Deciphering the ecoevolutionary recipe of milk microbiomes.

In a recent article, Keady et al. analyzed mammalian milk microbiomes across 47 species and found their assembly to be largely determined by stochastic (i.e.

Body Size Poorly Predicts Host-Associated Microbial Diversity in Wild Birds.

The composition and diversity of avian microbiota are shaped by many factors, including host ecologies and environmental variables. In this study, we examine microbial diversity across 214 bird species sampled in Malawi at five major body sites: blood, buccal cavity, gizzard, intestinal tract, and cloaca. Microbial community dissimilarity differed significantly across body sites.

Functional and Compositional Changes in the Fecal Microbiome of a Shorebird during Migratory Stopover.

Shorebirds migrate long distances twice annually, which requires intense physiological and morphological adaptations, including the ability to rapidly gain weight via fat deposition at stopover locations. The role of the microbiome in weight gain in avian hosts is unresolved, but there is substantial evidence to support the hypothesis that the microbiome is involved with host weight from mammalian microbiome literature. Here, we collected 100 fecal samples of Ruddy Turnstones to investigate microbiome composition and function during stopover weight gain in Delaware Bay, USA.

Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes.

16S rRNA amplicon sequences are predominantly used to identify the taxonomic composition of a microbiome, but they can also be used to generate simulated metagenomes to circumvent costly empirical shotgun sequencing. The effectiveness of using "simulated metagenomes" (shotgun metagenomes simulated from 16S rRNA amplicons using a database of full genomes closely related to the amplicons) in nonmodel systems is poorly known. We sought to determine the accuracy of simulated metagenomes in a nonmodel organism, the Canada goose (Branta canadensis), by comparing metagenomes and metatranscriptomes to simulated metagenomes derived from 16S amplicon sequencing.

Playing by their own rules: the vertebrate archaeome.

In a recent paper, Youngblut et al. used comparative methods to study the archaeal component of the vertebrate microbiome. This study showed that the vertebrate archaeome contains abundant variation, differs from the vertebrate bacteriome and lays a foundation for future comparative studies.

Sex Differences in Gut Microbial Development of Preterm Infant Twins in Early Life: A Longitudinal Analysis.

Infant gut microbiota plays a vital role in immune response, mediates neurobehavioral development and health maintenance. Studies of twins' gut microbiota found that gut microbiota composition and diversity tend to be mature and stable with increasing postnatal age (PNA). Preterm infant gut microbiome shifts dramatically when they were staying in the neonatal intensive care unit (NICU).

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.

Red Fluorescence of European Hedgehog (Erinaceus europaeus) Spines Results from Free-Base Porphyrins of Potential Microbial Origin.

Bioluminescence has been recognized as an important means for inter- and intra-species communication. A growing number of reports of red fluorescence occurring in keratinaceous materials have become available. The fluorophore(s) in these cases were shown to be, or suspected to be, free base porphyrins.

microbiome correlates with life stage, not the presence of human pathogens, in ticks submitted for diagnostic testing.

Ticks are globally distributed arthropods and a public health concern due to the many human pathogens they carry and transmit, including the causative agent of Lyme disease, . As tick species' ranges increase, so do the number of reported tick related illnesses. The microbiome is a critical part of understanding arthropod biology, and the microbiome of pathogen vectors may provide critical insight into disease transmission and management.

Spatial heterogeneity of the shorebird gastrointestinal microbiome.

The gastrointestinal tract (GIT) consists of connected structures that vary in function and physiology, and different GIT sections potentially provide different habitats for microorganisms. Birds possess unique GIT structures, including the oesophagus, proventriculus, gizzard, small intestine, caeca and large intestine. To understand birds as hosts of microbial ecosystems, we characterized the microbial communities in six sections of the GIT of two shorebird species, the Dunlin and Semipalmated Sandpiper, identified potential host species effects on the GIT microbiome and used microbial source tracking to determine microbial origin throughout the GIT.

Context Is Key: Comparative Biology Illuminates the Vertebrate Microbiome.

Microbes affect vertebrates on timescales from daily to evolutionary, and the cumulative effect of these interactions is immense. However, how microbiomes compare across (host) species is poorly understood, as most studies focus on relatively few species. A recent mBio article by S.

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea.

How the microbiome interacts with hosts across evolutionary time is poorly understood. Data sets including many host species are required to conduct comparative analyses. Here, we analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene.

No evidence for phylosymbiosis in western chipmunk species.

Phylosymbiosis refers to a congruent pattern between the similarity of microbiomes of different species and the branching pattern of the host phylogeny. Phylosymbiosis has been detected in a variety of vertebrate and invertebrate hosts, but has only been assessed in geographically isolated populations. We tested for phylosymbiosis in eight (sub)species of western chipmunks with overlapping ranges and ecological niches; we used a nuclear (Acrosin) and a mitochondrial (CYTB) phylogenetic marker because there are many instances of mitochondrial introgression in chipmunks.

Correction: Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons.

[This corrects the article DOI: 10.1371/journal.pone.

Microbiomes, Community Ecology, and the Comparative Method.

Microbiomes contain many levels of biological information, and integrating across the levels creates a holistic understanding of host-microbiome interactions. In my research on the evolution and ecology of avian microbiomes, I use two complementary frameworks: the microbiome as a community and the microbiome as a trait of the host. We draw on classic ecological and evolutionary theory and modern statistical models to advance our understanding in each of these frameworks and then integrate what we have learned into a better understanding of host-associated microbiomes, host evolution, and microbial biodiversity.

Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons.

Probiotics are bacterial species or assemblages that are applied to animals and plants with the intention of altering the microbiome in a beneficial way. Probiotics have been linked to positive health effects such as faster disease recovery times in humans and increased weight gain in poultry. Pigeon fanciers often feed their show pigeons probiotics with the intention of increasing flight performance.

Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria.

Although aquaria are common features of homes and other buildings, little is known about how environmental perturbations (i.e., tank cleaning, water changes, addition of habitat features) impact the diversity and succession of aquarium microbial communities.

The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status.

Waterfowl, especially ducks of the genus , are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards.

Evolutionary Biology Needs Wild Microbiomes.

The microbiome is a vital component to the evolution of a host and much of what we know about the microbiome derives from studies on humans and captive animals. But captivity alters the microbiome and mammals have unique biological adaptations that affect their microbiomes (e.g.

Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses.

Waterfowl, especially ducks and geese, are primary reservoirs for influenza A viruses (IAVs) that evolve and emerge as important pathogens in domestic animals and humans. In contrast to humans, where IAVs infect the respiratory tract and cause significant morbidity and mortality, IAVs infect the gastrointestinal tract of waterfowl and cause little or no pathology and are spread by fecal-oral transmission. For this reason, we examined whether IAV infection is associated with differences in the cloacal microbiome of mallards (), an important host of IAVs in North America and Eurasia.

Comparative Gut Microbiota of 59 Neotropical Bird Species.

The gut microbiota of vertebrates are essential to host health. Most non-model vertebrates, however, lack even a basic description of natural gut microbiota biodiversity. Here, we sampled 116 intestines from 59 Neotropical bird species and used the V6 region of the 16S rRNA molecule as a microbial fingerprint (average coverage per bird ~80,000 reads).

Evolution of the indoor biome.

Few biologists have studied the evolutionary processes at work in indoor environments. Yet indoor environments comprise approximately 0.5% of ice-free land area--an area as large as the subtropical coniferous forest biome.

Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater).

Brown-headed Cowbirds (Molothrus ater) are the most widespread avian brood parasite in North America, laying their eggs in the nests of approximately 250 host species that raise the cowbird nestlings as their own. It is currently unknown how these heterospecific hosts influence the cowbird gut microbiota relative to other factors, such as the local environment and genetics. We test a Nature Hypothesis (positing the importance of cowbird genetics) and a Nurture Hypothesis (where the host parents are most influential to cowbird gut microbiota) using the V6 region of 16S rRNA as a microbial fingerprint of the gut from 32 cowbird samples and 16 potential hosts from nine species.

Poor fit to the multispecies coalescent is widely detectable in empirical data.

Model checking is a critical part of Bayesian data analysis, yet it remains largely unused in systematic studies. Phylogeny estimation has recently moved into an era of increasingly complex models that simultaneously account for multiple evolutionary processes, the statistical fit of these models to the data has rarely been tested. Here we develop a posterior predictive simulation-based model check for a commonly used multispecies coalescent model, implemented in *BEAST, and apply it to 25 published data sets.

lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis.

Genomic enrichment methods and next-generation sequencing produce uneven coverage for the portions of the genome (the loci) they target; this information is essential for ascertaining the suitability of each locus for further analysis. lociNGS is a user-friendly accessory program that takes multi-FASTA formatted loci, next-generation sequence alignments and demographic data as input and collates, displays and outputs information about the data. Summary information includes the parameters coverage per locus, coverage per individual and number of polymorphic sites, among others.