Jessica L Metcalf — Metcalf lab

Curriculum Vitae

Microbial Ecology, Ancient DNA, Forensics, Conservation Genetics

Education

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

Funding

Expanding and validating microbiome database for estimating the postmortem interval. PI Jessica L Metcalf Co-PIs Rob Knight, Zachery Burcham, and David Carter. National Institute of Justice 15PNIJ-22-GG-04402-MUMU. $834,503

BII: Regional OneHealth Aerobiome Discovery Network (BROADN), National Science Foundation, PI Susan VandeWoude, Co-PIs Sonia Kreidenweis-Dandy, Angela Bosco-Lauth, Jan Leach, and Eugene Kelly Role: Jessica L. Metcalf Co-I and team co-lead for Theme 1 (of 4 themes). $12,499,974.

Human Decomposition: Effect of Indoor Versus Outdoor Decomposition on the Microbiome of Human Cadavers and Implications for Future Forensic Research. PI Sibyl Bucheli; Co-PIs Aaron Lynne, Jessica L Metcalf, Rob Knight. National Institute of Justice 2019-DU-BX-0025. $808,296

Evaluating low-biomass microbial communities associated with spontaneous canine tumors as a translational model for human disease. PI Jessica L Metcalf. Co-PIs: Susan Lana. $20,000

Dairy cattle as a model for studying the chronobiology of human milk and its microbiome. PI Jessica L Metcalf. Co-PIs: Meghan Azad, Catie Cramer. Canadian Institute for Advanced Research. $28,704 CAD.

One health and the Microbiome of North American Livestock Workers. PI Jessica L Metcalf. Co-PIs Melissa Melby, Mark Richter, Katherine Amato, Naama Geva-Zatorsky, Carolina Tropini. Canadian Institute for Advanced Research. $21,000 CAD.

Estimating the postmortem interval of human skeletal remains using rapid, inexpensive microbiome tools. PI Jessica L Metcalf. Co-PIs Sibyl Bucheli, Aaron Lynne. National Institute of Justice 2019-DU-BX-0010. $390,748.

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. https://www.nescent.org/science/awards.php

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, http://www.adelaide.edu.au/acad/events/workshop/

Publications

Martino C, Dilmore AH, Burcham ZM, Metcalf JL, Jeste D, Knight R. 2022. Microbiota succession throughout life from the cradle to the grave. Nature Reviews Microbiology. https://doi.org/10.1038/s41579-022-00768-z

Belk, AD, Frazier AN, Fuerniss L, Geornaras I, Delmore R, Martin JN, Metcalf JL. 2022. A Pilot Study: the Development of a Facility-Associated Microbiome and Its Association with the Presence of Listeria Spp. in One Small Meat Processing Facility. Microbiology Spectrum. DOI: https://doi.org/10.1128/spectrum.02045-22

Burcham LR, Burcham ZM, Akbari, Metcalf JL, Doran KS. 2022. MS, Interrelated Effects of Zinc Deficiency and the Microbiome on Group B Streptococcal Vaginal Colonization. DOI: https://doi.org/10.1128/msphere.00264-22

Deel, H.L., Montoya, S. King K, Emmons A, Huhn C, Lynne AM, Metcalf JL, Bucheli SR. 2022. The microbiome of fly organs and fly-human microbial transfer during decomposition. Forensic Science International. https://doi.org/10.1016/j.forsciint.2022.111425

Weinroth MD, Belk AD, Dean C, Noyes N, Dittoe DK, Rothrock MJ, Ricke SC, Myer PR, Henniger MT, Ramírez GA, Oakley BB, Summers KL, Miles AM, Ault-Seay TB, Yu Z, Metcalf, JL, Wells J E. (2022). Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies. Journal of Animal Science, 100(2). https://doi.org/10.1093/jas/skab346

Weinroth MD, Thomas KM, Doster E, Vikram A, Schmidt JW, Arthur TM, Wheeler TL, Parker JK, Hanes AS, Alekozai N, Wolfe C, Metcalf JL, Morley PS, Belk KE. 2022. Resistome and Microbiome of Meat Trimmings and Colon Content from Culled Cows raised in Conventional and Organic Production Systems. Animal Microbiome. https://doi.org/10.1186/s42523-022-00166-z

Fuerniss LK, Davis HE, Belk AD, Metcalf JL, Engle TE, Scanga JA, Garry FB, Bryant TC, Martin JN. 2022. Liver abscess microbiota of feedlot steers finished in natural and traditional management programs, Journal of Animal Science. skac252 https://doi.org/10.1093/jas/skac252

Deel, H, Emmons, AL, Kiely J, Damann, FE, Carter, DO, Lynne A, Knight R, Xu ZZ, Bucheli S, Metcalf, JL. 2021. A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition. mSphere, e0045521. DOI: https://doi.org/10.1128/mSphere.00455-21

Dillon MR, Bolyen E, Adamov A, A.D. Belk, Borsom E, Burcham Z, Debelius JW, Deel H, Emmons A, Estaki M, Herman C, Keefe CR, Morton JT, Oliveira RM, Sanchez A, Simard A, Vázquez-Baeza Y, Ziemski M, Miwa, HE, Kerere TA, Coote C, Bonneau R, Knight R, Oliveira G, Gopalasingam P, Kaehler PD, Cope EK, Metcalf JL, Robeson MS, Bokulich NA, Caporaso JG. 2021. Experience and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLOS Comp Bio. 17(6): e1009056 https://doi.org/10.1371/journal.pcbi.1009056

Burcham ZM, Weitzel MA, Hodges LD, Deel HL, Metcalf JL. A pilot study characterizing gravesoil bacterial communities a decade after swine decomposition. Forensic Sci Int. 2021 Apr 21;323:110782. doi: 10.1016/j.forsciint.2021.110782. Epub ahead of print. PMID: 33894685.

Belk AD, Duarte TL, Coil DA, Belk KE, Eisen JA, Quinn JC, Martin JN, Yang X, Metcalf JL. 2021. Air versus water chilling of chicken: a pilot study of quality, shelf-life, microbial ecology, and economics. mSystems.

Microbiome Centers Consortium COVID Committee. 2020. Coordinating and Assisting Research at the SARS-CoV-2/Microbiome Nexus. mSystems. 10.1128/mSystems.00999-20

Burcham ZM, Garneau NL, Comstock SS, Tucker RM, Knight R, Metcalf JL* & Genetics of Taste Lab Citizen Scientists. 2020. Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study. Scientific Reports, 10, 2133 https://doi.org/10.1038/s41598-020-59016-0

Poore GD, Kopylova E, Zhu Q, Carpenter C, Fraraccio S, Wandro S, TKosciolek T, Janssen S, Metcalf JL, Song S, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Knight R. 2020 Comprehensive cancer microbiome analyses suggest novel clinical diagnostics. Nature. 579, pages567–574

Song S, Sanders JG, Delsuc F, Metcalf JL, Amato K, Taylor MW, Mazel F, Lutz HL, Winker K, Graves GR, Humphrey G, Gilbert JA, Hackett SJ, White KP, Skeen HR, Kurtis SM, Withrow J, Braile T, Miller M, McCracken KG, Maley JM, Ezenwa VO, Williams A, Blanton JM, McKenzie V, Knight R. Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats 2020 mBio, 11 (1) e02901-19; DOI: 10.1128/mBio.02901-19

Increasing gender diversity in the STEM research workforce. 2019. Greider CW, Sheltzer JM, Cantalupo NC, Copeland WB, Dasgupta N, Hopkins N, Jansen JM, Joshua-Tor L, McDowell GS, Metcalf JL, McLaughlin B, Olivarius A, O'Shea EK, Raymond JL, Ruebain D, Steitz JA, Stillman B, Tilghman SM, Valian V, Villa-Komaroff L, Wong JY. Science. 8 Nov, 692-695. doi: 10.1126/science.aaz0649

Merrel SD, McAvoy TJ, King CM, Sittig M, Millare EV, Niero C, Metcalf JL, Blum FC, Testerman TL, Sardi A. Pre- and post-operative antibiotics in conjunction with cytoreductive surgery and heated intraperitoneal chemotherapy (HIPEC) should be considered for pseudomyxoma peritonei (PMP) treatment. 45 (9), 1723-1726. https://doi.org/10.1016/j.ejso.2019.01.223

Belk AD, Deel HL, Burcham ZM, Knight R, Carter DO, Metcalf JL*. 2019 Animal models for understanding microbial decomposition of human remains. Drug Discovery Today: Disease Models. 28, 117-125. https://doi.org/10.1016/j.ddmod.2019.08.013

Amato, KR., Mallott EK, McDonald D, Dominy NJ, Goldberg T, Lambert JE, Swedell L, Metcalf JL, Gomez A, Britton GA, Stumpf RM, Leigh S, Knight R. 2019. Convergence of Human and Old World Monkey Gut Microbiomes Demonstrates the Importance of Human Ecology over Phylogeny.” Genome Biology 20 (1): 201.

Weinroth MD, Martin JN, Doster E, Geornaras I, Parker JK, Carlson CR, Metcalf JL, Morley PS, Belk KE. 2019. Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes. Journal of Animal Science. https://doi.org/10.1093/jas/skz306

Weinroth MD, Britton BC, McCullough KR, Martin JN, Geornaras I, Knight R, Belk KE, Metcalf JL. 2019. Ground beef microbiome changes with antimicrobial decontamination interventions and product storage. PLoS One 14:e0217947.

Huebner KL, Martin JN, Weissend CJ, Holzer KL, Parker JK, Lakin SM, Doster E, Weinroth MD, Abdo Z, Woerner DR, Metcalf JL, Geornaras I, Bryant TC, Morley PS, Belk KE. 2019 “Effects of a Saccharomyces Cerevisiae Fermentation Product on Liver Abscesses, Fecal Microbiome, and Resistome in Feedlot Cattle Raised without Antibiotics.” Scientific Reports 9 (1): 2559.

McCullagh EA, Nowak K, Pogoriler A, Metcalf JL, Zaringhalam M, Zelikova TJ 2019 Request a woman scientist: A database for diversifying the public face of science. PLoS Biol 17(4): e3000212. https://doi.org/10.1371/journal.pbio.3000212

Song SS, Sanders JG, Baldassarre DT, Chaves JA, Johnson NS, Piaggio AJ, Stuckey MJ, Nováková E, Metcalf JL, Chomel BB, Aguilar-Setién A, Knight R, McKenzieVJ. 2019 Is there convergence of gut microbes in blood-feeding vertebrates? Phil. Trans. R. Soc. B. 374 https://doi.org/10.1098/rstb.2018.0249

Metcalf, JL*. 2019 Estimating the Postmortem Interval Using Microbes: Knowledge Gaps and a Path to Technology Adoption. Forensic Science International. Genetics 38 (January): 211–18.

Kodama WA, Xu ZZ, Metcalf JL, Song, S, Harrison N, Knight R, Carter DO, Happy CH. 2019 Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue. J.Forensic Sci. https://doi.org/10.1111/1556-4029.13949.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, Al-Ghalith GA… Metcalf JL… Caporaso JG. Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 22019 Nature Biotechnology, 37 (8), 852-857. https://doi.org/10.1038/s41587-019-0209-9. [52 citations]

Cochran, AT, Bauer, J, Metcalf, JL, Lovecka, P, Sura de Jong, M, Warris, S, Mooijman, PJW, van der Meer, I, Knight, R, and Pilon-Smits, EAH. 2018 Plant Selenium Hyperaccumulation Affects Rhizosphere: Enhanced Species Richness and Altered Species Composition Phytobiomes, PBIOMES-12-17-0051-R

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov A, Chen Y, Dorrestein PC, Dunn RR, Fahimpour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Kelley ST, Knights D, Ladau J, Leach J, Melnik A, Metcalf JL, Montassier E, Navas-Molina J, Peddada S, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Spector T, Thackray VG, Thompson LR, Vazquez Y. 2018 American Gut: an Open Platform for Citizen-Science Microbiome Research MSystems May, 3 (3) e00031-18; DOI: 101128/mSystems00031-18

Luna E, van Eck L, Campillo T, Michelle L Celia ML, Metcalf JL, Botha AM, Weinroth MD, Thannhauser TW, Pappin D, Tisserat NA, Argueso C, Laptian NLV, Ode PJ, and Leach JE. 2018 Bacteria Associated with Russian Wheat Aphid (Diuraphis noxia) Enhance Aphid Virulence to Wheat. Phytobiomes Journal . 2: 151–164

Amato, K R, G Sanders, J, Song, S J, Nute, M, Metcalf, JL, Thompson, L R, Morton, J T, Amir, A, J McKenzie, V, Humphrey, G, Gogul, G, Gaffney, J, L Baden, A, A O Britton, G, P Cuozzo, F, Di Fiore, A, J Dominy, N, L Goldberg, T, Gomez, A, Kowalewski, M M, J Lewis, R, Link, A, L Sauther, M, Tecot, S, A White, B, E Nelson, K, M Stumpf, R, Knight, R, and R Leigh, S 2019 Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes ISME J 13, 576-587 [15 citations]

Belk A, Xu ZZ, Carter DO, Lynne A, Bucheli S, Knight R, Metcalf JL*. 2018 Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models Genes, 9(2), 104 doi:103390/genes9020104

Boast AP, Weyrich LS, Wood JR, Metcalf JL, Knight R, Cooper A. 2018 Coprolites Reveal Ecological Interactions Lost With the Extinction of New Zealand Birds. Proceedings of the National Academy of Sciences 115 (7), 1546-1551. DOI:101073/pnas1712337115

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: http://dx.doi.org/10.1016/j.cub.2016.03.042.

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. http://aem.asm.org/content/early/2014/06/03/AEM.00957-14.long

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. http://www.springerreference.com/docs/html/chapterdbid/404233.html

Teaching Experience

Innovative Teaching - Massive Open Online Course: Gut Check: Exploring your microbiome, Oct 6 - Nov 15, 2014 https://www.coursera.org/course/microbiome

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 https://www.coursera.org/course/microbiome

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. http://nescent.org/science/awards_summary.php?id=263

International Union for Quaternary Research 2011 (INQUA XVIII). Extinction Events (session co-chair and speaker). http://www.inqua2011.ch/?a=programme&subnavi=sessions&id=30

Integrating datasets to investigate megafauna extinction in the late Quaternary. NESCent Catalysis (PI). Meeting May 25 – 30, 2010. https://www.nescent.org/science/awards.php