A mixed model approach for estimating drivers of microbiota community composition and differential taxonomic abundance

Amy Sweeny, Hannah Lemon, Anan Ibrahim, Kathryn Watt, Kenneth Wilson, Dylan Z. Childs, Daniel H Nussey, Andrew Free, Luke McNally

Research output: Contribution to journalArticlepeer-review


Next-generation sequencing (NGS) and metabarcoding approaches are increasingly applied to wild animal populations, but there is a disconnect between the widely-applied generalised linear mixed model (GLMM) approaches commonly used to study phenotypic variation and the statistical toolkit from community ecology typically applied to metabarcoding data. Here, we describe the suitability of a novel GLMM-based approach for analysing the taxon-specific sequence read counts derived from standard metabarcoding data. This approach allows decomposition of the contribution of different drivers to variation in community composition (e.g. age, season, individual), via interaction terms in the model random effects structure. We provide guidance to implementing this approach, and show how these models can identify how responsible specific taxonomic groups are for the effects attributed to different drivers. We applied this approach to two cross-sectional data sets from the Soay Sheep population of St. Kilda. GLMMs showed agreement to dissimilarity-based approaches highlighting substantial contribution of age and minimal contribution of season to microbiota community compositions, and simultaneously estimated contribution of other technical and biological factors. We further used model predictions to show that age effects were principally due to increases in taxa of the phylum Bacteroidetes and declines in taxa of the phylum Firmicutes. This approach offers a powerful means for understanding the influence of drivers of community structure derived from metabarcoding data. We discuss how our approach could be readily adapted to allow researchers to estimate contributions of additional factors such as host or microbe phylogeny to answer emerging questions surrounding the ecological and evolutionary roles of within-host communities.
Original languageEnglish
Number of pages28
Publication statusAccepted/In press - 8 May 2023


  • microbiota
  • metabarcoding
  • 16S
  • amplicon sequence variants
  • generalised linear mixed effects model
  • community composition
  • differential abundance
  • Bayesian estimation


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