Validating the use of trap-collected feces for studying the gut microbiota of a small mammal (<i>Neotoma lepida</i>)

Kohl, Kevin D.; Luong, Kyphuong; Dearing, M. Denise

doi:10.1093/jmammal/gyu008

Cited by 21 publications

(15 citation statements)

References 20 publications

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“…To address this concern, we collected fecal samples from woodrats in the wild and over a time series in captivity. We confirmed that feces collected from traps in nature were representative of aseptically collected samples ( Kohl et al, 2015 ). Woodrats retained a majority (>60%) of their natural gut microbes, even after 6 months in captivity ( Kohl and Dearing, 2014 ).…”

Section: Woodrats As a Tractable System For Gut Microbial Ecologysupporting

confidence: 71%

The Woodrat Gut Microbiota as an Experimental System for Understanding Microbial Metabolism of Dietary Toxins

Kohl

Dearing

2016

Front. Microbiol.

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The microbial communities inhabiting the alimentary tracts of mammals, particularly those of herbivores, are estimated to be one of the densest microbial reservoirs on Earth. The significance of these gut microbes in influencing the physiology, ecology and evolution of their hosts is only beginning to be realized. To understand the microbiome of herbivores with a focus on nutritional ecology, while evaluating the roles of host evolution and environment in sculpting microbial diversity, we have developed an experimental system consisting of the microbial communities of several species of herbivorous woodrats (genus Neotoma) that naturally feed on a variety of dietary toxins. We designed this system to investigate the long-standing, but experimentally neglected hypothesis that ingestion of toxic diets by herbivores is facilitated by the gut microbiota. Like several other rodent species, the woodrat stomach has a sacculated, non-gastric foregut portion. We have documented a dense and diverse community of microbes in the woodrat foregut, with several genera potentially capable of degrading dietary toxins and/or playing a role in stimulating hepatic detoxification enzymes of the host. The biodiversity of these gut microbes appears to be a function of host evolution, ecological experience and diet, such that dietary toxins increase microbial diversity in hosts with experience with these toxins while novel toxins depress microbial diversity. These microbial communities are critical to the ingestion of a toxic diet as reducing the microbial community with antibiotics impairs the host’s ability to feed on dietary toxins. Furthermore, the detoxification capacity of gut microbes can be transferred from Neotoma both intra and interspecifically to naïve animals that lack ecological and evolutionary history with these toxins. In addition to advancing our knowledge of complex host-microbes interactions, this system holds promise for identifying microbes that could be useful in the treatment of diseases in humans and domestic animals.

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Section: Woodrats As a Tractable System For Gut Microbial Ecologysupporting

confidence: 71%

The Woodrat Gut Microbiota as an Experimental System for Understanding Microbial Metabolism of Dietary Toxins

Kohl

Dearing

2016

Front. Microbiol.

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“…However, this study only used a single pooled faecal sample and so it is unclear whether the effects of time are larger or smaller than variation across individuals. Another controlled study with multiple individuals of wood rats found that individual microbial signatures were highly retained between fresh faeces and those collected from the floor of Sherman traps after the rodent hosts spent a night in the trap with cotton batting, apple slices and oatmeal bait for~10 h (Kohl et al 2015). Thus, further investigations into the different types of microbial samples and sources of variation are needed.…”

Section: Discussionmentioning

confidence: 99%

Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission

et al. 2016

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Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in-depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host-specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts.

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“…However, this study used a single pooled faecal sample, and so it is unclear whether the effects of time are larger or smaller than inter‐individual variation. A controlled study with multiple individuals of woodrats found that individual microbial signatures were highly retained between fresh faeces and those collected from the floor of Sherman traps after the rodent hosts spent a night in the trap with cotton batting, apple slices and oatmeal bait for ~10 hr (Kohl, Luong, & Dearing, ). Thus, it is unlikely that the effects of field conditions are solely responsible for the large differences in microbial community structure across populations.…”

Section: Discussionmentioning

confidence: 99%

Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets

Kohl

Varner

Wilkening

et al. 2017

Journal of Animal Ecology

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Gut microbial communities provide many physiological functions to their hosts, especially in herbivorous animals. We still lack an understanding of how these microbial communities are structured across hosts in nature, especially within a given host species. Studies on laboratory mice have demonstrated that host genetics can influence microbial community structure, but that diet can overwhelm these genetic effects. We aimed to test these ideas in a natural system, the American pika (Ochotona princeps). First, pikas are high-elevation specialists with significant population structure across various mountain ranges in the USA, allowing us to investigate whether similarities in microbial communities match host genetic differences. Additionally, pikas are herbivorous, with some populations exhibiting remarkable dietary plasticity and consuming high levels of moss, which is exceptionally high in fibre and low in protein. This allows us to investigate adaptations to an herbivorous diet, as well as to the especially challenging diet of moss. Here, we inventoried the microbial communities of pika caecal pellets from various populations using 16S rRNA sequencing to investigate structuring of microbial communities across various populations with different natural diets. Microbial communities varied significantly across populations, and differences in microbial community structure were congruent with genetic differences in host population structure, a pattern known as "phylosymbiosis." Several microbial members (Ruminococcus, Prevotella, Oxalobacter and Coprococcus) were detected across all samples, and thus likely represent a "core microbiome." These genera are known to perform a number of services for herbivorous hosts such as fibre fermentation and the degradation of plant defensive compounds, and thus are likely important for herbivory in pikas. Moreover, pikas that feed on moss harboured microbial communities highly enriched in Melainabacteria. This uncultivable candidate phylum has been proposed to ferment fibre for herbivores, and thus may contribute to the ability of some pika populations to consume high amounts of moss. These findings demonstrate that both host genetics and diet can influence the microbial communities of the American pika. These animals may be novel sources of fibre-degrading microbes. Last, we discuss the implications of population-specific microbial communities for conservation efforts in this species.

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Validating the use of trap-collected feces for studying the gut microbiota of a small mammal (Neotoma lepida)

Cited by 21 publications

References 20 publications

The Woodrat Gut Microbiota as an Experimental System for Understanding Microbial Metabolism of Dietary Toxins

The Woodrat Gut Microbiota as an Experimental System for Understanding Microbial Metabolism of Dietary Toxins

Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission

Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets

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