Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

Abstract

Despite their importance to host health and development, the communities of microorganisms associated with humans and other animals are characterized by a large degree of unexplained variation across individual hosts. The processes that drive such inter-individual variation are not well understood. To address this, we surveyed the microbial communities associated with the intestine of the zebrafish, Danio rerio, over developmental time. We compared our observations of community composition and distribution across hosts with that predicted by a neutral assembly model, which assumes that community assembly is driven solely by chance and dispersal. We found that as hosts develop from larvae to adults, the fit of the model to observed microbial distributions decreases, suggesting that the relative importance of non-neutral processes, such as microbe-microbe interactions, active dispersal, or selection by the host, increases as hosts mature. We also observed that taxa which depart in their distributions from the neutral prediction form ecologically distinct subgroups, which are phylogenetically clustered with respect to the full metacommunity. These results demonstrate that neutral processes are sufficient to generate substantial variation in microbiota composition across individual hosts, and suggest that potentially unique or important taxa may be identified by their divergence from neutral distributions.

Experimental Manipulation Shows a Greater Influence of Population than Dietary Perturbation on the Microbiome of Tyrophagus putrescentiae

“…We hypothesize that the different proportions of Cardinium/Wolbachia or Blattabacteriumlike/Wolbachia bacteria at the population level after perturbation could result in changes in population growth due to the various combinations of endosymbiotic bacteria in T. putrescentiae individuals. Similar changes have been observed in insects (2, 4) although the effects of these symbionts could also be the results of neutral processes (25). However, additional experiments are necessary to compare the effects of endosymbiotic bacteria on T. putrescentiae population growth.…”

Global-scale structure of the eelgrass microbiome

“…Generalized linear models with negative binomial error distributions were fitted to TMM-normalized OTU counts after removing underpowered OTUs (OTUs that were detected fewer than five times), and differentially abundant taxa on host samples were identified using a likelihood ratio test. We focused subsequent analyses on OTUs that were significantly host enriched (Benjamini-Hochberg adjusted P Ͻ 0.01), as these taxa represent portions of the microbiome that were most likely to be actively selected for by the host (61).…”

Assembly of seed-associated microbial communities within and across successive plant generations

“…The Sloan model predicts that abundant entities in the large community are widespread across samples because their dispersal could occur by chance, while rare members are more likely to be lost by ecological drift in the local community. We used a custom R script written by Burns and collaborators for fitting the Sloan neutral community model to OTU distribution (Burns et al 2016). Goodness of fit of was assessed with root mean squared errors (RMSE) and compared with the fit of a binomial distribution model using the Akaike information criterion (AIC).…”