@article{lafferty_mckenney_hubbard_trujillo_beasley_2024, title={A Path Forward: Creating an Academic Culture of Justice, Equity, Diversity, and Inclusion}, url={https://doi.org/10.1002/bes2.2117}, DOI={10.1002/bes2.2117}, abstractNote={Abstract}, journal={The Bulletin of the Ecological Society of America}, author={Lafferty, Diana J. R. and McKenney, Erin A. and Hubbard, Tru and Trujillo, Sarah and Beasley, DeAnna E.}, year={2024}, month={Jan} }
 @book{mckenney_2023, title={Applied Ecology}, url={https://doi.org/10.52750/147069}, DOI={10.52750/147069}, author={McKenney, Erin}, editor={McKenney, Erin and Rund, EmilyEditors}, year={2023}, month={Aug} }
 @misc{burnham_ange-van heugten_mckenney_minter_trivedi_2023, title={Conservation Innovations and Future Directions for the Study of Rhinoceros Gut Microbiome}, volume={4}, ISSN={["2673-5636"]}, url={https://www.mdpi.com/2673-5636/4/2/30}, DOI={10.3390/jzbg4020030}, abstractNote={Rhinoceros are among the largest and most endangered herbivores in the world. Three of the five extant species are critically endangered, with poaching and habitat loss contributing heavily to declines. The gut microbiome is an essential facet of host health and digestion, mediating a variety of immune and physiological functions. Certain microbes have the potential to serve as biomarkers for reproductive outcomes and predictors of disease susceptibility. Therefore, assessing gut microbial dynamics in relation to wild and managed rhinoceros populations has particular relevance for zoos and other conservation organizations that maintain assurance populations of these charismatic megafauna. The functional gut microbiomes associated with all rhinoceros species remain poorly studied, and many published reports are limited by small sample sizes and sex biases. In this review, we synthesize current research to examine the rhinoceros gut microbiome under human management and resulting conservation implications, address common pitfalls of wildlife gut microbiome studies, and propose future avenues of research in this field.}, number={2}, journal={JOURNAL OF ZOOLOGICAL AND BOTANICAL GARDENS}, author={Burnham, Christina M. and Ange-van Heugten, Kimberly and McKenney, Erin A. and Minter, Larry J. and Trivedi, Shweta}, year={2023}, month={Jun}, pages={396–412} }
 @article{burnham_mckenney_ange-van heugten_minter_trivedi_2023, title={Effect of fecal preservation method on captive southern white rhinoceros gut microbiome}, volume={3}, ISSN={["2328-5540"]}, DOI={10.1002/wsb.1436}, abstractNote={Abstract}, journal={WILDLIFE SOCIETY BULLETIN}, author={Burnham, Christina M. and McKenney, Erin A. and Ange-van Heugten, Kimberly and Minter, Larry J. and Trivedi, Shweta}, year={2023}, month={Mar} }
 @article{burnham_mckenney_ange-van heugten_minter_trivedi_2023, title={Effects of age, seasonality, and reproductive status on the gut microbiome of Southern White Rhinoceros (Ceratotherium simum simum) at the North Carolina zoo}, volume={5}, ISSN={["2524-4671"]}, DOI={10.1186/s42523-023-00249-5}, abstractNote={Abstract}, number={1}, journal={ANIMAL MICROBIOME}, author={Burnham, Christina M. M. and McKenney, Erin A. A. and Ange-van Heugten, Kimberly and Minter, Larry J. J. and Trivedi, Shweta}, year={2023}, month={May} }
 @article{mckenney_hale_anderson_larsen_grant_dunn_2023, title={Hidden diversity: comparative functional morphology of humans and other species}, volume={11}, ISSN={["2167-8359"]}, DOI={10.7717/peerj.15148}, abstractNote={Gastrointestinal (GI) morphology plays an important role in nutrition, health, and epidemiology; yet limited data on GI variation have been collected since 1885. Here we demonstrate that students can collect reliable data sets on gut morphology; when they do, they reveal greater morphological variation for some structures in the GI tract than has been documented in the published literature. We discuss trait variability both within and among species, and the implications of that variability for evolution and epidemiology. Our results show that morphological variation in the GI tract is associated with each organ’s role in food processing. For example, the length of many structures was found to vary significantly with feeding strategy. Within species, the variability illustrated by the coefficients of variation suggests that selective constraints may vary with function. Within humans, we detected significant Pearson correlations between the volume of the liver and the length of the appendix (t-value = 2.5278, df = 28, p = 0.0174, corr = 0.4311) and colon (t-value = 2.0991, df = 19, p = 0.0494, corr = 0.4339), as well as between the lengths of the small intestine and colon (t-value = 2.1699, df = 17, p = 0.0445, corr = 0.4657), which are arguably the most vital organs in the gut for nutrient absorption. Notably, intraspecific variation in the small intestine can be associated with life history traits. In humans, females demonstrated consistently and significantly longer small intestines than males (t-value15 = 2.245, p = 0.0403). This finding supports the female canalization hypothesis, specifically, increased female investment in the digestion and absorption of lipids.}, journal={PEERJ}, author={McKenney, Erin A. and Hale, Amanda R. and Anderson, Janiaya and Larsen, Roxanne and Grant, Colleen and Dunn, Robert R.}, year={2023}, month={Apr} }
 @article{mckenney_nichols_alvarado_hardy_kemp_polmanteer_shoemaker_dunn_2023, title={Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities}, volume={11}, ISSN={["2167-8359"]}, DOI={10.7717/peerj.16163}, abstractNote={The microbial fermentation behind sourdough bread is among our oldest technologies, yet there are many opportunities for sourdough science to learn from traditional bakers. We analyzed 16S rRNA sequences in R to assess the bacterial community structure and performance of 40 starters grown from 10 types of flour over 14 days, and identified six distinct stages of succession. At each stage, bacterial taxa correlate with determinants of bread quality including pH, rise, and aromatic profile. Day 1 starter cultures were dominated by microorganisms commonly associated with plants and flour, and by aromas similar to toasted grain/cereal. Bacterial diversity peaked from days 2–6 as taxa shifted from opportunistic/generalist bacteria associated with flour inputs, toward specialized climax bacterial communities (days 10–14) characterized by acid-tolerant taxa and fruity (p < 3.03e−03), sour (p < 1.60e−01), and fermented (p < 1.47e−05) aromas. This collection of traits changes predictably through time, regardless of flour type, highlighting patterns of bacterial constraints and dynamics that are conserved across systems and scales. Yet, while sourdough climax communities exhibit similar markers of maturity (i.e., pH ≤ 4 and enriched in Lactobacillus (mean abundance 48.1%), Pediococcus (mean abundance 22.7%), and/or Gluconobacter (mean abundance 19.1%)), we also detected specific taxa and aromas associated with each type of flour. Our results address important ecological questions about the relationship between community structure and starter performance, and may enable bakers to deliberately select for specific sourdough starter and bread characteristics.}, journal={PEERJ}, author={Mckenney, Erin A. and Nichols, Lauren M. and Alvarado, Samuel and Hardy, Shannon and Kemp, Kristen and Polmanteer, Rachael and Shoemaker, April and Dunn, Robert R.}, year={2023}, month={Oct} }
 @article{mckenney_2023, title={The Human Gut Microbiome}, url={https://doi.org/10.52750/219830}, DOI={10.52750/219830}, abstractNote={We evolved in a bacterial world.The gut microbiome affects our development, our behaviors and moods, our immune system and overall health, and our ability to break down toxins and harvest energy from the foods that we eat.Microbes affect our health, behavior, and other aspects of our lives and well-being.Decisions we make in our daily lives, from what foods we eat, to how much time we spend outdoors can help us make the most of our gut microbiome, and all the good that it can do for us.Erin McKenney's research incorporates microbial ecology, nutrition, and comparative gut morphology to investigate novel questions using perfect, unusual systems.For over a decade she has investigated evolutionary adaptation across scales and species, between non-human primates and rogue (herbivorous) carnivores and their gut microbes.More recently, she has engaged the public, particularly students, to study the microbes in sourdough starters and other fermented foods.In the classroom, Dr. McKenney cultivates critical thinking through active learning.She focuses on practicing current techniques to collect and analyze novel datasets.By designing her courses around authentic research experiences, she encourages student autonomy and foster practicing scientists.}, author={McKenney, Erin}, year={2023}, month={Jan} }
 @article{shoaf_french_clifford_mckenney_ott_2022, title={A gut microbiome tactile teaching tool and guided-inquiry activity promotes student learning}, volume={13}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2022.966289}, abstractNote={The gut microbiome and its physiological impacts on human and animal health is an area of research emphasis. Microbes themselves are invisible and may therefore be abstract and challenging to understand. It is therefore important to infuse this topic into undergraduate curricula, including Anatomy and Physiology courses, ideally through an active learning approach. To accomplish this, we developed a novel tactile teaching tool with guided-inquiry (TTT-GI) activity where students explored how the gut microbiome ferments carbohydrates to produce short chain fatty acids (SCFAs). This activity was implemented in two sections of a large-enrollment Human Anatomy and Physiology course at a research intensive (R1) university in the Spring of 2022 that was taught using a hyflex format. Students who attended class in person used commonly available building toys to assemble representative carbohydrates of varying structural complexity, whereas students who attended class virtually made these carbohydrate structures using a digital learning tool. Students then predicted how microbes within the gut would ferment different carbohydrates into SCFAs, as well as the physiological implications of the SCFAs. We assessed this activity to address three research questions, with 182 students comprising our sample. First, we evaluated if the activity learning objectives were achieved through implementation of a pre-and post-assessment schema. Our results revealed that all three learning objectives of this activity were attained. Next, we evaluated if the format in which this TTT-GI activity was implemented impacted student learning. While we found minimal and nonsignificant differences in student learning between those who attended in-person and those who attended remotely, we did find significant differences between the two course sections, which differed in length and spacing of the activity. Finally, we evaluated if this TTT-GI approach was impactful for diverse students. We observed modest and nonsignificant positive learning gains for some populations of students traditionally underrepresented in STEM (first-generation students and students with one or more disabilities). That said, we found that the greatest learning gains associated with this TTT-GI activity were observed in students who had taken previous upper-level biology coursework.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Shoaf, Parker T. and French, Katie S. and Clifford, Noah J. and McKenney, Erin A. and Ott, Laura E.}, year={2022}, month={Dec} }
 @article{trujillo_mckenney_hilderbrand_mangipane_rogers_joly_gustine_erlenbach_mangipane_lafferty_2022, title={Correlating gut microbial membership to brown bear health metrics}, volume={12}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-022-19527-4}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Trujillo, Sarah M. and McKenney, Erin A. and Hilderbrand, Grant V and Mangipane, Lindsey S. and Rogers, Matthew C. and Joly, Kyle and Gustine, David D. and Erlenbach, Joy A. and Mangipane, Buck A. and Lafferty, Diana J. R.}, year={2022}, month={Sep} }
 @article{trujillo_mckenney_hilderbrand_mangipane_rogers_joly_gustine_erlenbach_mangipane_lafferty_2022, title={Intrinsic and extrinsic factors influence on an omnivore's gut microbiome}, volume={17}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0266698}, DOI={10.1371/journal.pone.0266698}, abstractNote={Gut microbiomes (GMBs), complex communities of microorganisms inhabiting the gastrointestinal tracts of their hosts, perform countless micro-ecosystem services such as facilitating energy uptake and modulating immune responses. While scientists increasingly recognize the role GMBs play in host health, the role of GMBs in wildlife ecology and conservation has yet to be realized fully. Here, we use brown bears (Ursus arctos) as an ecological model to (1) characterize GMB community composition associated with location, season, and reproductive condition of a large omnivore; (2) investigate how both extrinsic and intrinsic factors influence GMB community membership and structure; and (3) quantify differences in GMB communities among different locations, seasons, sex, and reproductive conditions. To achieve these aims, we subsampled brown bear fecal samples collected during United States National Park Service research activities at three National Parks and Preserves (Katmai, Lake Clark, and Gates of the Arctic) and extracted microbial DNA for 16S rRNA amplicon sequencing and microbial taxonomic classification. We analyzed GMB communities using alpha and beta diversity indices, subsequently using linear mixed models to examine relationships between alpha diversity and extrinsic and intrinsic factors. Katmai brown bears hosted the greatest alpha diversity, whereas Gates brown bears hosted the least alpha diversity. Our results indicate that location and diet drive GMB variation, with bears hosting less phylogenetic diversity as park distance inland increases. Monitoring brown bear GMBs could enable managers to quickly detect and assess the impact of environmental perturbations on brown bear health. By integrating macro and micro-ecological perspectives we aim to inform local and landscape-level management decisions to promote long-term brown bear conservation and management.}, number={4}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Trujillo, Sarah M. and McKenney, Erin A. and Hilderbrand, Grant V and Mangipane, Lindsey S. and Rogers, Matthew C. and Joly, Kyle and Gustine, David D. and Erlenbach, Joy A. and Mangipane, Buck A. and Lafferty, Diana J. R.}, editor={Gorokhova, ElenaEditor}, year={2022} }
 @article{lafferty_gillman_jeakle_roell_mckenney_2022, title={Mink (Neovison vison) fecal microbiomes are influenced by sex, temperature, and time postdefecation}, volume={103}, ISSN={["1545-1542"]}, DOI={10.1093/jmammal/gyab140}, abstractNote={Abstract}, number={2}, journal={JOURNAL OF MAMMALOGY}, author={Lafferty, Diana J. R. and Gillman, Sierra J. and Jeakle, Lane K. and Roell, Brian J. and McKenney, Erin A.}, year={2022}, month={Apr}, pages={316–327} }
 @article{lafferty_mckenney_gillman_kailing_walimaa_kailing_roell_2022, title={The gut microbiome of wild American marten in the Upper Peninsula of Michigan}, volume={17}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0275850}, abstractNote={Carnivores are ecologically important and sensitive to habitat loss and anthropogenic disruption. Here we measured trophic level and gut bacterial composition as proxies of carnivore ecological status across the Upper Peninsula, Michigan, for wild American marten (Martes americana; hereafter marten). In contrast to studies that have focused on omnivorous and herbivorous species, we find that marten, like other carnivore species without a cecum, are dominated by Firmicutes (52.35%) and Proteobacteria (45.31%) but lack Bacteroidetes. Additionally, a majority of the 12 major bacterial genera (occurring at ≥1%) are known hydrogen producers, suggesting these taxa may contribute to host energy requirements through fermentative production of acetate. Our study suggests that live trapping and harvest methods yield similar marten gut microbiome data. In addition, preserving undisturbed forest likely impacts marten ecology by measurably increasing marten trophic level and altering the gut microbiome. Our study underscores the utility of the gut microbiome as a tool to monitor the ecological status of wild carnivore populations.}, number={11}, journal={PLOS ONE}, author={Lafferty, Diana J. R. and McKenney, Erin A. and Gillman, Sierra J. and Kailing, Chris D. and Walimaa, Myles C. and Kailing, Macy J. and Roell, Brian J.}, year={2022}, month={Nov} }
 @article{calvert_madden_nichols_haddad_lahne_dunn_mckenney_2021, title={A review of sourdough starters: ecology, practices, and sensory quality with applications for baking and recommendations for future research}, volume={5}, url={https://doi.org/10.7717/peerj.11389}, DOI={10.7717/peerj.11389}, abstractNote={The practice of sourdough bread-making is an ancient science that involves the development, maintenance, and use of a diverse and complex starter culture. The sourdough starter culture comes in many different forms and is used in bread-making at both artisanal and commercial scales, in countries all over the world. While there is ample scientific research related to sourdough, there is no standardized approach to using sourdough starters in science or the bread industry; and there are few recommendations on future directions for sourdough research. Our review highlights what is currently known about the microbial ecosystem of sourdough (including microbial succession within the starter culture), methods of maintaining sourdough (analogous to land management) on the path to bread production, and factors that influence the sensory qualities of the final baked product. We present new hypotheses for the successful management of sourdough starters and propose future directions for sourdough research and application to better support and engage the sourdough baking community.}, journal={PEERJ}, author={Calvert, Martha D. and Madden, Anne A. and Nichols, Lauren M. and Haddad, Nick M. and Lahne, Jacob and Dunn, Robert R. and McKenney, Erin A.}, year={2021}, month={May} }
 @article{eschweiler_clayton_moresco_mckenney_minter_suhr van haute_gasper_hayer_zhu_cooper_et al._2021, title={Host Identity and Geographic Location Significantly Affect Gastrointestinal Microbial Richness and Diversity in Western Lowland Gorillas (Gorilla gorilla gorilla) under Human Care}, volume={11}, ISSN={2076-2615}, url={http://dx.doi.org/10.3390/ani11123399}, DOI={10.3390/ani11123399}, abstractNote={The last few decades have seen an outpouring of gastrointestinal (GI) microbiome studies across diverse host species. Studies have ranged from assessments of GI microbial richness and diversity to classification of novel microbial lineages. Assessments of the “normal” state of the GI microbiome composition across multiple host species has gained increasing importance for distinguishing healthy versus diseased states. This study aimed to determine baselines and trends over time to establish “typical” patterns of GI microbial richness and diversity, as well as inter-individual variation, in three populations of western lowland gorillas (Gorilla gorilla gorilla) under human care at three zoological institutions in North America. Fecal samples were collected from 19 western lowland gorillas every two weeks for seven months (n = 248). Host identity and host institution significantly affected GI microbiome community composition (p < 0.05), although host identity had the most consistent and significant effect on richness (p = 0.03) and Shannon diversity (p = 0.004) across institutions. Significant changes in microbial abundance over time were observed only at Denver Zoo (p < 0.05). Our results suggest that individuality contributes to most of the observed GI microbiome variation in the study populations. Our results also showed no significant changes in any individual’s microbial richness or Shannon diversity during the 7-month study period. While some microbial taxa (Prevotella, Prevotellaceae and Ruminococcaceae) were detected in all gorillas at varying levels, determining individual baselines for microbial composition comparisons may be the most useful diagnostic tool for optimizing non-human primate health under human care.}, number={12}, journal={Animals}, publisher={MDPI AG}, author={Eschweiler, Katrina and Clayton, Jonathan B. and Moresco, Anneke and McKenney, Erin A. and Minter, Larry J. and Suhr Van Haute, Mallory J. and Gasper, William and Hayer, Shivdeep Singh and Zhu, Lifeng and Cooper, Kathryn and et al.}, year={2021}, month={Nov}, pages={3399} }
 @article{gillman_mckenney_lafferty_2021, title={Human-provisioned foods reduce gut microbiome diversity in American black bears (Ursus americanus)}, volume={12}, ISSN={["1545-1542"]}, DOI={10.1093/jmammal/gyab154}, abstractNote={Abstract}, journal={JOURNAL OF MAMMALOGY}, author={Gillman, Sierra J. and McKenney, Erin A. and Lafferty, Diana J. R.}, year={2021}, month={Dec} }
 @article{landis_oliverio_mckenney_nichols_kfoury_biango-daniels_shell_madden_shapiro_sakunala_et al._2021, title={The diversity and function of sourdough starter microbiomes}, volume={10}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/eLife.61644}, DOI={10.7554/eLife.61644}, abstractNote={Humans have relied on sourdough starter microbial communities to make leavened bread for thousands of years, but only a small fraction of global sourdough biodiversity has been characterized. Working with a community-scientist network of bread bakers, we determined the microbial diversity of 500 sourdough starters from four continents. In sharp contrast with widespread assumptions, we found little evidence for biogeographic patterns in starter communities. Strong co-occurrence patterns observed in situ and recreated in vitro demonstrate that microbial interactions shape sourdough community structure. Variation in dough rise rates and aromas were largely explained by acetic acid bacteria, a mostly overlooked group of sourdough microbes. Our study reveals the extent of microbial diversity in an ancient fermented food across diverse cultural and geographic backgrounds.}, journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Landis, Elizabeth A and Oliverio, Angela M and McKenney, Erin A and Nichols, Lauren M and Kfoury, Nicole and Biango-Daniels, Megan and Shell, Leonora K and Madden, Anne A and Shapiro, Lori and Sakunala, Shravya and et al.}, year={2021}, month={Jan} }
 @article{gillman_mckenney_lafferty_2020, title={Wild black bears harbor simple gut microbial communities with little difference between the jejunum and colon}, volume={10}, ISSN={["2045-2322"]}, url={https://doi.org/10.1038/s41598-020-77282-w}, DOI={10.1038/s41598-020-77282-w}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Gillman, Sierra J. and McKenney, Erin A. and Lafferty, Diana J. R.}, year={2020}, month={Dec} }
 @article{finn_scheuermann_holzknecht_gao_ibrahim_parker_granek_lin_mckenney_barbas_2019, title={The effect of levofloxacin on the lung microbiota of laboratory rats}, volume={45}, ISSN={["1521-0499"]}, DOI={10.1080/01902148.2019.1639225}, abstractNote={Abstract Aim: The aim of this study was to investigate the short-term effect of levofloxacin on the microbiota of healthy lungs. Material and methods: Male F344 rats received either no levofloxacin (n = 9), intravenous levofloxacin (n = 12), oral levofloxacin (n = 12), or subcutaneous levofloxacin (n = 14). Rats received a clinically applicable dose (5.56 mg/kg) of levofloxacin via the assigned delivery route once daily for three days. On day four, lung tissue was collected and the lung microbiota composition was investigated using 16S ribosomal RNA gene sequencing. Results: Untreated lungs showed a microbiota dominated by bacteria of the genera Serratia. After treatment with levofloxacin, bacteria of the genus Pantoea dominated the lung microbiota. This was observed for all routes of antibiotic administration, with a significant difference compared to no-antibiotic control group (PERMANOVA: P < 0.001; homogeneity of dispersions: P = 0.656). Conclusion: Our study is the first to demonstrate the effects of levofloxacin therapy on lung microbiota in laboratory rats. Levofloxacin treatment by any route of administration leads to profound changes in the rat lung microbiota, resulting in the predominance of bacteria belonging to the genus Pantoea. Further studies regarding the role of long-term application of broad spectrum antibiotics on induction of lung, allergic and autoimmune diseases are indicated. Abbreviations ASVs: Amplicon sequence variants; F344: Fischer 344; IV: Intravenous; NMDS: Non-metric multidimensional scaling; OTU: Operational taxonomic unit; PERMANOVA: Permutational multivariate analysis of variance; Subq: Subcutaneous.}, number={7}, journal={EXPERIMENTAL LUNG RESEARCH}, author={Finn, Sade M. B. and Scheuermann, Uwe and Holzknecht, Zoie E. and Gao, Qimeng and Ibrahim, Mohamed M. and Parker, William and Granek, Joshua A. and Lin, Shu S. and McKenney, Erin A. and Barbas, Andrew S.}, year={2019}, month={Aug}, pages={200–208} }
 @misc{greene_bornbusch_mckenney_harris_gorvetzian_yoder_drea_2019, title={The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs}, volume={81}, ISSN={["1098-2345"]}, DOI={10.1002/ajp.22974}, abstractNote={Abstract}, number={10-11}, journal={AMERICAN JOURNAL OF PRIMATOLOGY}, author={Greene, Lydia K. and Bornbusch, Sally L. and McKenney, Erin A. and Harris, Rachel L. and Gorvetzian, Sarah R. and Yoder, Anne D. and Drea, Christine M.}, year={2019}, month={Oct} }
 @article{finn_scheuermann_holzknecht_parker_granek_lin_mckenney_barbas_2018, title={Effect of gastric fluid aspiration on the lung microbiota of laboratory rats}, volume={44}, DOI={10.1080/01902148.2018.1482976}, abstractNote={Abstract Aim of the Study: The pulmonary microbiota is important for both normal homeostasis and the progression of disease, and may be affected by aspiration of gastric fluid. The aim of this study was to investigate changes in the lung microbiota induced by aspiration of gastric fluid in a laboratory rat model. Material and Methods: Using the intratracheal application method, male rats received aspiration with 0.9% normal saline (n = 11); gastric fluid (n = 24) or sterilized (gamma-irradiated) gastric fluid (n = 12) once-weekly for four weeks. On the fifth week, the animals were sacrificed, and the microbiota of the lung was assessed by 16S ribosomal RNA gene sequencing. Results: Lungs without aspiration and lungs after aspiration with normal saline had similar microbial compositions, dominated by bacteria of the genera Serratia, Ralstonia and Brucella. Evaluation of the microbiota following aspiration of gastric fluid revealed a much different profile that was dominated by bacteria from the genera Romboutsia and Turicibacter and largely independent of sterilization of the gastric fluid. Conclusion: In a laboratory rat model, aspiration with gastric fluid caused a substantial shift of the lung microbiota that could be characterized as a shift from Proteobacteria towards Firmicutes, possibly of enteric origin. Bacteria contained in the gastric fluid are not apparently responsible for this change.}, number={4-5}, journal={EXPERIMENTAL LUNG RESEARCH}, author={Finn, Sade M. B. and Scheuermann, Uwe and Holzknecht, Zoie E. and Parker, William and Granek, Joshua A. and Lin, Shu S. and McKenney, Erin and Barbas, Andrew S.}, year={2018}, pages={201–210} }
 @article{greene_mckenney_o’connell_drea_2018, title={The critical role of dietary foliage in maintaining the gut microbiome and metabolome of folivorous sifakas}, volume={8}, DOI={10.1038/s41598-018-32759-7}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Nature America, Inc}, author={Greene, Lydia K. and McKenney, Erin A. and O’Connell, Thomas M. and Drea, Christine M.}, year={2018}, month={Sep} }
 @article{mckenney_koelle_dunn_yoder_2018, title={The ecosystem services of animal microbiomes}, volume={27}, ISSN={["1365-294X"]}, url={https://doi.org/10.1111/mec.14532}, DOI={10.1111/mec.14532}, abstractNote={Abstract}, number={8}, journal={MOLECULAR ECOLOGY}, publisher={Wiley-Blackwell}, author={McKenney, E. A. and Koelle, K. and Dunn, R. R. and Yoder, A. D.}, year={2018}, month={Apr}, pages={2164–2172} }
 @article{greene_mckenney_2018, title={The inside tract: The appendicular, cecal, and colonic microbiome of captive aye-ayes}, volume={166}, DOI={10.1002/ajpa.23481}, abstractNote={Abstract}, number={4}, journal={American Journal of Physical Anthropology}, publisher={Wiley}, author={Greene, Lydia K. and McKenney, Erin A.}, year={2018}, month={Apr}, pages={960–967} }
 @article{bamboo specialists from two mammalian orders (primates, carnivora) share a high number of low-abundance gut microbes._2017, volume={11}, url={http://europepmc.org/abstract/med/29188302}, DOI={10.1007/s00248-017-1114-8}, abstractNote={Bamboo specialization is one of the most extreme examples of convergent herbivory, yet it is unclear how this specific high-fiber diet might selectively shape the composition of the gut microbiome compared to host phylogeny. To address these questions, we used deep sequencing to investigate the nature and comparative impact of phylogenetic and dietary selection for specific gut microbial membership in three bamboo specialists-the bamboo lemur (Hapalemur griseus, Primates: Lemuridae), giant panda (Ailuropoda melanoleuca, Carnivora: Ursidae), and red panda (Ailurus fulgens, Carnivora: Musteloideadae), as well as two phylogenetic controls-the ringtail lemur (Lemur catta) and the Asian black bear (Ursus thibetanus). We detected significantly higher Shannon diversity in the bamboo lemur (10.029) compared to both the giant panda (8.256; p = 0.0001936) and the red panda (6.484; p = 0.0000029). We also detected significantly enriched bacterial taxa that distinguished each species. Our results complement previous work in finding that phylogeny predominantly governs high-level microbiome community structure. However, we also find that 48 low-abundance OTUs are shared among bamboo specialists, compared to only 8 OTUs shared by the bamboo lemur and its sister species, the ringtail lemur (Lemur catta, a generalist). Our results suggest that deep sequencing is necessary to detect low-abundance bacterial OTUs, which may be specifically adapted to a high-fiber diet. These findings provide a more comprehensive framework for understanding the evolution and ecology of the microbiome as well as the host.}, journal={Microbial ecology}, year={2017}, month={Nov} }
 @article{down for the count: cryptosporidium infection depletes the gut microbiome in coquerel's sifakas._2017, url={http://europepmc.org/abstract/med/28740461}, DOI={10.1080/16512235.2017.1335165}, abstractNote={ABSTRACT Background: The gut microbiome (GMB) is the first line of defense against enteric pathogens, which are a leading cause of disease and mortality worldwide. One such pathogen, the protozoan Cryptosporidium, causes a variety of digestive disorders that can be devastating and even lethal. The Coquerel’s sifaka (Propithecus coquereli) – an endangered, folivorous primate endemic to Madagascar – is precariously susceptible to cryptosporidiosis under captive conditions. If left untreated, infection can rapidly advance to morbidity and death. Objective: To gain a richer understanding of the pathophysiology of this pathogen while also improving captive management of endangered species, we examine the impact of cryptosporidiosis on the GMB of a flagship species known to experience a debilitating disease state upon infection. Design: Using 16S sequencing of DNA extracted from sifaka fecal samples, we compared the microbial communities of healthy sifakas to those of infected individuals, across infection and recovery periods. Results: Over the course of infection, we found that the sifaka GMB responds with decreased microbial diversity and increased community dissimilarity. Compared to the GMB of unaffected individuals, as well as during pre-infection and recovery periods, the GMB during active infection was enriched for microbial taxa associated with dysbiosis and rapid transit time. Time to recovery was inversely related to age, with young animals being slowest to recover GMB diversity and full community membership. Antimicrobial treatment during infection caused a significant depletion in GMB diversity. Conclusions: Although individual sifakas show unique trajectories of microbial loss and recolonization in response to infection, recovering sifakas exhibit remarkably consistent patterns, similar to initial community assembly of the GMB in infants. This observation, in particular, provides biological insight into the rules by which the GMB recovers from the disease state. Fecal transfaunation may prove effective in restoring a healthy GMB in animals with specialized diets.}, journal={Microbial ecology in health and disease}, year={2017} }
 @article{evolution of the hygiene hypothesis into biota alteration theory: what are the paradigms and where are the clinical applications?_2017, volume={11}, url={http://europepmc.org/abstract/med/29133248}, DOI={10.1016/j.micinf.2017.11.001}, abstractNote={For thousands of years, changes in human cultures have altered the biota associated with the human body, and those alterations have strongly influenced human health. The hygiene hypothesis has evolved over the past 30 years into a nuanced biota alteration theory, but modern medical priorities and regulatory policies have resulted in tragic underutilization of the acquired knowledge.}, journal={Microbes and infection}, year={2017}, month={Nov} }
 @article{feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs._2017, volume={11}, url={http://europepmc.org/abstract/med/29182421}, DOI={10.1080/19490976.2017.1408762}, abstractNote={ABSTRACT Many studies have demonstrated the effects of host diet on gut microbial membership, metagenomics, and fermentation individually; but few have attempted to interpret the relationship among these biological phenomena with respect to host features (e.g. gut morphology). We quantitatively compare the fecal microbial communities, metabolic pathways, and fermentation products associated with the nutritional intake of frugivorous (fruit-eating) and folivorous (leaf-eating) lemurs. Our results provide a uniquely multidimensional and comparative perspective on the adaptive dynamics between host and microbiome. Shotgun metagenomic sequencing revealed significant differential taxonomic and metabolic pathway enrichment, tailored to digest and detoxify different diets. Frugivorous metagenomes feature pathways to degrade simple carbohydrates and host-derived glycosaminoglycans, while folivorous metagenomes are equipped to break down phytic acid and other phytochemical compounds in an anaerobic environment. We used nuclear magnetic resonance based metabolic profiling of fecal samples to link metabolic pathways to fermentation products, confirming that the dissimilar substrates provided in each diet select for specific microbial functions. Fecal samples from frugivorous lemurs contained significantly different profiles of short chain fatty acids, alcohol fermentation products, amino acids, glucose, and glycerol compared to folivorous lemurs. We present the relationships between these datasets as an integrated visual framework, which we refer to as microbial geometry. We use microbial geometry to compare empirical gut microbial profiles across different feeding strategies, and suggest additional utility as a tool for hypothesis-generation.}, journal={Gut microbes}, year={2017}, month={Nov} }
 @article{williamson_mckenney_holzknecht_belliveau_rawls_poulton_parker_bilbo_2016, title={Got worms? Perinatal exposure to helminths prevents persistent immune sensitization and cognitive dysfunction induced by early-life infection}, volume={51}, DOI={10.1016/j.bbi.2015.07.006}, abstractNote={The incidence of autoimmune and inflammatory diseases has risen dramatically in post-industrial societies. "Biome depletion" - loss of commensal microbial and multicellular organisms such as helminths (intestinal worms) that profoundly modulate the immune system - may contribute to these increases. Hyperimmune-associated disorders also affect the brain, especially neurodevelopment, and increasing evidence links early-life infection to cognitive and neurodevelopmental disorders. We have demonstrated previously that rats infected with bacteria as newborns display life-long vulnerabilities to cognitive dysfunction, a vulnerability that is specifically linked to long-term hypersensitivity of microglial cell function, the resident immune cells of the brain. Here, we demonstrate that helminth colonization of pregnant dams attenuated the exaggerated brain cytokine response of their offspring to bacterial infection, and that combined with post-weaning colonization of offspring with helminths (consistent with their mothers treatment) completely prevented enduring microglial sensitization and cognitive dysfunction in adulthood. Importantly, helminths had no overt impact on adaptive immune cell subsets, whereas exaggerated innate inflammatory responses in splenic macrophages were prevented. Finally, helminths altered the effect of neonatal infection on the gut microbiome; neonatal infection with Escherichia coli caused a shift from genera within the Actinobacteria and Tenericutes phyla to genera in the Bacteroidetes phylum in rats not colonized with helminths, but helminths attenuated this effect. In sum, these data point toward an inter-relatedness of various components of the biome, and suggest potential mechanisms by which this helminth might exert therapeutic benefits in the treatment of neuroinflammatory and cognitive disorders.}, journal={Brain, Behavior, and Immunity}, publisher={Elsevier BV}, author={Williamson, Lauren L. and McKenney, Erin A. and Holzknecht, Zoie E. and Belliveau, Christine and Rawls, John F. and Poulton, Susan and Parker, William and Bilbo, Staci D.}, year={2016}, month={Jan}, pages={14–28} }
 @article{mckenney_dunn_urban_stalls_millis_flythe_stevens_2016, title={Symbiosis in the Soil: Citizen Microbiology in Middle and High School Classrooms †}, volume={17}, ISSN={1935-7877 1935-7885}, url={http://dx.doi.org/10.1128/jmbe.v17i1.1016}, DOI={10.1128/jmbe.v17i1.1016}, abstractNote={Microorganisms are vital to environmental health, yet their association with disease often overshadows these benefits. Building citizen-science activities around the positive role of microorganisms and an understanding of their ubiquity can begin to dispel misconceptions while simultaneously engaging the public in research. Here, we describe a citizen-science microbiology project geared toward implementation in middle and high school classrooms. Students culture environmental microorganisms and document microbial diversity of plant root systems compared with adjacent bulk soil. Results contribute data toward research on microbiome recruitment of weeds and other successful plants while addressing core topics in science education.}, number={1}, journal={Journal of Microbiology & Biology Education}, publisher={American Society for Microbiology}, author={McKenney, Erin and Dunn, Robert R. and Urban, Julie M. and Stalls, Jennifer and Millis, Courtney and Flythe, Taylar and Stevens, Julia L.}, year={2016}, month={Mar}, pages={60–62} }
 @article{mckenney_williamson_yoder_rawls_bilbo_parker_2015, title={Alteration of the rat cecal microbiome during colonization with the helminthHymenolepis diminuta}, volume={6}, DOI={10.1080/19490976.2015.1047128}, abstractNote={The microbiome is now widely recognized as being important in health and disease, and makes up a substantial subset of the biome within the ecosystem of the vertebrate body. At the same time, multicellular, eukaryotic organisms such as helminths are being recognized as an important component of the biome that shaped the evolution of our genes. The absence of these macroscopic organisms during the early development and life of humans in Western culture probably leads to a wide range of human immunological diseases. However, the interaction between the microbiome and macroscopic components of the biome remains poorly characterized. In this study, the microbiome of the cecum in rats colonized for 2 generations with the small intestinal helminth Hymenolepis diminuta was evaluated. The introduction of this benign helminth, which is of considerable therapeutic interest, led to several changes in the cecal microbiome. Most of the changes were within the Firmicutes phylum, involved about 20% of the total bacteria, and generally entailed a shift from Bacilli to Clostridia species in the presence of the helminth. The results point toward ecological relationships between various components of the biome, with the observed shifts in the microbiome suggesting potential mechanisms by which this helminth might exert therapeutic effects.}, number={3}, journal={Gut Microbes}, publisher={Informa UK Limited}, author={McKenney, Erin A and Williamson, Lauren and Yoder, Anne D and Rawls, John F and Bilbo, Staci D and Parker, William}, year={2015}, month={May}, pages={182–193} }
 @article{mckenney_rodrigo_yoder_2015, title={Patterns of Gut Bacterial Colonization in Three Primate Species}, volume={10}, DOI={10.1371/journal.pone.0124618}, abstractNote={Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes). Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.}, number={5}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={McKenney, Erin A. and Rodrigo, Allen and Yoder, Anne D.}, editor={Heimesaat, Markus M.Editor}, year={2015}, month={May}, pages={e0124618} }
 @article{lambert_fellner_mckenney_hartstone-rose_2014, title={Binturong (Arctictis binturong) and Kinkajou (Potos flavus) Digestive Strategy: Implications for Interpreting Frugivory in Carnivora and Primates}, volume={9}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0105415}, DOI={10.1371/journal.pone.0105415}, abstractNote={Exclusive frugivory is rare. As a food resource, fruit is temporally and spatially patchy, low in protein, and variable in terms of energy yield from different carbohydrate types. Here, we evaluate the digestive physiology of two frugivorous Carnivora species (Potos flavus, Arctictis binturong) that converge with primates in a diversity of ecological and anatomical traits related to fruit consumption. We conducted feeding trials to determine mean digestive retention times (MRT) on captive animals at the Carnivore Preservation Trust (now Carolina Tiger Rescue), Pittsboro, NC. Fecal samples were collected on study subjects for in vitro analysis to determine methane, pH, and short chain fatty acid profiles; fiber was assayed using standard neutral detergent (NDF) and acid detergent (ADF) fiber methods. Results indicate that both carnivoran species have rapid digestive passage for mammals that consume a predominantly plant-based diet: A. binturong MRT = 6.5 hrs (0.3); P. flavus MRT = 2.5 hrs (1.6). In vitro experiments revealed no fermentation of structural polysaccharides – methane levels did not shift from 0 h to either 24 or 48 hours and no short chain fatty acids were detected. In both species, however, pH declined from one incubation period to another suggesting acidification and bacterial activity of microbes using soluble carbohydrates. A comparison with primates indicates that the study species are most similar in digestive retention times to Ateles – the most frugivorous anthropoid primate taxon.}, number={8}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Lambert, Joanna E. and Fellner, Vivek and McKenney, Erin and Hartstone-Rose, Adam}, editor={Taylor, Andrea B.Editor}, year={2014}, month={Aug}, pages={e105415} }
 @article{mckenney_ashwell_lambert_fellner_2014, title={Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong)}, volume={9}, ISSN={["1749-4869"]}, DOI={10.1111/1749-4877.12112}, abstractNote={Abstract}, number={5}, journal={INTEGRATIVE ZOOLOGY}, publisher={Wiley-Blackwell}, author={McKenney, Erin A. and Ashwell, Melissa and Lambert, Joanna E. and Fellner, Vivek}, year={2014}, month={Nov}, pages={557–569} }