The human microbiome is the collection of microorganisms that colonize the human body. Over the last year the analysis of the microbiome of 250 healthy subjects was initiated, focusing on five body sites (nasal, oral, vaginal, dermal, and gut) and many subsites. This study began to build a catalog of genome sequences of culturable bacteria that inhabit the human body as well as described the community structure formed by microbial species, allowing diversity to be assessed between body sites and between individuals. The goal of this study is to extend these initial probes in multiple directions. The study will add 1,000 genomes to the catalog of bacterial reference sequences of the human microbiome by using automated methods to isolate organisms and high throughput DNA sequencing to construct genome sequences. The study will also further characterize the metagenomes of the 250 individuals by directly comparing DNA sequences from organisms in the microbiome, thus deterimining what is common or variant between subjects. Going beyond bacteria, the project will characterize the virome, the component of the human microbiome formed by viruses, and take a census of eukaryotic microbes in the human microbiome. The last goal is to analyze the transcriptional patterns of microbes found in metagenomic communities, and by this means determine what functions are expressed in the different body niches. These studies will advance our growing knowledge of the human microbiome in healthy subjects, providing a baseline for disease studies as well as new tools for probing the microbiome.

Public Health Relevance

The human microbiome is the collection of microorganisms that colonize the human body. Over the last year the analysis of the microbiome of 250 healthy subjects was initiated, focusing on five body sites. This study began to build a catalog of genome sequences of organisms that inhabit the human body as well as described the diversity found between body sites and individuals. The goal of this study is to add 1,000 genomes to the catalog of reference sequences of the human microbiome, to further characterize differences in the metagenomes of 250 individuals by directly comparing shotgun sequences, to characterize the virome component of the human microbiome, to take a census of eukaryotic microbes in the human microbiome, and to analyze the transcriptional pattern found in metagenomic communities. These studies will advance our growing knowledge of the human microbiome in healthy subjects, providing a baseline for disease studies as well as new tools for probing the microbiome.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54HG004968-04
Application #
8333457
Study Section
Special Emphasis Panel (ZRG1-GGG-J (52))
Program Officer
Proctor, Lita
Project Start
2009-05-22
Project End
2014-04-30
Budget Start
2012-05-01
Budget End
2014-04-30
Support Year
4
Fiscal Year
2012
Total Cost
$1,806,483
Indirect Cost
$526,157
Name
Washington University
Department
Genetics
Type
Schools of Medicine
DUNS #
068552207
City
Saint Louis
State
MO
Country
United States
Zip Code
63130
Rossi, Flávia; Diaz, Lorena; Wollam, Aye et al. (2014) Transferable vancomycin resistance in a community-associated MRSA lineage. N Engl J Med 370:1524-31
Wylie, Kristine M; Mihindukulasuriya, Kathie A; Zhou, Yanjiao et al. (2014) Metagenomic analysis of double-stranded DNA viruses in healthy adults. BMC Biol 12:71
Zhou, Yanjiao; Mihindukulasuriya, Kathie A; Gao, Hongyu et al. (2014) Exploration of bacterial community classes in major human habitats. Genome Biol 15:R66
La Rosa, Patricio S; Warner, Barbara B; Zhou, Yanjiao et al. (2014) Patterned progression of bacterial populations in the premature infant gut. Proc Natl Acad Sci U S A 111:12522-7
Zhou, Yanjiao; Burnham, Carey-Ann D; Hink, Tiffany et al. (2014) Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study. J Clin Microbiol 52:4260-6
Kraal, Laurens; Abubucker, Sahar; Kota, Karthik et al. (2014) The prevalence of species and strains in the human microbiome: a resource for experimental efforts. PLoS One 9:e97279
Carl, Mike A; Ndao, I Malick; Springman, A Cody et al. (2014) Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. Clin Infect Dis 58:1211-8
Somarajan, Sudha R; Roh, Jung H; Singh, Kavindra V et al. (2014) CcpA is important for growth and virulence of Enterococcus faecium. Infect Immun 82:3580-7
Zhou, Yanjiao; Gao, Hongyu; Mihindukulasuriya, Kathie A et al. (2013) Biogeography of the ecosystems of the healthy human body. Genome Biol 14:R1
Tomida, Shuta; Nguyen, Lin; Chiu, Bor-Han et al. (2013) Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. MBio 4:e00003-13

Showing the most recent 10 out of 25 publications