PT  - JOURNAL ARTICLE
AU  - Johannes R. Björk
AU  - Francis KC. Hui
AU  - Robert B. O’Hara
AU  - Jose M. Montoya
TI  - Uncovering the drivers of host-associated microbiota with joint species distribution modeling
AID  - 10.1101/137943
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 137943
4099  - http://biorxiv.org/content/early/2018/04/14/137943.1.short
4100  - http://biorxiv.org/content/early/2018/04/14/137943.1.full
AB  - In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure, and therefore cannot explicitly account for the effect of the host in structuring the microbiota. We introduce a novel extension of joint species distribution models which can straightforwardly accommodate and discern between effects such as host phylogeny and traits, recorded covariates like diet and collection site, among other ecological processes. Our proposed methodology includes powerful yet familiar outputs seen in community ecology overall, including: (i) model-based ordination to visualize and quantify the main patterns in the data; (ii) variance partitioning to asses how influential the included host-specific factors are in structuring the microbiota; and (iii) co-occurrence networks to visualize microbe-to-microbe associations.