Microbes, herbivory and the evolution of social behavior

Commentary: The microbial dependence continuum: Towards a comparative physiology approach to understand host reliance on microbes

Comparative physiologists often compare physiological traits across organisms to understand the selective pressures influencing their evolution in different environments. Traditionally focused on the organisms themselves, comparative physiology has more recently incorporated studies of the microbiome-the communities of microbes living in and on animals that influence host physiology. In this commentary, we describe the utility of applying a comparative framework to study the microbiome, particularly in understanding how hosts vary in their dependence on microbial communities for physiological function, a concept we term the "microbial dependence continuum". This hypothesis suggests that hosts exist on a spectrum ranging from high to low reliance on their microbiota. Certain physiological traits may be highly dependent on microbes for proper function in some species but microbially independent in others. Comparative physiology can elucidate the selective pressures driving species along this continuum. Here, we discuss the microbial dependence continuum in detail and how comparative physiology can be useful to study it. Then, we discuss two example traits, herbivory and flight, where comparative physiology has helped reveal the selective pressures influencing host dependence on microbial communities. Lastly, we discuss useful experimental approaches for studying the microbial dependence continuum in a comparative physiology context.

Ecological and genetic variables co-vary with social group identity to shape the gut microbiome of a pair-living primate

Primates exhibit diverse social systems that are intricately linked to their biology, behavior, and evolution, all of which influence the acquisition and maintenance of their gut microbiomes (GMs). However, most studies of wild primate populations focus on taxa with relatively large group sizes, and few consider pair-living species. To address this gap, we investigate how a primate's social system interacts with key environmental, social, and genetic variables to shape the GM in pair-living, red-bellied lemurs (Eulemur rubriventer). Previous research on this species suggests that social interactions within groups influence interindividual microbiome similarity; however, the impacts of other nonsocial variables and their relative contributions to gut microbial variation remain unclear. We sequenced the 16S ribosomal RNA hypervariable V4-V5 region to characterize the GM from 26 genotyped individuals across 11 social groups residing in Ranomafana National Park, Madagascar. We estimated the degree to which sex, social group identity, genetic relatedness, dietary diversity, and home range proximity were associated with variation in the gut microbial communities residing in red-bellied lemurs. All variables except sex played a significant role in predicting GM composition. Our model had high levels of variance inflation, inhibiting our ability to determine which variables were most predictive of gut microbial composition. This inflation is likely due to red-bellied lemurs' pair-living, pair-bonded social system that leads to covariation among environmental, social, and genetic variables. Our findings highlight some of the factors that predict GM composition in a tightly bonded, pair-living species and identify variables that require further study. We propose that future primate microbiome studies should simultaneously consider environmental, social, and genetic factors to improve our understanding of the relationships among sociality, the microbiome, and primate ecology and evolution.

When is microbial strain sharing evidence for transmission?

In humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. However, social microbiome transmission can be difficult to identify if social partners also have other traits in common or live in a shared environment. Strain-resolved metagenomics has been proposed as a solution for tracking microbial transmission. Using a fecal microbiota transplant dataset, we show that strain sharing can recapitulate true transmission networks under ideal settings when donor-recipient pairs are unambiguous. However, gut metagenomes from a wild baboon population, where social networks predict compositional similarity, show that strain sharing is also driven by demographic and environmental factors that can override signals of social interactions. We conclude that strain-level analyses provide useful information about microbiome similarity, but other facets of study design, especially longitudinal sampling and careful consideration of host characteristics, are essential for conclusions about the underlying mechanisms.

Integrating microbiome science and evolutionary medicine into animal health and conservation

Microbiome science has provided groundbreaking insights into human and animal health. Similarly, evolutionary medicine - the incorporation of eco-evolutionary concepts into primarily human medical theory and practice - is increasingly recognised for its novel perspectives on modern diseases. Studies of host-microbe relationships have been expanded beyond humans to include a wide range of animal taxa, adding new facets to our understanding of animal ecology, evolution, behaviour, and health. In this review, we propose that a broader application of evolutionary medicine, combined with microbiome science, can provide valuable and innovative perspectives on animal care and conservation. First, we draw on classic ecological principles, such as alternative stable states, to propose an eco-evolutionary framework for understanding variation in animal microbiomes and their role in animal health and wellbeing. With a focus on mammalian gut microbiomes, we apply this framework to populations of animals under human care, with particular relevance to the many animal species that suffer diseases linked to gut microbial dysfunction (e.g. gut distress and infection, autoimmune disorders, obesity). We discuss diet and microbial landscapes (i.e. the microbes in the animal's external environment), as two factors that are (i) proposed to represent evolutionary mismatches for captive animals, (ii) linked to gut microbiome structure and function, and (iii) potentially best understood from an evolutionary medicine perspective. Keeping within our evolutionary framework, we highlight the potential benefits - and pitfalls - of modern microbial therapies, such as pre- and probiotics, faecal microbiota transplants, and microbial rewilding. We discuss the limited, yet growing, empirical evidence for the use of microbial therapies to modulate animal gut microbiomes beneficially. Interspersed throughout, we propose 12 actionable steps, grounded in evolutionary medicine, that can be applied to practical animal care and management. We encourage that these actionable steps be paired with integration of eco-evolutionary perspectives into our definitions of appropriate animal care standards. The evolutionary perspectives proposed herein may be best appreciated when applied to the broad diversity of species under human care, rather than when solely focused on humans. We urge animal care professionals, veterinarians, nutritionists, scientists, and others to collaborate on these efforts, allowing for simultaneous care of animal patients and the generation of valuable empirical data.

Microbial transmission in the social microbiome and host health and disease

Although social interactions are known to drive pathogen transmission, the contributions of socially transmissible host-associated mutualists and commensals to host health and disease remain poorly explored. We use the concept of the social microbiome-the microbial metacommunity of a social network of hosts-to analyze the implications of social microbial transmission for host health and disease. We investigate the contributions of socially transmissible microbes to both eco-evolutionary microbiome community processes (colonization resistance, the evolution of virulence, and reactions to ecological disturbance) and microbial transmission-based processes (transmission of microbes with metabolic and immune effects, inter-specific transmission, transmission of antibiotic-resistant microbes, and transmission of viruses). We consider the implications of social microbial transmission for communicable and non-communicable diseases and evaluate the importance of a socially transmissible component underlying canonically non-communicable diseases. The social transmission of mutualists and commensals may play a significant, under-appreciated role in the social determinants of health and may act as a hidden force in social evolution.

The role of diet and host species in shaping the seasonal dynamics of the gut microbiome

The gut microbiome plays an important role in the health and fitness of hosts. While previous studies have characterized the importance of various ecological and evolutionary factors in shaping the composition of the gut microbiome, most studies have been cross-sectional in nature, ignoring temporal variation. Thus, it remains unknown how these same factors might affect the stability and dynamics of the gut microbiome over time, resulting in variation across the tree of life. Here, we used samples collected in each of four seasons for three taxa: the herbivorous southern white rhinoceros (Ceratotherium simum simum, n = 5); the carnivorous Sumatran tiger (Panthera tigris sumatrae, n = 5); and the red panda (Ailurus fulgens, n = 9), a herbivorous carnivore that underwent a diet shift in its evolutionary history from carnivory to a primarily bamboo-based diet. We characterize the variability of the gut microbiome among these three taxa across time to elucidate the influence of diet and host species on these dynamics. Altogether, we found that red pandas exhibit marked seasonal variation in their gut microbial communities, experiencing both high microbial community turnover and high variation in how individual red panda's gut microbiota respond to seasonal changes. Conversely, while the gut microbiota of rhinoceros change throughout the year, all individuals respond in the same way to seasonal changes. Tigers experience relatively low levels of turnover throughout the year, yet the ways in which individuals respond to seasonal transitions are highly varied. We highlight how the differences in microbiome richness and network connectivity between these three species may affect the level of temporal stability in the gut microbiota across the year.

Climate change is not just global warming: Multidimensional impacts on animal gut microbiota

Climate change has rapidly altered many ecosystems, with detrimental effects for biodiversity across the globe. In recent years, it has become increasingly apparent that the microorganisms that live in and on animals can substantially affect host health and physiology, and the structure and function of these microbial communities can be highly sensitive to environmental variables. To date, most studies have focused on the effects of increasing mean temperature on gut microbiota, yet other aspects of climate are also shifting, including temperature variation, seasonal dynamics, precipitation and the frequency of severe weather events. This array of environmental pressures might interact in complex and non-intuitive ways to impact gut microbiota and consequently alter animal fitness. Therefore, understanding the impacts of climate change on animals requires a consideration of multiple types of environmental stressors and their interactive effects on gut microbiota. Here, we present an overview of some of the major findings in research on climatic effects on microbial communities in the animal gut. Although ample evidence has now accumulated that shifts in mean temperature can have important effects on gut microbiota and their hosts, much less work has been conducted on the effects of other climatic variables and their interactions. We provide recommendations for additional research needed to mechanistically link climate change with shifts in animal gut microbiota and host fitness.

Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation

During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.

Effects of short-term experimental manipulation of captive social environment on uropygial gland microbiome and preen oil volatile composition

Introduction

Avian preen oil, secreted by the uropygial gland, is an important source of volatile compounds that convey information about the sender’s identity and quality, making preen oil useful for the recognition and assessment of potential mates and rivals. Although intrinsic factors such as hormone levels, genetic background, and diet can affect preen oil volatile compound composition, many of these compounds are not the products of the animal’s own metabolic processes, but rather those of odor-producing symbiotic microbes. Social behavior affects the composition of uropygial microbial communities, as physical contact results in microbe sharing. We experimentally manipulated social interactions in captive dark-eyed juncos (Junco hyemalis) to assess the relative influence of social interactions, subspecies, and sex on uropygial gland microbial composition and the resulting preen oil odor profiles.

Methods

We captured 24 birds at Mountain Lake Biological Station in Virginia, USA, including birds from two seasonally sympatric subspecies – one resident, one migratory. We housed them in an outdoor aviary in three phases of social configurations: first in same-sex, same-subspecies flocks, then in male-female pairs, and finally in the original flocks. Using samples taken every four days of the experiment, we characterized their uropygial gland microbiome through 16S rRNA gene sequencing and their preen oil volatile compounds via GC-MS.

Results

We predicted that if social environment was the primary driver of uropygial gland microbiome composition, and if microbiome composition in turn affected preen oil volatile profiles, then birds housed together would become more similar over time. Our results did not support this hypothesis, instead showing that sex and subspecies were stronger predictors of microbiome composition. We observed changes in volatile compounds after the birds had been housed in pairs, which disappeared after they were moved back into flocks, suggesting that hormonal changes related to breeding condition were the most important factor in these patterns.

Discussion

Although early life social environment of nestlings and long-term social relationships have been shown to be important in shaping uropygial gland microbial communities, our study suggests that shorter-term changes in social environment do not have a strong effect on uropygial microbiomes and the resulting preen oil volatile compounds.

Gut mutualists can persist in host populations despite low fidelity of vertical transmission

Humans harbour diverse microbial communities, and this interaction has fitness consequences for hosts and symbionts. Understanding the mechanisms that preserve host-symbiont association is an important step in studying co-evolution between humans and their mutualist microbial partners. This association is promoted by vertical transmission, which is known to be imperfect. It is unclear whether host-microbial associations can generally be maintained despite 'leaky' vertical transmission. Cultural practices of the host are expected to be important in bacterial transmission as they influence the host's interaction with other individuals and with the environment. There is a need to understand whether and how cultural practices affect host-microbial associations. Here, we develop a mathematical model to identify the conditions under which the mutualist can persist in a population where vertical transmission is imperfect. We show with this model that several factors compensate for imperfect vertical transmission, namely, a selective advantage to the host conferred by the mutualist, horizontal transmission of the mutualist through an environmental reservoir and transmission of a cultural practice that promotes microbial transmission. By making the host-microbe association more likely to persist in the face of leaky vertical transmission, these factors strengthen the association which in turn enables host-mutualist co-evolution.

Social complexity as a driving force of gut microbiota exchange among conspecific hosts in non-human primates

The emergent concept of the social microbiome implies a view of a highly connected biological world, in which microbial interchange across organisms may be influenced by social and ecological connections occurring at different levels of biological organization. We explore this idea reviewing evidence of whether increasing social complexity in primate societies is associated with both higher diversity and greater similarity in the composition of the gut microbiota. By proposing a series of predictions regarding such relationship, we evaluate the existence of a link between gut microbiota and primate social behavior. Overall, we find that enough empirical evidence already supports these predictions. Nonetheless, we conclude that studies with the necessary, sufficient, explicit, and available evidence are still scarce. Therefore, we reflect on the benefit of founding future analyses on the utility of social complexity as a theoretical framework.

Unveiling the egg microbiota of the loggerhead sea turtle Caretta caretta in nesting beaches of the Mediterranean Sea

Microbes have central roles in the development and health of animals, being the introduction of specific microbial species a potential conservation strategy to protect animals from emerging diseases. Thus, insight into the microbiota of the species and their habitats is essential. In this manuscript, we report for the first time the bacterial composition of all the components (eggshells of hatched and unhatched eggs, internal content of unhatched eggs, intestinal content of hatchling and pipping sea turtles, and sand) of three nesting beaches of Caretta caretta along the Italian coasts of the Mediterranean Sea. The analysis of 26 amplicon samples was carried out using next-generation sequencing analysis, targeting V3–V4 regions of the bacterial 16S rRNA gene. Samples featured mainly Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, whose percentages depended on the sample type. Our results showed that, although from different sampling sites, the internal content of the unhatched eggs, intestinal content of hatchling and pipping sea turtles share the microbiota, which was yet different from that of eggshells and sand of the same nesting beach. This study suggests the maternal and environmental influence alongside a protective role of eggshells in shaping the egg microbiota of Caretta caretta sea turtles.

Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation

Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.

Disentangling the Relative Roles of Vertical Transmission, Subsequent Colonizations, and Diet on Cockroach Microbiome Assembly

A multitude of factors affect the assemblies of complex microbial communities associated with animal hosts, with implications for community flexibility, resilience, and long-term stability; however, their relative effects have rarely been deduced. Here, we use a tractable lab model to quantify the relative and combined effects of parental transmission (egg case microbiome present/reduced), gut inocula (cockroach versus termite gut provisioned), and varying diets (matched or unmatched with gut inoculum source) on gut microbiota structure of hatchlings of the omnivorous cockroach Shelfordella lateralis using 16S rRNA gene (rDNA) amplicon sequencing. We show that the presence of a preexisting bacterial community via vertical transmission of microbes on egg cases reduces subsequent microbial invasion, suggesting priority effects that allow initial colonizers to take a strong hold and which stabilize the microbiome. However, subsequent inoculation sources more strongly affect ultimate community composition and their ecological networks, with distinct host-taxon-of-origin effects on which bacteria establish. While this is so, communities respond flexibly to specific diets in ways that consequently impact predicted community functions. In conclusion, our findings suggest that inoculations drive communities toward different stable states depending on colonization and extinction events, through ecological host-microbe relations and interactions with other gut bacteria, while diet in parallel shapes the functional capabilities of these microbiomes. These effects may lead to consistent microbial communities that maximize the extended phenotype that the microbiota provides the host, particularly if microbes spend most of their lives in host-associated environments.IMPORTANCE When host fitness is dependent on gut microbiota, microbial community flexibility and reproducibility enhance host fitness by allowing fine-tuned environmental tracking and sufficient stability for host traits to evolve. Our findings lend support to the importance of vertically transmitted early-life microbiota as stabilizers, through interactions with potential colonizers, which may contribute to ensuring that the microbiota aligns within host fitness-enhancing parameters. Subsequent colonizations are driven by microbial composition of the sources available, and we confirm that host-taxon-of-origin affects stable subsequent communities, while communities at the same time retain sufficient flexibility to shift in response to available diets. Microbiome structure is thus the result of the relative impact and combined effects of inocula and fluctuations driven by environment-specific microbial sources and digestive needs. These affect short-term community structure on an ecological time scale but could ultimately shape host species specificities in microbiomes across evolutionary time, if environmental conditions prevail.

Neotropical Melyroidea group cockroaches reveal various degrees of (eu)sociality

Eusociality in its various degrees represents an animal social system characterised by cooperative brood care, differentiation into castes and generational overlap. The fossil record indicates that eusociality is likely to have originated in hymenopterans and blattodeans during the Cretaceous. In this study, we present findings from surveys in Peruvian (Villa Carmen) and Ecuadorian (Rio Bigal, El Reventador) cloud forests revealing the first extant cockroach species living in complex, structured groups (n = 90-200 individuals, ˃ 20 adults). We observed and described behaviours that suggest the existence of cooperative care, nest guarding, nest chamber preparation within hardwood Casearia sp. (Salicaceae) and bamboo (Bambusoideae), multiple overlapping generations ('different stages of' instars), colony translocation, possibly a sole reproductive female (1.25 times larger white 'queen', but no potential 'king' observed), and morphologically diversified immature stages. In order to define the lineage where this type of sociality originated and occurs, the forms of Melyroidea magnifica Shelford, 1912, M. ecuadoriana sp. n., M. mimetica Shelford, 1912 and an undescribed species from Peru are also described in a separate section of this study. Blattoid morphological characteristics such as typical styli suggest categorisation within distinct Oulopterygidae (Rehn, 1951), outside Corydiidae Saussure 1864. Transitional advanced sociality or semisociality in related Aclavoidea socialis gen. et sp. n. is documented in a rotting stump (n = 80 individuals, few adults). Close phylogenetic relation between the genera, conserved morphology of numerous characters and their diverse feeding strategies generally lacking specialisation suggests a rather recent origin of a social way of life in this group. Eusociality in invertebrates and vertebrates can thus originate in various phylogenetical and ecological trajectories including predation, parasitism, care for herbs and the new one, documented through diet shift from detritivory to fungivory and algaevory. Interdisciplinary approaches reveal the low degree of knowledge of rainforest ecosystems, with fundamental groups remaining still systematically and also behaviourally undescribed.

Host-microbiome coevolution can promote cooperation in a rock-paper-scissors dynamics

Cooperation is a fundamental behaviour observed in all forms of life. The evolution of cooperation has been widely studied, but almost all theories focused on the cooperating individual and its genes. We suggest a different approach, taking into account the microbes carried by the interacting individuals. Accumulating evidence reveals that microbes can affect their host's well-being and behaviour, yet hosts can evolve mechanisms to resist the manipulations of their microbes. We thus propose that coevolution of microbes with their hosts may favour microbes that induce their host to cooperate. Using computational modelling, we show that microbe-induced cooperation can evolve and be maintained in a wide range of conditions, including when facing hosts' resistance to the microbial effect. We find that host-microbe coevolution leads the population to a rock-paper-scissors dynamics that enables maintenance of cooperation in a polymorphic state. Our results suggest a mechanism for the evolution and maintenance of cooperation that may be relevant to a wide variety of organisms, including cases that are difficult to explain by current theories. This study provides a new perspective on the coevolution of hosts and their microbiome, emphasizing the potential role of microbes in shaping their host's behaviour.

Leveraging non-human primates for exploring the social transmission of microbes

Host social interactions can provide multiple complex pathways for microbial transmission. Here, we suggest non-human primates as models to study the social transmission of commensal or mutualistic microbes due to their high sociality, wide range of group compositions and dominance structures, and diverse group interactions. Microbial sharing from social interactions can positively impact host health by promoting microbial diversity and influencing immunity. Microbes may also drive their own transmission by shaping host behavior, which could lead to fitness benefits for both microbes and hosts. Variation in patterns of social interactions at both the individual and group scale make non-human primates an ideal system to explore the relationship between social behavior, microbial sharing, and their impact on host health and evolution.

Small to modest impact of social group on the gut microbiome of wild Costa Rican capuchins in a seasonal forest

The horizontal transmission of pathogenic and beneficial microbes has implications for health and development of socially living animals. Social group is repeatedly implicated as an important predictor of gut microbiome structure among primates, with individuals in neighboring social groups exhibiting distinct microbiomes. Here we examine whether group membership is a predictor of gut microbiome structure and diversity across three groups of white-faced capuchins (Cebus capucinus imitator) inhabiting a seasonal Costa Rican forest. We collected 62 fecal samples from 18 adult females during four sampling bouts. Sampling bouts spanned the dry-to-wet-to-dry seasonal transitions. To investigate gut microbial composition, we sequenced the V4 region of the 16S rRNA gene. We used the DADA2 pipeline to assign amplicon sequence variants and the RDP database to classify taxa. Our findings are: 1) gut microbiomes of capuchins clustered by social group in the late dry season, but this pattern was less evident in other sampling bouts; 2) social group was a significant variable in a PERMANOVA test of beta diversity, but it accounted for less variation than season; 3) social group was not an important predictor of abundance for the ten most abundant microbial taxa in capuchins; 4) when examining log2-fold abundances of microbes between social groups, there were significant differences in some pairwise comparisons. While this is suggestive of group-wide differences, individual variation may have a strong impact and should be assessed in future studies. Overall, we found a minor impact of social group membership on the gut microbiota of wild white-faced capuchins. Future research including home range overlap and resource use, as well as fine-scale investigation of individual variation, will further elucidate patterns of socially structured microbes.

The Neuroendocrinology of the Microbiota-Gut-Brain Axis: A Behavioural Perspective

The human gut harbours trillions of symbiotic bacteria that play a key role in programming different aspects of host physiology in health and disease. These intestinal microbes are also key components of the gut-brain axis, the bidirectional communication pathway between the gut and the central nervous system (CNS). In addition, the CNS is closely interconnected with the endocrine system to regulate many physiological processes. An expanding body of evidence is supporting the notion that gut microbiota modifications and/or manipulations may also play a crucial role in the manifestation of specific behavioural responses regulated by neuroendocrine pathways. In this review, we will focus on how the intestinal microorganisms interact with elements of the host neuroendocrine system to modify behaviours relevant to stress, eating behaviour, sexual behaviour, social behaviour, cognition and addiction.

Social behaviour in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

Social interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviours and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both eusocial and solitary bee species within the behaviourally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between social forms; most halictid species appear to share similar gut bacterial communities. However, several strains of Sodalis, a genus described as a symbiont in a variety of insects but yet to be characterized in bees, differ in abundance between eusocial and solitary bees. Phylogenetic reconstructions based on whole-genome alignments indicate that Sodalis has independently colonized halictids at least three times. These strains appear to be mutually exclusive within individual bees, although they are not host-species-specific and no signatures of vertical transmission were observed, suggesting that Sodalis strains compete for access to hosts. The symbiosis between halictids and Sodalis therefore appears to be in its early stages.

Reciprocal Interactions Between Gut Microbiota and Host Social Behavior

Animals harbor an extensive, dynamic microbial ecosystem in their gut. Gut microbiota (GM) supposedly modulate various host functions including fecundity, metabolism, immunity, cognition and behavior. Starting by analyzing the concept of the holobiont as a unit of selection, we highlight recent findings suggesting an intimate link between GM and animal social behavior. We consider two reciprocal emerging themes: (i) that GM influence host social behavior; and (ii) that social behavior and social structure shape the composition of the GM across individuals. We propose that, throughout a long history of coevolution, GM may have become involved in the modulation of their host’s sociality to foster their own transmission, while in turn social organization may have fine-tuned the transmission of beneficial endosymbionts and prevented pathogen infection. We suggest that investigating these reciprocal interactions can advance our understanding of sociality, from healthy and impaired social cognition to the evolution of specific social behaviors and societal structure.

Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality

Vertebrate gut microbiota form a key component of immunity and a dynamic link between an individual and the ecosystem. Microbiota might play a role in social systems as well, because microbes are transmitted during social contact and can affect host behaviour. Combining methods from behavioural and molecular research, we describe the relationship between social dynamics and gut microbiota of a group-living cooperative species of primate, the red-bellied lemur (Eulemur rubriventer). Specifically, we ask whether patterns of social contact (group membership, group size, position in social network, individual sociality) are associated with patterns of gut microbial composition (diversity and similarity) between individuals and across time. Red-bellied lemurs were found to have gut microbiota with slight temporal fluctuations and strong social group-specific composition. Contrary to expectations, individual sociality was negatively associated with gut microbial diversity. However, position within the social network predicted gut microbial composition. These results emphasize the role of the social environment in determining the microbiota of adult animals. Since social transmission of gut microbiota has the potential to enhance immunity, microbiota might have played an escalating role in the evolution of sociality.

Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk

According to a traditional view, the specific diet in vertebrates is one of the key factors structuring the composition of the gut microbiota. In this interpretation, the microbiota assumes a subordinate position, where the larger host shapes, through evolution and its fitness, the taxonomical composition of the hosted microbiota. The present contribution shows how the evolution of herbivory, framed within the new concept of holobiont, the possibility of inter-kingdom crosstalk and its epigenetic effects, could pave the way to a completely reversed interpretation: instead of being passively shaped, the microbiota can mold and shape the general host body structure to increase its fitness. Central elements to consider in this context are the inter-kingdom crosstalk, the possibility of transporting RNAs through nanovesicles in feces from parents to offspring, and the activation of epigenetic processes passed on vertically from generation to generation. The new hypothesis is that the gut microbiota could play a great role in the macroevolutionary dynamics of herbivorous vertebrates, causing directly through host-microbiota dialog of epigenetic nature (i.e., methylation, histone acetylation, etc.), major changes in the organisms phenotype. The vertical exchange of the same microbial communities from parents to offspring, the interaction of these microbes with fairly uniform genotypes, and the socially restricted groups where these processes take place, could all explain the reasons why herbivory has appeared several time (and independently) during the evolution of vertebrates. The new interpretation could also represent a key factor in understanding the convergent evolution of analogous body structures in very distant lineages.

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat

Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (Varanus komodoensis) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon's environment are similar to the Komodo dragon's salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals' environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions.

Growing up in a Bubble: Using Germ-Free Animals to Assess the Influence of the Gut Microbiota on Brain and Behavior

There is a growing recognition of the importance of the commensal intestinal microbiota in the development and later function of the central nervous system. Research using germ-free mice (mice raised without any exposure to microorganisms) has provided some of the most persuasive evidence for a role of these bacteria in gut-brain signalling. Key findings show that the microbiota is necessary for normal stress responsivity, anxiety-like behaviors, sociability, and cognition. Furthermore, the microbiota maintains central nervous system homeostasis by regulating immune function and blood brain barrier integrity. Studies have also found that the gut microbiota influences neurotransmitter, synaptic, and neurotrophic signalling systems and neurogenesis. The principle advantage of the germ-free mouse model is in proof-of-principle studies and that a complete microbiota or defined consortiums of bacteria can be introduced at various developmental time points. However, a germ-free upbringing can induce permanent neurodevelopmental deficits that may deem the model unsuitable for specific scientific queries that do not involve early-life microbial deficiency. As such, alternatives and complementary strategies to the germ-free model are warranted and include antibiotic treatment to create microbiota-deficient animals at distinct time points across the lifespan. Increasing our understanding of the impact of the gut microbiota on brain and behavior has the potential to inform novel management strategies for stress-related gastrointestinal and neuropsychiatric disorders.

Comparative analysis of the fecal bacterial community of five harbor seals (Phoca vitulina)

The gut microbiota has many beneficial effects on host metabolism and health, and its composition is determined by numerous factors. It is also assumed that there was a co‐evolution of mammals and the bacteria inhabiting their gut. Current knowledge of the mammalian gut microbiota mainly derives from studies on humans and terrestrial animals, whereas those on marine mammals are sparse. However, they could provide additional information on influencing factors, such as the role of diet and co‐evolution with the host. In this study, we investigated and compared the bacterial diversity in the feces of five male harbor seals (Phoca vitulina). Because this small population included two half‐brother pairs, each sharing a common father, it allowed an evaluation of the impact of host relatedness or genetic similarity on the gut microbial community. Fresh feces obtained from the seals by an enema were analyzed by fluorescence in situ hybridization and amplicon sequencing of 16S rRNA genes. The results showed that the bacterial communities in the seals' feces mainly consisted of the phyla Firmicutes (19–43%), Bacteroidetes (22–36%), Fusobacteria (18–32%), and Proteobacteria (5–17%) . Twenty‐one bacterial members present in the fecal samples of the five seals contributed an average relative abundance of 93.7 + 8.7% of the total fecal microbial community. Contrary to all expectations based on previous studies a comparison of the fecal community between individual seals showed a higher similarity between unrelated than related individuals.

Ecological Succession in the Honey Bee Gut: Shift in Lactobacillus Strain Dominance During Early Adult Development

In many vertebrates, social interactions and nutrition can affect the colonization of gut symbionts across generations. In the highly social honey bee, it is unknown to what extent the hive environment and older worker individuals contribute to the generational transmission of core gut bacteria. We used high-throughput sequencing to investigate the effect of nest materials and social contact on the colonization and succession of core hindgut microbiota in workers. With only brief exposure to hive materials following natural eclosion, gut bacterial communities at 3 and 7 days contained phylotypes typically found in the guts of mature adults regardless of treatment. Continuous exposure to nest materials or direct social interactions with mature adults did not affect the diversity or abundance of gut bacterial communities at the scale examined. Similarly, a common pollen supplement fed by beekeepers during pollen dearth had no effect. A consideration of unique OTUs revealed extensive microbial succession independent of treatment. The dominant Lactobacillus strain at 3 days was largely replaced by a different strain at day 7, revealing the colonization signature of a pioneer species. Similar but less pronounced patterns were evident in less abundant OTU's, many of which may influence community succession via alteration of the gut environment. Our results indicate that the process of bacterial community colonization in the hindgut is resilient to changes in the nutritional, hive, and social environment. Greater taxonomic resolution is needed to accurately resolve questions of ecological succession and typical proportional variation within and between core members of the gut bacterial community.

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions

As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.

Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise

Herbivorous vertebrates rely on complex communities of mutualistic gut bacteria to facilitate the digestion of celluloses and hemicelluloses. Gut microbes are often convergent based on diet and gut morphology across a phylogenetically diverse group of mammals. However, little is known about microbial communities of herbivorous hindgut-fermenting reptiles. Here, we investigate how factors at the individual level might constrain the composition of gut microbes in an obligate herbivorous reptile. Using multiplexed 16S rRNA gene sequencing, we characterized the faecal microbial community of a population of gopher tortoises (Gopherus polyphemus) and examined how age, genetic diversity, spatial structure and kinship influence differences among individuals. We recovered phylotypes associated with known cellulolytic function, including candidate phylum Termite Group 3, suggesting their importance for gopher tortoise digestion. Although host genetic structure did not explain variation in microbial composition and community structure, we found that fine-scale spatial structure, inbreeding, degree of relatedness and possibly ontogeny shaped patterns of diversity in faecal microbiomes of gopher tortoises. Our findings corroborate widespread convergence of faecal-associated microbes based on gut morphology and diet and demonstrate the role of spatial and demographic structure in driving differentiation of gut microbiota in natural populations.

Collective unconscious: how gut microbes shape human behavior

The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.

Friends with social benefits: host-microbe interactions as a driver of brain evolution and development?

The tight association of the human body with trillions of colonizing microbes that we observe today is the result of a long evolutionary history. Only very recently have we started to understand how this symbiosis also affects brain function and behavior. In this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. In particular, we explore the integration of human brain development with evolution, symbiosis, and RNA biology, which together represent a “social triangle” that drives human social behavior and cognition. We argue that, in order to understand how inter-kingdom communication can affect brain adaptation and plasticity, it is inevitable to consider epigenetic mechanisms as important mediators of genome-microbiome interactions on an individual as well as a transgenerational time scale. Finally, we unite these interpretations with the hologenome theory of evolution. Taken together, we propose a tighter integration of neuroscience fields with host-associated microbiology by taking an evolutionary perspective.

Biochemical and Microbiological Evidence for Fermentative Digestion in Free‐Living Land Iguanas (Conolophus pallidus) and Marine Iguanas (Amblyrhynchus cristatus) on the Galápagos Archipelago

Herbivorous lizards are potentially capable of high digestive efficiency, but the presence of an indigenous microbial population has been implied from measurements of activity rather than directly studied. This study is the first to provide direct biochemical and microbiological evidence for fermentative digestion in free-living land iguanas (Conolophus pallidus) and marine iguanas (Amblyrhynchus cristatus) from the Galapagos archipelago. In marine iguanas, the stomach and large capacious colon contained ca. 32% and 60%, respectively, of the weight of total gut content. Total volatile fatty acid concentration was ca. 150 and 180 mM, respectively, for marine and land iguanas. Molar proportions of acetate, propionate, and butyrate (80.3%, 9.5%, and 3.5%) in land iguana fecal samples were similar to those for marine iguanas. Examination of fecal samples using confocal and transmission electron microscopy, as well as cultivable counts, revealed a dense and diverse population of bacteria, with spores prominent. Total culturable counts of anaerobes (2.22x10(8) g(-1) wet weight of fecal material) outnumbered aerobes on average by a factor of ca. 700. Combined, these results strongly support the contention that these unique herbivorous lizards are largely dependent on the presence and metabolic activities of a resident bacterial population in order to hydrolyze and ferment plant polymers that are indigestible to the host.