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1. Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas

   https://doi.org/10.1186/s40168-020-00977-9  

   Baniel, Alice; Amato, Katherine R.; Beehner, Jacinta C.; Bergman, Thore J.; Mercer, Arianne; Perlman, Rachel F.; Petrullo, Lauren; Reitsema, Laurie; Sams, Sierra; Lu, Amy; et al (December 2021, Microbiome)

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   Abstract Background Adaptive shifts in gut microbiome composition are one route by which animals adapt to seasonal changes in food availability and diet. However, outside of dietary shifts, other potential environmental drivers of gut microbial composition have rarely been investigated, particularly in organisms living in their natural environments. Results Here, we generated the largest wild nonhuman primate gut microbiome dataset to date to identify the environmental drivers of gut microbial diversity and function in 758 samples collected from wild Ethiopian geladas ( Theropithecus gelada ). Because geladas live in a cold, high-altitude environment and have a low-quality grass-based diet, they face extreme thermoregulatory and energetic constraints. We tested how proxies of food availability (rainfall) and thermoregulatory stress (temperature) predicted gut microbiome composition of geladas. The gelada gut microbiome composition covaried with rainfall and temperature in a pattern that suggests distinct responses to dietary and thermoregulatory challenges. Microbial changes were driven by differences in the main components of the diet across seasons: in rainier periods, the gut was dominated by cellulolytic/fermentative bacteria that specialized in digesting grass, while during dry periods the gut was dominated by bacteria that break down starches found in underground plant parts. Temperature had a comparatively smaller, but detectable, effect on the gut microbiome. During cold and dry periods, bacterial genes involved in energy, amino acid, and lipid metabolism increased, suggesting a stimulation of fermentation activity in the gut when thermoregulatory and nutritional stress co-occurred, and potentially helping geladas to maintain energy balance during challenging periods. Conclusion Together, these results shed light on the extent to which gut microbiota plasticity provides dietary and metabolic flexibility to the host, and might be a key factor to thriving in changing environments. On a longer evolutionary timescale, such metabolic flexibility provided by the gut microbiome may have also allowed members of Theropithecus to adopt a specialized diet, and colonize new high-altitude grassland habitats in East Africa. 

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2. Covariation of diet and gut microbiome in African megafauna

   https://doi.org/10.1073/pnas.1905666116  

   Kartzinel, Tyler R.; Hsing, Julianna C.; Musili, Paul M.; Brown, Bianca R.; Pringle, Robert M. (November 2019, Proceedings of the National Academy of Sciences)

   A major challenge in biology is to understand how phylogeny, diet, and environment shape the mammalian gut microbiome. Yet most studies of nonhuman microbiomes have relied on relatively coarse dietary categorizations and have focused either on individual wild populations or on captive animals that are sheltered from environmental pressures, which may obscure the effects of dietary and environmental variation on microbiome composition in diverse natural communities. We analyzed plant and bacterial DNA in fecal samples from an assemblage of 33 sympatric large-herbivore species (27 native, 6 domesticated) in a semiarid East African savanna, which enabled high-resolution assessment of seasonal variation in both diet and microbiome composition. Phylogenetic relatedness strongly predicted microbiome composition ( r = 0.91) and was weakly but significantly correlated with diet composition ( r = 0.20). Dietary diversity did not significantly predict microbiome diversity across species or within any species except kudu; however, diet composition was significantly correlated with microbiome composition both across and within most species. We found a spectrum of seasonal sensitivity at the diet−microbiome nexus: Seasonal changes in diet composition explained 25% of seasonal variation in microbiome composition across species. Species’ positions on (and deviations from) this spectrum were not obviously driven by phylogeny, body size, digestive strategy, or diet composition; however, domesticated species tended to exhibit greater diet−microbiome turnover than wildlife. Our results reveal marked differences in the influence of environment on the degree of diet−microbiome covariation in free-ranging African megafauna, and this variation is not well explained by canonical predictors of nutritional ecology. 

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3. Early-life effects of juvenile Western diet and exercise on adult gut microbiome composition in mice

   https://doi.org/10.1242/jeb.239699  

   McNamara, Monica P.; Singleton, Jennifer M.; Cadney, Marcell D.; Ruegger, Paul M.; Borneman, James; Garland, Theodore (February 2021, Journal of Experimental Biology)

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   ABSTRACT Alterations to the gut microbiome caused by changes in diet, consumption of antibiotics, etc., can affect host function. Moreover, perturbation of the microbiome during critical developmental periods potentially has long-lasting impacts on hosts. Using four selectively bred high runner and four non-selected control lines of mice, we examined the effects of early-life diet and exercise manipulations on the adult microbiome by sequencing the hypervariable internal transcribed spacer region of the bacterial gut community. Mice from high runner lines run ∼3-fold more on wheels than do controls, and have several other phenotypic differences (e.g. higher food consumption and body temperature) that could alter the microbiome, either acutely or in terms of coevolution. Males from generation 76 were given wheels and/or a Western diet from weaning until sexual maturity at 6 weeks of age, then housed individually without wheels on standard diet until 14 weeks of age, when fecal samples were taken. Juvenile Western diet reduced bacterial richness and diversity after the 8-week washout period (equivalent to ∼6 human years). We also found interactive effects of genetic line type, juvenile diet and/or juvenile exercise on microbiome composition and diversity. Microbial community structure clustered significantly in relation to both line type and diet. Western diet also reduced the relative abundance of Muribaculum intestinale. These results constitute one of the first reports of juvenile diet having long-lasting effects on the adult microbiome after a substantial washout period. Moreover, we found interactive effects of diet with early-life exercise exposure, and a dependence of these effects on genetic background. 

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4. Altered precipitation has asymmetric impacts on annual plant communities in warm and cool growing seasons

   https://doi.org/10.1525/elementa.2021.00014  

   Spasojevic, Marko J.; Homyak, Peter M.; Jenerette, G. Darrel; Goulden, Mike L.; McFaul, Shane; Madsen-McQueen, Tesa; Schauer, Lisa; Solis, Miguel (January 2022, Elementa: Science of the Anthropocene)

   While altered precipitation regimes can greatly impact biodiversity and ecosystem functioning, we lack a comprehensive view of how these impacts are mediated by changes to the seasonality of precipitation (i.e., whether it rains more/less in one season relative to another). Over 2 years, we examined how altered seasonal precipitation influenced annual plant biomass and species richness, Simpson’s diversity, and community composition of annual plant communities in a dryland ecosystem that receives both winter and summer rainfall and has distinct annual plant communities in each season. Using a rainfall exclusion, collection, and distribution system, we excluded precipitation and added water during each season individually and compared responses to control plots which received ambient summer and winter precipitation. In control plots, we found five times greater annual plant biomass, twice as many species, and higher diversity in winter relative to summer. Adding water increased annual plant biomass in summer only, did not change richness or diversity in either summer or winter, and modestly shifted community composition. Excluding precipitation in either season reduced annual plant biomass, richness, and Simpson’s diversity. However, in the second winter season, biomass was higher in the plots where precipitation was excluded in the previous summer seasons suggesting that reduced productivity in the summer may facilitate biomass in the winter. Our results suggest that increased precipitation in summer may have stronger short-term impacts on annual plant biodiversity and ecosystem function relative to increased winter precipitation. In contrast, decreasing precipitation may have ubiquitous negative effects on annual plants across both summer and winter but may lead to increased biomass in the following off-seasons. These patterns suggest that annual plant communities exhibit asymmetries in their community and ecosystem responses to altered seasonal precipitation and that considering the seasonality of precipitation is important for predicting the effects of altered precipitation regimes. 

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5. Black‐throated blue warblers ( Setophaga caerulescens ) exhibit diet flexibility and track seasonal changes in insect availability

   https://doi.org/10.1002/ece3.70340  

   Kaiser, Sara A; Forg, Lindsey E; Stillman, Andrew N; Deitsch, John F; Sillett, T Scott; Clucas, Gemma V (September 2024, Ecology and Evolution)

   Abstract Changes in leaf phenology from warming spring and autumn temperatures have lengthened the temperate zone growing “green” season and breeding window for migratory birds in North America. However, the fitness benefits of an extended breeding season will depend, in part, on whether species have sufficient dietary flexibility to accommodate seasonal changes in prey availability. We used fecal DNA metabarcoding to test the hypothesis that seasonal changes in the diets of the insectivorous, migratory black‐throated blue warbler (Setophaga caerulescens) track changes in the availability of arthropod prey at the Hubbard Brook Experimental Forest, New Hampshire, USA. We examined changes across the breeding season and along an elevation gradient encompassing a 2‐week difference in green season length. From 98 fecal samples, we identified 395 taxa from 17 arthropod orders; 242 were identified to species, withCecrita guttivitta(saddled prominent moth),Theridion frondeum(eastern long‐legged cobweaver), andPhilodromus rufus(white‐striped running crab spider) occurring at the highest frequency. We found significant differences in diet composition between survey periods and weak differences among elevation zones. Variance in diet composition was highest late in the season, and diet richness and diversity were highest early in the season. Diet composition was associated with changes in prey availability surveyed over the green season. However, several taxa occurred in diets more or less than expected relative to their frequency of occurrence from survey data, suggesting that prey selection or avoidance sometimes accompanies opportunistic foraging. This study demonstrates that black‐throated blue warblers exhibit diet flexibility and track seasonal changes in prey availability, which has implications for migratory bird responses to climate‐induced changes in insect communities with longer green seasons. 

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