Summary: The human microbiome is the collection of microorganisms that reside in and on humans, including bacteria, archaea, protists, fungi and viruses. They have significant positive and negative effects on human health, including aiding digestion and interacting with our immune system. We’ll focus on papers that investigate the links between human genome variation and microbiome variation, and their joint impact on human health.
Coordinator this quarter: Sharon Browning (email@example.com)
Website: http://courses.washington.edu/b581/ (link to “current schedule” and also read the “how to” guide).
October 10: ASHG posters, presented by those who will be attending the ASHG meeting.
October 17: David, Bowen (Faculty advisor: Sharon Browning)
The Human Microbiome Project Consortium, 2012. Structure, Function and Diversity of the Healthy Human Microbiome. Nature 486:207-214. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564958/
An investigation into the human microbiome and inter-individual differences. This paper will serve as our introduction to the human microbiome.
October 24: Report back from ASHG, presented by those who attended the ASHG meeting.
October 31: Edward, Anya, Joe (Faculty advisor: Tim Thornton)
Frank DN, Robertson CE, Hamm CM, Kpadeh Z, Zhang T, et al. 2011. Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm. Bowel Dis. 17(1):179–84 http://onlinelibrary.wiley.com/doi/10.1002/ibd.21339/full
Interaction between genetic causes of inflammatory bowel disease (IBD) and the gut microbiome of IBD patients.
November 7: Kaleigh, Kelsey (Faculty advisor: Sharon Browning)
Davenport ER, Cusanovich DA, Michelini K, Barreiro LB, Ober C, Gilad Y. 2015. Genome-wide association studies of the human gut microbiota. PLOS ONE 10(11):e0140301 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140301
Study in Hutterites (a small founder population). “We examined the fecal microbiome from the Hutterites, a religious isolate living in North America. Importantly, members of this population live and eat on large communal farms, called colonies, limiting inter-individual variation in environmental exposures that might mask genetic effects on microbiome composition. In particular, meals are prepared and eaten in a communal kitchen and dining room, respectively.”
November 14: Zora, Xiaowen (Faculty advisor: Ellen Wijsman)
Lim MY, You HJ, Yoon HS, Kwon B, Lee JY, et al. 2017. The effect of heritability and host genetics on the gut microbiota and metabolic syndrome. Gut 66:1031–38 http://gut.bmj.com/content/66/6/1031
Korean twins and their families. Gut microbiome and metabolic syndrome. Heritability of microbiome.
November 21: Aaron, Alex, Yiqun (Faculty advisor: Sharon Browning)
Xu L, Paterson AD, Turpin W, Xu W. 2015. Assessment and selection of competing models for zero-inflated microbiome data. PLOS ONE 10(7):e0129606 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129606
“Typical data in a microbiome study consist of the operational taxonomic unit (OTU) counts that have the characteristic of excess zeros, which are often ignored by investigators. In this paper, we compare the performance of different competing methods to model data with zero inflated features through extensive simulations and application to a microbiome study. These methods include standard parametric and non-parametric models, hurdle models, and zero inflated models.”
November 28: Amarise, Krystal (Faculty advisor: Liz Blue)
Turpin W, Espin-Garcia O, Xu W, Silverberg MS, Kevans D, et al. 2016. Association of host genome with intestinal microbial composition in a large healthy cohort. Nat. Genet. 48(11):1413–17 https://www.nature.com/ng/journal/v48/n11/full/ng.3693.html
Heritability and genetic associations, using 1500+ individuals from Canada.
December 5: Anna Plantinga, presenting her microbiome research.
Extra papers for optional reading:
Goodrich JK, Davenport ER, Beaumont M, Jackson MA, Knight R, et al. 2016. Genetic determinants of the gut microbiome in UK twins. Cell Host Microbe 19(5):731–43 http://www.sciencedirect.com/science/article/pii/S1931312816301536
1000+ twin pairs from the UK. Heritable taxa, and an association between lactase persistence and Bifidobacterium.
Beaumont M, Goodrich JK, Jackson MA, Yet I, Davenport ER, et al. 2016. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biol. 17(1):189 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1052-7
Genetic variants affect your microbiome, which in turn affect your phenotype, in this case your body’s accumulation of fat.
Price et al. 2017. A wellness study of 108 individuals using personal, dense, dynamic data clouds. Nature Biotechnology 35:747-756. https://www.nature.com/nbt/journal/v35/n8/full/nbt.3870.html
Connecting human genome, microbiome and more. The current sample size is small, but the implications for the future of medicine could be large.