Assessing the drivers of gut microbiome composition in wild redfronted lemurs via longitudinal metacommunity analysis

The gut microbiome of Madagascar's lemurs from forest fragments in the central highlands

The gut microbiome is now understood to play essential roles in host nutrition and health and has become a dominant research focus in primatology. Over the past decade, research has clarified the evolutionary traits that govern gut microbiome structure across species and the ecological traits that further influence consortia within them. Nevertheless, we stand to gain resolution by sampling hosts in understudied habitats. We focus on the lemurs of Madagascar's central highlands. Madagascar's highlands have a deep history as heterogeneous grassland-forest mosaics, but due to significant anthropogenic modification, have long been overlooked as lemur habitat. We collected fecal samples from Verreaux's sifakas (Propithecus verreauxi), common brown lemurs (Eulemur fulvus), and Goodman's mouse lemurs (Microcebus lehilahytsara) inhabiting two protected areas in the highlands and used amplicon sequencing to determine gut microbiome diversity and membership. As expected, the lemurs harbored distinct gut consortia tuned to their feeding strategies. Mouse lemurs harbored abundant Bifidobacterium and Alloprevotella that are implicated in gum metabolism, sifakas harbored abundant Lachnospiraceae that are implicated in leaf-fiber metabolism, and brown lemurs harbored diverse consortia with abundant WCBH1-41 that could be associated with frugivory in harsh seasons and habitats. Within brown lemurs, a suite of bacteria varied between seed-packed and leaf-packed feces, a proxy for dietary intakes, collected from the same group over days. Our results underscore the evolutionary and ecological factors that govern primate gut microbiomes. More broadly, we showcase the forests of Madagascar's central highlands as rich habitat for future research of lemur ecology and evolution.

The costs and benefits of a dynamic host microbiome

All species host a rich community of microbes. This microbiome is dynamic, and displays seasonal, daily, and even hourly changes, but also needs to be resilient to fulfill important roles for the host. In evolutionary ecology, the focus of microbiome dynamism has been on how it can facilitate host adaptation to novel environments. However, an hitherto largely overlooked issue is that the host needs to keep its microbiome in check, which is costly and leads to trade-offs with investing in other fitness-related traits. Investigating these trade-offs in natural vertebrate systems by collecting longitudinal data will lead to deeper insight into the evolutionary mechanisms that shape host-microbiome interactions.

Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats in a novel sample type

The gut microbiome is a plastic phenotype; gut microbial composition is highly variable across an individual host's lifetime and between host social groups, and this variation has consequences for host health. However, we do not yet fully understand how longitudinal microbial dynamics and their social drivers may be influenced by ecological stressors, such as habitat degradation. Answering these questions is difficult in most wild animal systems, as it requires long-term collections of matched host, microbiome, and environmental trait data. To test if temporal and social influences on microbiome composition differ by the history of human disturbance, we leveraged banked, desiccated fecal samples collected over 5 months in 2004 from two ecologically distinct populations of wild, red-bellied lemurs (Eulemur rubriventer) that are part of a long-term study system. We found that social group explained more variation in microbiome composition than host population membership did, and that temporal variation in common microbial taxa was similar between populations, despite differences in history of human disturbance. Furthermore, we found that social group membership and collection month were both more important than individual lemur identity. Taken together, our results suggest that synchronized environments use can lead to synchronized microbial dynamics over time, even between habitats of varying quality, and that desiccated samples could become a viable approach for studying primate gut microbiota. Our work opens the door for other projects to utilize historic biological sample data sets to answer novel temporal microbiome questions in an ecological context.

Seasonal variation in aggression and physiological stress in wild female and male redfronted lemurs (Eulemur rufifrons)

Intraspecific competition with fellow group members represents an unavoidable cost of group living. However, the causes of competition can vary among group members, and ecological and reproductive challenges faced by individuals throughout the year can trigger physical conflicts and or physiological responses. To date, few studies in mammals have described both physiological and behavioral responses to competition simultaneously across the year in both males and females. However, such an approach may shed light on ultimate drivers of sex-specific competitive strategies. In this six-year study on multiple groups of wild redfronted lemurs (Eulemur rufifrons), a primate species from Madagascar, we intended to identify the relative importance of feeding vs. reproductive competition for both sexes. We combined data on fecal glucocorticoid metabolite (FGCM) levels, a proxy for the physiological stress response, with behavioral observations on agonistic interactions during ecologically and socially challenging phases across the year. We found that while FGCM levels increased in both sexes with decreasing fruit consumption, this increase was not accompanied by concomitant changes in agonistic behavior. Female aggression and FGCM levels instead peaked during the birth season, while for males, aggression remained fairly constant across the year. Our results suggest that redfronted lemurs have mechanisms to avoid direct competition through aggression at times when individuals may need to conserve energy.

Establishment and Validation of Fecal Secretory Immunoglobulin A Measurement for Intestinal Mucosal Health Assessment in Wild Lemurs

The measurement of biomarkers in blood and excreta can enable immune status assessment and provide prognostic information on individual health outcomes. In this respect, the fecal measurement of secretory immunoglobulin A (sIgA), the primary mammalian antibody for mucosal defense, has recently received increased interest in a few anthropoid primates, but a fecal sIgA assay for use in strepsirrhine primates has not yet been reported. Here, we develop and analytically validate a cost-effective in-house sandwich enzyme immunoassay for the extraction and measurement of sIgA in feces of redfronted lemurs (Eulemur rufifrons). We also tested a simple method for sIgA extraction that can be used under remote field conditions and undertook experiments to assess the robustness of sIgA concentrations to variation in processing and storage conditions of fecal extracts. Our analytical validation revealed that the assay recognizes immunoreactive sIgA in redfronted lemur feces, that sIgA can be measured accurately with no potential interference from the fecal matrix, and that assay reagents and performance are highly stable over time. The field-friendly extraction procedure produced sIgA results strongly correlated with those generated by a standard laboratory extraction method. Short-term storage at room temperature resulted in a slight decline in sIgA concentrations, whereas freezing extracts at -20°C kept sIgA levels stable for at least 3 months. Longer-term storage of >5 months, however, led to a significant decline of sIgA concentrations. Multiple freeze-thaw cycles did not affect sIgA levels. This study, therefore, provides the basis for measuring fecal sIgA in lemurs and possibly other strepsirrhines. When samples are processed properly and stored frozen, and when sIgA analysis can be performed within 3 months upon sample collection, fecal sIgA measurements can become a valuable tool for monitoring aspects of immunity and health in both zoo-housed and wild-living lemurs.

Differences in Gut Microbes Across Age and Sex Linked to Metabolism and Microbial Stability in a Hibernating Mammal

The gut microbiome has a well-documented relationship with host fitness, physiology, and behavior. However, most of what is known comes from captive animals where diets and environments are more homogeneous or controlled. Studies in wild populations that experience dynamic environments and have natural life history variation are less common but are key to understanding the drivers of variation in the gut microbiome. Here we examine a wild population of yellow-bellied marmots (Marmota flaviventer), an obligate winter hibernator, to quantify multivariate associations between host-associated factors (e.g., age, sex, environmental harshness, and social behavior) and gut microbial composition. Across 5 years and 143 individuals, we found that males had a higher relative abundance of microbes associated with mass gain and cellulose digestion, which suggests a metabolic investment in mass gain (such as phylum Firmicutes and family Lachnospiraceae). By contrast, females had higher relative abundances of microbes associated with inflammation and metabolism (from microbial groups such as Tenericutes and Ruminococcus), possibly reflecting the importance of lactation and offspring investment. Post hoc analyses of lactating females showed a negative relationship with the abundance of microbes associated with mass gain but a positive relationship with microbes associated with metabolic energy, suggesting a trade-off between investment in pups and maternal mass gain. Older animals also had reduced Proteobacteria relative abundance, a phylum associated with reduced inflammation. Results demonstrate that sex and age-based traits, not sociality or environmental harshness, are associated with microbe-mediated metabolism and inflammation in a wild, hibernating mammal.

Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases

Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.

Host-gut microbiota interactions during pregnancy

Mammalian pregnancy is characterized by a well-known suite of physiological changes that support fetal growth and development, thereby positively affecting both maternal and offspring fitness. However, mothers also experience trade-offs between current and future maternal reproductive success, and maternal responses to these trade-offs can result in mother-offspring fitness conflicts. Knowledge of the mechanisms through which these trade-offs operate, as well as the contexts in which they operate, is critical for understanding the evolution of reproduction. Historically, hormonal changes during pregnancy have been thought to play a pivotal role in these conflicts since they directly and indirectly influence maternal metabolism, immunity, fetal growth and other aspects of offspring development. However, recent research suggests that gut microbiota may also play an important role. Here, we create a foundation for exploring this role by constructing a mechanistic model linking changes in maternal hormones, immunity and metabolism during pregnancy to changes in the gut microbiota. We posit that marked changes in hormones alter maternal gut microbiome composition and function both directly and indirectly via impacts on the immune system. The gut microbiota then feeds back to influence maternal immunity and metabolism. We posit that these dynamics are likely to be involved in mediating maternal and offspring fitness as well as trade-offs in different aspects of maternal and offspring health and fitness during pregnancy. We also predict that the interactions we describe are likely to vary across populations in response to maternal environments. Moving forward, empirical studies that combine microbial functional data and maternal physiological data with health and fitness outcomes for both mothers and infants will allow us to test the evolutionary and fitness implications of the gestational microbiota, enriching our understanding of the ecology and evolution of reproductive physiology.

Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations

Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.