Beyond Microbial Variability: Disclosing the Functional Redundancy of the Core Gut Microbiota of Farmed Gilthead Sea Bream from a Bayesian Network Perspective

The significant microbiota variability represents a key feature that makes the full comprehension of the functional interaction between microbiota and the host an ongoing challenge. To overcome this limitation, in this study, fish intestinal microbiota was analyzed through a meta-analysis, identifyi...

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Bibliographic Details
Published in:Microorganisms (Basel) 2025-01, Vol.13 (1), p.198
Main Authors: Moroni, Federico, Naya-Català, Fernando, Hafez, Ahmed Ibrahem, Domingo-Bretón, Ricardo, Soriano, Beatriz, Llorens, Carlos, Pérez-Sánchez, Jaume
Format: Article
Language:English
Subjects:
Aquaculture
Bacteria
Bayesian analysis
Bream
Clustering
core microbiota
Data analysis
Datasets
Diet
Fish
fish gut microbiome
Functional plasticity
functional redundancy
Heterogeneity
Homogeneity
Intestinal microflora
Livestock
Mathematical models
Metabolism
Microbiota
microbiota biomarkers
Microorganisms
processed animal proteins
Redundancy
taxonomical variability
Taxonomy
Variability
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Summary:The significant microbiota variability represents a key feature that makes the full comprehension of the functional interaction between microbiota and the host an ongoing challenge. To overcome this limitation, in this study, fish intestinal microbiota was analyzed through a meta-analysis, identifying the core microbiota and constructing stochastic Bayesian network (BN) models with SAMBA. We combined three experiments performed with gilthead sea bream juveniles of the same hatchery batch, reared at the same season/location, and fed with diets enriched on processed animal proteins (PAP) and other alternative ingredients (NOPAP-PP, NOPAP-SCP). Microbiota data analysis disclosed a high individual taxonomic variability, a high functional homogeneity within trials and highlighted the importance of the core microbiota, clustering PAP and NOPAP fish microbiota composition. For both NOPAP and PAP BNs, >99% of the microbiota population were modelled, with a significant proportion of bacteria (55-69%) directly connected with the diet variable. Functional enrichment identified 11 relevant pathways expressed by different taxa across the different BNs, confirming the high metabolic plasticity and taxonomic heterogeneity. Altogether, these results reinforce the comprehension of the functional bacteria-host interactions and in the near future, allow the use of microbiota as a species-specific growth and welfare benchmark of livestock animals, and farmed fish in particular.
ISSN:2076-2607
2076-2607
DOI:10.3390/microorganisms13010198