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Baboons inform on human gut microbiota Commensal bacteria are found throughout an organism, but it is not known whether associations between gut bacteria and their host are heritable. Grieneisen et al. examined changes in the microbiomes of 585 wild baboons from fecal samples collected over 14 years (see the Perspective by Cortes-Ortiz and Amato). Almost all microbiome traits tested demonstrated some level of statistically significant heritability. Most heritability values were low but varied over time correlating with the age of the host. Baboons live in an environment similar to that postulated for early humans and have a microbiome similar to that of humans. Thus, this heritability of the microbiome may reflect similar genetic determinants in humans, for which similar datasets are not available. Science , aba5483, this issue p. 181 ; see also abj5287, p. 159

The aerial portion of plants (phyllosphere) harbors complex and diverse microbial communities that have been shown to influence host growth and fitness, tolerance to environmental stressors, diseas...

Human gut microbial dynamics are highly individualized, making it challenging to link microbiota to health and to design universal microbiome therapies. This individuality is typically attributed to variation in host genetics, diets, environments and medications but it could also emerge from fundamental ecological forces that shape microbiota more generally. Here, we leverage extensive gut microbial time series from wild baboons-hosts who experience little interindividual dietary and environmental heterogeneity-to test whether gut microbial dynamics are synchronized across hosts or largely idiosyncratic. Despite their shared lifestyles, baboon microbiota were only weakly synchronized. The strongest synchrony occurred among baboons living in the same social group, probably because group members range over the same habitat and simultaneously encounter the same sources of food and water. However, this synchrony was modest compared to each host's personalized dynamics. In support, host-specific factors, especially host identity, explained, on average, more than three times the deviance in longitudinal dynamics compared to factors shared with social group members and ten times the deviance of factors shared across the host population. These results contribute to mounting evidence that highly idiosyncratic gut microbiomes are not an artefact of modern human environments and that synchronizing forces in the gut microbiome (for example, shared environments, diets and microbial dispersal) are not strong enough to overwhelm key drivers of microbiome personalization, such as host genetics, priority effects, horizontal gene transfer and functional redundancy.

Humans are inextricably linked to each other and our natural world, and microorganisms lie at the nexus of those interactions. Microorganisms form genetically flexible, taxonomically diverse, and biochemically rich communities, i.e., microbiomes that are integral to the health and development of macroorganisms, societies, and ecosystems. Yet engagement with beneficial microbiomes is dictated by access to public resources, such as nutritious food, clean water and air, safe shelter, social interactions, and effective medicine. In this way, microbiomes have sociopolitical contexts that must be considered. The Microbes and Social Equity (MSE) Working Group connects microbiology with social equity research, education, policy, and practice to understand the interplay of microorganisms, individuals, societies, and ecosystems. Here, we outline opportunities for integrating microbiology and social equity work through broadening education and training; diversifying research topics, methods, and perspectives; and advocating for evidence-based public policy that supports sustainable, equitable, and microbial wealth for all.

SummaryA key aspect of microbiome research is analysis of longitudinal dynamics using time series data. A method to visualize both the proportional and absolute change in the abundance of multiple taxa across multiple subjects over time is needed. We developed BiomeHorizon, an open-source R package that visualizes longitudinal compositional microbiome data using horizon plots.Availability and ImplementationBiomeHorizon is available at https://github.com/blekhmanlab/biomehorizon/ and released under the MIT license. A guide with step-by-step instructions for using the package is provided at https://blekhmanlab.github.io/biomehorizon/. The guide also provides code to reproduce all plots in this manuscript.Contactlgrienei@umn.edu, blekhman@umn.edu, iafink@uchicago.eduSupplementary informationNone

Across group-living animals, linear dominance hierarchies lead to disparities in access to resources, health outcomes, and reproductive performance. Studies of how dominance rank affects these outcomes typically employ one of several dominance rank metrics without examining the assumptions each metric makes about its underlying competitive processes. Here we compare the ability of two dominance rank metrics—ordinal rank and proportional or ‘standardized’ rank—to predict 20 distinct traits in a well-studied wild baboon population in Amboseli, Kenya. We propose that ordinal rank best predicts outcomes when competition is density-dependent, while proportional rank best predicts outcomes when competition is density-independent. We found that for 75% (15/20) of the traits, one of the two rank metrics performed better than the other. Strikingly, all male traits were better predicted by ordinal than by proportional rank, while female traits were evenly split between being better predicted by proportional or ordinal rank. Hence, male and female traits are shaped by different competitive regimes: males’ competitive environments are largely driven by density-dependent resource access (e.g., access to estrus females), while females’ competitive environments are shaped by both density-independent resource access (e.g. distributed food resources) and density-dependent resource access. However, traits related to competition for social and mating partners are an exception to this sex-biased pattern: these traits were better predicted by ordinal rank than by proportional rank for both sexes. We argue that this method of comparing how different rank metrics predict traits of interest can be used as a way to distinguish between different competitive processes operating in animal societies.

Across group-living animals, linear dominance hierarchies lead to disparities in access to resources, health outcomes and reproductive performance. Studies of how dominance rank predicts these traits typically employ one of several dominance rank metrics without examining the assumptions each metric makes about its underlying competitive processes. Here, we compare the ability of two dominance rank metrics—simple ordinal rank and proportional or ‘standardized’ rank—to predict 20 traits in a wild baboon population in Amboseli, Kenya. We propose that simple ordinal rank best predicts traits when competition is density-dependent, whereas proportional rank best predicts traits when competition is density-independent. We found that for 75% of traits (15/20), one rank metric performed better than the other. Strikingly, all male traits were best predicted by simple ordinal rank, whereas female traits were evenly split between proportional and simple ordinal rank. Hence, male and female traits are shaped by different competitive processes: males are largely driven by density-dependent resource access (e.g. access to oestrous females), whereas females are shaped by both density-independent (e.g. distributed food resources) and density-dependent resource access. This method of comparing how different rank metrics predict traits can be used to distinguish between different competitive processes operating in animal societies.

Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed “easy to install,” and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software., Developing new software tools for analysis of large-scale biological data involves numerous unique challenges; this Perspective article surveys more than 36,000 software resources, concluding that a rigorous standardized approach is needed to ensure the installability and archival stability of software tools prior to their publication.

Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviours, environments, genetics and geographical distance. However, which factors are most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota) is detectable in admixed, closely related primates. We found little evidence of genetic effects: none of host genetic ancestry, host genetic relatedness nor genetic distance between host populations were strong predictors of baboon gut microbiota. Instead, gut microbiota were best explained by the baboons' environments, especially the soil's geologic history and exchangeable sodium. Indeed, soil effects were 15 times stronger than those of host–population F ST, perhaps because soil predicts which foods are present, or because baboons are terrestrial and consume soil microbes incidentally with their food. Our results support an emerging picture in which environmental variation is the dominant predictor of host-associated microbiomes. We are the first to show that such effects overshadow host species identity among members of the same primate genus.

To date, most insights into the processes shaping vertebrate gut microbiomes have emerged from studies with cross-sectional designs. While this approach has been valuable, emerging time series analyses on vertebrate gut microbiomes show that gut microbial composition can change rapidly from one day to the next, with consequences for host physical functioning, health, and fitness. Hence, the next frontier of microbiome research will require longitudinal perspectives. Here we argue that primatologists, with their traditional focus on tracking the lives of individual animals and familiarity with longitudinal fecal sampling, are well positioned to conduct research at the forefront of gut microbiome dynamics. We begin by reviewing some of the most important ecological processes governing microbiome change over time, and briefly summarizing statistical challenges and approaches to microbiome time series analysis. We then introduce five questions of general interest to microbiome science where we think field-based primate studies are especially well-positioned to fill major gaps: (1) Do early life events shape gut microbiome composition in adulthood? (2) Do shifting social landscapes cause gut microbial change? (3) Are gut microbiome phenotypes heritable across variable environments? (4) Does the gut microbiome show signs of host aging? And (5) do gut microbiome composition and dynamics predict host health and fitness? For all of these questions, we high-light areas where primatologists are uniquely positioned to make substantial contributions. We review preliminary evidence, discuss possible study designs, and suggest future directions.

Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through URLs published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed “easy to install,” and 28% of the tools failed to be installed at all due to problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software.

Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue ‘The role of the microbiome in host evolution’.

The microbes of the human intestinal tract play a profound role in our health. The complex interactions between our gut microbial communities and the external environment, and the resulting functional consequences, can be difficult to disentangle., The microbes of the human intestinal tract play a profound role in our health. The complex interactions between our gut microbial communities and the external environment, and the resulting functional consequences, can be difficult to disentangle. To address this problem, McDonald et al. (mSystems 3:e00031-18, 2018, https://doi.org/10.1128/mSystems.00031-18) present the first set of results from the American Gut Project, a citizen science-based data set currently comprised of over 10,000 gut microbiome samples and associated life history data. By combining this extensive data set with other published studies, the authors uncover novel relationships between gut microbiome structure and function. For example, they found that dietary plant diversity and recent antibiotic use predict both microbial and metabolomic diversity. McDonald et al. also demonstrate that there is high diversity across human gut microbiomes, even compared to the diversity of environmental microbiomes. The results from this study illuminate the potential of the citizen science approach to further our knowledge of host-associated microbial communities.

The microbes of the human intestinal tract play a profound role in our health. The complex interactions between our gut microbial communities and the external environment, and the resulting functional consequences, can be difficult to disentangle.The microbes of the human intestinal tract play a profound role in our health. The complex interactions between our gut microbial communities and the external environment, and the resulting functional consequences, can be difficult to disentangle. To address this problem, McDonald et al. (mSystems 3:e00031-18, 2018, https://doi.org/10.1128/mSystems.00031-18) present the first set of results from the American Gut Project, a citizen science-based data set currently comprised of over 10,000 gut microbiome samples and associated life history data. By combining this extensive data set with other published studies, the authors uncover novel relationships between gut microbiome structure and function. For example, they found that dietary plant diversity and recent antibiotic use predict both microbial and metabolomic diversity. McDonald et al. also demonstrate that there is high diversity across human gut microbiomes, even compared to the diversity of environmental microbiomes. The results from this study illuminate the potential of the citizen science approach to further our knowledge of host-associated microbial communities.

Gut bacterial communities play essential roles in host biology, but to date we lack information on the forces that shape gut microbiota between hosts and over time in natural populations. Understanding these forces in wild primates provides a valuable comparative context that enriches scientific perspectives on human gut microbiota. To this end, we tested predictors of gut microbial composition in a well-studied population of wild baboons. Using cross-sectional and longitudinal samples collected over 13 years, we found that baboons harbour gut microbiota typical of other omnivorous primates, albeit with an especially high abundance of Bifidobacterium. Similar to previous work in humans and other primates, we found strong effects of both developmental transitions and diet on gut microbial composition. Strikingly, baboon gut microbiota appeared to be highly dynamic such that samples collected from the same individual only a few days apart were as different from each other as samples collected over 10 years apart. Despite the dynamic nature of baboon gut microbiota, we identified a set of core taxa that is common among primates, supporting the hypothesis that microbiota codiversify with their host species. Our analysis identified two tentative enterotypes in adult baboons that differ from those of humans and chimpanzees.

The mammalian gut microbiome plays a profound role in the physiology, metabolism, and overall health of its host. However, biologists have only a nascent understanding of the forces that drive inter-individual heterogeneity in gut microbial composition, especially the role of host social environment. Here we used 178 samples from 78 wild yellow baboons (Papio cynocephalus) living in two social groups to test how host social context, including group living, social interactions within groups, and transfer between social groups (e.g., dispersal) predict inter-individual variation in gut microbial alpha and beta diversity. We also tested whether social effects differed for prevalent "core" gut microbial taxa, which are thought to provide primary functions to hosts, versus rare "non-core" microbes, which may represent relatively transient environmental acquisitions. Confirming prior studies, we found that each social group harbored a distinct gut microbial community. These differences included both non-core and core gut microbial taxa, suggesting that these effects are not solely driven by recent gut microbial exposures. Within social groups, close grooming partners had more similar core microbiomes, but not non-core microbiomes, than individuals who rarely groomed each other, even controlling for kinship and diet similarity between grooming partners. Finally, in support of the idea that the gut microbiome can be altered by current social context, we found that the longer an immigrant male had lived in a given social group, the more closely his gut microbiome resembled the gut microbiomes of the group's long-term residents. Together, these results reveal the importance of a host's social context in shaping the gut microbiome and shed new light onto the microbiome-related consequences of male dispersal.

Field studies of wild vertebrates are frequently associated with extensive collections of banked fecal samples, which are often collected from known individuals and sometimes also sampled longitudinally across time. Such collections represent unique resources for understanding ecological, behavioral, and phylogenetic effects on the gut microbiome, especially for species of particular conservation concern. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. This uncertainty arises in part because comparisons across storage methods to date generally include only a few (≤5) individuals, or analyze pooled samples. Here, we used n=52 samples from 13 rhesus macaque individuals to compare immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: storage in ethanol, lyophilization following ethanol storage, and storage in RNAlater. We found that the signature of individual identity consistently outweighed storage effects: alpha diversity and beta diversity measures were significantly correlated across methods, and while samples often clustered by donor, they never clustered by storage method. Provided that all analyzed samples are stored the same way, banked fecal samples therefore appear highly suitable for investigating variation in gut microbiota. Our results open the door to a much-expanded perspective on variation in the gut microbiome across species and ecological contexts.

The digestive system is home to a complex community of microbes—known as the gut microbiome—that contributes to our health and wellbeing by digesting food, producing essential vitamins, and preventing the growth of harmful bacteria. The recent development of rapid genome sequencing techniques has made it much easier to identify the species of microbes found in the gut microbiome, and how this microbiome's composition varies between individuals. Studies in humans and other primates suggest that direct contact during social interactions may alter the composition of the gut microbiome in an individual. This could explain why there is a strong association between social interactions and health in humans and other social animals. However, similarities in the gut microbiomes of individuals within a social group could also be due to a shared diet or a common environment. The information collected during long-term studies of wild primates offers an opportunity to analyze and assess the influence of diet, environment and social interaction on the gut microbiome. Here, Tung et al. studied the gut microbiomes of 48 wild baboons belonging to two different social groups in Amboseli, Kenya. Using a technique called shotgun metagenomic sequencing, they sequenced DNA extracted from samples of feces collected from individual baboons. The sequence data revealed that an individual's social group and social network can predict the species found in its gut microbiome. This remained the case even when other factors—such as diet, kinship, and shared environments—were taken into account. Tung et al.'s findings suggest that direct physical contact during social interactions may be important in transmitting gut microbiomes between members of the same social group. However, scientists still don't know whether this exchange is good or bad for the health of the baboons. Future work will try to understand whether baboons benefit from acquiring gut microbes from their group members, and if the gut microbes of some social groups are better than others.

Gut bacterial communities play essential roles in host biology, but to date we lack information on the forces that shape gut microbiota between hosts and over time in natural populations. Understanding these forces in wild primates provides a valuable comparative context that enriches scientific perspectives on human gut microbiota. To this end, we tested predictors of gut microbial composition in a well-studied population of wild baboons. Using cross-sectional and longitudinal samples collected over 13 years, we found that baboons harbour gut microbiota typical of other omnivorous primates, albeit with an especially high abundance of Bifidobacterium. Similar to previous work in humans and other primates, we found strong effects of both developmental transitions and diet on gut microbial composition. Strikingly, baboon gut microbiota appeared to be highly dynamic such that samples collected from the same individual only a few days apart were as different from each other as samples collected over 10 years apart. Despite the dynamic nature of baboon gut microbiota, we identified a set of core taxa that is common among primates, supporting the hypothesis that microbiota codiversify with their host species. Our analysis identified two tentative enterotypes in adult baboons that differ from those of humans and chimpanzees.

Social structure is proposed to influence the transmission of both directly and environmentally transmitted infectious agents. However in natural populations, many other factors also influence transmission, including variation in individual susceptibility and aspects of the environment that promote or inhibit exposure to infection. We used a population genetic approach to investigate the effects of social structure, environment, and host traits on the transmission of Escherichia coli infecting two populations of wild elephants: one in Amboseli National Park and another in Samburu National Reserve, Kenya. If E. coli transmission is strongly influenced by elephant social structure, E. coli infecting elephants from the same social group should be genetically more similar than E. coli sampled from members of different social groups. However, we found no support for this prediction. Instead, E. coli was panmictic across social groups, and transmission patterns were largely dominated by habitat and host traits. For instance, habitat overlap between elephant social groups predicted E. coli genetic similarity, but only in the relatively drier habitat of Samburu, and not in Amboseli, where the habitat contains large, permanent swamps. In terms of host traits, adult males were infected with more diverse haplotypes, and males were slightly more likely to harbor strains with higher pathogenic potential, as compared to adult females. In addition, elephants from similar birth cohorts were infected with genetically more similar E. coli than elephants more disparate in age. This age-structured transmission may be driven by temporal shifts in genetic structure of E. coli in the environment and the effects of age on bacterial colonization. Together, our results support the idea that, in elephants, social structure often will not exhibit strong effects on the transmission of generalist, fecal-oral transmitted bacteria. We discuss our results in the context of social, environmental, and host-related factors that influence transmission patterns.

Management and policy decisions regarding biological invasions and other aspects of global change such as the changing climate have the potential to influence one another. Recently, interest in harvest as an invasive species management strategy has surged. Researchers have speculated about the potential positive (e.g. population and impact reduction, economic losses recouped through new profits) and negative (e.g. generation of economic incentives to encourage further introductions) consequences of such management strategies, but few experimental analyses exist despite the fact that real-world 'experiments' in harvesting invasive species continue to accrue. This chapter provides the first comprehensive list of the many ways humankind has adapted to the presence of invasive species through harvest and considers trends that emerge from this list. The spectrum ranges from collection of feral invasive populations to cultivation of potential invaders as crops, and harvested invasive species serve a variety of purposes ranging from biofuels to foods. The costs of invasion and benefit from harvest can be difficult to quantify, and this difficulty is compounded by the fact that costs and benefits are often incurred by different stakeholders. Climate and other aspects of global change accompanying invasive species harvest have rarely been taken into account, and the climate effects of invasive species harvest should become an explicit consideration of harvest strategies moving forward. Ecologists, economists, environmental managers and stakeholders must work together to ensure the successful and responsible application of ongoing harvests and to inform future efforts.

White-nose syndrome (WNS), an emerging infectious disease caused by the novel fungus Pseudogymnoascus destructans , has devastated North American bat populations since its discovery in 2006. The little brown myotis, Myotis lucifugus , has been especially affected. The goal of this 2-year captive study was to determine the impact of hibernacula temperature and sex on WNS survivorship in little brown myotis that displayed visible fungal infection when collected from affected hibernacula. In study 1, we found that WNS-affected male bats had increased survival over females and that bats housed at a colder temperature survived longer than those housed at warmer temperatures. In study 2, we found that WNS-affected bats housed at a colder temperature fared worse than unaffected bats. Our results demonstrate that WNS mortality varies among individuals, and that colder hibernacula are more favourable for survival. They also suggest that female bats may be more negatively affected by WNS than male bats, which has important implications for the long-term survival of the little brown myotis in eastern North America.

White-nose syndrome (WNS), an emerging infectious disease that has killed over 5.5 million hibernating bats, is named for the causative agent, a white fungus (Geomyces destructans (Gd)) that invades the skin of torpid bats. During hibernation, arousals to warm (euthermic) body temperatures are normal but deplete fat stores. Temperature-sensitive dataloggers were attached to the backs of 504 free-ranging little brown bats (Myotis lucifugus) in hibernacula located throughout the northeastern USA. Dataloggers were retrieved at the end of the hibernation season and complete profiles of skin temperature data were available from 83 bats, which were categorized as: (1) unaffected, (2) WNS-affected but alive at time of datalogger removal, or (3) WNS-affected but found dead at time of datalogger removal. Histological confirmation of WNS severity (as indexed by degree of fungal infection) as well as confirmation of presence/absence of DNA from Gd by PCR was determined for 26 animals. We demonstrated that WNS-affected bats aroused to euthermic body temperatures more frequently than unaffected bats, likely contributing to subsequent mortality. Within the subset of WNS-affected bats that were found dead at the time of datalogger removal, the number of arousal bouts since datalogger attachment significantly predicted date of death. Additionally, the severity of cutaneous Gd infection correlated with the number of arousal episodes from torpor during hibernation. Thus, increased frequency of arousal from torpor likely contributes to WNS-associated mortality, but the question of how Gd infection induces increased arousals remains unanswered.