Experimental Evolution of a Mammalian Holobiont? Genetic and Maternal Effects on the Cecal Microbiome in Bank Voles Selectively Bred for Herbivorous Capability.

AbstractMammalian herbivory represents a complex adaptation requiring evolutionary changes across all levels of biological organization, from molecules to morphology to behavior. Explaining the evolution of such complex traits represents a major challenge in biology, as it is simultaneously muddled and enlightened by a growing awareness of the crucial role of symbiotic associations in shaping organismal adaptations. The concept of hologenomic evolution includes the partnered unit of the holobiont, the host with its microbiome, as a selection unit that may undergo adaptation.

Functional convergence in gastric lysozymes of foregut-fermenting rodents, ruminants, and primates is not attributed to convergent molecular evolution.

Convergent evolution is a widespread phenomenon. While there are many examples of convergent evolution at the phenotypic scale, convergence at the molecular level has been more difficult to identify. A classic example of convergent evolution across scales is that of the digestive lysozyme found in ruminants and Colobine monkeys.

Host avian species and environmental conditions influence the microbial ecology of brood parasitic brown-headed cowbird nestlings: What rules the roost?

The role of species interactions, as well as genetic and environmental factors, all likely contribute to the composition and structure of the gut microbiome; however, disentangling these independent factors under field conditions represents a challenge for a functional understanding of gut microbial ecology. Avian brood parasites provide unique opportunities to investigate these questions, as brood parasitism results in parasite and host nestlings being raised in the same nest, by the same parents. Here we utilized obligate brood parasite brown-headed cowbird nestlings (BHCO; Molothrus ater) raised by several different host passerine species to better understand, via 16S rRNA sequencing, the microbial ecology of brood parasitism.

Dietary tannins alter growth, behavior, and the gut microbiome of larval amphibians.

Research has shown that leached plant toxins negatively impact the growth and development of larval amphibians. However, tadpoles may encounter these same toxins in food material, and differential exposure routes and distribution of toxic chemicals can yield variable downstream effects on animals. To date, most research understanding the interactions between dietary plant toxins and herbivores has been conducted in terrestrial systems.

Ectotherm heat tolerance and the microbiome: current understanding, future directions and potential applications.

Climate change and increasing global temperatures are a leading threat to ectothermic animals worldwide. Ectotherm persistence under climate change will depend on a combination of host and environmental factors; recently it has become clear that host-associated microbial communities contribute significantly to the response of ectotherms to environmental warming. However, several unanswered questions about these relationships remain before accurate predictions can be made regarding the microbiome's influence on host ecology and evolution under climate warming.

Temperature and the microbial environment alter brain morphology in a larval amphibian.

Understanding how the global climate impacts the physiology of wildlife animals is of importance. Amphibians are particularly sensitive to climate change, and it is hypothesized that rising temperatures impair their neurodevelopment. Temperature influences the composition of the gut microbiota, which is critical to host neurodevelopment through the microbiota-gut-brain (MGB) axis.

Deficits in Accessibility across Field Research Stations for Scientists with Disabilities and/or Chronic Illness, and Proposed Solutions.

Equity and inclusivity in STEM research has become a larger topic of discussion in recent years; however, researchers and scientists with disabilities and/or chronic illnesses are often missing from these conversations. Further, while field research is a major research component for some STEM disciplines, it is unclear what accessibility barriers or accommodations exist across the field sciences. Field research can sometimes involve harsh environments, topography, and weather that present challenges to those with disabilities and/or chronic illnesses.

The microbiome buffers tadpole hosts from heat stress: a hologenomic approach to understand host-microbe interactions under warming.

Phenotypic plasticity is an important strategy that animals employ to respond and adjust to changes in their environment. Plasticity may occur via changes in host gene expression or through functional changes in their microbiomes, which contribute substantially to host physiology. Specifically, the presence and function of host-associated microbes can impact how animals respond to heat stress.

Skin bacterial microbiome diversity predicts lower activity levels in female, but not male, guppies, .

While the link between the gut microbiome and host behaviour is well established, how the microbiomes of other organs correlate with behaviour remains unclear. Additionally, behaviour-microbiome correlations are likely sex-specific because of sex differences in behaviour and physiology, but this is rarely tested. Here, we tested whether the skin microbiome of the Trinidadian guppy, , predicts fish activity level and shoaling tendency in a sex-specific manner.

Comparative digestive morphology and physiology of five species of Peromyscus under controlled environment and diet.

Digestive morphology and physiology differ across animal species, with many comparative studies uncovering relationships between animal ecology or diet, and the morphology and physiology of the gastrointestinal tract. However, many of these studies compare wild-caught animals feeding on uncontrolled diets and compare broadly related taxa. Thus, few studies have disentangled the phenotypic consequences of genetics from those potentially caused by the environment, especially across closely related species that occupy similar ecological niches.

Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies.

The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously.

The gut microbiome influences host diet selection behavior.

Diet selection is a fundamental aspect of animal behavior with numerous ecological and evolutionary implications. While the underlying mechanisms are complex, the availability of essential dietary nutrients can strongly influence diet selection behavior. The gut microbiome has been shown to metabolize many of these same nutrients, leading to the untested hypothesis that intestinal microbiota may influence diet selection.

Experimental manipulation of microbiota reduces host thermal tolerance and fitness under heat stress in a vertebrate ectotherm.

Identifying factors that influence how ectothermic animals respond physiologically to changing temperatures is of high importance given current threats of global climate change. Host-associated microbial communities impact animal physiology and have been shown to influence host thermal tolerance in invertebrate systems. However, the role of commensal microbiota in the thermal tolerance of ectothermic vertebrates is unknown.

Plant secondary compound- and antibiotic-induced community disturbances improve the establishment of foreign gut microbiota.

Fecal transplants are a powerful tool for manipulating the gut microbial community, but how these non-native communities establish in the presence of an intact host gut microbiome is poorly understood. We explored the microbiome of desert woodrats (Neotoma lepida) to determine whether disrupting existing microbial communities using plant secondary compounds (PSCs) or antibiotics increases the establishment of foreign microbes. We administered two fecal transplants between natural populations of adult woodrats that harbor distinct gut microbiota and have different natural dietary exposure to PSCs.

Microbiome stability and structure is governed by host phylogeny over diet and geography in woodrats ( 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 , we quantify how geography, diet, and host genetics, alongside neutral processes, influence microbiome structure and stability under natural and captive conditions.

Abundance and Compositions of B-Vitamin-Producing Microbes in the Mammalian Gut Vary Based on Feeding Strategies.

Mammals maintain close associations with gut microbes that provide numerous nutritional benefits, including vitamin synthesis. While most mammals obtain sufficient vitamins from their diets, deficiencies in various B vitamins (biotin, cobalamin, riboflavin, thiamine, etc.) are reported in captive animals.

Stabilization and optimization of host-microbe-environment interactions as a potential reason for the behavior of natal philopatry.

Many animals engage in a behavior known as natal philopatry, where after sexual maturity they return to their own birthplaces for subsequent reproduction. There are many proposed ultimate factors that may underlie the evolution of natal philopatry, such as genetic optimization, suitable living conditions, and friendly neighbors, which can improve the survival rates of offspring. However, here we propose that a key factor that has been overlooked could be the colonization of gut microbiota during early life and the effects these microorganisms have on host performance and fitness.

Changes in the gut microbial community of the eastern newt (Notophthalmus viridescens) across its three distinct life stages.

Understanding the forces that shape vertebrate gut microbial community assembly and composition throughout development is a major focus of the microbiome field. Here, we utilize the complex life cycle of the eastern newt (Notophthalmus viridescens) as a natural wild model to compare the effects of host and environmental factors on gut microbiome development. We compared bacterial inventories of each of the newt's three physiologically distinct developmental stages to determine if each hosted a unique community, or if the two stages which share an aquatic habitat (larvae and adults) harbored more similar communities than those of the third stage, the terrestrial juvenile eft.

Optimal integration between host physiology and functions of the gut microbiome.

Host-associated microbial communities have profound impacts on animal physiological function, especially nutrition and metabolism. The hypothesis of 'symmorphosis', which posits that the physiological systems of animals are regulated precisely to meet, but not exceed, their imposed functional demands, has been used to understand the integration of physiological systems across levels of biological organization. Although this idea has been criticized, it is recognized as having important heuristic value, even as a null hypothesis, and may, therefore, be a useful tool in understanding how hosts evolve in response to the function of their microbiota.

Coprophagy prevention alters microbiome, metabolism, neurochemistry, and cognitive behavior in a small mammal.

Many small mammals engage in coprophagy, or the behavior of consuming feces, as a means to meet nutritional requirements when feeding on low-quality foods. In addition to nutritional benefits, coprophagy may also help herbivores retain necessary gut microbial diversity and function, which may have downstream physiological effects, such as maintaining energy balance and cognitive function. Here, we used collars to prevent Brandt's vole (Lasiopodomys brandtii) from engaging in coprophagy and monitored changes in microbial community structure, energy metabolism, and cognitive performance.

Gut microbiota of invasive bullfrog tadpoles responds more rapidly to temperature than a noninvasive congener.

Environmental temperature can alter the composition, diversity, and function of ectothermic vertebrate gut microbial communities, which may result in negative consequences for host physiology, or conversely, increase phenotypic plasticity and persistence in harsh conditions. The magnitude of either of these effects will depend on the length of time animals are exposed to extreme temperatures, and how quickly the composition and function of the gut microbiota can respond to temperature change. However, the temporal effects of temperature on gut microbiota are currently unknown.

Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities.

Phylosymbiosis, where similarities in host-associated microbial communities recapitulate the phylogeny of their hosts, is a newly recognized yet pervasive pattern in the field of host-microbe interactions. While phylosymbiosis has been documented across many systems, we still have a poor understanding of the mechanisms that underlie this emergent pattern. Host selection of the microbiome is a widely cited mechanism, yet other basic ecological and evolutionary processes (dispersal, drift and diversification) may also be at play.

A bird's-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes.

In numerous animal clades, the evolutionary history of host species drives patterns of gut microbial community structure, resulting in more divergent microbiota with increasing phylogenetic distance between hosts. This phenomenon, termed phylosymbiosis, has been observed in diverse evolutionary lineages, but has been difficult to detect in birds. Previous tests of phylosymbiosis among birds have been conducted using wild individuals, and thus interspecific differences in diet and environment may have masked a phylogenetic signal.