On the Importance of the Microbiome and Pathobiome in Coral Health and Disease

Abstract

The term "microbiome" was first coined in 1988 and given the definition of a characteristic microbial community occupying a reasonably well defined habitat which has distinct physio-chemical properties. A more recent term has also emerged, taking this one step further and focusing on diseases in host organisms. The "pathobiome" breaks down the concept of "one pathogen = one disease" and highlights the role of the microbiome, more specifically certain members within the microbiome, in causing pathogenesis. The development of next generation sequencing has allowed large data sets to be amassed describing the microbial communities of many organisms and the field of coral biology is no exception. However, the choices made in the analytical process and the interpretation of these data can significantly affect the outcome and the overall conclusions drawn. In this review we explore the implications of these difficulties, as well as highlighting analytical tools developed in other research fields (such as network analysis) which hold substantial potential in helping to develop a deeper understanding of the role of the microbiome in disease in corals. We also make the case that standardization of methods will substantially improve the collective gain in knowledge across research groups.

Evidence for rapid, tide-related shifts in the microbiome of the coral Coelastrea aspera

“…The nearby coastline supports both oyster and fish farms, and two of the bacteria detected with a high frequency on Day 2 in *4-yr-old corals have been formerly associated with shellfish farms (Fulvivirga) and fish diseases (Piscirickettsiaceae) (Nedashkovskaya et al 2007;Rozas and Enríquez 2014). It has been proposed that the microbiome can be separated into microbes that can be classed as 'transient' and more sporadic versus those that are more stable or sometimes referred to as 'core' members (Ainsworth et al 2015;Hester et al 2015;Sweet and Bulling 2017). A large proportion of the bacterial phylotypes found in this study fall into the category of 'transient' members (i.e., only present in relatively few samples with little to no consistency among replicate colonies).…”

“…However, the exact definition of a 'core microbiome' is currently relatively arbitrary and lacks consistency among studies (reviewed in Sweet and Bulling 2017). Yet the definition can have important consequences when comparing studies.…”

Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience

“…The core microbiome is composed of common members, host-specific, of two or more microbial communities (Turnbaugh et al, 2007; Hamady and Knight, 2009; Hernandez-Agreda et al, 2016; Sweet and Bulling, 2017). Studies have suggested that identification of the operational taxonomic units (OTUs) that compose the core microbiome is vital because these populations may play key roles (potential BMC) due to their ability to maintain stability in the face of environmental changes (Shade and Handelsman, 2012; Shafquat et al, 2014; Ainsworth et al, 2015; Chu and Vollmer, 2016).…”

Symbiotic Microbes from Marine Invertebrates: Driving a New Era of Natural Product Drug Discovery

“…However, this adds an extra level of complexity to the culturing procedure, having to accommodate the needs of an entire complex holobiont. The conditions used would have to mimic the exact natural conditions of the host marine invertebrate to ensure it was in a state that promoted growth of the desired symbiont, as it has been shown that the microbial composition of certain marine invertebrates, like corals for example can vary significantly under ex-situ culturing conditions [110,111]. That said, recent advances in the design of new culture media, the development of nature-mimicking culture systems, the optimization of growth conditions in bioreactors, the development of efficient automated harvesting protocols for organisms with biotechnological potential, and the invention of different ways of co-cultivation and mixed culturing [8,112] appear to be addressing these issues, at least to some degree.…”