Evolutionary Biology Needs Wild Microbiomes

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.

Keywords: evolution; field biology; gut microbiome; host-associated microbiota; ornithology.

Figure 1

The 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.

Figure 2

Relationship 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., , 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 3

The 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).