What can chemical profiles tell us about animal physiology and health status?

Using both targeted and untargeted metabolomics, chemical profiling of biospecimens provides great insight into animals at the individual and population level. These tools have been powerful at understanding dietary readouts in humans [1] and phenotypes in a broad range of species, such as rhinoceros, linking phytoestrogen-profiles to fertility status of captive-born individuals [2]. We have also used hormone monitoring in endangered amphibians to better understand animal physiology, including pseudohermaphroditism [3] as well as supporting captive breeding efforts more broadly [4,5]. In bears, we have found chemical profiles from the skin of brown bears to display evidence of individuality and age-sex variation across individuals in the wild [6]. For captive giant pandas, we found similar results in urine, as well as identifying impending ovulation [7]. Currently we are analyzing skin swabs broadly across pandas, as well as comparisons to other bear species, including brown bears and polar bears, linking microbial production of pheromones to determine estrus [8]. Altogether, using chemical profiling using mass spectrometry, we can understand physiological state of both wild and captive animals without needing invasive sampling techniques.


  1. Gauglitz JM†, West K†, Bittremeiux W†, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Sayyari E, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Nguyen DS, Elijah EO, Wang M, Marotz C, Sprecher KE, Robles DV, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Gonzalez DJ, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC (2022). Enhancing untargeted metabolomics using metadata-based source annotation. Nature Biotechnology DOI:10.1038/s41587-022-01368-1. †contributed equally.
  2. Williams CL, Ybarra AR, Meredith AN, Durrant BS, Tubbs CW. (2019) Gut microbiota and phytoestrogen-associated infertility in southern white rhinoceros, mBio 10(2) e00311-19.
  3. Jacobs LE, Hammond TT, Gaffney PM, Curtis MJ, Shier DM, Durrant BS, Williams CL†, Calatayud NE† (2021). Using assisted reproductive technologies to assess the development of secondary sexual characteristics, ovarian senescence, and pseudohermaphroditism in an endangered frog, Rana muscosa, Reproduction, Fertility and Development 33(9) 610-614. †contributed equally.
  4. Calatayud NE, Jacobs LE, Williams CL, Steiner C, Shier D (2022). Recovering an endangered frog species using integrative reproductive technologies, Theriogenology 191: 141-152.
  5. Calatayud, NE, Howell L, Upton R, Tapley B, Johnson K, Browne R, Marcec R, Williams CL, O’Brien D, Hobbs R, Trudeau VT, Bower D, Clulow S, Clulow J, Della Tonga G. (2023) Amphibian Assisted Reproduction and Biobanking chapter for the IUCN/ASG Amphibian ARTs and Biobanking Working Group, accepted.
  6. Clapham M, Wilson AE, Williams CL, Sergiel A (2023). Brown bear skin-borne secretions display evidence of individuality and age-sex variation, Scientific Reports 13: 3163.
  7. Wilson A, Sparks D, Williams CL, Knott K, Kouba A, Willard S, Brown A (2023) Changes in the volatile composition of giant panda urine indicate sex, reproductive status, and impending ovulation, in preparation.
  8. Wilson AE†, Williams CL†, Sparks D, Crowe O, Knott K, Willard S, Brown A (2023) Pandas, pheromones, and the pursuit of anatomical estrus cues, in preparation. †contributed equally.