Complex communities of microbes are intimately associated with all plants and animals in nature: they influence the evolution, physiology and ecology of the host. The specific roles of microbes in these symbiotic relationships have been best elucidated for that subset of microbes grown in pure culture. However, the application of cultivation-independent molecular surveys reveals that many of these microbes have yet to be cultivated. We propose to cultivate a physiological subset of novel microbes from the human microbiome - the microaerobes - by incorporating unique approaches to isolation and cultivation. We are focusing on microaerobes because oxygen diffusing into the GI tract from host tissue creates a microoxic zone adjacent to the tissue that is likely to be colonized by microaerobes. As a result of the proximity to the host tissue, these microbes are likely to interact directly with the host and so are key to understanding the role of the microbiome in human health and disease. Microbes are typically isolated under an atmosphere of 21% oxygen or strictly anoxic conditions. While these conditions are suitable for the cultivation of many organisms, microaerobes thrive under reduced concentrations of oxygen. They have specialized respiratory enzymes to harvest oxygen at low concentrations, and as a result occupy niches not available to typical aerobes. Microaerobes, including populations of Helicobacter and Campylobacter, occupy the GI tracts of many animals. We propose to extend the availability of cultured microaerobes from the human microbiome as follows: 1) Exploit microoxic atmospheres and novel cultivation strategies to isolate microaerobes from the mucosa of the human GI tract, 2) Select representative microaerobes based on their distribution and abundance in the GI tract and their estimated prevalence in the human population, 3) Provide a physiological characterization of representative isolates that are sent for genome sequencing. Pure cultures of microaerophiles will not only enable direct sequencing of their genomes, but will be a valuable resource for genetic, biochemical and physiological experiments to test hypotheses generated from genome analyses. An improved understanding of the physiological ecology of these microbes and their impact on humans is most accessible when they are studied in pure and defined mixed cultures.

Public Health Relevance

Complex communities of microbes are intimately associated with the human body. To better understand their role in human health and disease, we proposed to cultivate these microbes in the laboratory to facilitate studies that will include the sequencing of their genomes.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project (R01)
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Special Emphasis Panel (ZRG1-IDM-P (50))
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Schloss, Jeffery
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Michigan State University
Schools of Arts and Sciences
East Lansing
United States
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Morris, Rachel L; Schmidt, Thomas M (2013) Shallow breathing: bacterial life at low O(2). Nat Rev Microbiol 11:205-12
Carmody, Lisa A; Zhao, Jiangchao; Schloss, Patrick D et al. (2013) Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Ann Am Thorac Soc 10:179-87
Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207-14
Zhao, Jiangchao; Schloss, Patrick D; Kalikin, Linda M et al. (2012) Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A 109:5809-14
Human Microbiome Project Consortium (2012) A framework for human microbiome research. Nature 486:215-21
Wang, Yunwei; Antonopoulos, Dionysios A; Zhu, Xiaorong et al. (2010) Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Appl Microbiol Biotechnol 88:1333-42