Kevin D. Kohl

Diversity and function of the avian gut microbiota

The intestinal microbiota have now been shown to largely affect host health through various functional roles in terms of nutrition, immunity, and other physiological systems. However, the majority of these studies have been carried out in mammalian hosts, which differ in their physiological traits from other taxa. For example, birds possess several unique life history traits, such as hatching from eggs, which may alter the interactions with and transmission of intestinal microbes compared to most mammals. This review covers the diversity of microbial taxa hosted by birds. It also discusses how avian microbial communities strongly influence nutrition, immune function, and processing of toxins in avian hosts, in manners similar to and different from mammalian systems. Finally, areas demanding further research are identified, along with descriptions of existing techniques that could be employed to answer these questions.

Gut microbes of mammalian herbivores facilitate intake of plant toxins.

The foraging ecology of mammalian herbivores is strongly shaped by plant secondary compounds (PSCs) that defend plants against herbivory. Conventional wisdom holds that gut microbes facilitate the ingestion of toxic plants; however, this notion lacks empirical evidence. We investigated the gut microbiota of desert woodrats (Neotoma lepida), some populations of which specialise on highly toxic creosote bush (Larrea tridentata). Here, we demonstrate that gut microbes are crucial in allowing herbivores to consume toxic plants. Creosote toxins altered the population structure of the gut microbiome to facilitate an increase in abundance of genes that metabolise toxic compounds. In addition, woodrats were unable to consume creosote toxins after the microbiota was disrupted with antibiotics. Last, ingestion of toxins by naïve hosts was increased through microbial transplants from experienced donors. These results demonstrate that microbes can enhance the ability of hosts to consume PSCs and therefore expand the dietary niche breadth of mammalian herbivores.

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History

Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern, whereby the ecological relatedness of host-associated microbial communities parallels the phylogeny of related host species. Here, we test the prevalence of phylosymbiosis and its functional significance under highly controlled conditions by characterizing the microbiota of 24 animal species from four different groups (Peromyscus deer mice, Drosophila flies, mosquitoes, and Nasonia wasps), and we reevaluate the phylosymbiotic relationships of seven species of wild hominids. We demonstrate three key findings. First, intraspecific microbiota variation is consistently less than interspecific microbiota variation, and microbiota-based models predict host species origin with high accuracy across the dataset. Interestingly, the age of host clade divergence positively associates with the degree of microbial community distinguishability between species within the host clades, spanning recent host speciation events (~1 million y ago) to more distantly related host genera (~108 million y ago). Second, topological congruence analyses of each groups complete phylogeny and microbiota dendrogram reveal significant degrees of phylosymbiosis, irrespective of host clade age or taxonomy. Third, consistent with selection on host–microbiota interactions driving phylosymbiosis, there are survival and performance reductions when interspecific microbiota transplants are conducted between closely related and divergent host species pairs. Overall, these findings indicate that the composition and functional effects of an animals microbial community can be closely allied with host evolution, even across wide-ranging timescales and diverse animal systems reared under controlled conditions.

Experience matters: prior exposure to plant toxins enhances diversity of gut microbes in herbivores

For decades, ecologists have hypothesised that exposure to plant secondary compounds (PSCs) modifies herbivore-associated microbial community composition. This notion has not been critically evaluated in wild mammalian herbivores on evolutionary timescales. We investigated responses of the microbial communities of two woodrat species (Neotoma bryanti and N. lepida). For each species, we compared experienced populations that independently converged to feed on the same toxic plant (creosote bush, Larrea tridentata) to naïve populations with no exposure to creosote toxins. The addition of dietary PSCs significantly altered gut microbial community structure, and the response was dependent on previous experience. Microbial diversity and relative abundances of several dominant phyla increased in experienced woodrats in response to PSCs; however, opposite effects were observed in naïve woodrats. These differential responses were convergent in experienced populations of both species. We hypothesise that adaptation of the foregut microbiota to creosote PSCs in experienced woodrats drives this differential response.

Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts

Many animals face unpredictable food sources and periods of prolonged fasting, which likely present significant challenges to gut microorganisms. While several studies have demonstrated that fasting impacts the gut microbiota, experiments have not been carried out in a comparative context. We used 16S rRNA gene sequencing to document changes in colonic and cecal microbiomes of animals representing five classes of vertebrates at four time points through prolonged fasting: tilapia, toads, geckos, quail, and mice. We found differences in the starvation-induced changes in the microbiome across host species and across gut regions. Microbial phylogenetic diversity increased as a result of fasting in the colons of fish, toads, and mice, while quail exhibited a decrease in diversity; geckos exhibited no change. Microbial diversity in the cecum decreased in fish and exhibited no change in mice. Alterations in relative abundances of microbial taxa varied across hosts. Fish exhibited the most significant changes due to fasting, while geckos maintained a stable community over 28 days of fasting. We uncovered several shared responses of the microbiota across hosts. For example, all tetrapods exhibited decreases in the abundances of Coprobacillus and Ruminococcus in response to fasting. We also discuss host-mediated physiological mechanisms that may underlie these community changes.

Restructuring of the amphibian gut microbiota through metamorphosis

Vertebrates maintain complex symbioses with a diverse community of microbes residing within their guts. The microbial players in these symbioses differ between major taxa of vertebrates, such that fish and amniotes maintain notably different communities. To date, there has not been a culture-independent inventory of an amphibian gut microbial community. Here, we compared gut microbial communities of tadpoles and frogs of the Northern leopard frog (Lithobates pipiens). We utilized Illumina sequencing, which allowed us to inventory more than 450 000 microbial sequences. We found that tadpoles and frogs differ markedly in the composition of their gut microbial communities, with tadpoles maintaining a community more similar to fish, whereas the frog community resembles that of amniotes. Additionally, frogs maintain a community with lower phylogenetic diversity compared with tadpoles. The significant restructuring of the microbiota is likely due to changes in diet as well as the large reorganization of the intestinal organ during metamorphosis. Overall, we propose that amphibians represent an important system in which to study regulation and selection of gut microbial communities.

Developmental adjustments of house sparrow (Passer domesticus) nestlings to diet composition.

SUMMARY House sparrow nestlings are fed primarily on insects during the first 3 days of their life, and seeds become gradually more important afterwards. We tested whether developmental changes in size and functional capacity of the digestive tract in young house sparrows are genetically hard-wired and independent of diet, or can be modified by food type. Under laboratory conditions, we hand-fed young house sparrows with either a starch-free insect-like diet, based mainly on protein and fat, or a starch-containing diet with a mix of substrates similar to that offered to older nestlings in natural nests when they are gradually weaned from an insect to a seed diet. Patterns of overall development in body size and thermoregulatory ability, and in alimentary organ size increase, were relatively similar in house sparrow nestlings developing on both diets. However, total intestinal maltase activity, important in carbohydrate breakdown, was at least twice as high in house sparrow nestlings fed the starch-containing diet (P<0.001). The change in maltase activity of nestlings was specific, as no change occurred in aminopeptidase-N activity in the same tissues. There was no significant diet effect on digesta retention time, but assimilation efficiency for radiolabeled starch tended to be higher (P=0.054) in nestlings raised on starch-containing diet. Future studies must test whether the diet-dependent increase in maltase activity during development is irreversible or reversible, reflecting, respectively, a developmental plasticity or a phenotypic flexibility.

Wild‐caught rodents retain a majority of their natural gut microbiota upon entrance into captivity

Experiments conducted on captive animals allow scientists to control many variables; however, these settings are highly unnatural. Previous research has documented a large difference in microbial communities between wild animals and captive-bred individuals. However, wild-caught animals brought into captivity might retain their natural microbiota and thus provide a better study system in which to investigate the ecology of the gut microbiome. We collected individuals of the desert woodrat (Neotoma lepida) from nature and investigated changes in the microbial community over 6 months in captivity. Additionally, we inventoried potential environmental sources of microbes (food, bedding) from the wild and captivity. We found that environmental sources do not make large contributions to the woodrat gut microbial community. We documented a slight decrease in several biodiversity metrics over 6 months in captivity, yet the magnitude of change was small compared with other studies. Wild and captive animals shared 64% of their microbial species, almost twice that observed in other studies of wild and captive-bred individuals (≤ 37% shared). We conclude that wild-caught animals brought into captivity retain a substantial proportion of their natural microbiota and represent an acceptable system in which to study the gut microbiome.

Herbivorous rodents (Neotoma spp.) harbour abundant and active foregut microbiota

Symbiotic gut microbes have facilitated the success of herbivorous mammals, which are generally grouped into foregut- and hindgut-fermenters. However, rodents are primarily herbivorous and exhibit a variety of gastrointestinal anatomies. Most rodents house microbes in hindgut chambers, such as the caecum and colon. Some rodents also exhibit stomach segmentation with a foregut chamber proximal to the stomach. For over a century, scientists have hypothesized that this foregut chamber houses a microbial community, yet this has never been explicitly examined. We investigated the capacity of each of the gut regions to house microbes by measuring size, pH, bacterial cell density, concentrations of microbial metabolites and digesta transit time in woodrats (Neotoma spp.). We also compared microbial communities across gut chambers, as well as faeces, using 16S rRNA sequencing. This allowed us to test the appropriateness of using faeces as a proxy for microbial communities of other gut chambers. We found that woodrats house foregut microbial communities with similar density and volatile fatty acid concentrations to rumen ecosystems. Resident microbial communities varied between gut chambers, and faecal bacterial communities were significantly different from caecal and colonic communities. The foregut microbiota may provide a number of physiological services to the host.

Captivity results in disparate loss of gut microbial diversity in closely related hosts

We compared microbial community structure in two rodent species before and after captivity. One species lost a greater proportion of diversity in captivity, which was not rescued when they were returned to their natural diet. Mothers effectively transmitted microbiota to their offspring. These results have implications for captive breeding programs.