About this Research Topic

Submission closed

Background

The microbiota of aquatic animals are highly species- and tissue-specific, underlying the balance that exists among the host respiratory, skin and gastrointestinal microbiota. Most of the research on host-microbiome interactions has been developed on aquaculture species, highlighting the importance of the microbiome for the health, performance and most physiological functions. It is now clear that the composition of the fish gastrointestinal microbiota is essential for the host fitness, is strongly modulated by host diet or local environmental factors and has wide effects on the animal physiology. Besides optimizing nutrient uptake, the gut microbiome is involved in immunomodulation, maintaining mucosal tolerance, and enhancing the host’s resilience against infectious diseases. Consequently, understanding microbiome dynamics in aquaculture species plays an indispensable role in promoting animal health and industrial sustainability. On the other hand, studies with an integrative approach on how the ever-increasing known and emerging stressors (eutrophication, ocean acidification, pollution agents) in aquatic ecosystems impact host-associated and free-living bacterial communities, are falling behind. Advanced knowledge on the composition and physiological functions of tissue-specific microbiomes, in relation to how aquatic environment stress factors influence their structure, is fundamental in order to explore the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems.

Based on the amassed contextual description/quantification of microbiome composition in different species and physiological challenges, research can now progress and ascertain the upshots of this wealth of information, implement its use to routinely test the adequacy of rearing systems and parameters, feeding formulas, new sources of protein in feedings, immune reactions and animal densities, etc., and include that data in the panel of physiological markers currently used to diagnose animal welfare. Equally, we need now to focus on the functional relevance of the microbiome and of its alterations to the aquatic organisms’ physiology and how this impacts their ability to overcome stressors in a global change context.

This Research Topic is aimed at compiling both research and review papers on the latest research on the microbiota/microbiome of aquatic animals, with emphasis on aquaculture species and a physiological context, to highlight key advances and outcomes. To this end, we welcome papers related to:

i) Microbiome composition as both an element and a consequence of host physiology and environmental stressors.
ii) Understanding agents of alterations in the microbiota interaction with their hosts, that bring about reduced host performance and welfare, i.e. compromised physiological performance.
iii) Improvement of methodology for microbiome dysbiosis as a biomarker, adequate to implement in routine diagnostic.
iv) Identification of pro- and prebiotics in relation to new sources of protein-based feeds, and their physiological consequences.
v) Identification of knowledge gaps (both methodological and conceptual) and priorities in microbiome research

Keywords: Microbiota, Dysbiosis, Gastrointestinal tract, Plant-based feeds, Gut bacteria, animal nutrition and production, anti-nutritional factors, digestive capacity, carbohydrolytic capacity, proteolytic capacity, fish gut epithelium, physiological and inflammatory imbalances, 16S rRNA, new probiotics

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

Topic editors

filomena fonseca
University of Algarve
Faro, Portugal

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