Human Microbiome Project
The Human Microbiome Project (HMP) was a United States National Institutes of Health initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans (the human microbiome). Launched in 2008, it was a five-year project, best characterized as a feasibility study, and had a total budget of $115 million. The ultimate goal of this and similar NIH-sponsored microbiome projects was to test how changes in the human microbiome are associated with human health or disease. This topic is currently not well understood.
Important components of the Human Microbiome Project were culture-independent methods of microbial community characterization, such as metagenomics (which provides a broad genetic perspective on a single microbial community), as well as extensive whole genome sequencing (which provides a "deep" genetic perspective on certain aspects of a given microbial community, i.e. of individual bacterial species). The latter served as reference genomic sequences — 3000 such sequences of individual bacterial isolates are currently planned — for comparison purposes during subsequent metagenomic analysis. The microbiology of five body sites was emphasized: oral, skin, vaginal, gut, and nasal/lung. The project also financed deep sequencing of bacterial 16S rRNA sequences amplified by polymerase chain reaction from human subjects.
Total microbial cells found in association with humans may exceed the total number of cells making up the human body by a factor of ten-to-one. The total number of genes associated with the human microbiome could exceed the total number of human genes by a factor of 100-to-one. Many of these organisms have not been successfully cultured, identified, or otherwise characterized. Organisms thought to be found in the human microbiome, however, may generally be categorized as bacteria (the majority), members of domain Archaea, yeasts, and single-celled eukaryotes as well as various helminth parasites and viruses, the latter including viruses that infect the cellular microbiome organisms (e.g., bacteriophages, the viruses of bacteria).
The HMP will address some of the most inspiring, vexing and fundamental scientific questions today. Importantly, it also has the potential to break down the artificial barriers between medical microbiology and environmental microbiology. It is hoped that the HMP will not only identify new ways to determine health and predisposition to diseases but also define the parameters needed to design, implement and monitor strategies for intentionally manipulating the human microbiota, to optimize its performance in the context of an individual's physiology.
The HMP has been described as "a logical conceptual and experimental extension of the Human Genome Project." In 2007 the Human Microbiome Project was listed on the NIH Roadmap for Medical Research as one of the New Pathways to Discovery. Organized characterization of the human microbiome is also being done internationally under the auspices of the International Human Microbiome Consortium. The Canadian Institutes of Health Research, through the CIHR Institute of Infection and Immunity, is leading the Canadian Microbiome Initiative to develop a coordinated and focused research effort to analyze and characterize the microbes that colonize the human body and their potential alteration during chronic disease states.
The HMP includes the following goals:
- To develop a reference set of microbial genome sequences and to perform preliminary characterization of the human microbiome
- To explore the relationship between disease and changes in the human microbiome
- To develop new technologies and tools for computational analysis
- To establish a resource repository
- To study the ethical, legal, and social implications of human microbiome research
The impact to date of the Human Microbiome Project may be partially assessed by examination of research sponsored by the HMP. Over 190 peer-reviewed publications are listed on the HMP website from June 2009 through August 2012.
Major categories of work funded by HMP include:
- Development of new database systems allowing efficient organization, storage, access, search and annotation of massive amounts of data. These include IMG, the Integrated Microbial Genomes database and comparative analysis system; IMG/M, a related system that integrates metagenome data sets with isolate microbial genomes from the IMG system; CharProtDB, a database of experimentally characterized protein annotations; and the Genomes OnLine Database (GOLD), for monitoring the status of genomic and metagenomic projects worldwide and their associated metadata.
- Development of tools for comparative analysis that facilitate the recognition of common patterns, major themes and trends in complex data sets. These include RAPSearch2, a fast and memory-efficient protein similarity search tool for next-generation sequencing data; Boulder ALignment Editor (ALE), a web-based RNA alignment tool; WebMGA, a customizable web server for fast metagenomic sequence analysis; and DNACLUST, a tool for accurate and efficient clustering of phylogenetic marker genes
- Development of new methods and systems for assembly of massive sequence data sets. No single assembly algorithm addresses all the known problems of assembling short-length sequences, so next-generation assembly programs such as AMOS are modular, offering a wide range of tools for assembly. Novel algorithms have been developed for improving the quality and utility of draft genome sequences.
- Assembly of a catalog of sequenced reference genomes of pure bacterial strains from multiple body sites, against which metagenomic results can be compared. The original goal of 600 genomes has been far surpassed; the current goal is for 3000 genomes to be in this reference catalog, sequenced to at least a high-quality draft stage. As of March 2012[update], 742 genomes have been cataloged.
- Establishment of the Data Analysis and Coordination Center (DACC), which serves as the central repository for all HMP data.
- Various studies exploring legal and ethical issues associated with whole genome sequencing research.
Developments funded by HMP include:
- New predictive methods for identifying active transcription factor binding sites.
- Identification, on the basis of bioinformatic evidence, of a widely distributed, ribosomally produced electron carrier precursor
- Time-lapse "moving pictures" of the human microbiome.
- Identification of unique adaptations adopted by segmented filamentous bacteria (SFB) in their role as gut commensals. SFB are medically important because they stimulate T helper 17 cells, thought to play a key role in autoimmune disease.
- Identification of factors distinguishing the microbiota of healthy and diseased gut.
- Identification of a hitherto unrecognized dominant role of Verrucomicrobia in soil bacterial communities.
- Identification of factors determining the virulence potential of Gardnerella vaginalis strains in vaginosis.
- Identification of a link between oral microbiota and atherosclerosis.
- Demonstration that pathogenic species of Neisseria involved in meningitis, septicemia, and sexually transmitted disease exchange virulence factors with commensal species.
Reference database established
On 13 June 2012, a major milestone of the Human Microbiome Project (HMP) was announced by the NIH director Francis Collins. The announcement was accompanied with a series of coordinated articles published in Nature  and several journals in the Public Library of Science (PLoS) on the same day. By mapping the normal microbial make-up of healthy humans using genome sequencing techniques, the researchers of the HMP have created a reference database and the boundaries of normal microbial variation in humans. 
From 242 healthy U.S. volunteers, more than 5,000 samples were collected from tissues from 15 (men) to 18 (women) body sites such as mouth, nose, skin, lower intestine (stool) and vagina. All the DNA, human and microbial, were analyzed with DNA sequencing machines. The microbial genome data were extracted by identifying the bacterial specific ribosomal RNA, 16S rRNA. The researchers calculated that more than 10,000 microbial species occupy the human ecosystem and they have identified 81 – 99% of the genera. In addition to establishing the human microbiome reference database, the HMP project also discovered several "surprises", which include:
- Microbes contribute more genes responsible for human survival than humans' own genes. It is estimated that bacterial protein-coding genes are 360 times more abundant than human genes.
- Microbial metabolic activities; for example, digestion of fats; are not always provided by the same bacterial species. The presence of the activities seems to matter more.
- Components of the human microbiome change over time, affected by a patient disease state and medication. However, the microbiome eventually returns to a state of equilibrium, even though the composition of bacterial types has changed.
Among the first clinical applications utilizing the HMP data, as reported in several PLoS papers, the researchers found a shift to less species diversity in vaginal microbiome of pregnant women in preparation for birth, and high viral DNA load in the nasal microbiome of children with unexplained fevers. Other studies using the HMP data and techniques include role of microbiome in various diseases in the digestive tract, skin, reproductive organs and childhood disorders.
Pharmaceutical microbiologists have considered the implications of the HMP data in relation to the presence / absence of 'objectionable' microorganisms in non-sterile pharmaceutical products and in relation to the monitoring of microorganisms within the controlled environments in which products are manufactured. The latter also has implications for media selection and disinfectant efficacy studies 
- "Human Microbiome Project: Diversity of Human Microbes Greater Than Previously Predicted". ScienceDaily. Retrieved 8 March 2012.
- "Human Microbiome Project". The NIH Common Fund. Retrieved 8 March 2012.
- Turnbaugh, P. J.; Ley, R. E.; Hamady, M.; Fraser-Liggett, C. M.; Knight, R.; Gordon, J. I. (2007). "The Human Microbiome Project". Nature 449 (7164): 804–810. doi:10.1038/nature06244. PMID 17943116.
- "About the NIH Roadmap". The NIH Common Fund. Retrieved 8 March 2012.
- "The International Human Microbiome Consortium". Retrieved 8 March 2012.
- "Canadian Microbiome Initiative". Canadian Institutes of Health Research. Retrieved 8 March 2012.
- "Human Microbiome Project / Program Initiatives". The NIH Common Fund. Retrieved 8 March 2012.
- "Human Microbiome Project / Science Publications". The NIH Common Fund. Retrieved 8 March 2012.
- Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.; Chu, K.; Szeto, E.; Grechkin, Y.; Ratner, A.; Jacob, B.; Huang, J.; Williams, P.; Huntemann, M.; Anderson, I.; Mavromatis, K.; Ivanova, N. N.; Kyrpides, N. C. (2011). "IMG: The integrated microbial genomes database and comparative analysis system". Nucleic Acids Research 40 (Database issue): D115–D122. doi:10.1093/nar/gkr1044. PMC 3245086. PMID 22194640.
- Markowitz, V. M.; Chen, I. -M. A.; Chu, K.; Szeto, E.; Palaniappan, K.; Grechkin, Y.; Ratner, A.; Jacob, B.; Pati, A.; Huntemann, M.; Liolios, K.; Pagani, I.; Anderson, I.; Mavromatis, K.; Ivanova, N. N.; Kyrpides, N. C. (2011). "IMG/M: The integrated metagenome data management and comparative analysis system". Nucleic Acids Research 40 (Database issue): D123–D129. doi:10.1093/nar/gkr975. PMC 3245048. PMID 22086953.
- Madupu, R.; Richter, A.; Dodson, R. J.; Brinkac, L.; Harkins, D.; Durkin, S.; Shrivastava, S.; Sutton, G.; Haft, D. (2011). "CharProtDB: A database of experimentally characterized protein annotations". Nucleic Acids Research 40 (Database issue): D237–D241. doi:10.1093/nar/gkr1133. PMC 3245046. PMID 22140108.
- Pagani, I.; Liolios, K.; Jansson, J.; Chen, I. -M. A.; Smirnova, T.; Nosrat, B.; Markowitz, V. M.; Kyrpides, N. C. (2011). "The Genomes OnLine Database (GOLD) v.4: Status of genomic and metagenomic projects and their associated metadata". Nucleic Acids Research 40 (Database issue): D571–D579. doi:10.1093/nar/gkr1100. PMC 3245063. PMID 22135293.
- Zhao, Y.; Tang, H.; Ye, Y. (2011). "RAPSearch2: A fast and memory-efficient protein similarity search tool for next-generation sequencing data". Bioinformatics 28 (1): 125–126. doi:10.1093/bioinformatics/btr595. PMC 3244761. PMID 22039206.
- Stombaugh, J.; Widmann, J.; McDonald, D.; Knight, R. (2011). "Boulder ALignment Editor (ALE): A web-based RNA alignment tool". Bioinformatics 27 (12): 1706–1707. doi:10.1093/bioinformatics/btr258. PMC 3106197. PMID 21546392.
- Wu, S.; Zhu, Z.; Fu, L.; Niu, B.; Li, W. (2011). "WebMGA: A customizable web server for fast metagenomic sequence analysis". BMC Genomics 12: 444. doi:10.1186/1471-2164-12-444. PMC 3180703. PMID 21899761.
- Ghodsi, M.; Liu, B.; Pop, M. (2011). "DNACLUST: Accurate and efficient clustering of phylogenetic marker genes". BMC Bioinformatics 12: 271. doi:10.1186/1471-2105-12-271. PMC 3213679. PMID 21718538.
- Yao, G.; Ye, L.; Gao, H.; Minx, P.; Warren, W. C.; Weinstock, G. M. (2011). "Graph accordance of next-generation sequence assemblies". Bioinformatics 28 (1): 13–16. doi:10.1093/bioinformatics/btr588. PMC 3244760. PMID 22025481.
- Treangen, T. J.; Sommer, D. D.; Angly, F. E.; Koren, S.; Pop, M. (2011). "Next Generation Sequence Assembly with AMOS". In Andreas D. Baxevanis. Current Protocols in Bioinformatics. pp. Unit Un11.8. doi:10.1002/0471250953.bi1108s33. ISBN 0471250953. PMC 3072823. PMID 21400694.
- Koren, S.; Miller, J. R.; Walenz, B. P.; Sutton, G. (2010). "An algorithm for automated closure during assembly". BMC Bioinformatics 11: 457. doi:10.1186/1471-2105-11-457. PMC 2945939. PMID 20831800.
- "Human Microbiome Project / Reference Genomes Data". Data Analysis and Coordination Center (DACC) for the National Institutes of Health (NIH). Retrieved 8 March 2012.
- "Data Analysis and Coordination Center (DACC)". National Institutes of Health (NIH) Common Fund. Retrieved 11 March 2012.
- Schwab, A. P.; Frank, L.; Gligorov, N. (2011). "Saying Privacy, Meaning Confidentiality". The American Journal of Bioethics 11 (11): 44–45. doi:10.1080/15265161.2011.608243. PMID 22047127.
- Rhodes, R.; Azzouni, J.; Baumrin, S. B.; Benkov, K.; Blaser, M. J.; Brenner, B.; Dauben, J. W.; Earle, W. J.; Frank, L.; Gligorov, N.; Goldfarb, J.; Hirschhorn, K.; Hirschhorn, R.; Holzman, I.; Indyk, D.; Jabs, E. W.; Lackey, D. P.; Moros, D. A.; Philpott, S.; Rhodes, M. E.; Richardson, L. D.; Sacks, H. S.; Schwab, A.; Sperling, R.; Trusko, B.; Zweig, A. (2011). "De MinimisRisk: A Proposal for a New Category of Research Risk". The American Journal of Bioethics 11 (11): 1–7. doi:10.1080/15265161.2011.615588. PMID 22047112.
- McGuire, A. L.; Lupski, J. R. (2010). "Personal genome research : What should the participant be told?". Trends in Genetics 26 (5): 199–201. doi:10.1016/j.tig.2009.12.007. PMC 2868334. PMID 20381895.
- Sharp, R. R.; Achkar, J. P.; Brinich, M. A.; Farrell, R. M. (2009). "Helping Patients Make Informed Choices About Probiotics: A Need for Research". The American Journal of Gastroenterology 104 (4): 809–813. doi:10.1038/ajg.2008.68. PMC 2746707. PMID 19343022.
- Cuellar-Partida, G.; Buske, F. A.; McLeay, R. C.; Whitington, T.; Noble, W. S.; Bailey, T. L. (2011). "Epigenetic priors for identifying active transcription factor binding sites". Bioinformatics 28 (1): 56–62. doi:10.1093/bioinformatics/btr614. PMC 3244768. PMID 22072382.
- Haft, D. H. (2011). "Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners". BMC Genomics 12: 21. doi:10.1186/1471-2164-12-21. PMC 3023750. PMID 21223593.
- Caporaso, J. G.; Lauber, C. L.; Costello, E. K.; Berg-Lyons, D.; Gonzalez, A.; Stombaugh, J.; Knights, D.; Gajer, P.; Ravel, J.; Fierer, N.; Gordon, J. I.; Knight, R. (2011). "Moving pictures of the human microbiome". Genome Biology 12 (5): R50. doi:10.1186/gb-2011-12-5-r50. PMC 3271711. PMID 21624126.
- Sczesnak, A.; Segata, N.; Qin, X.; Gevers, D.; Petrosino, J. F.; Huttenhower, C.; Littman, D. R.; Ivanov, I. I. (2011). "The Genome of Th17 Cell-Inducing Segmented Filamentous Bacteria Reveals Extensive Auxotrophy and Adaptations to the Intestinal Environment". Cell Host & Microbe 10 (3): 260–272. doi:10.1016/j.chom.2011.08.005. PMC 3209701. PMID 21925113.
- Ballal, S. A.; Gallini, C. A.; Segata, N.; Huttenhower, C.; Garrett, W. S. (2011). "Host and gut microbiota symbiotic factors: Lessons from inflammatory bowel disease and successful symbionts". Cellular Microbiology 13 (4): 508–517. doi:10.1111/j.1462-5822.2011.01572.x. PMID 21314883.
- Bergmann, G. T.; Bates, S. T.; Eilers, K. G.; Lauber, C. L.; Caporaso, J. G.; Walters, W. A.; Knight, R.; Fierer, N. (2011). "The under-recognized dominance of Verrucomicrobia in soil bacterial communities". Soil Biology and Biochemistry 43 (7): 1450–1455. doi:10.1016/j.soilbio.2011.03.012. PMC 3260529. PMID 22267877.
- Yeoman, C. J.; Yildirim, S.; Thomas, S. M.; Durkin, A. S.; Torralba, M.; Sutton, G.; Buhay, C. J.; Ding, Y.; Dugan-Rocha, S. P.; Muzny, D. M.; Qin, X.; Gibbs, R. A.; Leigh, S. R.; Stumpf, R.; White, B. A.; Highlander, S. K.; Nelson, K. E.; Wilson, B. A. (2010). Li, Wenjun, ed. "Comparative Genomics of Gardnerella vaginalis Strains Reveals Substantial Differences in Metabolic and Virulence Potential". PLoS ONE 5 (8): e12411. doi:10.1371/journal.pone.0012411. PMC 2928729. PMID 20865041.
- Koren, O.; Spor, A.; Felin, J.; Fak, F.; Stombaugh, J.; Tremaroli, V.; Behre, C. J.; Knight, R.; Fagerberg, B.; Ley, R. E.; Backhed, F. (2010). "Colloquium Paper: Human oral, gut, and plaque microbiota in patients with atherosclerosis". Proceedings of the National Academy of Sciences 108 (Supplement_1): 4592–4598. doi:10.1073/pnas.1011383107. PMC 3063583. PMID 20937873.
- Marri, P. R.; Paniscus, M.; Weyand, N. J.; Rendón, M. A. A.; Calton, C. M.; Hernández, D. R.; Higashi, D. L.; Sodergren, E.; Weinstock, G. M.; Rounsley, S. D.; So, M. (2010). Ahmed, Niyaz, ed. "Genome Sequencing Reveals Widespread Virulence Gene Exchange among Human Neisseria Species". PLoS ONE 5 (7): e11835. doi:10.1371/journal.pone.0011835. PMC 2911385. PMID 20676376.
- "NIH Human Microbiome Project defines normal bacterial makeup of the body". NIH News. 13 June 2012.
- The Human Microbiome Project Consortium, Barbara A.; Nelson, Karen E.; Pop, Mihai; Creasy, Heather H.; Giglio, Michelle G.; Huttenhower, Curtis; Gevers, Dirk; Petrosino, Joseph F. et al. (2012). "A framework for human microbiome research". Nature 486 (7402): 215–221. doi:10.1038/nature11209. PMC 3377744. PMID 22699610.
- The Human Microbiome Project Consortium, Curtis; Gevers, Dirk; Knight, Rob; Abubucker, Sahar; Badger, Jonathan H.; Chinwalla, Asif T.; Creasy, Heather H.; Earl, Ashlee M. et al. (2012). "Structure, function and diversity of the healthy human microbiome". Nature 486 (7402): 207–214. doi:10.1038/nature11234. PMC 3564958. PMID 22699609.
- Manuscript Summaries
- Wilder, C., Sandle, T., Sutton, S. (June 2013). "Implications of the Human Microbiome on Pharmaceutical Microbiology". American Pharmaceutical Review.
- Human Microbiome Project
- Data Analysis and Coordination Center
- The CIHR Canadian Microbiome Initiative
- The International Human Microbiome Consortium
- 2006, Lay summary of colon microbiome study (the actual study: Gill et al., 2006)
- Olivia Judson Microbes ‘R’ Us New York Times 22 July 2009
- Gina Kolata Good Health? Thank Your 100 Trillion Bacteria New York Times 13 June 2012