Key Drivers of Ecological Assembly in the Hindgut of Atlantic Cod (Gadus morhua) when Fed with a Macroalgal Supplemented diet – How Robust Is the Gut to Taxonomic Perturbation?

Abstract

The microbiota in the gastrointestinal tract of any species is shaped by internal and external cues in addition to random events which can be difficult to disentangle from a range of interacting variables. Estimating ecological assembly processes can help elucidate these factors. In our study, farmed Atlantic cod (Gadus morhua) were fed a diet of 10% macroalgae supplement (Ulva rigida species [ULVA] or Ascophyllum nodosum [ASCO] or a non-amended control diet [CTRL]) over a 12-week period and the ecological assembly processes quantified. The CTRL samples showed selection (variable selection - divergence in communities related to selective environmental conditions) as a key assembly process, while dispersal limitation (limited movement results in divergent communities through stochastic processes) was a driver of the gut microbiome for fish fed the macroalgae supplemented diet at Week 12 (i.e., ASCO and ULVA). Fish from the ASCO grouping diverged into ASCO_N (normal) and ASCO_LG (lower growth), where ASCO_LG individuals found the diet unpalatable. The recruitment of new taxa over time was altered in the ASCO_LG fish, with the gut microbiome showing phylogenetic under dispersion (nepotistic recruitment of species). Finally, the gut microbiome (CTRL and ULVA only) showed increasing robustness to taxonomic disturbance over time and an increase in functional redundancy. This study advances our understanding of the ecological assembly and succession in the hindgut of juvenile Atlantic cod across dietary regimes. Understanding the processes driving ecological assembly in the gut microbiome, in fish research specifically, could allow us to manipulate the microbiome for improved health or resilience to disease for improved aquaculture production.

Beyond Basic Diversity Estimates—Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data

“…This will allow for basic diversity statistics, the identification of discriminant taxa and a core microbiome (e.g., [ 43 ]). However, for more advanced ecological modelling to be applied, usually a minimum of five to six replicates are required; this will usually satisfy criteria for the null models which often underpin community assembly analysis (e.g., [ 18 , 44 , 45 ]). Finally, for even more involved methods such as network inferences, upwards of 35 samples per category are often necessary to obtain reliable results (e.g., [ 46 , 47 ]).…”

“…Using simulated stochastic and deterministic metacommunities, Tucker et al (2016) were able to use the abundance-based ß-null deviation measures to differentiate between niche and neutral community assembly. This has since been applied to understand the community assembly of fish (Atlantic cod) microbiomes [ 45 ] and marine bioplankton [ 19 ].…”

“…In contrast, if D < 0, then phylogenetically similar taxa are preferentially added to the community (underdispersed—or nepotistic ). This model has been implemented to understand recruitment trends in microbiomes [ 45 , 121 ] where the communities were generally nepotistic and recruitment was disrupted in ‘perturbed’ communities.…”