Cloacal bacterial communities of tree swallows (Tachycineta bicolor): Similarity within a population, but not between pair-bonded social partners

Sexual transmission may drive pair similarity of the cloacal microbiome in a polyandrous species

All animals host a microbial community within and on their reproductive organs, known as the reproductive microbiome. In free-living birds, studies on the sexual transmission of bacteria have typically focused on a few pathogens instead of the bacterial community as a whole, despite a potential link to reproductive function. Theory predicts higher sexual transmission of the reproductive microbiome in females via the males' ejaculates and higher rates of transmission in promiscuous systems. We studied the cloacal microbiome of breeding individuals of a socially polyandrous, sex-role-reversed shorebird, the red phalarope (Phalaropus fulicarius). We expected (i) higher microbial diversity in females compared to males; (ii) low compositional differentiation between sexes; (iii) lower variation in composition between individuals (i.e. microbiome dispersion) in females than in males; (iv) convergence in composition as the breeding season progresses as a consequence of sexual transmission and/or shared habitat use; and (v) higher similarity in microbial composition between social pair members than between two random opposite-sex individuals. We found no or small between-sex differences in cloacal microbiome diversity/richness and composition. Dispersion of predicted functional pathways was lower in females than in males. As predicted, microbiome dispersion decreased with sampling date relative to clutch initiation of the social pair. Microbiome composition was significantly more similar among social pair members than among two random opposite-sex individuals. Pair membership explained 21.5% of the variation in taxonomic composition and 10.1% of functional profiles, whereas temporal and sex effects explained only 0.6%-1.6%. Consistent with evidence of functional convergence of reproductive microbiomes within pairs, some select taxa and predicted functional pathways were less variable between social pair members than between random opposite-sex individuals. As predicted if sexual transmission of the reproductive microbiome is high, sex differences in microbiome composition were weak in a socially polyandrous system with frequent copulations. Moreover, high within-pair similarity in microbiome composition, particularly for a few taxa spanning the spectrum of the beneficial-pathogenic axis, demonstrates the link between mating behaviour and the reproductive microbiome. Our study is consistent with the hypothesis that sexual transmission plays an important role in driving reproductive microbiome ecology and evolution.

Advances in the study of microbiota in reproductive biology: A short review of recent research, following Leclaire et al. (2022)

Research on microbiota dynamics in humans (Gilbert et al., 2018), model organisms (Douglas, 2019), and free-ranging, wild animals (Grond et al., 2018) has taken off in the past decades, and even in nonmodel organisms, research has already shifted from initial characterization studies to those examining associations with behaviour and fitness (Bodawatta et al., 2022; Corl et al., 2020; Risely et al., 2018; Turjeman et al., 2020). The microbiota is known to change through pregnancy and parturition (Koren et al., 2012), and there is also evidence in humans that infertility may be associated with microbiota composition (Silva & Giacobini, 2019), but how the microbiota is related to reproductive fitness in free-ranging species is largely understudied or primarily focused on pathogen transmission (sexually transmitted infection) (Lombardo, 1998; Sheldon, 1993). In a From the Cover article in this issue of Molecular Ecology, Leclaire et al. (2022) begin to tease apart the relationship between the microbiota and reproductive fitness using the black-legged kittiwake (Rissa tridactyla) as their study species. Following characterization of the microbiota in multiple body sites of breeders and nonbreeders, they discovered that breeding and nonbreeding females had distinct microbiota, that higher performing female breeders had lower abundances of potentially pathogenic taxa, and that feathers of these birds were characterized by reduced microbiota diversity compared to low-performance breeders. Leclaire and her colleagues provide some of the first evidence of body-wide differences in microbiota composition in relation to breeding status. Their research further supports the relationship between the microbiota and host fitness, and additional studies focusing on this topic can continue to unravel intricacies in host-microbiota-reproductive strategy evolution (Comizzoli et al., 2021; Rowe et al., 2020). Here, I review the results of Leclaire et al. (2022) and provide a wider context for their research by reviewing other studies in the field, focusing on avian species.

The cloacal microbiome of a cavity-nesting raptor, the lesser kestrel (Falco naumanni)

Background

Microbial communities are found on any part of animal bodies exposed to the environment, and are particularly prominent in the gut, where they play such a major role in the host metabolism and physiology to be considered a "second genome". These communities, collectively known as "microbiome", are well studied in humans and model species, while studies on wild animals have lagged behind. This is unfortunate, as different studies suggested the central role of the gut microbiome in shaping the evolutionary trajectories of species and their population dynamics. Among bird species, only few descriptions of raptor gut microbiomes are available, and mainly carried out on captive individuals.

Objectives

In this study, we aimed at improving the knowledge of raptor microbiomes by providing the first description of the gut microbiome of the lesser kestrel (Falco naumanni), a cavity-nesting raptor.

Results

The gut microbiome of the lesser kestrel was dominated by Actinobacteria (83.9%), Proteobacteria (8.6%) and Firmicutes (4.3%). We detected no differences in microbiome composition between males and females. Furthermore, the general composition of the microbiome appears similar to that of phylogenetically distant cavity-nesting species.

Conclusions

Our results broaden the knowledge of raptor gut microbial communities and let us hypothesize that the distinct nest environment in terms of microclimate and presence of organic material from previous breeding attempts, to which cavity-nesting species that reuse the nest are exposed, might be an important driver shaping microbiomes.

Antibiotic perturbation of gut bacteria does not significantly alter host responses to ocular disease in a songbird species

Bacterial communities in and on wild hosts are increasingly appreciated for their importance in host health. Through both direct and indirect interactions, bacteria lining vertebrate gut mucosa provide hosts protection against infectious pathogens, sometimes even in distal body regions through immune regulation. In house finches (Haemorhous mexicanus), the bacterial pathogen Mycoplasma gallisepticum (MG) causes conjunctivitis, with ocular inflammation mediated by pro- and anti-inflammatory cytokines and infection triggering MG-specific antibodies. Here, we tested the role of gut bacteria in host responses to MG by using oral antibiotics to perturb bacteria in the gut of captive house finches prior to experimental inoculation with MG. We found no clear support for an impact of gut bacterial disruption on conjunctival pathology, MG load, or plasma antibody levels. However, there was a non-significant trend for birds with intact gut communities to have greater conjunctival pathology, suggesting a possible impact of gut bacteria on pro-inflammatory cytokine stimulation. Using 16S bacterial rRNA amplicon sequencing, we found dramatic differences in cloacal bacterial community composition between captive, wild-caught house finches in our experiment and free-living finches from the same population, with lower bacterial richness and core communities composed of fewer genera in captive finches. We hypothesize that captivity may have affected the strength of results in this experiment, necessitating further study with this consideration. The abundance of anthropogenic impacts on wildlife and their bacterial communities, alongside the emergence and spread of infectious diseases, highlights the importance of studies addressing the role of commensal bacteria in health and disease, and the consequences of gut bacterial shifts on wild hosts.

Experimental test of microbiome protection across pathogen doses reveals importance of resident microbiome composition

The commensal microbes inhabiting a host tissue can interact with invading pathogens and host physiology in ways that alter pathogen growth and disease manifestation. Prior work in house finches (Haemorhous mexicanus) found that resident ocular microbiomes were protective against conjunctival infection and disease caused by a relatively high dose of Mycoplasma gallisepticum. Here, we used wild-caught house finches to experimentally examine whether protective effects of the resident ocular microbiome vary with the dose of invading pathogen. We hypothesized that commensal protection would be strongest at low M. gallisepticum inoculation doses because the resident microbiome would be less disrupted by invading pathogen. Our five M. gallisepticum dose treatments were fully factorial with an antibiotic treatment to perturb resident microbes just prior to M. gallisepticum inoculation. Unexpectedly, we found no indication of protective effects of the resident microbiome at any pathogen inoculation dose, which was inconsistent with the prior work. The ocular bacterial communities at the beginning of our experiment differed significantly from those previously reported in local wild-caught house finches, likely causing this discrepancy. These variable results underscore that microbiome-based protection in natural systems can be context dependent, and natural variation in community composition may alter the function of resident microbiomes in free-living animals.

Avian gut microbiomes taking flight

Birds harbor complex gut bacterial communities that may sustain their ecologies and facilitate their biological roles, distribution, and diversity. Research on gut microbiomes in wild birds is surging and it is clear that they are diverse and important - but strongly influenced by a series of environmental factors. To continue expanding our understanding of how the internal ecosystems of birds work in their natural settings, we believe the most pressing needs involve studies on the functional and evolutionary aspects of these symbioses. Here we summarize the state of the field and provide a roadmap for future studies on aspects that are pivotal to understanding the biology of avian gut microbiomes, emphasizing prospects for integrating gut microbiome work in avian conservation and host health monitoring.

Assessing age, breeding stage, and mating activity as drivers of variation in the reproductive microbiome of female tree swallows

Sexually transmitted microbes are hypothesized to influence the evolution of reproductive strategies. Though frequently discussed in this context, our understanding of the reproductive microbiome is quite nascent. Indeed, testing this hypothesis first requires establishing a baseline understanding of the temporal dynamics of the reproductive microbiome and of how individual variation in reproductive behavior and age influence the assembly and maintenance of the reproductive microbiome as a whole. Here, we ask how mating activity, breeding stage, and age influence the reproductive microbiome. We use observational and experimental approaches to explain variation in the cloacal microbiome of free-living, female tree swallows (Tachycineta bicolor). Using microsatellite-based parentage analyses, we determined the number of sires per brood (a proxy for female mating activity). We experimentally increased female sexual activity by administering exogenous 17ß-estradiol. Lastly, we used bacterial 16S rRNA amplicon sequencing to characterize the cloacal microbiome. Neither the number of sires per brood nor the increased sexual activity of females significantly influenced female cloacal microbiome richness or community structure. Female age, however, was positively correlated with cloacal microbiome richness and influenced overall community structure. A hypothesis to explain these patterns is that the effect of sexual activity and the number of mates on variation in the cloacal microbiome manifests over an individual's lifetime. Additionally, we found that cloacal microbiome alpha diversity (Shannon Index, Faith's phylogenetic distance) decreased and community structure shifted between breeding stages. This is one of few studies to document within-individual changes and age-related differences in the cloacal microbiome across successive breeding stages. More broadly, our results contribute to our understanding of the role that host life history and behavior play in shaping the cloacal microbiomes of wild birds.

The call of the wild: using non-model systems to investigate microbiome-behaviour relationships

On and within most sites across an animal's body live complex communities of microorganisms. These microorganisms perform a variety of important functions for their hosts, including communicating with the brain, immune system and endocrine axes to mediate physiological processes and affect individual behaviour. Microbiome research has primarily focused on the functions of the microbiome within the gastrointestinal tract (gut microbiome) using biomedically relevant laboratory species (i.e. model organisms). These studies have identified important connections between the gut microbiome and host immune, neuroendocrine and nervous systems, as well as how these connections, in turn, influence host behaviour and health. Recently, the field has expanded beyond traditional model systems as it has become apparent that the microbiome can drive differences in behaviour and diet, play a fundamental role in host fitness and influence community-scale dynamics in wild populations. In this Review, we highlight the value of conducting hypothesis-driven research in non-model organisms and the benefits of a comparative approach that assesses patterns across different species or taxa. Using social behaviour as an intellectual framework, we review the bidirectional relationship between the gut microbiome and host behaviour, and identify understudied mechanisms by which these effects may be mediated.