The desert woodrat (Neotoma lepida) induces a diversity of biotransformation genes in response to creosote bush resin

Liver biotransformation enzymes have long been thought to enable animals to feed on diets rich in xenobiotic compounds. However, despite decades of pharmacological research in humans and rodents, little is known about hepatic gene expression in specialized mammalian herbivores feeding on toxic diets. Leveraging a recently identified population of the desert woodrat (Neotoma lepida) found to be highly tolerant to toxic creosote bush (Larrea tridentata), we explored the expression changes of suites of biotransformation genes in response to diets enriched with varying amounts of creosote resin. Analysis of hepatic RNA-seq data indicated a dose-dependent response to these compounds, including the upregulation of several genes encoding transcription factors and numerous phase I, II, and III biotransformation families. Notably, elevated expression of five biotransformation families - carboxylesterases, cytochromes P450, aldo-keto reductases, epoxide hydrolases, and UDP-glucuronosyltransferases - corresponded to species-specific duplication events in the genome, suggesting that these genes play a prominent role in N. lepida's adaptation to creosote bush. Building on pharmaceutical studies in model rodents, we propose a hypothesis for how the differentially expressed genes are involved in the biotransformation of creosote xenobiotics. Our results provide some of the first details about how these processes likely operate in the liver of a specialized mammalian herbivore.

Differential Effects of Two Common Antiparasitics on Microbiota Resilience

BACKGROUND

Parasitic infections challenge vertebrate health worldwide, and off-target effects of antiparasitic treatments may be an additional obstacle to recovery. However, there have been few investigations of the effects of antiparasitics on the gut microbiome in the absence of parasites.

METHODS

We investigated whether two common antiparasitics-albendazole (ALB) and metronidazole (MTZ)-significantly alter the gut microbiome of parasite-free mice. We treated mice with ALB or MTZ daily for 7 days and sampled the fecal microbiota immediately before and after treatment and again after a two-week recovery period.

RESULTS

ALB did not immediately change the gut microbiota, while MTZ decreased microbial richness by 8.5% and significantly changed community structure during treatment. The structural changes caused by MTZ included depletion of the beneficial family Lachnospiraceae, and predictive metagenomic analysis revealed that these losses likely depressed microbiome metabolic function. Separately, we compared the fecal microbiotas of treatment groups after recovery, and there were minor differences in community structure between the ALB, MTZ, and sham-treated control groups.

CONCLUSIONS

These results suggest that a healthy microbiome is resilient after MTZ-induced depletions of beneficial gut microbes, and ALB may cause slight, latent shifts in the microbiota but does not deplete healthy gut microbiota diversity.

Seasonal restructuring facilitates compositional convergence of gut microbiota in free-ranging rodents

Gut microbes provide essential services to their host and shifts in their composition can impact host fitness. However, despite advances in our understanding of how microbes are assembled in the gut, we understand little about the stability of these communities within individuals, nor what factors influence its composition over the life of an animal. For this reason, we conducted a longitudinal survey of the gut microbial communities of individual free-ranging woodrats (Neotoma spp.) across a hybrid zone in the Mojave Desert, USA, using amplicon sequencing approaches to characterize gut microbial profiles and diet. We found that gut microbial communities were individualized and experienced compositional restructuring as a result of seasonal transitions and changes in diet. Turnover of gut microbiota was highest amongst bacterial subspecies and was much lower at the rank of Family, suggesting there may be selection for conservation of core microbial functions in the woodrat gut. Lastly, we identified an abundant core gut bacterial community that may aid woodrats in metabolizing a diet of plants and their specialized metabolites. These results demonstrate that the gut microbial communities of woodrats are highly dynamic and experience seasonal restructuring which may facilitate adaptive plasticity in response to changes in diet.

Hybridization in the absence of an ecotone favors hybrid success in woodrats (Neotoma spp.)

Hybridization is a common process that has broadly impacted the evolution of multicellular eukaryotes; however, how ecological factors influence this process remains poorly understood. Here, we report the findings of a 3-year recapture study of the Bryant's woodrat (Neotoma bryanti) and desert woodrat (N. lepida), two species that hybridize within a creosote bush (Larrea tridentata) shrubland in Whitewater, CA, USA. We used a genotype-by-sequencing approach to characterize the ancestry distribution of individuals across this hybrid zone coupled with Cormack-Jolly-Seber modeling to describe demography. We identified a high frequency of hybridization at this site with ~40% of individuals possessing admixed ancestry, which is the result of multigenerational backcrossing and advanced hybrid-hybrid crossing. F1, F2 and advanced generation hybrids had apparent survival rates similar to parental N. bryanti, while parental and backcross N. lepida had lower apparent survival rates and were far less abundant. Compared to bimodal hybrid zones where hybrids are often rare and selected against, we find that hybrids at Whitewater are common and have comparable survival to the dominant parental species, N. bryanti. The frequency of hybridization at Whitewater is therefore likely limited by the abundance of the less common parental species, N. lepida, rather than selection against hybrids.

Demonstrating the role of symbionts in mediating detoxification in herbivores

Plant toxins constitute an effective defense against herbivorous animals. However, many herbivores have evolved adaptations to cope with dietary toxins through detoxification, excretion, sequestration, target site insensitivity and/or via behavioral avoidance. While these adaptations are often directly encoded in herbivore genomes, evidence is accumulating that microbial symbionts can reduce the dose of plant toxins by metabolizing or sequestering them prior to absorption by the herbivore. Here, we describe a few well-studied examples to assess such symbiont-mediated detoxification and showcase different approaches that have been used for their analyses. These include: (i) a host phenotypic route in which the symbiotic association is manipulated to reveal host fitness costs upon toxin exposure in the presence/absence of detoxifying symbionts, including function restoration after symbiont re-infection, (ii) a molecular microbiological approach that focuses on the identification and characterization of microbial genes involved in plant toxin metabolism, and (iii) an analytical chemical route that aims to characterize the conversion of the toxin to less harmful metabolites in vivo and link conversion to the activities of a detoxifying symbiont. The advantages and challenges of each approach are discussed, and it is argued that a multi-pronged strategy combining phenotypic, molecular, and chemical evidence is needed to unambiguously demonstrate microbial contributions to plant toxin reduction and the importance of these processes for host fitness. Given the interdisciplinary nature of the topic, we aim to provide a guideline to researchers interested in symbiont-mediated detoxification and hope to encourage future studies that contribute to a more comprehensive and mechanistic understanding of detoxification in herbivores and their symbionts.

PINWORMS ARE ASSOCIATED WITH TAXONOMIC BUT NOT FUNCTIONAL DIFFERENCES IN THE GUT MICROBIOME OF WHITE-THROATED WOODRATS (NEOTOMA ALBIGULA)

Vertebrates rely on their gut microbiome for digestion, and changes to gut microbial communities can impact host health. Past work, primarily in model organisms, has revealed that endoparasites disrupt the gut microbiome. Here, using wild-caught white-throated woodrats (Neotoma albigula), we tested whether naturally acquired parasite infections are associated with different microbiome structure and function. We surveyed wild N. albigula in eastern Utah for gastrointestinal parasites in the spring and fall of 2019, using traditional fecal float methods and testing a PCR-based approach to detect infection. We tested whether the host gut microbiome structure and function differed based on infection with the most prevalent parasite, the pinworm Lamotheoxyuris ackerti. In spring, infected and uninfected animals had significantly different microbiomes, but these differences were not detected in the fall. However, for both sampling periods, infection was associated with differences in particular microbial taxa determined by differential abundance analysis. As N. albigula rely on their microbiomes to digest both fiber and the plant defensive compound oxalate, we compared microbiome function by measuring dry matter digestibility and oxalate intake in infected and uninfected animals. Although we expected infected animals to have reduced fiber degradation and oxalate intake, we found no difference in microbiome function using these assays. This work suggests that parasite effects on the microbiome may be difficult to detect in complex natural systems, and more studies in wild organisms are warranted.

Toxin tolerance across landscapes: Ecological exposure not a prerequisite

Little is known about the tolerances of mammalian herbivores to plant specialized metabolites across landscapes.We investigated the tolerances of two species of herbivorous woodrats, Neotoma lepida (desert woodrat) and Neotoma bryanti (Bryant's woodrat) to creosote bush (Larrea tridentata), a widely distributed shrub with a highly toxic resin. Woodrats were sampled from 13 locations both with and without creosote bush across a 900 km transect in the US southwest. We tested whether these woodrat populations consume creosote bush using plant metabarcoding of feces and quantified their tolerance to creosote bush through feeding trials using chow amended with creosote resin.Toxin tolerance was analyzed in the context of population structure across collection sites with microsatellite analyses. Genetic differentiation among woodrats collected from different locations was minimal within either species. Tolerance differed substantially between the two species, with N. lepida persisting 20% longer than N. bryanti in feeding trials with creosote resin. Furthermore, in both species, tolerance to creosote resin was similar among woodrats near or within creosote bush habitat. In both species, woodrats collected greater than 25 km from creosote had markedly lower tolerances to creosote resin compared to animals from within the range of creosote bush.The results imply that mammalian herbivores are adapted to the specialized metabolites of plants in their diet, and that this tolerance can extend several kilometers outside of the range of dietary items. That is, direct ecological exposure to the specialized chemistry of particular plant species is not a prerequisite for tolerance to these compounds. These findings lay the groundwork for additional studies to investigate the genetic mechanisms underlying toxin tolerance and to identify how these mechanisms are maintained across landscape-level scales in mammalian herbivores.

Addressing nontarget amplification in DNA metabarcoding studies of arthropod-feeding rodents

High-throughput sequencing approaches have revolutionized how we study animal diets by enabling the detection of dietary components from the metabarcoding of DNA in excrement. Mitochondrial cytochrome oxidase C subunit I (mtCOI) DNA metabarcoding is commonly used to study the diets of arthropod-feeding animals; however, this approach is susceptible to nontarget amplification of the consumer species mtCOI locus. Nontarget amplification is often an unforeseen complication that can drastically reduce the quality and utility of the results generated by high-throughput amplicon sequencing. By interrogating the diets of new world rodents in the genus Neotoma (woodrats) in both natural and captive settings, we demonstrate that nontarget amplification can drastically reduce the total read abundance of detected arthropod taxa in fecal samples and inhibit downstream analyses of dietary diversity and composition metrics. Using the results from these investigations, we offer a guide on how to identify concerns for nontarget amplification when selecting degenerate primers for DNA metabarcoding studies and recommend several approaches that can reduce or eliminate nontarget amplification. Lastly, for the community interested in investigating the diets of arthropod-feeding rodents, we generated a database containing the degree of mismatch between publicly available Rodentia mtCOI sequences and four common universal mtCOI primer sets to be used as a resource for inferring the relative risk of nontarget amplification when designing arthropod metabarcoding studies in rodent systems. This guide will be especially useful for researchers working with consumer species that have not previously been studied.

Mammalian cytochrome P450 biodiversity: Physiological importance, function, and protein and genomic structures of cytochromes P4502B in multiple species of woodrats with different dietary preferences

The vast diversity of cytochrome P450 enzymes in mammals has been proposed to result in large measure from plant-animal warfare, whereby evolution of chemical defenses such as phenolics and terpenoids in plants led to duplication and divergence of P450 genes in herbivores. Over evolutionary time, natural selection is predicted to have produced P450s with high affinity and enhanced metabolism of substrates that are ingested regularly by herbivores. Interestingly, however, almost all knowledge of the interactions of mammalian P450 enzymes with substrates stems from studies of the metabolism of drugs and model compounds rather than studies on wild mammalian herbivores and their respective PSMs. A question of particular interest centers on the role of individual P450 enzymes in the ability of certain herbivores to specialize on plants that are lethal to most other species, including those from the same genus as the specialists. We tackled this intricate problem using a tractable natural system (herbivorous woodrats, genus Neotoma) focusing on comparisons of the specialist N. stephensi, the facultative specialist N. lepida, and the generalist N. albigula, and employing a cross-disciplinary approach involving ecology, biochemistry, pharmacology, structural biology, and genomics. Based on multiple findings suggesting the importance of CYP2B enzymes for ingestion of juniper and a major constituent, α-pinene, we characterized the structure, function and activity of several CYP2B enzymes in woodrats with different dietary habits. Results to date suggest that differences in CYP2B gene copy number may contribute to differential tolerance of PSMs among woodrat species, although additional work is warranted to firmly link gene copy number to juniper tolerance.

Warmer Ambient Temperatures Depress Detoxification and Food Intake by Marsupial Folivores

Ambient temperature is an underappreciated determinant of foraging behaviour in wild endotherms, and the requirement to thermoregulate likely influences food intake through multiple interacting mechanisms. We investigated relationships between ambient temperature and hepatic detoxification capacity in two herbivorous marsupials, the common ringtail possum (Pseudocheirus peregrinus) and common brushtail possum (Trichosurus vulpecula) that regularly feed on diets rich in plant toxins. As an indicator of hepatic detoxification capacity, we determined the functional clearance rate of an anaesthetic agent, Alfaxalone, after possums were acclimated to 10°C [below the thermoneutral zone (TNZ)], 18°C [approximately lower critical temperature (LCT)], and 26°C [approximately upper critical temperature (UCT)] for either 7 days or less than 24 h. We then measured intake of foods with high or low plant secondary metabolite (PSM) concentrations under the same temperature regimes. After 7 days of acclimation, we found a positive correlation between the functional clearance rate of Alfaxalone and ambient temperature, and a negative relationship between ambient temperature and intake of foods with high or low PSM concentrations for both species. The effect of ambient temperature on intake of diets rich in PSMs was absent or reduced when possums were kept at temperatures for less than 24 h. Our results underscore the effects of ambient temperature in hepatic metabolism particularly with respect intake of diets containing PSMs. Given that the planet is warming, it is vital that effects of ambient temperature on metabolism, nutrition and foraging by mammalian herbivores is taken into account to predict range changes of species and their impact on ecosystems.

Metabolic Enabling and Detoxification by Mammalian Gut Microbes

The longstanding interactions between mammals and their symbionts enable thousands of mammal species to consume herbivorous diets. The microbial communities in mammals degrade both plant fiber and toxins. Microbial toxin degradation has been repeatedly documented in domestic ruminants, but similar work in wild mammals is more limited due to constraints on sampling and manipulating the microbial communities in these species. In this review, we briefly describe the toxins commonly encountered in mammalian diets, major classes of biotransformation enzymes in microbes and mammals, and the gut chambers that house symbiotic microbes. We next examine evidence for microbial detoxification in domestic ruminants before providing case studies on microbial toxin degradation in both foregut- and hindgut-fermenting wild mammals. We end by discussing species that may be promising for future investigations, and the advantages and limitations of approaches currently available for studying degradation of toxins by mammalian gut microbes. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal

DNA metabarcoding is widely used to determine wild animal diets, however whether this technique provides accurate, quantitative measurements is still under debate. To test our ability to accurately estimate abundance of dietary items using metabarcoding, we fed wild caught desert woodrats (Neotoma lepida) diets comprised of constant amounts of juniper (Juniperus osteosperma, 15%) and varying amounts of creosote (Larrea tridentata, 1-60%), or cactus (Opuntia sp., 0-100%), and commercial chow (0-85%). Using metabarcoding, we compared the representation of items in the original diet samples to that in the fecal samples to test the sensitivity and accuracy of diet metabarcoding, the performance of different bioinformatic pipelines, and our ability to correct sequence counts. Metabarcoding, using standard trnL primers, detected creosote, juniper, and chow. Different pipelines for assigning taxonomy performed similarly. While creosote was detectable at dietary proportions as low as 1%, we failed to detect cactus in most samples, likely due to a primer mismatch. Creosote read counts increased as its proportion in the diet increased, and we could differentiate when creosote was a minor and major component of the diet. However, we found that estimates of juniper and creosote varied. Using previously suggested methods to correct these errors did not improve accuracy estimates of creosote, but did reduce error for juniper and chow. Our results indicate that metabarcoding can provide quantitative information on dietary composition, but may be limited. We suggest that researchers use caution in quantitatively interpreting diet metabarcoding results unless they first experimentally determine the extent of possible biases.

Wild herbivorous mammals (genus Neotoma) host a diverse but transient assemblage of fungi

Fungi are often overlooked in microbiome research and, as a result, little is known about the mammalian mycobiome. Although frequently detected in vertebrate guts and known to contribute to digestion in some herbivores, whether these eukaryotes are a persistent part of the mammalian gut microbiome remains contentious. To address this question, we sampled fungi from wild woodrats (Neotoma spp.) collected from 25 populations across the southwestern United States. For each animal, we collected a fecal sample in the wild, and then re-sampled the same individual after a month in captivity on a controlled diet. We characterized and quantified fungi using three techniques: ITS metabarcoding, shotgun metagenomics and qPCR. Wild individuals contained diverse fungal assemblages dominated by plant pathogens, widespread molds, and coprophilous taxa primarily in Ascomycota and Mucoromycota. Fungal abundance, diversity and composition differed between individuals, and was primarily influenced by animal geographic origin. Fungal abundance and diversity significantly declined in captivity, indicating that most fungi in wild hosts came from diet and environmental exposure. While this suggests that these mammals lack a persistent gut mycobiome, natural fungal exposure may still impact fungal dispersal and animal health.

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

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 genus Neotoma, 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.

Diet alters rodent fecal pellet size: implications for paleoecological and demographic studies using fecal dimensions

Measurements of fecal pellet size can provide important information about wild mammals, such as body size and demographic information. Previous studies have not rigorously tested whether diet can confound these measurements. Furthermore, it is unknown whether diet might alter fecal dimensions directly or through changes in animal physiology. Here, we studied three closely related rodent species that differ in natural feeding strategies. Individuals were fed diets that varied in protein and fiber content for 5 weeks. We then measured body size, fecal widths and lengths, and the radius of the large intestine. Diet composition significantly changed fecal widths in all species. High-fiber content significantly increased fecal widths and would cause overestimations of body size if applied to wild feces. Using path analysis, we found that fiber can increase fecal widths both directly and indirectly through increasing the large intestine radius. Protein affected each species differently, suggesting that protein effects vary by species feeding strategy and existing physiology. Overall, diet and large intestine morphology can alter fecal pellet measurements. Studies using fecal measurements therefore must consider these effects in their conclusions.

The secret social lives of African crested rats, Lophiomys imhausi

The crested rat, Lophiomys imhausi, is the only mammal known to sequester plant toxins. Found in eastern Africa, this large rodent is thought to defend against predation by coating specialized hairs along its sides with cardenolide toxins from the poison arrow tree, Acokanthera schimperi. To better understand the ecology of this unusual poisonous mammal, we used camera traps, livetrapping, and captive behavioral observations, to study L. imhausi in central Kenya. Although crested rats were rarely detected with camera traps, 25 individuals were caught in live traps, with estimated densities of up to 15 rats/km² at one of nine trapping sites. Trapping records and behavioral observations suggest that L. imhausi live in male-female pairs, with juveniles that might exhibit delayed dispersal. We observed chewing of A. schimperi and/or anointing in 10 of 22 individuals, confirming the previous poison sequestration observation. We monitored crested rat activity using cameras and found that chewing on A. schimperi and cardenolide exposure had no effect on feeding, movement, or total activity. One crested rat also fed on milkweed (Gomphocarpus physocarpus; Gentaniales: Apocynaceae), but did not anoint with this cardenolide containing plant. This observation, combined with L. imhausi's selective use of A. schimperi, suggests the potential for use of alternative poison sources. This research provides novel insight into the ecology of L. imhausi, while also suggesting that more field observations, feeding trials, and chemical analyses are needed to understand their behavior and physiology. Furthermore, their complex social interactions, slow life history, and fragmented populations suggest that L. imhausi could be at risk of decline.

Strategies in herbivory by mammals revisited: The role of liver metabolism in a juniper specialist (Neotoma stephensi) and a generalist (Neotoma albigula)

Although herbivory is widespread among mammals, few species have adopted a strategy of dietary specialization. Feeding on a single plant species often exposes herbivores to high doses of plant secondary metabolites (PSMs), which may exceed the animal's detoxification capacities. Theory predicts that specialists will have unique detoxification mechanisms to process high levels of dietary toxins. To evaluate this hypothesis, we compared liver microsomal metabolism of a juniper specialist, Neotoma stephensi (diet >85% juniper), to a generalist, N. albigula (diet ≤30% juniper). Specifically, we quantified the concentration of a key detoxification enzyme, cytochrome P450 2B (CYP2B) in liver microsomes, and the metabolism of α-pinene, the most abundant terpene in the juniper species consumed by the specialist woodrat. In both species, a 30% juniper diet increased the total CYP2B concentration (2-3×) in microsomes and microsomal α-pinene metabolism rates (4-fold). In N. stephensi, higher levels of dietary juniper (60% and 100%) further induced CYP2B and increased metabolism rates of α-pinene. Although no species-specific differences in metabolism rates were observed at 30% dietary juniper, total microsomal CYP2B concentration was 1.7× higher in N. stephensi than in N. albigula (p < .01), suggesting N. stephensi produces one or more variant of CYP2B that is less efficient at processing α-pinene. In N. stephensi, the rates of α-pinene metabolism increased with dietary juniper and were positively correlated with CYP2B concentration. The ability of N. stephensi to elevate CYP2B concentration and rate of α-pinene metabolism with increasing levels of juniper in the diet may facilitate juniper specialization in this species.

Natural diets promote retention of the native gut microbiota in captive rodents

Wild animals entering captivity experience radical lifestyle changes resulting in microbiome alterations. However, little is known about the factors that drive microbial community shifts in captivity, and what actions could mitigate microbial changes. Using white-throated woodrats (Neotoma albigula), we tested whether offering natural diets in captivity facilitates retention of native microbial communities of captive animals. Wild-caught woodrats were brought to laboratory conditions. Woodrats received either a natural diet of Opuntia cactus or an artificial diet of commercial chow over three weeks. Microbial inventories from woodrat feces at the time of capture and in captivity were generated using Illumina 16S rRNA sequencing. We found that providing woodrats with wild-natural diets significantly mitigated alterations in their microbiota, promoting a 90% retention of native microbial communities across the experiment. In contrast, the artificial diet significantly impacted microbial structure to the extent that 38% of the natural microflora was lost. Core bacteria including Bifidobacterium and Allobaculum were lost, and abundances of microbes related to oxalate degradation decreased in individuals fed artificial but not natural diets. These results highlight the importance of supplementing captive diets with natural foods to maintain native microbiomes of animals kept in artificial conditions for scientific or conservation purposes.

Metagenomic sequencing provides insights into microbial detoxification in the guts of small mammalian herbivores (Neotoma spp.)

Microbial detoxification of plant toxins influences the use of plants as food sources by herbivores. Stephen's woodrats (Neotoma stephensi) specialize on juniper, which is defended by oxalate, phenolics and monoterpenes, while closely related N. albigula specialize on cactus, which only contains oxalate. Woodrats maintain two gut chambers harboring dense microbial communities: a foregut chamber proximal to the major site of toxin absorption, and a cecal chamber in their hindgut. We performed several experiments to investigate the location and nature of microbial detoxification in the woodrat gut. First, we measured toxin concentrations across gut chambers of N. stephensi. Compared to food material, oxalate concentrations were immediately lower in the foregut, while concentrations of terpenes remained high in the foregut, and were lowest in the cecal chamber. We conducted metagenomic sequencing of the foregut chambers of both woodrat species and cecal chambers of N. stephensi to compare microbial functions. We found that most genes associated with detoxification were more abundant in the cecal chambers of N. stephensi. However, some genes associated with degradation of oxalate and phenolic compounds were more abundant in the foregut chambers. Thus, microbial detoxification may take place in various chambers depending on the class of chemical compound.

Symbiotic microbes and potential pathogens in the intestine of dead southern right whale (Eubalaena australis) calves

Between 2003 and 2017, at least 706 southern right whale (Eubalaena australis) calves died at the Península Valdés calving ground in Argentina. Pathogenic microbes are often suggested to be the cause of stranding events in cetaceans; however, to date there is no evidence supporting bacterial infections as a leading cause of right whale calf deaths in Argentina. We used high-throughput sequencing and culture methods to characterize the bacterial communities and to detect potential pathogens from the intestine of stranded calves. We analyzed small and large intestinal contents from 44 dead calves that stranded at Península Valdés from 2005 to 2010 and found 108 bacterial genera, most identified as Firmicutes or Bacteroidetes, and 9 genera that have been previously implicated in diseases of marine mammals. Only one operational taxonomic unit was present in all samples and identified as Clostridium perfringens type A. PCR results showed that all C. perfringens isolates (n = 38) were positive for alpha, 50% for beta 2 (n = 19) and 47% for enterotoxin (CPE) genes (n = 18). The latter is associated with food-poisoning and gastrointestinal diseases in humans and possibly other animals. The prevalence of the cpe gene found in the Valdés' calves is unusually high compared with other mammals. However, insufficient histologic evidence of gastrointestinal inflammation or necrosis (the latter possibly masked by autolysis) in the gut of stranded calves, and absence of enterotoxin detection precludes conclusions about the role of C. perfringens in calf deaths. Further work is required to determine whether C. perfringens or other pathogens detected in this study are causative agents of calf deaths at Península Valdés.

Cytochrome P450 2B diversity in a dietary specialist—the red tree vole (Arborimus longicaudus)

Although herbivores rely on liver enzymes to biotransform plant secondary metabolites ingested in plant-based diets, only a few enzymes from a handful of species have been characterized at the genomic level. In this study, we examined cytochrome P450 2B (CYP2B) sequence diversity and gene copy number in a conifer specialist, the red tree vole (Arborimus longicaudus). We fed captive individuals exclusively Douglas-fir (Pseudotsuga menziesii) foliage, cloned and sequenced their liver CYP2B cDNA, and estimated CYP2B gene copy number. We identified 21 unique CYP2B nucleotide sequences, and 20 unique CYP2B amino acid sequences. Gene copy number of CYP2B was estimated at 7.7 copies per haploid genome. We compared red tree vole CYP2B with CYP2B sequences of a generalist, the prairie vole (Microtus ochrogaster), found in GenBank. Our study revealed that the CYP2B enzymes of red tree voles possess unique sequences compared to CYP2B enzymes of other herbivorous species. The unique combination of amino acid residues at key substrate recognition sites of CYP2B enzymes may underlie the ability of the red tree vole to specialize on a highly toxic diet of Douglas-fir.

Beyond Fermentation: Other Important Services Provided to Endothermic Herbivores by their Gut Microbiota

For decades, comparative biologists have recognized the importance of microbial partners in facilitating herbivory as a successful feeding strategy. Most of this success is attributed to the ability of gut microbes to digest recalcitrant dietary fiber and provides usable nutrients to their hosts. Gut microbes can also provide numerous other functions, such as vitamin synthesis, nitrogen recycling, and the detoxification of plant secondary compounds. Here, we review these microbial functions in herbivorous mammals and birds, highlighting studies that utilize recently developed metagenomic techniques. Several of these studies emphasize that microbial services are the product of interactions and exchanges within a complex microbial community, rather than the product of an individual member. Additionally, a number of these microbial functions are interdependent. For example, levels of dietary nitrogen or plant toxins can influence fiber digestibility. Further studies into the variety of microbial services provided to herbivorous hosts, and how these services might interact will broaden our understanding of host-microbe interactions.

Microbial communities exhibit host species distinguishability and phylosymbiosis along the length of the gastrointestinal tract

Host-associated microbial communities consist of stable and transient members that can assemble through purely stochastic processes associated with the environment or by interactions with the host. Phylosymbiosis predicts that if host-microbiota interactions impact assembly patterns, then one conceivable outcome is concordance between host evolutionary histories (phylogeny) and the ecological similarities in microbial community structures (microbiota dendrogram). This assembly pattern has been demonstrated in several clades of animal hosts in laboratory and natural populations, but in vertebrates, it has only been investigated using samples from faeces or the distal colon. Here, we collected the contents of five gut regions from seven rodent species and inventoried the bacterial communities by sequencing the 16S rRNA gene. We investigated how community structures varied across gut regions and whether the pattern of phylosymbiosis was present along the length of the gut. Gut communities varied by host species and gut region, with Oscillospira and Ruminococcus being more abundant in the stomach and hindgut regions. Gut microbial communities were highly distinguishable by host species across all gut regions, with the strength of the discrimination increasing along the length of the gut. Last, the pattern of phylosymbiosis was found in all five gut regions, as well as faeces. Aspects of the gut environment, such as oxygen levels, production of antimicrobials or other factors, may shift microbial communities across gut regions. However, regardless of these differences, host species maintain distinguishable, phylosymbiotic assemblages of microbes that may have functional impacts for the host.

With a Little Help from My Friends: Microbial Partners in Integrative and Comparative Biology-An Introduction to the Symposium

The role that host-associated microbes play in animal biology is gaining attention in comparative biology. Numerous research groups study the roles that microbes play in human health and nutrition, or in enhancing the production of agricultural animals. However, inclusion of host-associated microbes into research questions of integrative and comparative biology has lagged behind. We hosted a symposium to bring together top researchers in the field of host-associated microbes who also incorporate aspects of integrative and comparative biology. In this introduction, we highlight recent research demonstrating the profound roles that host-associated microbes play in many aspects of animal biology, such as immune function, endocrinology, and even behavior. It is our hope that integrative and comparative biologists will begin to include aspects of host-associated microbes into their research programs, enhancing both the fields of comparative biology and host-microbe interactions.

Patterns of host gene expression associated with harboring a foregut microbial community

BACKGROUND

Harboring foregut microbial communities is considered a key innovation that allows herbivorous mammals to colonize new ecological niches. However, the functions of these chambers have only been well studied at the molecular level in ruminants. Here, we investigate gene expression in the foregut chamber of herbivorous rodents and ask whether these gene expression patterns are consistent with results in ruminants. We compared gene expression in foregut tissues of two rodent species: Stephen's woodrat (Neotoma stephensi), which harbors a dense foregut microbial community, and the lab rat (Rattus norvegicus), which lacks such a community.

RESULTS

We found that woodrats have higher abundances of transcripts associated with smooth muscle processes, specifically a higher expression of the smoothelin-like 1 gene, which may assist in contractile properties of this tissue to retain food material in the foregut chamber. The expression of genes associated with keratinization and cornification exhibited a complex pattern of differences between the two species, suggesting distinct molecular mechanisms. Lab rats exhibited higher abundances of transcripts associated with immune function, likely to inhibit microbial growth in the foregut of this species.

CONCLUSIONS

Some of our results were consistent with previous findings in ruminants (high expression of facilitative glucose transporters, lower expression of B4galnt2), suggestive of possible convergent evolution, while other results were unclear, and perhaps represent novel host-microbe interactions in rodents. Overall, our results suggest that harboring a foregut microbiota is associated with changes to the functions and host-microbe interactions of the foregut tissues.

Intestinal Lymphatic Transport: an Overlooked Pathway for Understanding Absorption of Plant Secondary Compounds in Vertebrate Herbivores

Herbivores employ numerous strategies to reduce their exposure to toxic plant secondary chemicals (PSCs). However, the physiological mechanisms of PSC absorption have not been extensively explored. In particular, the absorption of PSCs via intestinal lymphatic absorption has been largely overlooked in herbivores, even though this pathway is well recognized for pharmaceutical uptake. Here, we investigated for the first time whether PSCs might be absorbed by lymphatic transport. We fed woodrats (Neotoma albigula) diets with increasing concentrations of terpene-rich juniper (Juniperus monosperma) either with or without a compound that blocks intestinal lymphatic absorption (Pluronic L-81). Woodrats consuming diets that contained the intestinal lymphatic absorption blocker exhibited increased food intakes and maintained higher body masses on juniper diets. Our study represents the first demonstration that PSCs may be absorbed by intestinal lymphatic absorption. This absorption pathway has numerous implications for the metabolism and distribution of PSCs in the systemic circulation, given that compounds absorbed via lymphatic transport bypass first-pass hepatic metabolism. The area of lymphatic transport of PSCs represents an understudied physiological pathway in plant-herbivore interactions.

Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation

Gut microbes are essential for the degradation of dietary oxalate, and this function may play a role in decreasing the incidence of kidney stones. However, many oxalate-degrading bacteria are susceptible to antibiotics and the use of oxalate-degrading probiotics has only led to an ephemeral reduction in urinary oxalate. The objective of the current study was to determine the efficacy of using whole-community microbial transplants from a wild mammalian herbivore, Neotoma albigula, to increase oxalate degradation over the long term in the laboratory rat, Rattus norvegicus. We quantified the change in total oxalate degradation in lab rats immediately after microbial transplants and at 2- and 9-month intervals following microbial transplants. Additionally, we tracked the fecal microbiota of the lab rats, with and without microbial transplants, using high-throughput Illumina sequencing of a hyper-variable region of the 16S rRNA gene. Microbial transplants resulted in a significant increase in oxalate degradation, an effect that persisted 9 months after the initial transplants. Functional persistence was corroborated by the transfer, and persistence of a group of bacteria previously correlated with oxalate consumption in N. albigula, including an anaerobic bacterium from the genus Oxalobacter known for its ability to use oxalate as a sole carbon source. The results of this study indicate that whole-community microbial transplants are an effective means for the persistent colonization of oxalate-degrading bacteria in the mammalian gut.

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

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.

Experimental Evolution on a Wild Mammal Species Results in Modifications of Gut Microbial Communities

Comparative studies have shown that diet, life history, and phylogeny interact to determine microbial community structure across mammalian hosts. However, these studies are often confounded by numerous factors. Selection experiments offer unique opportunities to validate conclusions and test hypotheses generated by comparative studies. We used a replicated, 15-generation selection experiment on bank voles (Myodes glareolus) that have been selected for high swim-induced aerobic metabolism, predatory behavior toward crickets, and the ability to maintain body mass on a high-fiber, herbivorous diet. We predicted that selection on host performance, mimicking adaptive radiation, would result in distinct microbial signatures. We collected foregut and cecum samples from animals that were all fed the same nutrient-rich diet and had not been subjected to any performance tests. We conducted microbial inventories of gut contents by sequencing the V4 region of the 16S rRNA gene. We found no differences in cecal microbial community structure or diversity between control lines and the aerobic or predatory lines. However, the cecal chambers of voles selected for herbivorous capability harbored distinct microbial communities that exhibited higher diversity than control lines. The foregut communities of herbivorous-selected voles were also distinct from control lines. Overall, this experiment suggests that differences in microbial communities across herbivorous mammals may be evolved, and not solely driven by current diet or other transient factors.

Structure-Function Analysis of Mammalian CYP2B Enzymes Using 7-Substituted Coumarin Derivatives as Probes: Utility of Crystal Structures and Molecular Modeling in Understanding Xenobiotic Metabolism

Crystal structures of CYP2B35 and CYP2B37 from the desert woodrat were solved in complex with 4-(4-chlorophenyl)imidazole (4-CPI). The closed conformation of CYP2B35 contained two molecules of 4-CPI within the active site, whereas the CYP2B37 structure demonstrated an open conformation with three 4-CPI molecules, one within the active site and the other two in the substrate access channel. To probe structure-function relationships of CYP2B35, CYP2B37, and the related CYP2B36, we tested the O-dealkylation of three series of related substrates-namely, 7-alkoxycoumarins, 7-alkoxy-4-(trifluoromethyl)coumarins, and 7-alkoxy-4-methylcoumarins-with a C1-C7 side chain. CYP2B35 showed the highest catalytic efficiency (kcat/KM) with 7-heptoxycoumarin as a substrate, followed by 7-hexoxycoumarin. In contrast, CYP2B37 showed the highest catalytic efficiency with 7-ethoxy-4-(trifluoromethyl)coumarin (7-EFC), followed by 7-methoxy-4-(trifluoromethyl)coumarin (7-MFC). CYP2B35 had no dealkylation activity with 7-MFC or 7-EFC. Furthermore, the new CYP2B-4-CPI-bound structures were used as templates for docking the 7-substituted coumarin derivatives, which revealed orientations consistent with the functional studies. In addition, the observation of multiple -Cl and -NH-π interactions of 4-CPI with the aromatic side chains in the CYP2B35 and CYP2B37 structures provides insight into the influence of such functional groups on CYP2B ligand binding affinity and specificity. To conclude, structural, computational, and functional analysis revealed striking differences between the active sites of CYP2B35 and CYP2B37 that will aid in the elucidation of new structure-activity relationships.

Ambient temperature influences tolerance to plant secondary compounds in a mammalian herbivore

Growing evidence suggests that plant secondary compounds (PSCs) ingested by mammals become more toxic at elevated ambient temperatures, a phenomenon known as temperature-dependent toxicity. We investigated temperature-dependent toxicity in the desert woodrat (Neotoma lepida), a herbivorous rodent that naturally encounters PSCs in creosote bush (Larrea tridentata), which is a major component of its diet. First, we determined the maximum dose of creosote resin ingested by woodrats at warm (28-29°C) or cool (21-22°C) temperatures. Second, we controlled the daily dose of creosote resin ingested at warm, cool and room (25°C) temperatures, and measured persistence in feeding trials. At the warm temperature, woodrats ingested significantly less creosote resin; their maximum dose was two-thirds that of animals at the cool temperature. Moreover, woodrats at warm and room temperatures could not persist on the same dose of creosote resin as woodrats at the cool temperature. Our findings demonstrate that warmer temperatures reduce PSC intake and tolerance in herbivorous rodents, highlighting the potentially adverse consequences of temperature-dependent toxicity. These results will advance the field of herbivore ecology and may hone predictions of mammalian responses to climate change.

Using the Specialization Framework to Determine Degree of Dietary Specialization in a Herbivorous Woodrat

To be considered a dietary specialist, mammalian herbivores must consume large quantities of a plant species considered "difficult" with respect to nutrient or toxin content, and possess specialized adaptations to deal with plant defensive compounds or low nutritional content. Populations of Neotoma lepida in the Great Basin consume Juniperus osteosperma, a plant heavily defended by terpenes, but a detailed dietary analysis of this population is lacking. Therefore, we investigated the extent of dietary specialization in this species in comparison with the better-studied specialist species, N. stephensi. Microhistological analysis of feces from N. lepida revealed that greater than 90% of their diet in nature was comprised of juniper. In laboratory tolerance trials, N. lepida tolerated a diet of 80% J. osteosperma, similar to that observed for N. stephensi. There was no difference in the abilities of N. lepida and N. stephensi to metabolize hexobarbital, a proxy compound for terpene metabolism. In preference tests of native and non-native juniper species, N. lepida did not exhibit a preference for its native or co-occurring juniper, J. osteosperma, over the non-native species, J. monosperma, whereas N. stephensi preferred its native or co-occurring juniper J. monosperma over non-native J. osteosperma. Behavioral and habitat differences between these woodrat species lead to the categorization of N. stephensi as an obligate juniper specialist with a small range that overlaps that of its preferred food, J. monosperma, and N. lepida as a facultative juniper specialist with a large range, and only a portion of its distribution containing populations that feed extensively on J. osteosperma.

Evolutionary irony: evidence that 'defensive' plant spines act as a proximate cue to attract a mammalian herbivore

Many plants produce structural defenses to deter feeding by herbivores. However, many previous studies testing whether spines are effective at defending against mammalian herbivores have produced equivocal results. These ambiguous results are hypothesized to be due to herbivore counter-adaptations. We investigated potential counter-adaptations in a population of white-throated woodrats Neotoma albigua that specialize on cactus by investigating feeding behavior and preference for cacti varying in spinescence. Neotoma albigula exhibited a unique behavior of clipping cactus spines, which renders these defenses ineffective. Strikingly, these woodrats chose to collect spiny cacti over experimentally de-spined cacti, demonstrating that spines act as a proximal cue that attracts woodrats. This attraction is likely due to the higher protein and lower fiber content of spiny cacti compared to naturally non-spiny cacti. Thus, the 'defensive' spines of cacti are ineffective against a specialist herbivore and instead serve as an indicator of nutritional quality that promotes herbivory. Our results support the 'rule-of-thumb' hypothesis of foraging, which states that herbivores forage according to obvious visual cues that are indicative of nutritional content, rather than sampling nutrient composition of plants. We propose that specialist herbivores are unique systems in which to study other counter-adaptations to structural defenses and 'rule-of-thumb' foraging strategies.

Small intestinal hydrolysis of plant glucosides: higher glucohydrolase activities in rodents than passerine birds

Glycosides are a major group of plant secondary compounds characterized by one or more sugars conjugated to a lipophilic, possibly toxic aglycone, which is released upon hydrolysis. We compared small intestinal homogenate hydrolysis activity of three rodent and two avian species against four substrates: amygdalin and sinigrin, two plant-derived glucosides, the sugar lactose, whose hydrolysis models some activity against flavonoid and isoflavonoid glucosides, and the disaccharide sugar maltose (from starch), used as a comparator. Three new findings extend our understanding of physiological processing of plant glucosides: (1) the capacity of passerine birds to hydrolyze plant glucosides seems relatively low, compared with rodents; (2) in this first test of vertebrates' enzymic capacity to hydrolyze glucosinolates, sinigrin hydrolytic capacity seems low; (3) in laboratory mice, hydrolytic activity against lactose resides on the enterocytes' apical membrane facing the intestinal lumen, but activity against amygdalin seems to reside inside enterocytes.

Larval exposure to polychlorinated biphenyl 126 (PCB-126) causes persistent alteration of the amphibian gut microbiota

Interactions between gut microbes and anthropogenic pollutants have been under study. The authors investigated the effects of larval exposure to polychlorinated biphenyl 126 (PCB-126) on the gut microbial communities of tadpoles and frogs. Frogs treated with PCBs exhibited increased species richness in the gut and harbored communities significantly enriched in Fusobacteria. These results suggest that anthropogenic pollutants alter gut microbial populations, which may have health and fitness consequences for hosts.

Translating physiological signals to changes in feeding behaviour in mammals and the future effects of global climate change

Mammals cannot avoid ingesting secondary metabolites, often in significant amounts. Thus, their intake must be regulated to avoid intoxication. Three broad mechanisms have been described by which this can be achieved. These are conditioned aversions mediated by nausea, non-conditioned aversions and the recognition of limits to detoxification. Although there is some overlap between these, we know little about the way that mechanisms of toxin avoidance interact with regulation of nutrient intake and whether one has priority over the other. Nonetheless, regulation of meal length and inter-meal length allows the intake of some plant secondary metabolites to be matched with an animal’s capacity for detoxification and its nutritional requirements. Toxicity itself is not a fixed limitation and recent work suggests that ambient temperature can be a major determinant of the toxicity of plant secondary metabolites, largely through effects on liver function. These effects are likely to be of major importance in predicting the impact of global climate change on herbivores.