A major goal of the Human Microbiome Project is to identify all of the organisms that are associated with the human body (the human microbiota) and determine the genomic sequence of most if not all of them. The detected diversity of the human microbiota reaches thousands of species and strains, the vast majority of which have not been isolated in pure culture. Our goal is to develop a robust and rapid approach for the targeted genomic characterization of any uncultured constituent of the human microbiota at single cell level and also to allow population genetic studies of selected groups of organisms that may have some cultured isolates. Our strategy utilizes the high phylogenetic resolution that the small subunit ribosomal RNA (SSU rRNA) provides in distinguishing microbial phylotypes. We plan to label and isolate single cells representing uncultured microbial lineages as well as populations of cells of specific phylotypes from complex microbiota samples and amplify their DNA to levels that enable genomic sequencing. This approach will bridge the gap between sequencing the limited number of individual cultured organisms and whole community shotgun sequencing (metagenomics) which generally does not provide sufficient depth and resolution to comprehensively sequence the microbiome. Initial feasibility studies indicate that our approach can be applied to any microbial consortia and is not dependent on the abundance of the target organism. Based on this, the focus of this proposal is to determine optimum experimental design and improved technical procedures for targeted single cell and population genomics of microbes from the human microbiota.
The specific aims are to: 1.
Aim 1. Separate single cells and populations of target uncultured microbial phylotypes from gut microbiota samples. We will use fluorescence in situ hybridization (FISH) combined with flow cytometry to obtain single cells and populations of targeted phylotypes, uncultured or with few cultured representatives 2.
Aim 2. Amplification and sequencing of genomes from single cells representing the uncultured gut microbiota. We will amplify the genomes of target cells using multiple displacement amplification and sequence the DNA to obtain draft genomic assemblies. The experimental and computational approaches will be optimized for the human microbiota characteristics. 3.
Aim 3. Pangenomic characterization of targeted populations of uncultured and cultured microbial phylotypes. We will isolate populations of specific bacterial phylotypes representing uncultured organisms as well as cell populations representing species/genera that have representatives in culture and one or few genomes sequenced. We will amplify and sequence the cell population genomic DNA to obtain composite genomes/pangenomes.

Public Health Relevance

Targeted genomics of uncultured microbiota will enable selective access to the genetic blueprint of any of the organisms that inhabit the human body. This approach, which relies upon specific isolation of single cells or specific cell populations from complex human microbial consortia and sequencing their genomes or a part of, complements whole genome sequencing from individual cultivated organisms and global community metagenomics.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
1R01HG004857-01A1
Application #
7696060
Study Section
Special Emphasis Panel (ZRG1-IDM-Q (50))
Program Officer
Garges, Susan
Project Start
2009-08-17
Project End
2012-07-31
Budget Start
2009-08-17
Budget End
2010-07-31
Support Year
1
Fiscal Year
2009
Total Cost
$426,363
Indirect Cost
Name
UT-Battelle, LLC-Oak Ridge National Lab
Department
Type
DUNS #
099114287
City
Oak Ridge
State
TN
Country
United States
Zip Code
37831
Campbell, Alisha G; Schwientek, Patrick; Vishnivetskaya, Tatiana et al. (2014) Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. Environ Microbiol 16:2635-43
Beall, Clifford J; Campbell, Alisha G; Dayeh, Daniel M et al. (2014) Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia. PLoS One 9:e89398
Campbell, James H; O'Donoghue, Patrick; Campbell, Alisha G et al. (2013) UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci U S A 110:5540-5
Zhou, Yanjiao; Gao, Hongyu; Mihindukulasuriya, Kathie A et al. (2013) Biogeography of the ecosystems of the healthy human body. Genome Biol 14:R1
Shakya, Migun; Quince, Christopher; Campbell, James H et al. (2013) Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ Microbiol 15:1882-99
Campbell, Alisha G; Campbell, James H; Schwientek, Patrick et al. (2013) Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity. PLoS One 8:e59361
Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207-14
Campbell, James H; Foster, Carmen M; Vishnivetskaya, Tatiana et al. (2012) Host genetic and environmental effects on mouse intestinal microbiota. ISME J 6:2033-44
Human Microbiome Project Consortium (2012) A framework for human microbiome research. Nature 486:215-21