| Literature DB >> 28487687 |
Abstract
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., milk). Birds represent over 30% of known tetrapod diversity and possess their own suite of adaptations relevant to the microbiome. In a previous study, we showed that 59 species of birds displayed immense variation in their microbiomes and host (bird) taxonomy and ecology were most correlated with the gut microbiome. In this Frontiers Focused Review, I put those results in a broader context by discussing how collecting and analyzing wild microbiomes contributes to the main goals of evolutionary biology and the specific ways that birds are unique microbial hosts. Finally, I outline some of the methodological considerations for adding microbiome sampling to the research of wild animals and urge researchers to do so. To truly understand the evolution of a host, we need to understand the millions of microorganisms that inhabit it as well: evolutionary biology needs wild microbiomes.Entities:
Keywords: evolution; field biology; gut microbiome; host-associated microbiota; ornithology
Year: 2017 PMID: 28487687 PMCID: PMC5404107 DOI: 10.3389/fmicb.2017.00725
Source DB: PubMed Journal: Front Microbiol ISSN: 1664-302X Impact factor: 5.640
Figure 1The goals of evolutionary biology are to describe and understand living things, including their distribution, lifestyles, and history. Without microbiomes, we are missing not only the majority of living things on the planet (bacteria) but also important interactions between dynamic forces. Arrows on figure show how different levels of biological organization can affect each other. E.g., eating a butterfly affects (in a broad sense) a bird; the microbiome of the butterfly can also affect the bird, as well as directly affect the microbiome of the bird. Genes and genomes of all living pieces of this “foodweb” interact at many scales and the evolution of all the pieces are connected to many others.
The three main goals of evolutionary biology, applied to the microbiome (MB).
| What is here? (including: What lives here? What's passing through? What's living? What dead?) | Where does the MB come from? How is the MB seeded (from where)? (Metacommunity dynamics) | Roles of different layers of selection? (on host, on MB, on microbe, on genomes, on genes) |
| What always lives here? (“core microbiome”) | How does the MB change over time? (succession) | Role of social contact between hosts (microbial migration) |
| Why is it here? (Resident or transient; living; or dead) | Analysis of phylogeny of microbes within host (including concepts of adaptive radiation, HGT, gut biogeography) | Role of pathogens (disturbed state, succession dynamics, or source-sink dynamics); role of disease or illness of host on MB |
| How many unique taxa? What is new to science? (endemism) | Analysis of phylogeny of particular microbes across hosts (including concepts from phylogeography) | (How) Does MB aid adaptability of host? (How) Does the MB adapt to new environments? |
| Estimate phylogeny of bacteria within a host; estimate phylogeny of bacteria (or clade) across hosts | What is the maternal contribution (vertical and pseudo-vertical inheritance)? | Testing for, identifying, quantifying coevolution between host and microbe(s). Differentiating from co-diversification |
| Defining a bacterial species, a pan-genome | What is the neonatal environment's contribution? | What is the community structure? |
| Which taxa co-occur? | What is host ecology's contribution (e.g., diet)? | Extinction/speciation: of microbe and host |
Figure 2Relationship between bacteria and birds. (A) Phylogenetic tree of bacteria belonging to the order Fusobacteriales and which hosts the bacteria were found in. All members in the original dataset belonging to five bird families are shown for comparative purposes; bird orders are grouped by color and the first six letters of each name represent the species (see Hird et al., 2015, for more information about samples). Whether a particular OTU was found in a particular bird is shown in columns where the letter denotes which sampling locality the bird came from (on map shown in B) and the size of the letter refers to the abundance of the OTU. Patterns of note are shown on the figure.
Figure 3The steps required to collect microbiome data from wild organisms. Note that the cost of each step is shown: dollar signs represent cost of raw materials and clocks represent time investment. Values shown are estimates of the expected minimum cost but can vary, sometimes by quite a bit. Notably, time equals money in many cases (e.g., personnel).