Recent findings from human microbiome research suggest that a core microbiome can be defined at the functional rather than the taxonomic level (Lloyd-Price et al., 2016).

Yet, what constitutes a core still remains elusive and depends on the question of interest.

A recent assessment of US microbiome research, for example, highlights the importance of microbiome studies for tackling current world problems, such as food production, human, and ecosystem health (Stulberg et al., 2016).

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Host-associated microbial communities are dynamic, changing throughout the hosts’ life, and are not passive players but actively engage in host development, metabolism, immunity, and health as found in established model systems, like corals, worms, insects, mice, and Hydra (Ley et al., 2008; Fraune and Bosch, 2010; Fukuda et al., 2011; Naik et al., 2012; Lee and Brey, 2013; Sommer and Bäckhed, 2013; Mc Fall-Ngai, 2014; Thompson et al., 2015).

How microbes increase the host’s stress tolerance and modulate its niche breath are active fields of research (Mueller and Sachs, 2015).

However, deciphering the different types of interactions among community members, with their hosts and their interplay with their environment is still a challenge of major proportion.

The emerging fields of synthetic microbial ecology and community systems biology have the potential to decrypt these complex relationships. doi: 10.1038/ismej.2014.239 Cross Ref Full Text | Google Scholar Fraune, S., and Bosch, T.

Central for the ability to predict and manage the function of host-associated microbial communities is the knowledge about the factors determining their dynamics and stability. doi: 10.1073/pnas.1304960110 Cross Ref Full Text | Google Scholar Franzenburg, S., Fraune, S., Künzel, S., Baines, J.

The concept of a core microbiome (taxa or functional core) has been very helpful in addressing the stability of this core and how it changes with age, diet, geographic location, time, or other factors. The existence of such a unifying term indicates the significance of the microbial community for understanding the biology of any host. These host-associated microbial communities (microbiomes) live on host surfaces, are associated with different tissues, and can reside inter- and intracellularly (Huttenhower et al., 2012; Kostic et al., 2013). In Hydra, microbial communities of wild caught and domesticated animals have been found to be surprisingly similar and to share a core microbiota at the taxonomic level (Fraune and Bosch, 2007). It is likely that the microbiome (like microbial communities associated with abiotic environments) is affected by various extrinsic and intrinsic factors, e.g., temperature, p H, resource availability, microbe–microbe interactions, but also by interactions with the host. Through in vivo, in vitro, and in silico approaches the interaction structure of host-associated microbial communities and the effects of the host on the microbiota and its interactions can be disentangled. Disturbing epithelial homeostasis in the metazoan Hydra leads to drastic changes in associated microbiota.