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Research Output 1999 2019

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Article
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
Cercopithecidae
Microbiota
Phylogeny
Ecology
primate

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

primate
Primates
physiology
niche
niches

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

Lemur
deforestation
endangered species
digestive system
Madagascar

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

Phylogeography
Viruses
Microbiota
Primates
Bacteroidetes

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

Gorilla gorilla
Sex Factors
Age Factors
infant
Group

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
Microbiota
Primates
Haplorhini
Cercopithecidae
Population

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

preservative
captivity
preservatives
ethanol
sampling
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

Gorilla gorilla
Bacterial Genes
Physiological Stress
Clostridium
rRNA Genes

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

Gorilla gorilla
Parasitic Diseases
Microbiota
Entamoeba
Parasites

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

Lemuridae
social behavior
social network
immunity
intestinal microorganisms
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

Gait
Walking
Foot
Extremities
Posture

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. A., 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

intestinal microorganisms
primate
Primates
gender
microbial communities
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

Gorilla gorilla
Gorilla
antibiotics
lowlands
Central African Republic

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

Microbiota
Amino Acids
Xenobiotics
Ecology
Metabolites

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., 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

intestinal microorganisms
habitat type
habitat
habitats
disturbance

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

intestinal microorganisms
primate
Primates
phylogenetics
phylogeny

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

Gorilla gorilla
Gorilla
Primates
temporal variation
digestive system
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

Gorilla gorilla
Metabolomics
metabolomics
Ecology
primate

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., 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

sexually transmitted disease
sexually transmitted diseases
Pongidae
Trichomonadida
Pan troglodytes

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. D., Mackie, R. I., Yeoman, C. J., Stumpf, R., 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

Alouatta
intestinal microorganisms
diet
energy
relative abundance

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

Primates
Cercopithecus aethiops
Microbiota
Diet
Animal Models
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

Colobus
Erythrocebus patas
Uganda
national park
Primates

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

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

Research output: Contribution to journalArticle

Disease control
Vaccines
Pan troglodytes
Vaccination
Pathogens

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

Species Specificity
Microbiota
Lactobacillus
primate
Primates

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

Alouatta
Primates
Diet
Ruminococcus
Lactococcus

Timing is everything: Expanding the cost of sexual attraction hypothesis

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

Research output: Contribution to journalArticle

Colobus
cost
mating behavior
plasticity
genitalia
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

Bacterial Vaginosis
metabolomics
Mobiluncus
Dialister
Metabolomics

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

Alouatta
Ecosystem
degradation
habitat
habitats

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

social networks
network analysis
infectious disease
social network
Pan troglodytes
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

Papio
bacterial communities
bacterium
primate
phylogenetics

Sexual conflict in primates

Stumpf, R., 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

interaction
evidence
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

Papio
primate
physiology
Primates
microorganisms

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., Dec 9 2010, In : PloS one. 5, 11, e13963.

Research output: Contribution to journalArticle

Microbiota
Primates
microbial communities
Colobus
microbiome

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

Gardnerella vaginalis
Bacterial Vaginosis
Genomics
Virulence
virulence
Infanticide
Pongo
infanticide
Coercion
Pongo pygmaeus

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

aggression
Pan troglodytes
sexual conflict
mating success
mating behavior
2009

Antibiotic resistance genes in the vaginal microbiota of primates not normally exposed to antibiotics

Jeters, R. T., Rivera, A. J., Boucek, L. M., Stumpf, R. M., Leigh, S. R. & Salyers, A. A., Dec 1 2009, In : Microbial Drug Resistance. 15, 4, p. 309-315 7 p.

Research output: Contribution to journalArticle

Microbiota
Microbial Drug Resistance
Primates
Anti-Bacterial Agents
Genes

Heterogeneity of vaginal microbial communities within individuals

Kim, T. K., Thomas, S. M., Ho, M., Sharma, S., Reich, C. I., Frank, J. A., Yeater, K. M., Biggs, D. R., Nakamura, N., Stumpf, R., Leigh, S. R., Tapping, R. I., Blanke, S. R., Slauch, J. M., Gaskins, H. R., Weisbaum, J. S., Olsen, G. J., Hoyer, L. L. & Wilson, B. A., Apr 1 2009, In : Journal of Clinical Microbiology. 47, 4, p. 1181-1189 9 p.

Research output: Contribution to journalArticle

Microbiota
Ecosystem
Gene Library
rRNA Genes
Cervix Uteri

The context of female dispersal in Kanyawara chimpanzees

Stumpf, R. M., Emery Thompson, M., Muller, M. N. & Wrangham, R. W., Apr 1 2009, In : Behaviour. 146, 4-5, p. 629-656 28 p.

Research output: Contribution to journalArticle

Pan troglodytes
Emigration and Immigration
dispersal behavior
Physiological Stress
Uganda
2008

A comparison of female mating strategies in Pan troglodytes and Pongo spp.

Stumpf, R., Emery Thompson, M. & Knott, C. D., Aug 1 2008, In : International Journal of Primatology. 29, 4, p. 865-884 20 p.

Research output: Contribution to journalArticle

Pongo
Pan troglodytes
Pongo pygmaeus
mating behavior
paternity

Female reproductive strategies and competition in apes: An introduction

Emery Thompson, M., Stumpf, R. & Pusey, A. E., Aug 1 2008, In : International Journal of Primatology. 29, 4, p. 815-821 7 p.

Research output: Contribution to journalArticle

competition (ecology)
female behavior
Pongidae
primate
reproductive strategy
2006

The efficacy of female choice in chimpanzees of the Taï forest, Côte d'Ivoire

Stumpf, R. & Boesch, C., Oct 1 2006, In : Behavioral Ecology and Sociobiology. 60, 6, p. 749-765 17 p.

Research output: Contribution to journalArticle

Pan troglodytes
mating success
mating behavior
behavioral resistance
paternity
2005
Pan troglodytes
national parks
national park
mating behavior
female behavior

Morphological variation in populations of Eulemur albocollaris and E. fulvus rufus

Johnson, S. E., Gordon, A. D., Stumpf, R., Overdorff, D. J. & Wright, P. C., Dec 1 2005, In : International Journal of Primatology. 26, 6, p. 1399-1416 18 p.

Research output: Contribution to journalArticle

dimorphism
Lemuridae
sperm competition
dogs
body mass
2002

Genetic assessment of a white-collared x red-fronted lemur hybrid zone at Andringitra, Madagascar

Wyner, Y. M., Johnson, S. E., Stumpf, R. M. & Desalle, R., Jul 30 2002, In : American journal of primatology. 57, 2, p. 51-66 16 p.

Research output: Contribution to journalArticle

hybrid zone
Lemur
Madagascar
gene
ferroxidase
1999

Species concepts and the determination of historic gene flow patterns in the Eulemur fulvus (Brown Lemur) complex

Wyner, Y., Absher, R., Amato, G., Sterling, E., Stumpf, R., Rumpler, Y. & Desalle, R., Jan 1999, In : Biological Journal of the Linnean Society. 66, 1, p. 39-56 18 p.

Research output: Contribution to journalArticle

species concept
Lemur
flow pattern
subspecies
gene flow