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Table 1 Outstanding questions in host-microbiome research. Host-microbiome research is an emerging field. Knowledge gaps include the eukaryotic and viral components of the microbiome [35,36,37], novel bacterial clades and uncultured microbes [38,39,40], and large gaps in the geography and host taxa sampled for microbiome studies. Most studies to date have focused on human or other mammalian gut microbiomes, agricultural plants, and fish studies focused on aquaculture, leaving other vertebrate and invertebrate hosts underrepresented. Wild samples are needed to overcome alterations due to captivity [41, 42]. Recent efforts to place microbiomes within a macroecology context described patterns across scales [43], or metacommunity or community ecology contexts to learn about microbial migration [44, 45], community assembly and succession [46], and functions for host health [12, 47,48,49]

From: Host-associated microbiomes are predicted by immune system complexity and climate

Frontiers in host-microbiome research
1) Are there dormant and active microbiome subsets of the host microbiome, and how do these subsets change with environmental conditions [50]? How does microbial antagonism and interaction protect hosts or facilitate host invasion [11]?
2) What are the effects of environmental change on colonization, dysbiosis, or adaptive microbiomes? Do abiotic conditions have stronger effects on ectotherms compared with endothermic hosts? Are microbial therapies effective [17, 51,52,53]?
3) What is the significance of core (stable through time and prevalent among individuals) vs peripheral (transitory or rare) microbiomes or gene functions including metabolic pathways in host populations, and is there a trade-off or shift in core microbiome with host immunity, anatomy, life stage, or environmental conditions? Are core microbiomes likely to be of use in personalized medicine or disease diagnostics? Are core microbiomes, particularly of non-human hosts, lost with industrialization [31, 54, 55]?
4) Metabolomics and functional analyses are a research frontier; do they require a renewed focus on culture-based research and genome sequencing [56,57,58]?