Curriculum Vitae

Microbial Ecology, Ancient DNA, Forensics, Conservation Genetics


2007 Ph.D. University of Colorado, Ecology and Evolutionary Biology
2000 B.S. University of Georgia, Chemistry, Biology Minor

Professional Experience

2018 - current     Associate Professor, Department of Animal Sciences, CSU                                                                                                                                          2016 – 2018        Assistant Professor, Department of Animal Sciences, CSU
2015 – 2016        Assistant Project Scientist step IV, University of San Diego, CA
2013 – 2016        Senior Research Associate, University of Colorado, Boulder, CO
2010 – 2013        Post-doc, University of Colorado, Boulder, CO
2008 – 2010       Post-doc, Australian Centre for Ancient DNA, Adelaide, Australia
2003 – 2007      Contracts w/ Pisces Molecular, CDOW, USFS, USFWS
2001 – 2002       TA, University of Colorado, Boulder, CO

Merit Awards

2005-2007 AAAS/Science Program for Excellence in Science
2003-2006 National Science Foundation Graduate Fellowship
1996- 2000 Barry Goldwater Scholarship for Math, Science, and Engineering, UGA Chemistry Student of the Year, UGA Honors

Recent Funding

Utilizing microbiome and bioinformatic tools to reduce energy use and food waste in poultry. Innovation Institute for Food and Health. 2017-2019. PI Jessica L Metcalf. Co-PIs Jennifer N. Martin, Keith Belk, Jonathan Eisen, David Coil and Xiang Yang. $210,950.

Improving estimates of the postmortem interval with metagenomics and metabolomics.  PI Jessica L. Metcalf. . National Institutes of Justice. 2016-DN-BX-4194. Co-PIs: Pieter Dorrestein, Rob Knight, and David Carter.  $684,273.

Microbial clocks for estimating the postmortem interval of human remains at three anthropological research facilities. National Institutes of Justice. 2015-DN-BX-K016. 01/2016 – 12/31/2018. PI Jessica L. Metcalf, CU Boulder. Co-PIs Rob Knight, David O. Carter, Franklin Damann. $863,485

Evaluating the skin microbiome as trace evidence. National Institutes of Justice. 01/2015 – 12/2016.  PI Rob Knight. Co-PIs Jessica L. Metcalf (primary project designer and writer), Jack Gilbert, David Carter.  $637,484.

Characterization of bacterial and fungal communities associated with corpse decomposition using next generation sequencing. 2012 - 2013. Department of Justice.  PI Rob Knight. Co-PIs Jessica L. Metcalf (primary project designer and writer), Noah Fierer, David O. Carter, and Arpad A. Vass.  $894,629

National Evolutionary Synthesis Center Catalysis Meeting (NESCent).  2009. Integrating datasets to investigate megafauna extinction in the late Quaternary.  Co-PIs Jessica L. Metcalf, Robert Guralnick and Alan Cooper.  Meeting June 2010.

Environmental Futures Network, University of Adelaide.  Early Career Research Grant. PI. Jessica L. Metcalf $13,500.  Workshop: Methods Bioinformatics & Molecular Evolution. 14-17 April, 2009,


Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E,  Amir A, Willerslev E, Knight R, McKenzie V, Orlando L. 2017. Does domestication and captivity shape the horse gut microbiome? Scientific Reports.  Vol. 7, 1-9.

Weinroth MD, Carlson CR, Martin JN, Metcalf JL, Morley PS, Belk KE., 2017. 16S rRNA Characterization of Liver Abscesses in Feedlot Cattle from Three States in the United States. Journal of Animal Sciences. doi:10.2527/asasann.2017.093

McKenzie VJ, Song SJ, Frédéric D, Prest TL, Oliverio AM, Korpita TM, Alexiev A, Amato KR, Metcalf JL, Kowalewski M, Avenant NL, Link A, Di Fiore T, Seguin-Orlando A, Feh CO, Orlando L, Mendelson JR, Sanders J, Knight R., 2017. The effects of captivity on the mammalian gut microbiome. Integrative and Comparative Biology, Volume 57, Issue 4, 1 October 2017, Pages 690–704

Metcalf JL, Xu Z, Boulsimani A, Dorrestein P, Knight R. Microbiome tools for forensic science. Trends in Biotechnology. 23 (9) p814-823. DOI:10.1016/j.tibtech.2017.03.006

Morton JT, Toran L, Edlund A, Metcalf JL, Lauber C, Knight R. Uncovering the horseshoe effect in microbial analyses. mSystems. Feb 2017, 2 (1) e00166-16; DOI: 10.1128/mSystems.00166-16.

Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vázquez-Baeza Y, Navas-Molina JA, Song SJ, Metcalf JL, Hyde ER, Lladser M, Dorrestein PC, Knight R. 2017. Balance trees reveal microbial niche differentiation. mSystems. Jan 2017, 2 (1) e00162-16; DOI: 10.1128/mSystems.00162-16.

Metcalf JL, Carter DO, Knight R. 2016. Microbiology of Death. Current Biology. 26:13. DOI:

Metcalf JL, Xu Z, Van Treuren W, Hyde ER, Haarmann D, Amir A,Weiss S, Song S, Lauber C, Bibat, A, Ackermann G, Nicholas C, Gebert M, Humphrey G, Carter DO, Lynne A, Bucheli S, Knight R. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. DOI: 10.1126/science.aad2646. 

Weiss S, Carter DO, Metcalf JL, Knight R. 2015. Carcass mass has little influence on the structure of gravesoil microbial communities. International Journal of Legal Medicine. 10.1007/s00414-015-1206-2.

Obregon-Tito AJ, Tito RY, Metcalf JL, Clemente J, Ursell LK, Van Treuren W, Knight R, Spicer P, Lawson P, Marin-Reyes L, Trujillo-Villarroel O, Foster M, Guija-Poma E, Troncoso-Corzo L, Ozga AT, Lewis CM. 2015. Amazonian Hunter-gatherers have taxonomically simple but metabolically complex microbiomes relative to other human populations. Nature Communications. 6:6505. doi:10.1038/ncomms7505.

Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Noya-Alarcón O, Contreras M, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez SM, Metcalf JL, Knight R, Dantas G, Dominguez-Bello MG. 2015. The microbiome of uncontacted Amerindians. Science Advances. 1:3 DOI: 10.1126/sciadv.1500183.

Carter. DO*, Metcalf JL*, Bibat A, Knight R. 2015. Seasonal variation of postmortem microbial communities. 2015. Forensic Science, Medicine, and Pathology. 10.1007/s12024-015-9667-7.  *Authors contributed equally.

Stowell SML, Kennedy C.M, Beals SC, Metcalf J L, Martin AP. 2015. The genetic legacy of more than a century of stocking trout: a case study in Rocky Mountain National Park, Colorado, USA. Canadian Journal of Fisheries and Aquatic Sciences 72, 1565-1574, doi:10.1139/cjfas-2015-0009.

Weiss S, Amir A, Hyde ER, Metcalf JL, Song S and Knight R. 2014. Tracking down the sources of experimental contamination in microbiome studies. Genome Biology, 15:564  doi:10.1186/s13059-014-0564-2. 

Llamas B, Brotherton P, Mitchell KJ, Templeton J, Thomson VA, Metcalf JL, Armstrong KN, Kasper M, Richards SM, Camens AB, Lee MSY, Cooper A. 2014. Late Pleistocene Australian marsupial DNA clarifies the affinities of extinct megafaunal kangaroos and wallabies. Molecular Biology and Evolution. DOI: 10.1093/molbev/msu338 .

Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell, LK, Vazquez-Baeza, Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert, J. A.Longitudinal analysis of microbial interaction between humans and the indoor environment. Science. 2014, 345(6200):1048-1052.

Metcalf JL, Ursell LK, Knight R. Ancient human oral plaque preserves a wealth of biological data. 2014. Nature Genetics. 46, 321–323. doi:10.1038/ng.2930.

Lauber CL, Metcalf JL, Keepers K, Ackermann G, Carter DO, Knight R. 2014. Vertebrate Decomposition is Accelerated by Soil Microbes. Applied and Environmental Microbiology. EPub ahead of print.

Metcalf JL, Prost S, Nogues-Bravo D, Dechaine EG, Anderson C, Batra P, Araujo MB, Cooper A, Guralnick R. 2014. Integrating multiple lines of evidence into historical biogeography hypothesis testing: a Bison bison case study. Proceedings of the Royal Society B. online early.  doi:10.1098/rspb.2013.2782.

Metcalf JL, Parfrey LW, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Fierer N, Carter DO, Knight R. 2013. A microbial clock provides an accurate estimate of the postmortem interval. eLife, DOI: 10.7554/eLife.01104.  Coverage by National Public Radio

Delsuc F, Metcalf JL, Wegener Parfrey L, Song SJ, González A, Knight R. 2013. Convergence of gut microbiomes in myrmecophagous mammals. Molecular Ecology, online in advance of print. doi:10.1111/mec.12501

Ursell, LK, Treuren, WV, Metcalf, JL, Pirrung M, Gewirtz A, and Knight R. (2013), Replenishing our defensive microbes. 2013. Bioessays, 35: 810–817. doi: 10.1002/bies.201300018

McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Lošo T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ. 2013. Proceedings of the National Academy of Sciences. 110(9):3229-36. doi: 10.1073/pnas.1218525110. 

Tito RY, Knights D, Metcalf JL, Obregon-Tito AJ, Cleeland L, Najar F, Roe B, Reinhard R, Sobolik K, Belknap S, Foster M, Spicer P, Knight R, Lewis CM. 2012. Insights from Characterizing Extinct Human Gut Microbiomes.PLoS ONE, 7 (12): e51146 DOI:10.1371/journal.pone.0051146.

Metcalf JL, Love Stowell S, Kennedy CM, Rogers KB, Epp J, Keepers K, Cooper A, Austin JJ, Martin AP. 2012. Historical stocking records and a comparison of 19th to 21st century DNA reveals the extent of human-induced changes to native diversity and distribution of cutthroat trout. Molecular Ecology, 21: 5194-5207.

Rawlence, NJ, Metcalf, JL, Wood, JR, Worthy, TH, Austin, JA, Cooper, A. 2012. The effect of climate and environmental change on the megafaunal moa of New Zealand in the absence of humans.Quaternary Science Reviews, 50:141-153.

Bray SCE, Austin JJ, Metcalf JL, Østbye K, Østbye E, Lauritzen S., Aaris-Sørensen K, Valdiosera C, Adler CJ, Cooper A. 2012. Ancient DNA identifies post-glacial recolonisation, not recent bottlenecks, as the primary driver of contemporary mtDNA phylogeography and diversity in Scandinavian brown bears. Diversity and Distributions.   DOI: 10.1111/j.1472-4642.2012.00923.x

Ursell LK, Metcalf JL, Parfrey LW, Knight R. 2012. Defining the human microbiome. Nutritional Reviews. 538-544.

Gonzalez A, King A, Robeson MS, Song S, Shade A, Metcalf JL, Knight R. 2011. Characterizing microbial communities through space and time. Current Opinion Biotechnology. 35(9):810-7. doi: 10.1002/bies.201300018.

Gonzalez A, Clemente JC, Shade A, Metcalf JL, Song S, Prithiviraj B, Palmer BE, and Knight, R. Our microbial selves: what ecology can teach us. EMBO reports. 12, 775–784. doi:10.1038/embor.2011.137

Orlando, L, Metcalf JL, Alberdi MT, Telles-Antunes M, Bonjean D, Otte M, Martin F, Eisenmann V, Mashkour M, Morello F, Prado JL, Salas-Gismondi R, Shockey B, Wrinn PJ, Vasil’ev SK, Ovodov ND, Cherry MI, Hopwood B, Male D, Austin JJ, Hanni C, Cooper A. 2009. Revising the recent evolutionary history of equids using ancient DNA. 2009. Proceedings of the National Academy of Sciences. 106(51) 21754-21759.

Pritchard VL, Metcalf JL, Jones K, Martin AP, Cowley DE. 2008. Population structure and genetic management of Rio Grande cutthroat trout (Oncorhynchus clarkii virginalis). Conservation Genetics, doi: 10.1007/s10592-008-9652-8.

Osborne AS, Som P, Metcalf JL, Phillips RS. 2008. Regioselective nitration of N-alpha,N-1-bis(trifluoroacetyl)-L-tryptophan methyl ester: Efficient synthesis of 2-nitro and 6-nitro-N-trifluoroacetyl-L-tryptophan methyl ester. Bioorganic & Medicinal Chemistry Letters. 18(21) 5750-5752.

Metcalf, JL, VL Pritchard, SM Silvestri, JB Jenkins, JS Wood, DE Cowley, RP Evans, DK Shiozawa, & AP Martin. 2007 Across the great divide: genetic forensics reveals misidentification of populations of an endangered species. Molecular Ecology Fast-Track. 16(21):4445-54. highlighted in ScienceNOW and Nature News

Metcalf JL, Siegle MR, Martin AP. 2008. Hybridization dynamics of native greenback cutthroat trout and introduced rainbow trout.The Journal of Heredity. 99(2):149-56.

Pritchard VL, Jones K, Metcalf JL, Martin AP, Wilkinson P., and Cowley DE. 2007. Characterization of tetranucleotide microsatellites for Rio Grande cutthroat trout and rainbow trout, and their cross-amplification in other cutthroat trout subspecies. Molecular Ecology Notes. 7 (4): 594-596.

Freiburger BJ, Breed MD, Metcalf JL. 2004. Mating frequency, within-colony relatedness and male production in a yellow jacket wasp, Dolichovespu arenaria. Molecular Ecology. 13 (12): 3703-3707

Metcalf, JL. 2000. Broadening your undergraduate experiences. In Chemistry.  Feb/March. 11-13.


Books and chapters

Forensic Microbiology. Editors Carter DO, Tomberlin JK, Benbow EM, and Metcalf JL.  2017. ISBN: 978-1-119-06255-4. Sponsored by the American Academy of Forensic Sciences.

Carter DO, Tomberlin JK, Benbow EM, and Metcalf JL.  2017. Perspectives on the future of forensic microbiology. Forensic Microbiology. Editors Carter DO, Tomberlin JK, Benbow EM, and Metcalf JL.. ISBN: 978-1-119-06255-4

Hyde ER, Metcalf JL, Bucheli SR, Lynne AM, Knight R. Microbial Communities Associated with Decomposing Corpses. Forensic Microbiology. Editors Carter DO, Tomberlin JK, Benbow EM, and Metcalf JL.. ISBN: 978-1-119-06255-4.

Metcalf JL, Carter D.O, Knight R. Microbiome studies of carrion decomposition. in Carrion Ecology, Eds. Eric M. Benbow , Jeffrey K. Tomberlin, and Aaron M. Tarone. 2015.

Metcalf, JL and Wheeler J. Domestication of South American Camelids. Invited Chapter for Encyclopedia of Global Archaeology. Springer. 2014.


Teaching Experience

Innovative Teaching - Massive Open Online Course: Gut Check: Exploring your microbiome, Oct 6 - Nov 15, 2014

Guest Lecturer: CU-Boulder, Science Writing, Center for Environmental Journalism, Fall 2012, 2013, 2014.

Guest Lecturer: CU – Boulder, Conservation Biology Course, 75 students, Fall 2011, 2012, 2014,  “Conservation Genetics using ancient DNA”

Teaching assistant: CU-Boulder, Microbiology (EBIO 3400), 2001


Invited Talks

University of Colorado Denver, Department of Pharmaceutical Sciences, June 11, 2015 "The microbiome as a biomarker for human health"

Colorado State University, September 2, 2014 “Fecal Transplants, Viking Poop and Crime Scenes: What’s Next In the Wild World of Microbiome Research?”

66th annual American Academy of Forensic Sciences workshop Forensic Microbiology, Where Do We Begin? February 17th, 2014:  “Current Microbiology & Forensic Microbiology”

66th annual American Academy of Forensic Sciences workshop Forensic Microbiology, Where Do We Begin?, February 17th, 2014: “Perspective on Forensic Microbiology”

Sam Houston State University, March 25, 2014 “A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system”

Illumina Midwest User’s meeting, November 6, 2013 “A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system”

Denver University, October 14th, 2013 “From endangered trout to viking latrines: ancient DNA as a tool for conservation and evolutionary biology”

Colorado College, April 4, 2013, “The Journey of Cutthroat Trout in Colorado”

Northern Arizona University, November 1, 2012 “From endangered trout to viking poo -Ancient DNA as a tool for conservation and evolutionary biology”


Public Outreach

Campus Creek Middle School, December 4, 2015, "The human microbiome: stories of a poologist"

Contributor DMNS Blog, November 2014, “Gut Check

Massive Open Online Course (MOOC): Gut Check: Exploring your microbiome, October 6 - Nov 15, 2014

Biotech panel at Denver Museum of Nature and Science, September 9, 2014

Teen Science Café, Denver Botanic Gardens, October 9, 2014 “Reconstructing gut microbiomes from poo (new and old)”

Teen Science Café, CU-Boulder Museum of Natural History, October 29, 2014 “Reconstructing gut microbiomes from poo (new and old)”

University of Colorado, Colorado Springs Café Scientifique series, September 10, 2013, “The Journey of Cutthroat Trout in Colorado”

Aspen Center for Environmental Studies, January 11, 2013 “The Journey of Cutthroat Trout in Colorado”


Recent workshops and meetings

Recent Advances in Biomolecular Archeology (co-moderator and presenter). International Committee of Archeozoology. September 22-25, 2014.

Pathology/Biology “Microbes” session (co-moderator and presenter). 66th annual American Academy of Forensic Sciences.

Forensic Microbiology: Where Do We Begin? Workshop at the 66th annual American Academy of Forensic Sciences (presenter). February 17th, 2014.

The origin and evolution of animal-microbe interactions. NESCent Catalysis meeting (participant). October 23-27, 2011.

International Union for Quaternary Research 2011 (INQUA XVIII).  Extinction Events (session co-chair and speaker).

Integrating datasets to investigate megafauna extinction in the late Quaternary. NESCent Catalysis (PI). Meeting May 25 – 30, 2010.


Popular Media/Press

Microbes and forensic science

eLife pod cast, episode 5, and five year anniversary follow up interview in episode 42

Science Magazine podcast: Dancing dinosaurs, naked black holes, and more

The New York Times Magazine:

KGNU Science Show, How on Earth:

National Public Radio:

The Atlantic:


CU Press Release:

Microbiome highlight

The Denver Post:

Early Career highlight by eLIFE

2014 greenback cutthroat trout coverage

Highlight of recent microbial forensics research

CU Connections Faculty and Staff Highlight: Five Questions for Jessica Metcalf

2012 cutthroat trout research media coverage

Caving expedition in search of well-preserved Australian megafauna with National Geographic.

Interviewed for the New York Times about a publication on ancient horses

Media coverage about native cutthroat trout genetics research