Use of Bayes factors to evaluate the effects of host genetics, litter and cage on the rabbit cecal microbiota
Velasco-Galilea, María (Centre de Recerca en Agrigenòmica)
Piles, Miriam (Institut de Recerca i Tecnologia Agroalimentàries)
Ramayo-Caldas, Yuliaxis (Institut de Recerca i Tecnologia Agroalimentàries)
Varona, Luis (Universidad de Zaragoza)
Sánchez, Juan Pablo (Institut de Recerca i Tecnologia Agroalimentàries)

Fecha:	2022
Resumen:	The rabbit cecum hosts and interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. Although the influence of host genetics on microbial diversity and specific microbial taxa has been studied in several species (e. g. , humans, pigs, or cattle), it has not been investigated in rabbits. Using a Bayes factor approach, the aim of this study was to dissect the effects of host genetics, litter and cage on 984 microbial traits that are representative of the rabbit microbiota. Analysis of 16S rDNA sequences of cecal microbiota from 425 rabbits resulted in the relative abundances of 29 genera, 951 operational taxonomic units (OTU), and four microbial alpha-diversity indices. Each of these microbial traits was adjusted with mixed linear and zero-inflated Poisson (ZIP) models, which all included additive genetic, litter and cage effects, and body weight at weaning and batch as systematic factors. The marginal posterior distributions of the model parameters were estimated using MCMC Bayesian procedures. The deviance information criterion (DIC) was used for model comparison regarding the statistical distribution of the data (normal or ZIP), and the Bayes factor was computed as a measure of the strength of evidence in favor of the host genetics, litter, and cage effects on microbial traits. According to DIC, all microbial traits were better adjusted with the linear model except for the OTU present in less than 10% of the animals, and for 25 of the 43 OTU with a frequency between 10 and 25%. On a global scale, the Bayes factor revealed substantial evidence in favor of the genetic control of the number of observed OTU and Shannon indices. At the taxon-specific level, significant proportions of the OTU and relative abundances of genera were influenced by additive genetic, litter, and cage effects. Several members of the genera Bacteroides and Parabacteroides were strongly influenced by the host genetics and nursing environment, whereas the family S24-7 and the genus Ruminococcus were strongly influenced by cage effects. This study demonstrates that host genetics shapes the overall rabbit cecal microbial diversity and that a significant proportion of the taxa is influenced either by host genetics or environmental factors, such as litter and/or cage.
Ayudas:	Agencia Estatal de Investigación PID2019-108829RB-I00 Agencia Estatal de Investigación CEX2019-000902-S Ministerio de Ciencia e Innovación RTA2011-00064-00-00 European Commission 633531 Agencia Estatal de Investigación RTI2018-097610R-I00 Ministerio de Economía y Competitividad RTA2014-00015-C2-01 Ministerio de Ciencia e Innovación RYC2019-027244-I
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Publicado en:	Genetics, selection, evolution, Vol. 54 (June 2022) , art. 46, ISSN 1297-9686

DOI: 10.1186/s12711-022-00738-2
PMID: 35761200

15 p, 1.6 MB

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