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Abstract Background The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer. Integrative approaches which aim at associating the composition of the human microbiome with other available information, such as clinical covariates and environmental predictors, are paramount to develop a more complete understanding of the role of microbiome in disease development. Results In this manuscript, we propose a Bayesian Dirichlet-Multinomial regression model which uses spike-and-slab priors for the selection of significant associations between a set of available covariates and taxa from a microbiome abundance table. The approach allows straightforward incorporation of the covariates through a log-linear regression parametrization of the parameters of the Dirichlet-Multinomial likelihood. Inference is conducted through a Markov Chain Monte Carlo algorithm, and selection of the significant covariates is based upon the assessment of posterior probabilities of inclusions and the thresholding of the Bayesian false discovery rate. We design a simulation study to evaluate the performance of the proposed method, and then apply our model on a publicly available dataset obtained from the Human Microbiome Project which associates taxa abundances with KEGG orthology pathways. The method is implemented in specifically developed R code, which has been made publicly available. Conclusions Our method compares favorably in simulations to several recently proposed approaches for similarly structured data, in terms of increased accuracy and reduced false positive as well as false negative rates. In the application to the data from the Human Microbiome Project, a close evaluation of the biological significance of our findings confirms existing associations in the literature.

README file for packageDescribes all files in package and provides external links to additional documentation.SILVA-to-NCBI mappingContains a mapping of Genbank accession numbers to NCBI taxon ids and names. The accessions are those that are the reference sequences for SILVA clusters.accessions.tgzOTT amendmentsThe taxonomy amendments used in preparation of OTT. Includes all amendments in https://github.com/OpenTreeOfLife/amendments-1 at the time that we built the version of OTT described in the article. Each amendment is a json file that includes the change being proposed as well as sources that support the change.amendments.tgzmapping of source ids to OTT idsCumulative mapping of identifiers in sources to OTT identifiers. Format of each line is source:sourceid,OTTid.by_qid.tgzOTT version2.10This is the previous version of the Open Tree Taxonomy. It is included because we use the previous version during identifier assignment (ott2.10 required to build ott3.0). See the enclosed README for details on files and formats.ott2.10.tgzOTT version 3.0Version of the Open Tree Taxonomy described in the manuscript. See the enclosed README for details on files and formats.ott3.0.tgzseparation taxonomyThe 'separation taxonomy' described in the manuscript. Contains a list of taxa and a list of synonyms.separation.tgz Taxonomy and nomenclature data are critical for any project that synthesizes biodiversity data, as most biodiversity data sets use taxonomic names to identify taxa. Open Tree of Life is one such project, synthesizing sets of published phylogenetic trees into comprehensive summary trees. No single published taxonomy met the taxonomic and nomenclatural needs of the project. Here we describe a system for reproducibly combining several source taxonomies into a synthetic taxonomy, and we discuss the challenges of taxonomic and nomenclatural synthesis for downstream biodiversity projects.

Figs 6–12. Gondwanoscurus jezeki sp. nov. 6 – male genital tract, hypandrium, gonopods, and aedeagus, dorsal view; 7 – epandrium, proctiger and epandrial claspers, dorsal view; 8 – wing; 9 – female genitalia, ventral view; 10 – left gonopod, dorsal view; 11 – flagellomere 5, with ascoids, dorsal view; 12 – apical flagellomeres, ascoids removed, dorsal view. Abbreviations: aed – aedeagus; eja – ejaculatory apodem; ejd – ejaculatory duct; prm – paramere; tes – testes; vsd – vasa deferentia. Scale bars: 6–7 = 0.25 mm; 8 = 1 mm; 9–12 = 0.10 mm. Published as part of Curler, Gregory R., Priyadarsanan, Dharma Rajan & Atree, 2015, Descriptions of Psychodidae (Diptera) from the Western Ghats of India, pp. 473-483 in Acta Entomologica Musei Nationalis Pragae 55 (2) on page 479, DOI: 10.5281/zenodo.5372805

Supplemental Movie 1. At 40% RH, 50 µL, 5 µL, and 1 µL droplets dry at different times and develop similar feather-like interior crystals. Droplets of DMEM were placed on a 6-well polystyrene plate and imaged every 10 minutes. 50 µL droplets were placed in the top left and bottom right wells, 5 µL droplets were placed in the top middle and bottom middle wells, and the 1 µL droplets were placed in the top right and bottom left wells. Images were combined at 10 frames per second to generate videos of droplets at 40% RH over a 24-hour period.