A (growing) collection of important papers on specific topics. No list is ever complete; just trying to make a good starting point for a literature search or grant proposal. Please send suggestions for additional key papers by leaving a comment. Updated August 2016, Elisabeth Bik, Stanford University

General Microbiome Reviews

Human microbiome papers:

• Human Oral Microbiome
• Human Respiratory Microbiome
• Human Vaginal Microbiome (also see Pregnancy)
• Human Skin Microbiome
• Human Beard Microbiome
• Human Stomach Microbiome
• Human Gut Microbiome
• Human Pregnancy Microbiome
• Human Breast Milk Microbiome
• Infant Colonization 
• Wound Microbiome

Other, non-human microbiome papers:

• Animal Microbiome
• Plant, Root, Soil Microbiome
• Water Microbiome
• Outdoor Air Microbiome
• Indoor Air and Surface Microbiome
• Microbes in Space
• Archaeological Microbiology
• Microbiome of Death
• Forensic Microbiology
• Food Microbiology
• Beer and Wine Microbiology
• Microbiome Vocabulary
• Microbiome, Speciation, Evolution
• Synthetic Microbial Communities
• Sample Storage

My favorite microbiome datasets (list might change over time):

1. Diversity of the human intestinal microbial flora, 2005. Eckburg PB, Science (shameless self plug)
2. Host lifestyle affects human microbiota on daily timescales – Lawrence A David – Genome Biology. Gut and oral samples from 2 persons followed for over a year. Showed that microbiotas are different between persons, relatively stable over time, with big disturbances created by travel or illness. Beautiful graphs (figure 1 is the best!)
3. Human gut microbiome viewed across age and geography – Tanya Yatsunenko – Nature 2012.  One of the first papers to include non-Western subjects. Also shows that the gut communities of kids are starting to become “adult-like” around age 3.
4. A very new paper, so fresh in my mind, but very nice: Walls talk: Microbial biogeography of homes spanning urbanization – Jean F. Ruiz-Calderon – Science Advances – 2016
5. Continental-scale distributions of dust-associated bacteria and fungi – Albert Barberán – PNAS – April 2015.
6. Bacterial Community Variation in Human Body Habitats Across Space and Time – Elizabeth K. Costello – 2007 – Science.
7. The Soil Microbiome Influences Grapevine-Associated Microbiota – Iratxe Zarraonaindia – 2015 – mBio
8. Succession of microbial consortia in the developing infant gut microbiome – Jeremy E. Koenig – PNAS 2010 – How a healthy baby get colonized over time
9. Cohabiting family members share microbiota with one another and with their dogs – Se Jin Song – 2013 – eLIFE
10. Persistent gut microbiota immaturity in malnourished Bangladeshi children – Sathish Subramanian – 2014 Nature