FEMS Microbiology Letters, 366, 2019, fnz117 doi: 10.1093/femsle/fnz117 Advance Access Publication Date: 27 May 2019 Minireviews Downloaded from https://academic.oup.com/femsle/article-abstract/366/10/fnz117/5499024 by University of Colorado user on 12 July 2019 M I N I REV I EW S – Environmental Microbiology Not all animals need a microbiome Tobin J. Hammer1,*,†, Jon G. Sanders2,‡ and Noah Fierer3,4 1Department of Integrative Biology, University of Texas at Austin, 2506 Speedway, NMS 4.216, Austin, TX 78712, USA, 2Cornell Institute of Host–Microbe Interactions and Disease, Cornell University, E145 Corson Hall, Ithaca, NY 14853, USA, 3Department of Ecology & Evolutionary Biology, University of Colorado at Boulder, 216 UCB, Boulder, CO 80309, USA and 4Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, CIRES Bldg. Rm. 318, Boulder, CO 80309, USA ∗Corresponding author: 2506 Speedway, NMS 4.216, Austin, TX 78712, USA. Tel: +1 (512) 232-9419; E-mail: [email protected] One sentence summary: Contrary to a prevailing paradigm, some animals do not host nor rely on a microbiome. Editor: Daniel Tamarit †Tobin J. Hammer, http://orcid.org/0000-0002-7308-8440 ‡Jon G. Sanders, http://orcid.org/0000-0001-6077-4014 ABSTRACT It is often taken for granted that all animals host and depend upon a microbiome, yet this has only been shown for a small proportion of species. We propose that animals span a continuum of reliance on microbial symbionts. At one end are the famously symbiont-dependent species such as aphids, humans, corals and cows, in which microbes are abundant and important to host fitness. In the middle are species that may tolerate some microbial colonization but are only minimallyor facultatively dependent. At the other end are species that lack beneficial symbionts altogether. While their existence may seem improbable, animals are capable of limiting microbial growth in and on their bodies, and a microbially independent lifestyle may be favored by selection under some circumstances. There is already evidence for several ‘microbiome-free’ lineages that represent distantly related branches in the animal phylogeny. We discuss why these animals have received such little attention, highlighting the potential for contaminants, transients, and parasites to masquerade as beneficial symbionts. We also suggest ways to explore microbiomes that address the limitations of DNA sequencing. We call for further research on microbiome-free taxa to provide a more complete understanding of the ecology and evolution of macrobe-microbe interactions. Keywords: microbiota; holobiont; symbiosis; gut bacteria; endosymbiont; 16S rRNA gene INTRODUCTION sis then fell out of fashion and laid relatively dormant until methodological advances, particularly cultivation-independent Beginning with Antonie van Leeuwenhoek and continuing into DNA sequencing, spurred a second wave of microbial explo- the early 20th century, microbiologists and zoologists discov- ration (Moran 2006). ered a seemingly ubiquitous world of microbial life in and on There has been a recent explosion of studies finding the bodies of animals. From minute beetles to humans, microor- microbes on and in a wide range of animals, reviving the view ganisms were repeatedly observed in intimate association with that all macroscopic organisms are hosts to microbial sym- animal tissues (Buchner 1965 and references therein). Such find- bionts or microbiomes (Table S1, Supporting Information). Fur- ings led to a widespread opinion among these early pioneers thermore, in a number of host groups, symbionts have been that microbial symbiosis must be ‘an elementary principle of shown to play critical and often surprising roles in development, all organisms’ (Buchner 1965, p. 69). But the study of symbio- physiology, behavior, defense from enemies and a variety of Received: 21 February 2019; Accepted: 25 May 2019 C FEMS 2019. All rights reserved. For permissions, please e-mail: [email protected] 1 2 FEMS Microbiology Letters, 2019, Vol. 366, No. 10 Downloaded from https://academic.oup.com/femsle/article-abstract/366/10/fnz117/5499024 by University of Colorado user on 12 July 2019 Figure 1. A schematic of microbial associations for three animal species across the microbial dependency spectrum, exemplified by a cow, red panda, and Crematogaster ant (see text for more information on these species). All species contain some transient and parasitic/pathogenic microbes, but differ in the degree to which they are colonized by beneficial symbionts. Shown is a section of the gut, but the same principles could apply to non-gut symbioses as well. Inset:n classificatio of individual microbes by their effect on host fitness, from negative ( − ) to neutral ( 0 ) to positive ( + ). Note that microbial residency and function categories can be fluid and context-dependent (not shown). For clarity, we do not depict the case of an animal highly dependent on transient microbes as food. other traits (e.g. Ezenwa et al. 2012; McFall-Ngai et al. 2013; What is a microbiome anyway? Sommer and Backhed¨ 2013; Douglas 2014; Gerardo and Parker 2014). The apparent ubiquity of microbiomes, combined with Whether all animals do or do not have microbiomes, micro- evidence that symbionts mediate certain traits in certain ani- biota or symbionts depends upon one’s definition of these terms. mals, gives an impression that the microbiome has far-reaching It is almost certainly true that every animal interacts with influences on the biology of all animals (Table S1, Supporting microbes in some way, for at least part of its life cycle. But Information). terms such as microbiome (Lederberg and McCray 2001)are But is the paradigm that all animals have and depend upon so all-encompassing that the same word lumps very different microbial symbionts actually supported by firm evidence? We kinds of microbial associations into a single concept, glossing argue that the field has overcorrected from the days when sym- over fundamental differences across animal species (also see biont roles in animal biology were underappreciated. Now, rein- Harris 1993). To highlight these differences, we focus on two forced by methodological issues (discussed below) and partic- axes of variation—residency and function—that are of partic- ularly exciting case studies, researchers often assume micro- ular significance in characterizing microbiomes and their con- biomes where there may be none. Many authors have claimed stituent members (Fig. 1). Both categories can be fluid and highly that all (or ‘virtually all’) animals host a microbiome (Table context-dependent (e.g. Weeks et al. 2007;Masonet al. 2011; S1,Supporting Information), but in fact, next to nothing is known Chamberland et al. 2017; Douglas 2018). Nevertheless, they are about microbial associations for the majority of animal species a useful way to roughly categorize both microbes and micro- on the planet. We suggest that the presence of a resident and biomes by their average or typical effects, as shown by the main- functionally relevant microbiome is not the appropriate null stream use of related terms like ‘pathogen’, ‘transient’ and ‘ben- hypothesis for explorations into these uncharted waters. It is eficial microbiome’. important to not just ask ‘who are the microbes?’ and ‘what are By residency, we refer to the degree to which a micro- they doing?’, but also whether there is even a microbiome in the bial population remains stably associated with a host. Resi- first place. dent microbes, also known as symbionts [‘living together’ (Dou- Moreover, by generalizing all animals as microbe-rich holo- glas 1994)], differ from transient microbes in that they replicate bionts, this paradigm obscures an interesting aspect of animal inside a host at a rate exceeding loss due to death or excretion. diversity—that animals vary strongly in the degree to which they Microbiologists and ecologists have long placed an important host and depend upon microbial symbionts. This more nuanced distinction between these two categories (e.g. Janzen 1977; Har- perspective encourages us to rethink the approaches we use to ris 1993;Berg1996;SnellTayloret al. 2018), and an increasing study animal microbiomes, and prompts new questions about number of animal microbiome studies are making efforts to dif- how and why animals evolve along the spectrum of microbiome ferentiate resident from transient taxa as well (David et al. 2014; dependence. Lee et al. 2016; Hammer et al. 2017; Auchtung et al. 2018). Hammer et al. 3 By ‘function’, we refer to the types and degree of microbial including bacteria, archaea, fungi and other eukaryotes (Table effects on host fitness. Transient microbes could have positive, S1, Supporting Information). For example, unlike bacteria, fungi negative, or negligible effects on hosts. Due to their growth and have been shown to be only transiently present in the healthy metabolic activity, resident microbes are likely to have some human gut and typically derived from food or the mouth effect on their host, but it could be negative—in which case (Auchtung et al. 2018). In invertebrates, resident microbiomes they would traditionally be described as parasites or pathogens. are often dominated by only one or a few species (e.g. Haynes Alternatively, resident microbes could increase host fitness; in et al. 2003; Dubilier, Bergin and Lott 2008; Salem et al. 2017;Mat- these cases, the benefits to hosts can take many forms, and can suura et al. 2018), not a diverse