The role of microbes as a part of animal systems has historically been an under-appreciated aspect of animal life histories. Recently, evidence has emerged that microbes have wide-ranging influences on animal behaviour. Elucidating the complex relationships between host-microbe interactions and behaviour requires an expanded ecological perspective, involving the host, the microbiome and the environment; which, in combination, is termed the holobiont. We begin by seeking insights from the literature on host-parasite interactions, then expand to consider networks of interactions between members of the microbial community. A central aspect of the environment is host nutrition. We describe how interactions between the nutrient environment, the metabolic and behavioural responses of the host and the microbiome can be studied using an integrative framework called Nutritional Geometry (NG), which integrates and maps multiple aspects of the host and microbial response in multidimensional nutrient intake spaces.

Summary: 16SpeB ( 16 S rRNA-based Spe cies B oundary) is a package of Perl programs that evaluates total sequence variation of a bacterial species at the levels of the whole 16S rRNA sequences or single hypervariable (V) regions, using publicly-available sequences. The 16SpeB pipelines filter sequences from duplicated strains and of low quality, extracts a V region of interest using general primer sequences, and calculates sequence percentage identity (%ID) through all possible pairwise alignments. Results: The minimum %ID of 16S rRNA gene sequences for 15 clinically-important bacterial species, as determined by 16SpeB, ranged from 82.6% to 99.8%. The relationship between minimum %ID of V2/V6 regions and full-gene sequences varied among species, indicating that %ID species limits should be resolved independently for each region of the 16S rRNA gene and bacterial species. Availability: 16SpeB and user manual are freely available for download from: https://github.com/pnpnpn/16SpeB . A video tutorial is available at: https://youtu.be/Vd6YmMhyBiA Contact: cw442@cornell.edu Supplementary information: Supplementary data are available at Bioinformatics online.