Body site-specific microbiota reflect sex and age-class among wild spotted hyenas

Microbial metabolites as engines of behavioral variation across animals

The microbiome, especially that present in the gut, has emerged as a key modulator of animal behavior. However, the extent of its influence across species and behavioral repertoires, as well as the underlying mechanisms, remains poorly understood. Increasing evidence suggests that microbial metabolites play an important role in driving behavioral variation. In this review, we synthesize findings from vertebrates to invertebrates, spanning both model and non-model organisms, to define key groups of microbial-derived metabolites involved in modulating seven distinct behaviors: nutrition, olfaction, circadian rhythms, reproduction, locomotion, aggression, and social interactions. We discuss how these microbial metabolites interact with host chemosensory systems, neurotransmitter signaling, and epigenetic modifications to shape behavior. Additionally, we highlight critical gaps in mechanistic understanding, including the need to map additional host receptors and signaling pathways, as well as the untapped potential of microbial biosynthetic gene clusters as sources for novel bioactive compounds. Advancing these areas will enhance understanding of the microbiome's role in behavioral modulation and open new avenues for microbiome-based interventions for behavioral disorders.

Social organization and physical environment shape the microbiome of harvester ants

All animals harbor microbiomes, which are obtained from the surrounding environment and are impacted by host behavior and life stage. To determine how two non-mutually exclusive drivers - physical environment and social organization - affect an organism's microbiome, we examined the bacterial communities within and around nests of harvester ants (Veromessor andrei). We collected soil and nest content samples from five different ant nests. We used 16S rRNA gene sequencing and calculated alpha and beta diversity to compare bacterial diversity and community composition across samples. To test the hypotheses that physical environment and/or social organization impact ant colonies' community of microbes we compared our samples across (i) sample types (ants, brood, seeds and reproductives (winged alates), and soil), (ii) soil inside and outside the nest, and (iii) soil from different chamber types. Interestingly, we found that both the environment and social organization impact the bacterial communities of the microbiome of V. andrei colonies. Soil from the five nests differed from one another in a way that mapped onto their geographical distance. Furthermore, soil from inside the nests resembled the surrounding soil, supporting the physical environment hypothesis. However, the bacterial communities associated with the contents within the nest chambers, i.e., ants, brood, seeds, and reproductives, differed from one another and from the surrounding soil, supporting the social organization hypotheses. This study highlights the importance of considering environmental and social factors in understanding microbiome dynamics.

Bats, Bacteria, and Bat Smell V.2.0: Repeatable Sex-Specific Differences in Scent Organ Microbiota

Reproducibility is a fundamental principle in science, ensuring reliable and valid findings. However, replication studies are scarce, particularly in ecology, due to the emphasis on novelty for publication. We explored the possibility of replicating original findings in the field of microbial and chemical ecology by conducting a conceptual replication of a previous study analysing the sex-specific differences in the microbial communities inhabiting the wing sacs, a scent organ with crucial functions in olfactory communication, of greater sac-winged bat (Saccopteryx bilineata). In the original study, the skin swabs from the antebrachial wing sacs of the males and wing sac rudiments of the females were analysed using culture-dependent methods to test sex-specific differences. The authors demonstrated that males have lower microbial richness and different microbial composition than females. We attempted to reproduce these findings using 16S rRNA sequencing, which offers improved accuracy in pinpointing microbial members than culture-dependent methods because of advanced statistical methods. Our study validated the original study's findings: Males had a lower microbial richness, and the community composition differed between the sexes. Furthermore, in the current study, males had an increased abundance of bacteria that might potentially be involved in odour production and degradation of malodorous substances and antimicrobial production. Our conceptual replication study corroborated that microbes can play a role in shaping their host's olfactory phenotype and consequently influence sexual selection. Furthermore, the current study emphasises the importance of replication efforts and hopefully encourages a culture that values replication studies in scientific practice.

The bacteria of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) are site-specific and distinct from freshwater environment

Bacteria play an essential role in the health of marine mammals, and the bacteria of marine mammals are widely concerned, but less is known about freshwater mammals. In this study, we investigated the bacteria of various body sites of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) and analyzed their association with freshwater environmental bacteria. The bacterial community and function of Yangtze finless porpoise showed apparent site-specificity. Various body sites have distinct differences in bacteria and have their dominant bacteria. Romboutsia, Plesiomonas, Actinobacillus, Candidatus Arthromitus dominated in the intestine (fecal and rectal samples). Fusobacterium, Streptococcus, and Acinetobacter dominated in the oral. The dominant genera in the blowhole include Suttonella, Psychrobacter, and two uncultured genera. Psychrobacter, Flavobacterium, and Acinetobacter were dominant in the skin. The alpha diversity of intestinal (fecal and rectal) bacteria was the lowest, while that of skin was the highest. The oral and skin bacteria of Yangtze finless porpoise significantly differed between the natural and semi-natural conditions, but no sex difference was observed. A clear boundary was found between the animal and the freshwater environmental bacteria. Even the skin bacteria, which are more affected by the environment, are significantly different from the environmental bacteria and harbor indigenous bacteria. Our results provide a comprehensive preliminary exploration of the bacteria of Yangtze finless porpoise and its association with bacteria in the freshwater environment.

The value of individual identification in studies of free-living hyenas and aardwolves

From population estimates to social evolution, much of our understanding of the family Hyaenidae is drawn from studies of known individuals. The extant species in this family (spotted hyenas, Crocuta crocuta, brown hyenas, Parahyaena brunnea, striped hyenas, Hyaena hyaena, and aardwolves, Proteles cristata) are behaviorally diverse, presenting an equally diverse set of logistical constraints on capturing and marking individuals. All these species are individually identifiable by their coat patterns, providing a useful alternative to man-made markings. Many studies have demonstrated the utility of this method in answering a wide range of research questions across all four species, with some employing a creative fusion of techniques. Despite its pervasiveness in basic research on hyenas and aardwolves, individual identification has rarely been applied to the conservation and management of these species. We argue that individual identification using naturally occurring markings in applied research could prove immensely helpful, as this could further improve accuracy of density estimates, reveal characteristics of suitable habitat, identify threats to population persistence, and help to identify individual problem animals.

Symbiotic microbiota and odor ensure mating in time for giant pandas

To achieve reproduction, male solitary mammals need to locate females using chemical communication with high levels of precision. In the case of giant pandas, the total estrus period of females was usually 15 days each year, however, successful mating activity is finished within 3 days from respective home range. The mating pattern of giant pandas, where multiple males compete for each female requires females employ efficient systems to communicate their estrus phases. To verifying whether the scent secretions of giant pandas changes by gender and estrus progression, the microbiota and compounds in 29 anogenital gland samples from 14 individuals during estrus were analyzed by 16S rRNA sequencing and GC-MS. We show that the microbiota communities covary by gender with 4 particular compounds of scent secretions. Among 597 genera, 34 were identified as biomarkers that could be used to distinguish between different estrus phases. By bacterial-compounds co-analysis, 3 fatty ester acids and squalene compounds covaried with the development of estrus in the bacterial communities of female giant pandas. This study helps clarify how a large, solitary mammal expresses accurate information to improve the likelihood of successful reproduction by changing the composition of microbiota and odor compounds of anogenital glands during estrus.

Hair Microbiome Diversity within and across Primate Species

Primate hair and skin are substrates upon which social interactions occur and are host-pathogen interfaces. While human hair and skin microbiomes display body site specificity and immunological significance, little is known about the nonhuman primate (NHP) hair microbiome. Here, we collected hair samples (n = 158) from 8 body sites across 12 NHP species housed at three zoological institutions in the United States to examine the following: (1) the diversity and composition of the primate hair microbiome and (2) the factors predicting primate hair microbiome diversity and composition. If both environmental and evolutionary factors shape the microbiome, then we expect significant differences in microbiome diversity across host body sites, sexes, institutions, and species. We found our samples contained high abundances of gut-, respiratory-, and environment-associated microbiota. In addition, multiple factors predicted microbiome diversity and composition, although host species identity outweighed sex, body site, and institution as the strongest predictor. Our results suggest that hair microbial communities are affected by both evolutionary and environmental factors and are relatively similar across nonhuman primate body sites, which differs from the human condition. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome. IMPORTANCE We created the most comprehensive primate hair and skin data set to date, including data from 12 nonhuman primate species sampled from 8 body regions each. We find that the nonhuman primate hair microbiome is distinct from the human hair and skin microbiomes in that it is relatively uniform-as opposed to distinct-across body regions and is most abundant in gut-, environment-, and respiratory-associated microbiota rather than human skin-associated microbiota. Furthermore, we found that the nonhuman primate hair microbiome varies with host species identity, host sex, host environment, and host body site, with host species identity being the strongest predictor. This result demonstrates that nonhuman primate hair microbiome diversity varies with both evolutionary and environmental factors and within and across primate species. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome.

Disentangling host-microbiota complexity through hologenomics

Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.

Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations

In recent years, emerging sequencing technologies and computational tools have driven a tidal wave of research on host-associated microbiomes, particularly the gut microbiome. These studies demonstrate numerous connections between the gut microbiome and vital host functions, primarily in humans, model organisms, and domestic animals. As the adaptive importance of the gut microbiome becomes clearer, interest in studying the gut microbiomes of wild populations has increased, in part due to the potential for discovering conservation applications. The study of wildlife gut microbiomes holds many new challenges and opportunities due to the complex genetic, spatial, and environmental structure of wild host populations, and the potential for these factors to interact with the microbiome. The emerging picture of adaptive coevolution in host-microbiome relationships highlights the importance of understanding microbiome variation in the context of host population genetics and landscape heterogeneity across a wide range of host populations. We propose a conceptual framework for understanding wildlife gut microbiomes in relation to landscape variables and host population genetics, including the potential of approaches derived from landscape genetics. We use this framework to review current research, synthesize important trends, highlight implications for conservation, and recommend future directions for research. Specifically, we focus on how spatial structure and environmental variation interact with host population genetics and microbiome variation in natural populations, and what we can learn from how these patterns of covariation differ depending on host ecological and evolutionary traits.

Measuring salivary cortisol in wild carnivores

Salivary hormone analyses provide a useful alternative to fecal and urinary hormone analyses in non-invasive studies of behavioral endocrinology. Here, we use saliva to assess cortisol levels in a wild population of spotted hyenas (Crocuta crocuta), a gregarious carnivore living in complex social groups. We first describe a novel, non-invasive method of collecting saliva from juvenile hyenas and validate a salivary cortisol assay for use in this species. We then analyze over 260 saliva samples collected from nearly 70 juveniles to investigate the relationships between cortisol and temporal and social variables in these animals. We obtain some evidence of a bimodal daily rhythm with salivary cortisol concentrations dropping around dawn and dusk, times at which cub activity levels are changing substantially. We also find that dominant littermates have lower cortisol than singleton juveniles, but that cortisol does not vary with age, sex, or maternal social rank. Finally, we examine how social behaviors such as aggression or play affect salivary cortisol concentrations. We find that inflicting aggression on others was associated with lower cortisol concentrations. We hope that the detailed description of our methods provides wildlife researchers with the tools to measure salivary cortisol in other wild carnivores.

The microbiome impacts host hybridization and speciation

Microbial symbiosis and speciation profoundly shape the composition of life's biodiversity. Despite the enormous contributions of these two fields to the foundations of modern biology, there is a vast and exciting frontier ahead for research, literature, and conferences to address the neglected prospects of merging their study. Here, we survey and synthesize exemplar cases of how endosymbionts and microbial communities affect animal hybridization and vice versa. We conclude that though the number of case studies remain nascent, the wide-ranging types of animals, microbes, and isolation barriers impacted by hybridization will likely prove general and a major new phase of study that includes the microbiome as part of the functional whole contributing to reproductive isolation. Though microorganisms were proposed to impact animal speciation a century ago, the weight of the evidence supporting this view has now reached a tipping point.

Noninvasively measured immune responses reflect current parasite infections in a wild carnivore and are linked to longevity

Host immune defenses are important components of host-parasite interactions that affect the outcome of infection and may have fitness consequences for hosts when increased allocation of resources to immune responses undermines other essential life processes. Research on host-parasite interactions in large free-ranging wild mammals is currently hampered by a lack of verified noninvasive assays. We successfully adapted existing assays to measure innate and adaptive immune responses produced by the gastrointestinal mucosa in spotted hyena (Crocuta crocuta) feces, including enzyme-linked immunosorbent assays (ELISAs), to quantify fecal immunoglobulins (total IgA, total IgG) and total fecal O-linked oligosaccharides (mucin). We investigated the effect of infection load by an energetically costly hookworm (Ancylostoma), parasite richness, host age, sex, year of sampling, and clan membership on immune responses and asked whether high investment in immune responses during early life affects longevity in individually known spotted hyenas in the Serengeti National Park, Tanzania. Fecal concentrations of IgA, IgG, and mucin increased with Ancylostoma egg load and were higher in juveniles than in adults. Females had higher mucin concentrations than males. Juvenile females had higher IgG concentrations than juvenile males, whereas adult females had lower IgG concentrations than adult males. High IgA concentrations during the first year of life were linked to reduced longevity after controlling for age at sampling and Ancylostoma egg load. Our study demonstrates that the use of noninvasive methods can increase knowledge on the complex relationship between gastrointestinal parasites and host local immune responses in wild large mammals and reveal fitness-relevant effects of these responses.

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.

Microbiome Analyses Demonstrate Specific Communities Within Five Shark Species

Profiles of symbiotic microbial communities (“microbiomes”) can provide insight into the natural history and ecology of their hosts. Using high throughput DNA sequencing of the 16S rRNA V4 region, microbiomes of five shark species in South Florida (nurse, lemon, sandbar, Caribbean reef, and tiger) have been characterized for the first time. The microbiomes show species specific microbiome composition, distinct from surrounding seawater. Shark anatomical location (gills, teeth, skin, cloaca) affected the diversity of microbiomes. An in-depth analysis of teeth communities revealed species specific microbial communities. For example, the genus Haemophilus, explained 7.0% of the differences of the teeth microbiomes of lemon and Caribbean reef sharks. Lemon shark teeth communities (n = 11) contained a high abundance of both Vibrio (10.8 ± 26.0%) and Corynebacterium (1.6 ± 5.1%), genera that can include human pathogenic taxa. The Vibrio (2.8 ± 6.34%) and Kordia (3.1 ± 6.0%) genera and Salmonella enterica (2.6 ± 6.4%) were the most abundant members of nurse shark teeth microbial communities. The Vibrio genus was highly represented in the sandbar shark (54.0 ± 46.0%) and tiger shark (5.8 ± 12.3%) teeth microbiomes. The prevalence of genera containing potential human pathogens could be informative in shark bite treatment protocols and future research to confirm or deny human pathogenicity. We conclude that South Florida sharks host species specific microbiomes that are distinct from their surrounding environment and vary due to differences in microbial community composition among shark species and diversity and composition among anatomical locations. Additionally, when considering the confounding effects of both species and location, microbial community diversity and composition varies.

Wild black bears harbor simple gut microbial communities with little difference between the jejunum and colon

The gut microbiome (GMB), comprising the commensal microbial communities located in the gastrointestinal tract, has co-evolved in mammals to perform countless micro-ecosystem services to facilitate physiological functions. Because of the complex inter-relationship between mammals and their gut microbes, the number of studies addressing the role of the GMB on mammalian health is almost exclusively limited to human studies and model organisms. Furthermore, much of our knowledge of wildlife-GMB relationships is based on studies of colonic GMB communities derived from the feces of captive specimens, leaving our understanding of the GMB in wildlife limited. To better understand wildlife-GMB relationships, we engaged hunters as citizen scientists to collect biological samples from legally harvested black bears (Ursus americanus) and used 16S rRNA gene amplicon sequencing to characterize wild black bear GMB communities in the colon and jejunum, two functionally distinct regions of the gastrointestinal tract. We determined that the jejunum and colon of black bears do not harbor significantly different GMB communities: both gastrointestinal sites were dominated by Firmicutes and Proteobacteria. However, a number of bacteria were differentially enriched in each site, with the colon harboring twice as many enriched taxa, primarily from closely related lineages.