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Research Output

2020

Biodiversity of protists and nematodes in the wild nonhuman primate gut

Mann, A. E., Mazel, F., Lemay, M. A., Morien, E., Billy, V., Kowalewski, M., Di Fiore, A., Link, A., Goldberg, T. L., Tecot, S., Baden, A. L., Gomez, A., Sauther, M. L., Cuozzo, F. P., Rice, G. A. O., Dominy, N. J., Stumpf, R., Lewis, R. J., Swedell, L., Amato, K. & 1 others, Wegener Parfrey, L., Feb 1 2020, In : ISME Journal. 14, 2, p. 609-622 14 p.

Research output: Contribution to journalArticle

The gut microbiota communities of wild arboreal and ground-feeding tropical primates are affected differently by habitat disturbance

Barelli, C., Barelli, C., Barelli, C., Albanese, D., Stumpf, R. M., Stumpf, R., Asangba, A., Donati, C., Rovero, F., Rovero, F. & Hauffe, H. C., Jun 2020, In : mSystems. 5, 3, e00061-20.

Research output: Contribution to journalArticle

Open Access
2019

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny

Amato, K. R., Mallott, E. K., McDonald, D., Dominy, N. J., Goldberg, T., Lambert, J. E., Swedell, L., Metcalf, J. L., Gomez, A., Britton, G. A. O., Stumpf, R. M., Leigh, S. R. & Knight, R., Oct 8 2019, In : Genome biology. 20, 1, 201.

Research output: Contribution to journalArticle

Open Access

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes

Amato, K. R., G. Sanders, J., Song, S. J., Nute, M., Metcalf, J. L., 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. & 9 others, J. Lewis, R., Link, A., L. Sauther, M., Tecot, S., A. White, B., E. Nelson, K., M. Stumpf, R., Knight, R. & R. Leigh, S., Mar 1 2019, In : ISME Journal. 13, 3, p. 576-587 12 p.

Research output: Contribution to journalArticle

Extensive variability in the gut microbiome of a highly-specialized and critically endangered lemur species across sites

Donohue, M. E., Asangba, A. E., Ralainirina, J., Weisrock, D. W., Stumpf, R. M. & Wright, P. C., Oct 1 2019, In : American journal of primatology. 81, 10-11, e23046.

Research output: Contribution to journalArticle

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K., Barr, J. J., Bibby, K., Brouns, S. J. J., Cazares, A., de Jonge, P. A., Desnues, C., Díaz Muñoz, S. L., Fineran, P. C., Kurilshikov, A., Lavigne, R., Mazankova, K. & 97 others, McCarthy, D. T., Nobrega, F. L., Reyes Muñoz, A., Tapia, G., Trefault, N., Tyakht, A. V., Vinuesa, P., Wagemans, J., Zhernakova, A., Aarestrup, F. M., Ahmadov, G., Alassaf, A., Anton, J., Asangba, A., Billings, E. K., Cantu, V. A., Carlton, J. M., Cazares, D., Cho, G. S., Condeff, T., Cortés, P., Cranfield, M., Cuevas, D. A., De la Iglesia, R., Decewicz, P., Doane, M. P., Dominy, N. J., Dziewit, L., Elwasila, B. M., Eren, A. M., Franz, C., Fu, J., Garcia-Aljaro, C., Ghedin, E., Gulino, K. M., Haggerty, J. M., Head, S. R., Hendriksen, R. S., Hill, C., Hyöty, H., Ilina, E. N., Irwin, M. T., Jeffries, T. C., Jofre, J., Junge, R. E., Kelley, S. T., Khan Mirzaei, M., Kowalewski, M., Kumaresan, D., Leigh, S. R., Lipson, D., Lisitsyna, E. S., Llagostera, M., Maritz, J. M., Marr, L. C., McCann, A., Molshanski-Mor, S., Monteiro, S., Moreira-Grez, B., Morris, M., Mugisha, L., Muniesa, M., Neve, H., Nguyen, N. P., Nigro, O. D., Nilsson, A. S., O’Connell, T., Odeh, R., Oliver, A., Piuri, M., Prussin, A. J., Qimron, U., Quan, Z. X., Rainetova, P., Ramírez-Rojas, A., Raya, R., Reasor, K., Rice, G. A. O., Rossi, A., Santos, R., Shimashita, J., Stachler, E. N., Stene, L. C., Strain, R., Stumpf, R., Torres, P. J., Twaddle, A., Ugochi Ibekwe, M. A., Villagra, N., Wandro, S., White, B., Whiteley, A., Whiteson, K. L., Wijmenga, C., Zambrano, M. M., Zschach, H. & Dutilh, B. E., Oct 1 2019, In : Nature Microbiology. 4, 10, p. 1727-1736 10 p.

Research output: Contribution to journalArticle

Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors

Pafčo, B., Sharma, A. K., Petrželková, K. J., Vlčková, K., Todd, A., Yeoman, C. J., Wilson, B. A., Stumpf, R., White, B. A., Nelson, K. E., Leigh, S. & Gomez, A., Jul 2019, In : American journal of physical anthropology. 169, 3, p. 575-585 11 p.

Research output: Contribution to journalArticle

Moving forward with the primate microbiome: Introduction to a special issue of the American Journal of Primatology

Amato, K. R. & Stumpf, R. M., Oct 1 2019, In : American journal of primatology. 81, 10-11, e23060.

Research output: Contribution to journalEditorial

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints

Gomez, A., Sharma, A. K., Mallott, E. K., Petrzelkova, K. J., Jost Robinson, C. A., Yeoman, C. J., Carbonero, F., Pafco, B., Rothman, J. M., Ulanov, A., Vlckova, K., Amato, K. R., Schnorr, S. L., Dominy, N. J., Modry, D., Todd, A., Torralba, M., Nelson, K. E., Burns, M. B., Blekhman, R. & 8 others, Remis, M., Stumpf, R. M., Wilson, B. A., Gaskins, H. R., Garber, P. A., White, B. A., Leigh, S. R. & Mcmahon, K., Jul 31 2019, In : mSphere. 4, 4, 14 p.

Research output: Contribution to journalArticle

Open Access

Variations in the microbiome due to storage preservatives are not large enough to obscure variations due to factors such as host population, host species, body site, and captivity

Asangba, A. E., Donohue, M. E., Lamb, A., Wright, P. C., Halajian, A., Leigh, S. R. & Stumpf, R. M., Oct 1 2019, In : American journal of primatology. 81, 10-11, e23045.

Research output: Contribution to journalArticle

2018

Impact of stress on the gut microbiome of free-ranging western lowland gorillas

Vlčková, K., Shutt-Phillip, K., Heisterman, M., Pafčo, B., Petrželkov, K. J., Todd, A., Modrý, D., Nelson, K. E., Wilson, B. A., Stumpf, R. M., White, B. A., Leigh, S. R. & Gomez, A., Jan 2018, In : Microbiology (United Kingdom). 164, 1, p. 40-44 5 p., 000587.

Research output: Contribution to journalArticle

Relationships between gastrointestinal parasite infections and the fecal microbiome in free-ranging western lowland gorillas

Vlčková, K., Pafčo, B., Petrželková, K. J., Modrý, D., Todd, A., Yeoman, C. J., Torralba, M., Wilson, B. A., Stumpf, R. M., White, B. A., Nelson, K. E., Leigh, S. R. & Gomez, A., Jun 15 2018, In : Frontiers in Microbiology. 9, JUN, 1202.

Research output: Contribution to journalArticle

Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality

Raulo, A., Ruokolainen, L., Lane, A., Amato, K., Knight, R., Leigh, S., Stumpf, R., White, B., Nelson, K. E., Baden, A. L. & Tecot, S. R., Mar 2018, In : Journal of Animal Ecology. 87, 2, p. 388-399 12 p.

Research output: Contribution to journalArticle

The gut microbiome of nonhuman primates: Lessons in ecology and evolution

Clayton, J. B., Gomez, A., Amato, K., Knights, D., Travis, D. A., Blekhman, R., Knight, R., Leigh, S., Stumpf, R., Wolf, T., Glander, K. E., Cabana, F. & Johnson, T. J., Jun 2018, In : American journal of primatology. 80, 6, e22867.

Research output: Contribution to journalReview article

2017

Limb dominance, foot orientation and functional asymmetry during walking gait

Polk, J. D., Stumpf, R. M. & Rosengren, K. S., Feb 1 2017, In : Gait and Posture. 52, p. 140-146 7 p.

Research output: Contribution to journalArticle

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate

Amato, K. R., Van Belle, S., Di Fiore, A., Estrada, A., Stumpf, R., White, B., Nelson, K. E., Knight, R. & Leigh, S. R., Jul 1 2017, In : Microbial Ecology. 74, 1, p. 250-258 9 p.

Research output: Contribution to journalArticle

2016

Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla)

Vlčková, K., Gomez, A., Petrželková, K. J., Whittier, C. A., Todd, A. F., Yeoman, C. J., Nelson, K. E., Wilson, B. A., Stumpf, R. M., Modrý, D., White, B. A. & Leigh, S. R., Nov 1 2016, In : Microbial Ecology. 72, 4, p. 943-954 12 p.

Research output: Contribution to journalArticle

Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns

Gomez, A., Petrzelkova, K. J., Burns, M. B., Yeoman, C. J., Amato, K. R., Vlckova, K., Modry, D., Todd, A., Jost Robinson, C. A., Remis, M. J., Torralba, M. G., Morton, E., Umaña, J. D., Carbonero, F., Gaskins, H. R., Nelson, K. E., Wilson, B. A., Stumpf, R. M., White, B. A., Leigh, S. R. & 1 others, Blekhman, R., Mar 8 2016, In : Cell Reports. 14, 9, p. 2142-2153 12 p.

Research output: Contribution to journalArticle

Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta)

Bennett, G., Malone, M., Sauther, M. L., Cuozzo, F. P., White, B., Nelson, K. E., Stumpf, R. M., Knight, R., Leigh, S. R. & Amato, K. R., Aug 1 2016, In : American journal of primatology. 78, 8, p. 883-892 10 p.

Research output: Contribution to journalArticle

Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications

Stumpf, R. M., Gomez, A., Amato, K. R., Yeoman, C. J., Polk, J. D., Wilson, B. A., Nelson, K. E., White, B. A. & Leigh, S. R., Jul 1 2016, In : Biological Conservation. 199, p. 56-66 11 p.

Research output: Contribution to journalComment/debate

Pan troglodytes—Common Chimpanzee

Hicks, T. C., Stumpf, R., Watts, D., Sanz, C. & Morgan, D., 2016, All The Worlds Primates. Rowe, N. & Myers, M. (eds.). Pogonias Press

Research output: Chapter in Book/Report/Conference proceedingChapter

Pan troglodytes ellioti—Nigeria-Cameroon Chimpanzee

Stumpf, R., 2016, All The Worlds Primates. Rowe, N. & Myers, M. (eds.). Pogonias Press

Research output: Chapter in Book/Report/Conference proceedingChapter

Pan troglodytes verus—Western Chimpanzee

Stumpf, R., 2016, All The Worlds Primates. Rowe, N. & Myers, M. (eds.). Pogonias Press

Research output: Chapter in Book/Report/Conference proceedingChapter

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species

Amato, K. R., Martinez-Mota, R., Righini, N., Raguet-Schofield, M., Corcione, F. P., Marini, E., Humphrey, G., Gogul, G., Gaffney, J., Lovelace, E., Williams, L. S., Luong, A., Dominguez-Bello, M. G., Stumpf, R. M., White, B., Nelson, K. E., Knight, R. & Leigh, S. R., Mar 1 2016, In : Oecologia. 180, 3, p. 717-733 17 p.

Research output: Contribution to journalArticle

Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp

Gomez, A., Rothman, J. M., Petrzelkova, K., Yeoman, C. J., Vlckova, K., Umaña, J. D., Carr, M., Modry, D., Todd, A., Torralba, M., Nelson, K. E., Stumpf, R. M., Wilson, B. A., Blekhman, R., White, B. A. & Leigh, S. R., Feb 1 2016, In : ISME Journal. 10, 2, p. 514-526 13 p.

Research output: Contribution to journalArticle

2015

Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology

Gomez, A., Petrzelkova, K., Yeoman, C. J., Vlckova, K., Mrázek, J., Koppova, I., Carbonero, F., Ulanov, A., Modry, D., Todd, A., Torralba, M., Nelson, K. E., Gaskins, H. R., Wilson, B., Stumpf, R. M., White, B. A. & Leigh, S. R., May 1 2015, In : Molecular ecology. 24, 10, p. 2551-2565 15 p.

Research output: Contribution to journalArticle

Screening wild and semi-free ranging great apes for putative sexually transmitted diseases: Evidence of Trichomonadidae infections

Rushmore, J., Allison, A. B., Edwards, E. E., Bagal, U., Altizer, S., Cranfield, M. R., Glenn, T. C., Liu, H., Mudakikwa, A., Mugisha, L., Muller, M. N., Stumpf, R. M., Thompson, M. E., Wrangham, R. & Yabsley, M. J., Oct 1 2015, In : American journal of primatology. 77, 10, p. 1075-1085 11 p.

Research output: Contribution to journalArticle

The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra)

Amato, K. R., Leigh, S. R., Kent, A., Mackie, R. I., Yeoman, C. J., Stumpf, R. M., Wilson, B. A., Nelson, K. E., White, B. A. & Garber, P. A., Feb 1 2015, In : Microbial Ecology. 69, 2, p. 434-443 10 p.

Research output: Contribution to journalArticle

Variable responses of human and non-human primate gut microbiomes to a Western diet

Amato, K. R., Yeoman, C. J., Cerda, G., Schmitt, C. A., Cramer, J. D., Miller, M. E. B., Gomez, A., Turner, T. R., Wilson, B. A., Stumpf, R. M., Nelson, K. E., White, B. A., Knight, R. & Leigh, S. R., Nov 16 2015, In : Microbiome. 3, 1 p.

Research output: Contribution to journalArticle

2014

Female red colobus monkeys maintain their densities through flexible feeding strategies in logged forests in Kibale National Park, Uganda

Milich, K. M., Stumpf, R., Chambers, J. M. & Chapman, C. A., Jan 1 2014, In : American journal of physical anthropology. 154, 1, p. 52-60 9 p.

Research output: Contribution to journalArticle

Network-based vaccination improves prospects for disease control in wild chimpanzees

Rushmore, J., Caillaud, D., Hall, R. J., Stumpf, R. M., Meyers, L. A. & Altizer, S., Aug 6 2014, In : Journal of the Royal Society Interface. 11, 97, 20140349.

Research output: Contribution to journalArticle

Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance

Yildirim, S., Yeoman, C. J., Janga, S. C., Thomas, S. M., Ho, M., Leigh, S. R., Consortium, P. M., White, B. A., Wilson, B. A. & Stumpf, R. M., Jan 1 2014, In : ISME Journal. 8, 12, p. 2431-2444 14 p.

Research output: Contribution to journalArticle

The role of gut microbes in satisfying the nutritional demands of adult and juvenile wild, black howler monkeys (Alouatta pigra)

Amato, K. R., Leigh, S. R., Kent, A., Mackie, R. I., Yeoman, C. J., Stumpf, R. M., Wilson, B. A., Nelson, K. E., White, B. A. & Garber, P. A., Dec 1 2014, In : American journal of physical anthropology. 155, 4, p. 652-664 13 p.

Research output: Contribution to journalArticle

Timing is everything: Expanding the cost of sexual attraction hypothesis

Milich, K. M., Bahr, J. M., Stumpf, R. M. & Chapman, C. A., Feb 1 2014, In : Animal Behaviour. 88, p. 219-224 6 p.

Research output: Contribution to journalArticle

2013

A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease

Yeoman, C. J., Thomas, S. M., Miller, M. E. B., Ulanov, A. V., Torralba, M., Lucas, S., Gillis, M., Cregger, M., Gomez, A., Ho, M., Leigh, S. R., Stumpf, R., Creedon, D. J., Smith, M. A., Weisbaum, J. S., Nelson, K. E., Wilson, B. A. & White, B. A., Feb 6 2013, In : PloS one. 8, 2, e56111.

Research output: Contribution to journalArticle

Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes

Amato, K. R., Yeoman, C. J., Kent, A., Righini, N., Carbonero, F., Estrada, A., Rex Gaskins, H., Stumpf, R. M., Yildirim, S., Torralba, M., Gillis, M., Wilson, B. A., Nelson, K. E., White, B. A. & Leigh, S. R., Jul 1 2013, In : ISME Journal. 7, 7, p. 1344-1353 10 p.

Research output: Contribution to journalArticle

Social network analysis of wild chimpanzees provides insights for predicting infectious disease risk

Rushmore, J., Caillaud, D., Matamba, L., Stumpf, R., Borgatti, S. P. & Altizer, S., Sep 1 2013, In : Journal of Animal Ecology. 82, 5, p. 976-986 11 p.

Research output: Contribution to journalArticle

The primate vaginal microbiome: comparative context and implications for human health and disease.

Stumpf, R. M., Wilson, B. A., Rivera, A., Yildirim, S., Yeoman, C. J., Polk, J. D., White, B. A. & Leigh, S. R., Dec 2013, In : American journal of physical anthropology. 152 Suppl 57, p. 119-134 16 p.

Research output: Contribution to journalReview article

2011

Differences between the normal vaginal bacterial community of baboons and that of humans

Rivera, A. J., Frank, J. A., Stumpf, R., Salyers, A. A., Wilson, B. A., Olsen, G. J. & Leigh, S., Feb 1 2011, In : American journal of primatology. 73, 2, p. 119-126 8 p.

Research output: Contribution to journalArticle

Sexual conflict in primates

Stumpf, R. M., Martinez-Mota, R., Milich, K. M., Righini, N. & Shattuck, M. R., Mar 1 2011, In : Evolutionary anthropology. 20, 2, p. 62-75 14 p.

Research output: Contribution to journalArticle

Towards an evolutionary model of animal-associated microbiomes

Yeoman, C. J., Chia, N., Yildirim, S., Berg Miller, M. E., Kent, A., Stumpf, R., Leigh, S. R., Nelson, K. E., White, B. A. & Wilson, B. A., Mar 2011, In : Entropy. 13, 3, p. 570-594 25 p.

Research output: Contribution to journalReview article

2010

Baboon vaginal microbiota: An overlooked aspect of primate physiology

Rivera, A. J., Stumpf, R. M., Wilson, B., Leigh, S. & Salyers, A. A., Jun 1 2010, In : American journal of primatology. 72, 6, p. 467-474 8 p.

Research output: Contribution to journalArticle

Behavioral data collection for primate field studies

Campbell, C. J., Crofoot, M. C., MacKinnon, K. C. & Stumpf, R., 2010, Primates in Perspective. Campbell, C. J., Fuentes, A., MacKinnon, K. C., Bearder, S. K. & Stumpf, R. M. (eds.). 2 ed. Oxford University Press

Research output: Chapter in Book/Report/Conference proceedingChapter

Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities

Yildirim, S., Yeoman, C. J., Sipos, M., Torralba, M., Wilson, B. A., Goldberg, T. L., Stumpf, R. M., Leigh, S. R., White, B. A. & Nelson, K. E., 2010, In : PloS one. 5, 11, e13963.

Research output: Contribution to journalArticle

Chimpanzees and bonobos: Inter- and intra-species diversity

Stumpf, R., 2010, Primates in Perspective. Campbell, C. J., Fuentes, A., MacKinnon, K. C., Bearder, S. K. & Stumpf, R. M. (eds.). 2 ed. Oxford University Press

Research output: Chapter in Book/Report/Conference proceedingChapter

Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential

Yeoman, C. J., Yildirim, S., Thomas, S. M., Durkin, A. S., Torralba, M., Sutton, G., Buhay, C. J., Ding, Y., Dugan-Rocha, S. P., Muzny, D. M., Qin, X., Gibbs, R. A., Leigh, S. R., Stumpf, R., White, B. A., Highlander, S. K., Nelson, K. E. & Wilson, B. A., Oct 20 2010, In : PloS one. 5, 8, e12411.

Research output: Contribution to journalArticle

Male aggression and sexual coercion in wild West African chimpanzees, Pan troglodytes verus

Stumpf, R. M. & Boesch, C., Feb 1 2010, In : Animal Behaviour. 79, 2, p. 333-342 10 p.

Research output: Contribution to journalArticle

Primates in Perspective

Campbell, C. J. (ed.), Fuentes, A. (ed.), MacKinnon, K. C. (ed.), Bearder, S. K. (ed.) & Stumpf, R. (ed.), Apr 23 2010, 2 ed. Oxford University Press. 864 p.

Research output: Book/Report/Conference proceedingBook

The future of primate research

Campbell, C. J., Fuentes, A., Bearder, S. K., MacKinnon, K. C. & Stumpf, R., 2010, Primates in Perspective. Campbell, C. J., Fuentes, A., Bearder, S. K., MacKinnon, K. C. & Stumpf, R. M. (eds.). 2 ed. Oxford University Press

Research output: Chapter in Book/Report/Conference proceedingChapter