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

   https://doi.org/10.1002/ajpa.23842  

   Pafčo, Barbora ; Sharma, Ashok K. ; Petrželková, Klára J. ; Vlčková, Klára ; Todd, Angelique ; Yeoman, Carl J. ; Wilson, Brenda A. ; Stumpf, Rebecca ; White, Bryan A. ; Nelson, Karen E. ; et al ( April 2019 , American Journal of Physical Anthropology)

   Environmental and ecological factors, such as geographic range, anthropogenic pressure, group identity, and feeding behavior are known to influence the gastrointestinal microbiomes of great apes. However, the influence of individual host traits such as age and sex, given specific dietary and social constraints, has been less studied. The objective of this investigation was to determine the associations between an individual's age and sex on the diversity and composition of the gut microbiome in wild western lowland gorillas.

   Publicly available 16S rRNA data generated from fecal samples of different groups ofGorilla gorillagorillain the Central African Republic were downloaded and bioinformatically processed. The groups analyzed included habituated, partially habituated and unhabituated gorillas, sampled during low fruit (dry,n = 28) and high fruit (wet,n = 82) seasons. Microbial community analyses (alpha and beta diversity and analyses of discriminant taxa), in tandem with network‐wide approaches, were used to (a) mine for specific age and sex based differences in gut bacterial community composition and to (b) asses for gut community modularity and bacterial taxa with potential functional roles, in the context of seasonal food variation, and social group affiliation.

   Both age and sex significantly influenced gut microbiome diversity and composition in wild western lowland gorillas. However, the largest differences were observed between infants and adults in habituated groups and between adults and immature gorillas within all groups, and across dry and wet seasons. Specifically, although adults always showed greater bacterial richness than infants and immature gorillas, network‐wide analyses showed higher microbial community complexity and modularity in the infant gorilla gut. Sex‐based microbiome differences were not evident among adults, being only detected among immature gorillas.

   The results presented point to a dynamic gut microbiome inGorillaspp., associated with ontogeny and individual development. Of note, the gut microbiomes of breastfeeding infants seemed to reflect early exposure to complex, herbaceous vegetation. Whether increased compositional complexity of the infant gorilla gut microbiome is an adaptive response to an energy‐limited diet and an underdeveloped gut needs to be further tested. Overall, age and sex based gut microbiome differences, as shown here, maybe mainly attributed to access to specific feeding sources, and social interactions between individuals within groups.

    

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2. Microbiome stability and structure is governed by host phylogeny over diet and geography in woodrats ( Neotoma spp.)

   https://doi.org/10.1073/pnas.2108787118  

   Weinstein, Sara B. ; Martínez-Mota, Rodolfo ; Stapleton, Tess E. ; Klure, Dylan M. ; Greenhalgh, Robert ; Orr, Teri J. ; Dale, Colin ; Kohl, Kevin D. ; Dearing, M. Denise ( November 2021 , Proceedings of the National Academy of Sciences)

   The microbiome is critical for host survival and fitness, but gaps remain in our understanding of how this symbiotic community is structured. Despite evidence that related hosts often harbor similar bacterial communities, it is unclear whether this pattern is due to genetic similarities between hosts or to common ecological selection pressures. Here, using herbivorous rodents in the genusNeotoma, we quantify how geography, diet, and host genetics, alongside neutral processes, influence microbiome structure and stability under natural and captive conditions. Using bacterial and plant metabarcoding, we first characterized dietary and microbiome compositions for animals from 25 populations, representing seven species from 19 sites across the southwestern United States. We then brought wild animals into captivity, reducing the influence of environmental variation. In nature, geography, diet, and phylogeny collectively explained ∼50% of observed microbiome variation. Diet and microbiome diversity were correlated, with different toxin-enriched diets selecting for distinct microbial symbionts. Although diet and geography influenced natural microbiome structure, the effects of host phylogeny were stronger for both wild and captive animals. In captivity, gut microbiomes were altered; however, responses were species specific, indicating again that host genetic background is the most significant predictor of microbiome composition and stability. In captivity, diet effects declined and the effects of host genetic similarity increased. By bridging a critical divide between studies in wild and captive animals, this work underscores the extent to which genetics shape microbiome structure and stability in closely related hosts.

    

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3. A test of the Niche Variation Hypothesis in a ruminant herbivore

   https://doi.org/10.1111/1365-2656.13351  

   Jesmer, Brett R. ; Kauffman, Matthew J. ; Murphy, Melanie A. ; Goheen, Jacob R. ; Jackson, ed., Andrew ( October 2020 , Journal of Animal Ecology)

   Despite the shared prediction that the width of a population's dietary niche expands as food becomes limiting, the Niche Variation Hypothesis (NVH) and Optimal Foraging Theory (OFT) offer contrasting views about how individuals alter diet selection when food is limited.

   Classical OFT predicts that dietary preferences do not change as food becomes limiting, so individuals expand their diets as they compensate for a lack of preferred foods. In contrast, the NVH predicts that among‐individual variation in cognition, physiology or morphology create functional trade‐offs in foraging efficiency, thereby causing individuals to specialize on different subsets of food as food becomes limiting.

   To evaluate (a) the predictions of the NVH and OFT and (b) evidence for physiological and cognitive‐based functional trade‐offs, we used DNA microsatellites and metabarcoding to quantify the diet, microbiome and genetic relatedness (a proxy for social learning) of 218 mooseAlces alcesacross six populations that varied in their degree of food limitation.

   Consistent with both the NVH and OFT, dietary niche breadth increased with food limitation. Increased diet breadth of individuals—rather than increased diet specialization—was strongly correlated with both food limitation and dietary niche breadth of populations, indicating that moose foraged in accordance with OFT. Diets were not constrained by inheritance of the microbiome or inheritance of diet selection, offering support for the little‐tested hypothesis that functional trade‐offs in food use (or lack thereof) determine whether populations adhere to the predictions of the NVH or OFT.

   Our results indicate that both the absence of strong functional trade‐offs and the digestive physiology of ruminants provide contexts under which populations should forage in accordance with OFT rather than the NVH. Also, because dietary niche width increased with increased food limitation, OFT and the NVH provide theoretical support for the notion that plant–herbivore interaction networks are plastic rather than static, which has important implications for understanding interspecific niche partitioning. Lastly, because population‐level dietary niche breadth and calf recruitment are correlated, and because calf recruitment can be a proxy for food limitation, our work demonstrates how diet data can be employed to understand a populations' proximity to carrying capacity.

    

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4. Movement ecology and sex are linked to barn owl microbial community composition

   https://doi.org/10.1111/mec.15398  

   Corl, Ammon ; Charter, Motti ; Rozman, Gabe ; Toledo, Sivan ; Turjeman, Sondra ; Kamath, Pauline L. ; Getz, Wayne M. ; Nathan, Ran ; Bowie, Rauri C. K. ( April 2020 , Molecular Ecology)

   The behavioural ecology of host species is likely to affect their microbial communities, because host sex, diet, physiology, and movement behaviour could all potentially influence their microbiota. We studied a wild population of barn owls (Tyto alba) and collected data on their microbiota, movement, diet, size, coloration, and reproduction. The composition of bacterial species differed by the sex of the host and female owls had more diverse bacterial communities than their male counterparts. The abundance of two families of bacteria, Actinomycetaceae and Lactobacillaceae, also varied between the sexes, potentially as a result of sex differences in hormones and immunological function, as has previously been found with Lactobacillaceae in the microbiota of mice. Male and female owls did not differ in the prey they brought to the nest, which suggests that dietary differences are unlikely to underlie the differences in their microbiota. The movement behaviour of the owls was associated with the host microbiota in both males and females because owls that moved further from their nest each day had more diverse bacterial communities than owls that stayed closer to their nests. This novel result suggests that the movement ecology of hosts can impact their microbiota, potentially on the basis of their differential encounters with new bacterial species as the hosts move and forage across the landscape. Overall, we found that many aspects of the microbial community are correlated with the behavioural ecology of the host and that data on the microbiota can aid in generating new hypotheses about host behaviour.

    

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5. Mechanisms of individual variation in large herbivore diets: Roles of spatial heterogeneity and state‐dependent foraging

   https://doi.org/10.1002/ecy.3921  

   Walker, Reena H. ; Hutchinson, Matthew C. ; Potter, Arjun B. ; Becker, Justine A. ; Long, Ryan A. ; Pringle, Robert M. ( January 2023 , Ecology)

   Many populations of consumers consist of relatively specialized individuals that eat only a subset of the foods consumed by the population at large. Although the ecological significance of individual‐level diet variation is recognized, such variation is difficult to document, and its underlying mechanisms are poorly understood. Optimal foraging theory provides a useful framework for predicting how individuals might select different diets, positing that animals balance the “opportunity cost” of stopping to eat an available food item against the cost of searching for something more nutritious; diet composition should be contingent on the distribution of food, and individual foragers should be more selective when they have greater energy reserves to invest in searching for high‐quality foods. We tested these predicted mechanisms of individual niche differentiation by quantifying environmental (resource heterogeneity) and organismal (nutritional condition) determinants of diet in a widespread browsing antelope (bushbuck,Tragelaphus sylvaticus) in an African floodplain‐savanna ecosystem. We quantified individuals' realized dietary niches (taxonomic richness and composition) using DNA metabarcoding of fecal samples collected repeatedly from 15 GPS‐collared animals (range 6–14 samples per individual, median 12). Bushbuck diets were structured by spatial heterogeneity and constrained by individual condition. We observed significant individual‐level partitioning of food plants by bushbuck both within and between two adjacent habitat types (floodplain and woodland). Individuals with home ranges that were closer together and/or had similar vegetation structure (measured using LiDAR) ate more similar diets, supporting the prediction that heterogeneous resource distribution promotes individual differentiation. Individuals in good nutritional condition had significantly narrower diets (fewer plant taxa), searched their home ranges more intensively (intensity‐of‐use index), and had higher‐quality diets (percent digestible protein) than those in poor condition, supporting the prediction that animals with greater endogenous reserves have narrower realized niches because they can invest more time in searching for nutritious foods. Our results support predictions from optimal foraging theory about the energetic basis of individual‐level dietary variation and provide a potentially generalizable framework for understanding how individuals' realized niche width is governed by animal behavior and physiology in heterogeneous landscapes.

    

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