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Open Access Highly Accessed Research article

The intestinal microbiome of fish under starvation

Jun Hong Xia1, Grace Lin1, Gui Hong Fu1, Zi Yi Wan1, May Lee1, Le Wang1, Xiao Jun Liu1 and Gen Hua Yue12*

Author Affiliations

1 Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore

2 Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore

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BMC Genomics 2014, 15:266  doi:10.1186/1471-2164-15-266

Published: 5 April 2014

Abstract

Background

Starvation not only affects the nutritional and health status of the animals, but also the microbial composition in the host’s intestine. Next-generation sequencing provides a unique opportunity to explore gut microbial communities and their interactions with hosts. However, studies on gut microbiomes have been conducted predominantly in humans and land animals. Not much is known on gut microbiomes of aquatic animals and their changes under changing environmental conditions. To address this shortcoming, we determined the microbial gene catalogue, and investigated changes in the microbial composition and host-microbe interactions in the intestine of Asian seabass in response to starvation.

Results

We found 33 phyla, 66 classes, 130 orders and 278 families in the intestinal microbiome. Proteobacteria (48.8%), Firmicutes (15.3%) and Bacteroidetes (8.2%) were the three most abundant bacteria taxa. Comparative analyses of the microbiome revealed shifts in bacteria communities, with dramatic enrichment of Bacteroidetes, but significant depletion of Betaproteobacteria in starved intestines. In addition, significant differences in clusters of orthologous groups (COG) functional categories and orthologous groups were observed. Genes related to antibiotic activity in the microbiome were significantly enriched in response to starvation, and host genes related to the immune response were generally up-regulated.

Conclusions

This study provides the first insights into the fish intestinal microbiome and its changes under starvation. Further detailed study on interactions between intestinal microbiomes and hosts under dynamic conditions will shed new light on how the hosts and microbes respond to the changing environment.

Keywords:
Fish; Microbiome; Starvation; Stress; Interaction; Nutrition