A primary aim of microbial ecology is to determine patterns and drivers of community distribution, interaction, and assembly amidst complexity and uncertainty. Microbial community composition has been shown to change across gradients of environment, geographic distance, salinity, temperature, oxygen, nutrients, pH, day length, and biotic factors 1-6 . These patterns have been identified mostly by focusing on one sample type and region at a time, with insights extra polated across environments and geography to produce generalized principles. To assess how microbes are distributed across environments globally-or whether microbial community dynamics follow funda mental ecological 'laws' at a planetary scale-requires either a massive monolithic cross environment survey or a practical methodology for coordinating many independent surveys. New studies of microbial environments are rapidly accumulating; however, our ability to extract meaningful information from across datasets is outstripped by the rate of data generation. Previous meta analyses have suggested robust gen eral trends in community composition, including the importance of salinity 1 and animal association 2 . These findings, although derived from relatively small and uncontrolled sample sets, support the util ity of meta analysis to reveal basic patterns of microbial diversity and suggest that a scalable and accessible analytical framework is needed.The Earth Microbiome Project (EMP, http://www.earthmicrobiome. org) was founded in 2010 to sample the Earth's microbial communities at an unprecedented scale in order to advance our understanding of the organizing biogeographic principles that govern microbial commu nity structure 7,8 . We recognized that open and collaborative science, including scientific crowdsourcing and standardized methods 8 , would help to reduce technical variation among individual studies, which can overwhelm biological variation and make general trends difficult to detect 9 . Comprising around 100 studies, over half of which have yielded peer reviewed publications (Supplementary Table 1), the EMP has now dwarfed by 100 fold the sampling and sequencing depth of earlier meta analysis efforts 1,2 ; concurrently, powerful analysis tools have been developed, opening a new and larger window into the distri bution of microbial diversity on Earth. In establishing a scalable frame work to catalogue microbiota globally, we provide both a resource for the exploration of myriad questions and a starting point for the guided acquisition of new data to answer them. As an example of using this Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of r...

Mammals are exposed to a diverse array of parasites and infectious diseases, many of which affect host survival and reproduction. Species that live in dense populations, large social groups, or with promiscuous mating systems may be especially vulnerable to infectious diseases owing to the close proximity and higher contact rates among individuals. We review the effects of host density and social contacts on parasite spread and the importance of promiscuity and mating structure for the spread and evolution of sexually transmitted diseases. Host social organization and mating system should influence not only parasite diversity and prevalence but may also determine the fitness advantages of different transmission strategies to parasites.

Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all vertebrate lineages. Here, we assessed gut microbiomes from ∼900 vertebrate species, including 315 mammals and 491 birds, assessing contributions of diet, phylogeny, and physiology to structuring gut microbiomes. In most nonflying mammals, strong correlations exist between microbial community similarity, host diet, and host phylogenetic distance up to the host order level. In birds, by contrast, gut microbiomes are only very weakly correlated to diet or host phylogeny. Furthermore, while most microbes resident in mammalian guts are present in only a restricted taxonomic range of hosts, most microbes recovered from birds show little evidence of host specificity. Notably, among the mammals, bats host especially bird-like gut microbiomes, with little evidence for correlation to host diet or phylogeny. This suggests that host-gut microbiome phylosymbiosis depends on factors convergently absent in birds and bats, potentially associated with physiological adaptations to flight. Our findings expose major variations in the behavior of these important symbioses in endothermic vertebrates and may signal fundamental evolutionary shifts in the cost/benefit framework of the gut microbiome. IMPORTANCE In this comprehensive survey of microbiomes of >900 species, including 315 mammals and 491 birds, we find a striking convergence of the microbiomes of birds and animals that fly. In nonflying mammals, diet and short-term evolutionary relatedness drive the microbiome, and many microbial species are specific to a particular kind of mammal, but flying mammals and birds break this pattern with many microbes shared across different species, with little correlation either with diet or with relatedness of the hosts. This finding suggests that adaptation to flight breaks long-held relationships between hosts and their microbes.

Feedbacks between microbiomes and their hosts affect a range of animal behaviors.

Vultures (Accipitridae and Cathartidae) are the only known obligate scavengers. They feed on rotting carcasses and are the most threatened avian functional group in the world. Possible effects of vulture declines include longer persistence of carcasses and increasing abundance of and contact between facultative scavengers at these carcasses. These changes could increase rates of transmission of infectious diseases, with carcasses serving as hubs of infection. To evaluate these possibilities, we conducted a series of observations and experimental tests of the effects of vulture extirpation on decomposition rates of livestock carcasses and mammalian scavengers in Kenya. We examined whether the absence of vultures changed carcass decomposition time, number of mammalian scavengers visiting carcasses, time spent by mammals at carcasses, and potential for disease transmission at carcasses (measured by changes in intraspecific contact rates). In the absence of vultures, mean carcass decomposition rates nearly tripled. Furthermore, the mean number of mammals at carcasses increased 3-fold (from 1.5 to 4.4 individuals/carcass), and the average time spent by mammals at carcasses increased almost 3-fold (from 55 min to 143 min). There was a nearly 3-fold increase in the mean number of contacts between mammalian scavengers at carcasses without vultures. These results highlight the role of vultures in carcass decomposition and level of contact among mammalian scavengers. In combination, our findings lead us to hypothesize that changes in vulture abundance may affect patterns of disease transmission among mammalian carnivores.

The emergence of several high profile infectious diseases in recent years has focused attention on our need to understand the ecological factors contributing to the spread of infectious diseases. West Nile virus (WNV) is a mosquito-borne zoonotic disease that was first detected in the United States in 1999. The factors accounting for variation in the prevalence of WNV are poorly understood, but recent ideas suggesting links between high biodiversity and reduced vector-borne disease risk may help account for distribution patterns of this disease. Since wild birds are the primary reservoir hosts for WNV, we tested associations between passerine (Passeriform) bird diversity, non-passerine (all other orders) bird diversity and virus infection rates in mosquitoes and humans to examine the extent to which bird diversity is associated with WNV infection risk. We found that non-passerine species richness (number of nonpasserine species) was significantly negatively correlated with both mosquito and human infection rates, whereas there was no significant association between passerine species richness and any measure of infection risk. Our findings suggest that non-passerine diversity may play a role in dampening WNV amplification rates in mosquitoes, minimizing human disease risk.

Summary1. Heterogeneity in the ability of hosts to transmit pathogens is among the most fundamental concepts in disease dynamics and has major implications for disease control strategies. 2. The number of secondary infections produced by an infected individual is a function of three components: an individual's infectiousness, the rate at which it contacts susceptible individuals and the duration of infection. Individual-level variation can emerge in each of these components through a combination of behavioural and physiological mechanisms. 3. In this review, we describe mechanisms that promote variation in the number of individuals to which an individual transmits a pathogen, emphasizing insights that can be gained by understanding which components of transmission (infectiousness, contact rate, infection duration) are primarily affected. We also discuss how behavioural and physiological processes generate transmission heterogeneities across multiple scales, from individual-level variation to heterogeneity among species. 4. Strategies for quantifying each transmission component are presented, and we discuss why studies focusing on only one component of the infection process may be misleading. 5. To conclude, we describe how future research focusing on variation in transmission across all three components can provide a more holistic view of heterogeneity in pathogen transmission.

Epidemiological studies typically focus on single-parasite systems, although most hosts harbor multiple parasite species; thus, the potential impacts of co-infection on disease dynamics are only beginning to be recognized. Interactions between macroparasites, such as gastrointestinal nematodes, and microparasites causing diseases like TB, AIDS, and malaria are particularly interesting because co-infection may favor transmission and progression of these important diseases. Here we present evidence for strong interactions between gastrointestinal worms and bovine tuberculosis (TB) in free-ranging African buffalo (Syncerus caffer). TB and worms are negatively associated at the population, among-herd, and within-herd scales, and this association is not solely the result of demographic heterogeneities in infection. Combining data from 1362 buffalo with simple mechanistic models, we find that both accelerated mortality of co-infected individuals and TB transmission heterogeneity caused by trade-offs in immunity to the two types of parasites likely contribute to observed infection patterns. This study is one of the first to examine the relevance of within-host immunological trade-offs for understanding parasite distribution patterns in natural populations.