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Cecil Lewis

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Cecil M. Lewis, Jr.

Ph.D. University of New Mexico, 2005

Office: Dale Hall Tower 805A

Laboratory:  Stephenson Research and Technology Center (SRTC), Room #1098
Phone: (405) 325-3415 (MAL)

Websites:  or

Research Interests

  • Human diversity
  • The microbiome
  • Multiomic methods (aka, panomics and integrated omics)
  • Community engagement
  • Ethics


Dr. Cecil M. Lewis Jr. is a Professor of Anthropology at University of Oklahoma (OU), primarily focusing on the evolution of the human microbiome. Dr. Lewis early career focused on human population genetics; he was awarded and National Science Foundation Career Award in this area. Dr. Lewis began to study the human microbiome during the early days of the discipline; he is arguably the first anthropologist to lead human microbiome research. Dr. Lewis published the first  ancient human microbiome profile using next generation DNA sequencing technologies in 2008. This was the same year the U.S. National Institutes of Health (NIH) announced their Human Microbiome Project (HMP). Dr. Lewis became a member of the HMP consortium. Included in his NIH HMP supported studies was an active push toward expanding community engagement, with a particular focus on Native and descended communities that are stakeholders in molecular anthropological studies. His work includes microbiome studies with hunter gatherer and rural agriculturalist communities, and Native communities in the US. For one example, after a four year engagement with Cheyenne and Arapaho tribes, Dr. Lewis led the first gut microbiome study conducted in partnership with American Indian tribes. His initial studies catalyzed a 12-year career in innovating microbiome science, while advocating, where applicable, a community-first perspective. At OU, Dr. Lewis is the founding director of the Laboratories of Molecular Anthropology and Microbiome Research (LMAMR). Highly successful in all metrics of research, mentoring, and community engage impact, LMAMR includes a set of shared staff support, laboratories and equipment for faculty representing biochemical, biological, and anthropological sciences. Dr. Lewis also serves as the director for OU Consolidated Core Laboratory for genomic services, which uses shared equipment and external partnerships to pipeline genomic data generation for OU. Dr. Lewis contributions repeatedly garner national press, represent a series of anthropological and microbiome research milestones, and has been supported repeatedly by NSF, NIH, and other foundations, including aforementioned CAREER Award and a current NIH Center for Excellence.
Courses and Seminars: Dr. Lewis has taught a wide range of courses as a faculty member, including introductory courses to Anthropology and Biological Anthropology, the core course for the OU's PhD and "Health and Human Biology", various genetics courses, and a classic class in biological sciences - the “Introduction to Population Genetics”. He has organized numerous workshops for science education, explaining evolution and health, genetics and the microbiome, both internationally and nationally, including within rural areas of Oklahoma. This includes partnering with Native education programs. In the last 12 years, his lab has trained 4 postdoctoral fellows, 11 graduate students, 11 undergraduate students, and 3 high school students. Moreover, the broader research group he founded, and now co-directs, has over 40+ members that include faculty, staff, students, and other professionals.

Recent/Significant Publications

2020 Jacobson DK, Honap TP, Monroe C, Lund J, Houk BA, Novotny AC, Robin C, Marini E, Lewis Jr CM. Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus. Phil. Trans. R. Soc. B 375: 20190586.

2020 Stone AC, Lewis Jr CM Schuenemann VJ Insights into health and disease from ancient biomolecules. Phil. Trans. R. Soc. B 375: 20190568.

2020 Honap TP, Sankaranarayanan K, Schnorr ST, Ozga A, Warinner C, Lewis Jr. CM. Biogeographic study of human gut associated CrAssphage suggests impacts from industrialization. PLoS One. 2020 Jan 15;15(1):e0226930. doi: 10.1371/journal.pone.0226930. eCollection 2020

2019 Hagan RW, Hofman CA, Hübner A, Reinhard K, Schnorr S, Lewis Jr CM, Sankaranarayanan K, Warinner C. Comparison of extraction methods for recovering ancient microbial DNA from paleofeces. 30 November 2019

2019 Lewis Jr. CM, McCall LI, Sharp R, Spicer P. Ethical Priority of the Most Actionable System of Biomolecules - the Metabolome. American Journal of Physical Anthropology. Feb;171(2):177-181. doi: 10.1002/ajpa.23943. Epub 2019 Oct 23.

2019 Patel NB, Obregón-Tito AJ, Tito RY, Trujillo-Villaroel O, Marin-Reyes L, Troncoso-Corzo L, Guija-Poma E, Lewis Jr. CM, Lawson PA. Citroniellla saccharovorans gen. nov., sp. nov. isolated from feces from a hunter-gatherer community in Peru. Int J Syst Evol Microbiol. 69(4):1142-1148. doi: 10.1099/ijsem.0.003287

2019 Schnorr SL, Hofman C, Shandukani R, Duncan FD, Honap TA, Lesnik J, Lewis Jr. CM Taxonomic features and comparisons of the gut microbiome from two edible fungus-farming termites (Macrotermes falciger; M. natalensis) harvested in the Vhembe district of Limpopo, South Africa. BMC Microbiology. 17;19(1):164. doi: 10.1186/s12866-019-1540-5.

2018 Ziesemer KA, Ramos-Madrigal J, Mann AE, Brandt B, Sankaranarayanan K, Ozga A, Hoogland M, Hofman C, Salazar-Garcia D, Frohlich B, Milner G, Stone AC, Aldenderfer M, Lewis Jr. CM, Hofman CL, Warinner C, Schroeder H. The efficacy of whole human genome and high-throughput sequencing on ancient dental calculus. AJPA. 2018, online. doi: 10.1002/ajpa.23763

2018 Mann AE, Sabin S, Ziesemer K, Vagene AJ, Schroeder H, Ozga AT, Sankaranarayanan K, Hofman CA, Fellows Yates JA, Salazar-Garcia DC, Frohlich B, Aldenderfer M, Hoogland M, Read C, Milner GR, Stone AC, Lewis CM, Jr., Krause J, Hofman C, Bos KI, Warinner C. Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Sci Rep. 2018,8(1):9822. doi: 10.1038/s41598-018-28091-9.2018

2018 McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vazquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, American Gut C, Knight R. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018,3(3). doi: 10.1128/mSystems.00031-18.

Courses Taught

  • ANTH 1113 What Makes Us Human
  • ANTH 3203 Introduction to Biological Anthropology
  • ANTH 4083 Genetic Perspectives on Human Evolution
  • ANTH 5423 Introduction of Population Genetics
  • ANTH 6843 Foundation in Medical and Biological Anthropology