/1757-4749-5-1

Published: 1 February 2013

Abstract

Background

The diverse bacterial communities colonizing the gut (gastrointestinal tract) of infants as commensal flora, which play an important role in nutrient absorption and determining the state of health, are known to alter due to diarrhea.

Method

Bacterial community dynamics in children suffering from cholera and during recovery period were examined in the present study by employing metagenomic tool, followed by DNA sequencing and analysis. For this, bacterial community DNA was extracted from fecal samples of nine clinically confirmed cholera children (age 2–3 years) at day 0 (acute cholera), day 2 (antibiotic therapy), day 7 and, and day 28, and the variable region of 16S rRNA genes were amplified by universal primer PCR.

Results

454 parallel sequencing of the amplified DNA followed by similarity search of the sequenced data against an rRNA database allowed us to identify V. cholerae, the cause of cholera, in all nine children at day 0, and as predominant species in six children, accounting for 35% of the total gut microbiota on an average in all the nine children. The relative abundance (mean ± sem %) of bacteria belonging to phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, was 55 ± 7, 18 ± 4, 13 ± 4, and 8 ± 4, respectively, at day 0, while these values were 12 ± 4, 43 ± 4, 33 ± 3, and 12 ± 2, respectively, at day 28. As antibiotic therapy began, V. cholerae count declined significantly (p< 0.001) and was found only in four children at day 2 and two children at day 7 with the relative abundance of 3.7% and 0.01%, respectively, which continued up to day 28 in the two children. Compared to acute cholera condition (day 0), the relative abundance of Escherichia coli, Enterococcus, and Veillonella increased at day 2 (antibiotic therapy) while Bifidobacterium, Bacteroides, and Ruminococcus decreased.

Conclusion

Cholera results expulsion of major commensal bacteria of phyla Bacteroidetes, Firmicutes, and Actinobacteria, and increase of harmful Proteobacteria to colonize the gut during acute and convalescence states. The observed microbiota disruption might explain the prevalent malnutrition in children of Bangladesh where diarrheal diseases are endemic.

Keywords:
Cholera; Microbiota; Gut; 16S rDNA; Children