Human physiology and health is highly dependent on the activities of billions of microorganisms that inhabit multiple niches within and on the human body. Few of these microorganisms have been characterized, in large part because the majority are yet to be cultivated. As such, the impact this vast number of species has on human health remains to be elucidated. This proposal presents the J. Craig Venter Institute's approach to generating the genomic sequences of a significant number of reference species including bacteria, fungi, viruses and phage that are associated with the human body. We also describe how we will generate metagenomic sequences from DNA samples collected from various body sites of multiple individuals.
The specific aims i nclude the sequencing, assembly and annotation of 400 microbial genomes (60 of which will be closed) to provide reference genomes for metagenomic data;characterization of the microbiota from multiple body sites via shotgun sequencing of these samples, and the use of our state-of-the-art assembly and analysis tools to further interpret this data. We will also investigate microeukaryotic diversity, focusing on the 28S rRNA gene and internal transcribed spacer regions. Cell sorting, combined with whole genome amplification will be employed to obtain genomic DNA from previously uncultured prokaryotes. Finally, the dynamic range of expressed RNA from marker genes identified through metagenomic analyses will be interrogated using a novel mRNA transcript capture and amplification approach. This study will be conducted using cutting edge technologies including next generation approaches to sequencing. We will continue outreach and education to research clinicians, and will make all data readily available. Without a doubt, the findings from the proposed study will increase current understanding of the microbial diversity associated with the human body and the impact of these species on health and disease.
This broad genomic and metagenomic survey of the human microbiome will lay a foundation for future efforts to understand the impact the microbes that inhabit the human body have on human health and disease.
|Danaher, Robert J; Fouts, Derrick E; Chan, Agnes P et al. (2017) HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences. J Neurovirol 23:171-185|
|Lloyd-Price, Jason; Mahurkar, Anup; Rahnavard, Gholamali et al. (2017) Strains, functions and dynamics in the expanded Human Microbiome Project. Nature 550:61-66|
|Bondy-Denomy, Joseph; Qian, Jason; Westra, Edze R et al. (2016) Prophages mediate defense against phage infection through diverse mechanisms. ISME J 10:2854-2866|
|Sizova, Maria V; Chilaka, Amanda; Earl, Ashlee M et al. (2015) High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae. Stand Genomic Sci 10:37|
|McCorrison, Jamison M; Venepally, Pratap; Singh, Indresh et al. (2014) NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly. BMC Bioinformatics 15:357|
|Sizova, Maria V; Muller, Paul A; Stancyk, David et al. (2014) Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium. Int J Syst Evol Microbiol 64:2642-9|
|Yang, Youngik; Yooseph, Shibu (2013) SPA: a short peptide assembler for metagenomic data. Nucleic Acids Res 41:e91|
|Fitzsimons, Michael S; Novotny, Mark; Lo, Chien-Chi et al. (2013) Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Res 23:878-88|
|Depew, Jessica; Zhou, Bin; McCorrison, Jamison M et al. (2013) Sequencing viral genomes from a single isolated plaque. Virol J 10:181|
|Shkoporov, A N; Efimov, B A; Khokhlova, E V et al. (2013) Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp. longum Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from Two Children after a 5-Year Time Period. Genome Announc 1:|
Showing the most recent 10 out of 23 publications