About

Rebecca M. Stumpf is a professor in the Department of Anthropology at the Illinois College of Liberal Arts & Sciences. Her research interests include host-microbial diversity and interactions, evolution, emerging diseases and transmission patterns, antimicrobial resistance distribution, primate comparative biology, behavioral ecology and ontogeny, reproductive and sexual behavior and evolution, behavioral endocrinology, and conservation. She holds a Ph.D. in Anthropological Sciences from Stony Brook University and an M.A. in the same field from the same institution, as well as a B.A. from Oberlin College. Throughout her career, Dr. Stumpf has contributed significantly to understanding microbiomes, pathogen transmission, and primate biology, with numerous funded projects including studies on primate pathogens in Uganda, antimicrobial resistance, and the impact of environmental changes on primate health. She has been recognized with awards such as the J.S. Guggenheim Foundation Fellowship and has been promoted to Full Professor with distinction. Her work integrates microbiology, anthropology, and conservation, and she is actively involved in teaching courses related to human origins, primate behavior, and biological anthropology.

Research topics

• Biology
• Ecology
• Evolutionary biology
• Genetics
• Neuroscience
• Bioinformatics
• Geography

Selected publications

• Integrating microbiomes into One Health: insights from the 2025 One Health World Microbiome Partnership Summit

  The Lancet Microbe · 2026-01-09

  articleOpen access

  Research across multiple disciplines is showing that microbial communities are crucial for many facets of health and resilience, from human, plant, and animal health to disease resistance, ecosystem adaptability, and planetary climate regulation. Recognising this importance, the World Microbiome Partnership (WMP) was launched to integrate microbiome science into global health, agricultural, environmental, and regulatory systems.1 The One Health World Microbiome Partnership Summit, convened on June 20, 2025, under the High Patronage of French President Emmanuel Macron, brought together more than 40 leading microbiome experts and stakeholders from all sectors representing 16 countries and including a large online audience, with the goal of catalysing a coordinated, cross-sectoral microbiome research and innovation agenda aligned with One Health principles.

  PublisherOA PDFDOI

• Ancestral Knowledge and River Systems: Pathways to Sustainability, Peace, and Community Resilience

  Water · 2025-06-30 · 2 citations

  articleOpen accessSenior author

  This study offers a unique perspective on the role of ancestral knowledge in sustainable river management and community resilience. Specifically, this study draws on (1) a systematic literature review using the PRISMA methodology and (2) a qualitative analysis of community surveys conducted with 39 women in Zambrano, Colombia, to examine the impact of ancestral knowledge on sustainability, peace promotion, and community development. The findings highlight that women’s traditional water management practices significantly contribute to environmental sustainability, conflict resolution, and social cohesion. Women play a central role in transmitting and applying ancestral water knowledge, yet they remain marginalized in decision-making processes, often facing barriers to participation in governance structures. Finally, these findings proposed strategies for integrating ancestral knowledge into sustainable resource management policies. This study underscores the urgent need for legal recognition, intercultural dialogue, gender-inclusive governance, and educational programs to ensure the transmission and adaptation of these practices in contemporary contexts. Integrating ancestral knowledge into water management policies is essential for strengthening gender equity, community resilience, and fostering governance models that harmoniously combine traditional and scientific approaches.

  PublisherOA PDFDOI

• Why Didn't the Sifaka Cross the Road? Divergence of <i>Propithecus edwardsi</i> Gut Microbiomes Across Geographic Barriers in Ranomafana National Park, Madagascar

  American Journal of Primatology · 2025-02-01

  articleOpen access

  This study uses a biogeographic framework to identify patterns of gut microbiome divergence in an endangered lemur species endemic to Madagascar's southeastern rainforests, the Milne-Edwards's sifaka (Propithecus edwardsi). Specifically, we tested the effects of (1) geographic barriers, (2) habitat disturbance, and (3) geographic distance on gut microbiome alpha and beta diversity. We selected 10 social groups from 4 sites in Ranomafana National Park with varied histories of selective logging. Sites were spaced between 4 and 17 km apart falling on either side of two parallel barriers to animal movement: the Namorona River and the RN25 highway. Using 16S rRNA metabarcoding, we found the greatest beta diversity differentiation to occur between social groups, with significant divisions on opposite sides of geographic barriers (road/river). Habitat disturbance had the most significant effect on alpha diversity, though, contrary to many other studies, disturbance was associated with higher microbial species richness. Without biomedical context, it is unclear whether microbiome differences observed herein are neutral, adaptive, or maladaptive. However, microbiome divergence associated with the road/river may be a symptom of reduced host gene flow, warranting further investigation and perhaps conservation action (e.g., construction of wildlife bridges). Finally, this work demonstrates that significant microbiome variation can accrue over small sampling areas, lending new insight into host-microbe-environmental interactions.

  PublisherOA PDFDOI

• Large Comparative Analyses of Primate Body Site Microbiomes Indicate that the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates

  Microbiology Spectrum · 2022 · 16 citations

  Senior authorCorresponding
  • Biology
  • Evolutionary biology
  • Genetics

  The microbiome is critical to host health and disease, but much remains unknown about the determinants, levels, and evolution of host-microbial diversity. The relationship between hosts and their associated microbes is complex. Most studies to date have focused on the gut microbiome; however, large gaps remain in our understanding of host-microbial diversity, coevolution, and levels of variation in microbiomes across multiple body sites and host species. To better understand the patterns of variation and evolutionary context of host-microbial communities, we conducted one of the largest comparative studies to date, which indicated that the oral microbiome was distinct from the microbiomes of all other body sites and convergent across host species, suggesting conserved niche specialization within the Primates order. We also show the importance of host species differences in shaping the microbiome within specific body sites. This large, comparative study contributes valuable information on key patterns of variation among hosts and body sites, with implications for understanding host-microbial dynamics and human-microbial coevolution.

  PublisherDOI

• Erratum for Gomez et al., “Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints”

  mSphere · 2021-03-16

  erratumOpen access

  Volume 4, no. 4, e00271-19, 2019, https://doi.org/10.1128/mSphere.00271-19. The following sentence should be added to the end of the first paragraph of the Acknowledgments section: “Collection and export of fecal samples was also facilitated by the Filoha Hamadryas Project with the generous permission of the Ethiopian Wildlife Conservation Authority.”

  PublisherDOI

• Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions

  mSystems · 2020 · 26 citations

  • Ecology
  • Biology
  • Evolutionary biology

  The results of this study highlight parallel gut microbiome traits in human and nonhuman primates, depending on subsistence strategy. Although these similarities have been reported before, the functional and ecological bases of this convergence are not fully understood. Here, we show that this parallelism is, in part, likely modulated by the complexity of plant carbohydrates consumed and by exposures to diverse xenobiotics of natural and artificial origin. Furthermore, we discuss how divergence from these parallel microbiome traits is typically associated with adverse health outcomes in human populations living under culturally westernized subsistence patterns. This is important information as we trace the specific dietary and environmental triggers associated with the loss and gain of microbial functions as humans adapt to various dietary niches.

  PublisherDOI

• The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance

  mSystems · 2020 · 70 citations

  • Ecology
  • Biology
  • Geography

  Gut microbiota diversity has become the subject of extensive research in human and nonhuman animals, linking diversity and composition to gut function and host health. Because wild primates are good indicators of tropical ecosystem health, we developed the idea that they are a suitable model to observe the consequences of advancing global change (e.g., habitat degradation) on gut microbiota. So far, most of the studies focus mainly on gut bacteria; however, they are not the only component of the gut: fungi also serve essential functions in gut homeostasis. Here, for the first time, we explore and measure diversity and composition of both bacterial and fungal microbiota components of two tropical primate species living in highly different habitat types (intact versus degraded forests). Results on their microbiota diversity and composition are discussed in light of conservation issues and potential applications.

  PublisherDOI

• 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

  American Journal of Primatology · 2019-08-31 · 10 citations

  articleSenior author

  The study of the primate microbiome is critical in understanding the role of the microbial community in the host organism. To be able to isolate the main factors responsible for the differences observed in microbiomes within and between individuals, confounding factors due to technical variations need to be removed. To determine whether alterations due to preservatives outweigh differences due to factors such as host population, host species, body site, and habitat, we tested three methods (no preservative, 96% ethanol, and RNAlater) for preserving wild chimpanzee (fecal), wild lemur (fecal), wild vervet monkey (rectal, oral, nasal, otic, vaginal, and penile), and captive vervet monkey (rectal) samples. All samples were stored below - 20°C (short term) at the end of the field day and then at - 80°C until DNA extraction. Using 16S rRNA gene sequencing, we show a significant preservative effect on microbiota composition and diversity. Samples stored in ethanol and RNAlater appear to be less different compared with samples not stored in any preservative (none). Our differential analysis revealed significantly higher amounts of Enterococcaceae and Family XI in no preservative samples, Prevotellaceae and Spirochaetaceae in ethanol and RNAlater preserved samples, Oligosphaeraceae in ethanol-preserved samples, and Defluviitaleaceae in RNAlater preserved samples. While these preservative effects on the microbiome are not large enough to remove or outweigh the differences arising from biological factors (e.g., host species, body site, and habitat differences) they may promote misleading interpretations if they have large enough effect sizes compared to the biological factors (e.g., host population).

  PublisherDOI

• Additional file 3: of Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny

  Figshare · 2019-01-01

  datasetOpen access

  Table S3. Shared gut microbial taxa between host taxonomic groups. (XLSX 56 kb)

  PublisherDOI

• Moving forward with the primate microbiome: Introduction to a special issue of the <i>American Journal of Primatology</i>

  American Journal of Primatology · 2019-10-01

  articleSenior author

  Primate microbiome research is a quickly growing field with exciting potential for informing our understanding of primate biology, ecology, and evolution as well as host-microbe interactions more broadly. This introductory essay to a special section of the American Journal of Primatology provides a cross-sectional snapshot of current activity in these areas by briefly summarizing the diversity of contributed papers and their relationships to key themes in host-associated microbiome research. It then uses this survey as a foundation for consolidating a set of key research questions to broadly guide future research. It also argues for the importance of methods standardization to facilitate comparative analyses and the identification of generalizable patterns and relationships. While primatology will benefit greatly from the integration of microbial datasets, it is uniquely positioned to address important questions regarding microbiology and macro-ecology and evolution more generally. We are eager to see where the primate microbiome leads us.

  PublisherDOI

Recent grants

• Microbes, Diet, and Hominin Evolution: Comparative and Metagenomic Approaches

  NSF · $2.4M · 2009–2018

• Female Sociality, Dispersal, and Comparative Microbial Community Composition in Pan troglodytes

  NSF · $376k · 2014–2020

• Comparative Primate Microbial Ecology

  NSF · $300k · 2008–2015

Frequent coauthors

• Steven R. Leigh

  67 shared

• Bryan A. White

  University of Auckland

  36 shared

• Brenda A. Wilson

  University of Illinois Urbana-Champaign

  33 shared

• William Nelson

  Pacific Northwest National Laboratory

  33 shared

• Klára J. Petrželková

  Czech Academy of Sciences, Institute of Vertebrate Biology

  30 shared

• David Modrý

  Masaryk University

  28 shared

• Katherine R. Amato

  Canadian Institute for Advanced Research

  28 shared

• Carl J. Yeoman

  Montana State University

  26 shared

Labs

• Stumpf LaboratoryPI

  Behavioral, hormone and microbiome studies of wild chimpanzees in Kibale National Park, Uganda.

Awards & honors

• Notre Dame Institute for Advanced Study Fellowship, Notre Da…
• Fulbright Specialist Program Faculty (2021-2024)
• Faculty Fellowship, Center for Advanced Study, University of…
• University Scholar: for Excellence in Scholarship, Teaching…
• Campus Award for Excellence in Undergraduate Teaching. Unive…