It has been estimated that the human body harbors 10 times more bacterial cells than human cells;many of those bacteria are yet uncultured. Historically, cultivable bacteria have been instrumental in human development, health, and diseases. It is reasonable to speculate that uncultured bacterial groups, which comprise nearly 80% of the human gut and 68% of the human oral microbial consortia, participate in similar functions. TM7, one of many candidate divisions of Bacteria, is comprised entirely of uncultured members, and has been associated with the human body (skin, mouth, gut, and vaginal fluid). Recently TM7 were associated with human oral diseases. This year, as part of our first SC3 funding cycle, we identified and published an environmental source for a TM7 bacterium with >99% identity to a human-associated oral TM7, based on 16S ribosomal DNA gene (16S rDNA) sequence analysis (Dinis et al. 2011). Surprisingly, our environmental TM7 bacterium has higher sequence homology to the human oral-associated TM7 than most other TM7 bacteria found elsewhere in the human body and up to five times more abundant than TM7 in the human oral cavity. We hypothesize that environmental TM7 bacteria can serve as a model organism for understanding human diseases. In this renewal application, we propose to sequence and annotate the whole genome of the environmental TM7 model organism in our samples. A genome sequence can help us make predictions for putative function of genes to pathogenicity, metabolic pathways, nutrient requirements, motility capabilities, and other biological attributes o this potential emerging human pathogen.

Public Health Relevance

This project seeks to establish a model of the emerging and uncultured bacterium TM7, which has been associated with human oral diseases, to better understand the role TM7 plays in human health. Our past publications proposed that an environmental TM7 with over 99% identity to a human-associated TM7 could serve as that model organism in the study of pathogenic genes using metagenomics and circumvent problems related to intrusive methods when collecting samples from humans.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Continuance Award (SC3)
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Special Emphasis Panel (ZGM1-MBRS-9 (SC))
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Okita, Richard T
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San Jose State University
Schools of Arts and Sciences
San Jose
United States
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Caldwell, Adam Collins; Silva, Lívia Carneiro Fidéles; da Silva, Cynthia Canêdo et al. (2015) Prokaryotic Diversity in the Rhizosphere of Organic, Intensive, and Transitional Coffee Farms in Brazil. PLoS One 10:e0106355
Dinis, Jorge M; Barton, David E; Ghadiri, Jamsheed et al. (2011) In search of an uncultured human-associated TM7 bacterium in the environment. PLoS One 6:e21280
Smits, Samuel A; Ouverney, Cleber C (2010) jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web. PLoS One 5:e12267
Smits, Samuel A; Ouverney, Cleber C (2010) Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship network perspective. BMC Bioinformatics 11 Suppl 6:S18