In humans, the digestive-tract microbiota is a complex community composed out of hundreds of species. This microbiome provides humans with an amazing repertoire of biochemical processes that far exceed those encoded by the animal's genome. As an animal matures or switches diets the microbiome can change in composition. How this change affects the overall physiology of the microbiome and its contribution to the host is poorly understood. The information gained from the Human Microbiome Project has produced a wealth of genome information and is providing insight into possible functions, but functional data from animals with their native microbiome are lacking. The sheer complexity of the microbiome has hindered identifying the genes that the microbiome expresses, the metatranscriptome. This application investigates a naturally occurring simple microbiome that resides in the digestive tract of the medicinal leech. Two bacteria dominate the microbial community and for one genetic tools are available. The composition of the microbiome changes during the first two weeks after the leeches hatch from the cocoon and also after they consume a blood meal. If the blood was partially lysed, a Clostridium species that is minor member of the microbiome became very abundant. Massively parallel sequencing will be used to monitor changes in the composition and in the metatranscriptome of the microbiome as the animals mature and change diet. This will be confirmed using qPCR and qRT-PCR, respectively. This analysis allows one to determine if under specific conditions a particular allele or strain is more abundant. Using gfp-fusions, the exact location of the cells expressing the genes will be determined. Environmental parameter such as electron acceptors, sugars and short chained fatty acids will be measured. Because the bacteria are present both in pelagic and microcolony phases, compare niche specific gene expression can be determined by using Illumina sequencing of FACS sorted cells. This work will determine new principles using a simple system that are applicable to the more complex human system and apply technologies that will become more feasible to use in highly complex systems as the sequencing throughput and computational power increase.

Public Health Relevance

The digestive-tract microbiome is essential for the well-being of humans, but the complexity of the community has hindered a direct assessment of its function. In this application, we utilize a naturally occurring, simple microbiome to establish techniques that identify the transcriptomes of the microbiome and allow one to elucidate its functions as it changes in composition of subpopulations occupying different niches.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZGM1-GDB-2 (MC))
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Singh, Shiva P
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University of Connecticut
Schools of Arts and Sciences
United States
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