Exploring fish microbial communities to mitigate emerging diseases in aquaculture

Abstract

Aquaculture is the fastest growing animal food sector worldwide and expected to further increase to feed the growing human population. However, existing and (re-)emerging diseases are hampering fish and shellfish cultivation and yield. For many diseases, vaccination protocols are not in place and the excessive use of antibiotics and other chemicals is of substantial concern. A more sustainable disease control strategy to protect fish and shellfish from (re-)emerging diseases could be achieved by introduction or augmentation of beneficial microbes. To establish and maintain a 'healthy' fish microbiome, a fundamental understanding of the diversity and temporal-spatial dynamics of fish-associated microbial communities and their impact on growth and health of their aquatic hosts is required. This review describes insights in the diversity and functions of the fish bacterial communities elucidated with next-generation sequencing and discusses the potential of the microbes to mitigate (re-)emerging diseases in aquaculture.

Spatiotemporal successions of shrimp gut microbial colonization: high consistency despite distinct species pool

“…First, comprehensive study on the gut microbiota of invertebrates lags far behind our understanding on vertebrates, such as human and fishes. On these biases, and given the functional importance of gut microbiota in improving host fitness (Mcfall-Ngai et al, 2013), a better understanding of the host-bacterial colonization pattern could afford an initial step to reestablish and sustain a 'healthy' gut microbiota (de Bruijn et al, 2017;Xiong, 2018). Furthermore, L. vannamei is the most valuable aquaculture shrimp species worldwide, while its aquaculture is being threatened by diverse diseases (Thitamadee et al, 2016).…”

“…Furthermore, L. vannamei is the most valuable aquaculture shrimp species worldwide, while its aquaculture is being threatened by diverse diseases (Thitamadee et al, 2016). On these biases, and given the functional importance of gut microbiota in improving host fitness (Mcfall-Ngai et al, 2013), a better understanding of the host-bacterial colonization pattern could afford an initial step to reestablish and sustain a 'healthy' gut microbiota (de Bruijn et al, 2017;Xiong, 2018). The isogenous shrimp in distant farms provides a natural setup to inquire convergence, divergence and repeatability in patterns of gut microbiota dynamics as a function of the host age and environment.…”

Using fish models to investigate the links between microbiome and social behaviour: The next step for translational microbiome research?

“…The use of fish in microbiome‐related research is expanding (Llewellyn et al., ), although currently the research is mostly ecological or diet focused on farmed or commercially valuable fish species (Box ). Similar to mammals, the gut microbiome of fish seems to play an important role in the innate immune response (e.g., de Bruijn et al., ; Gómez & Balcázar, ; Tarnecki et al., ), fish have also been shown to exhibit ontogenetic shifts in microbiome composition (Falcinelli et al., ; Hall et al., ; Roeslers et al., ; Shin et al., ), and there is also a diluting effect in microbiome differences caused by social proximity (Burns et al., ).…”

“…Similar to mammals, the gut microbiome of fish seems to play an important role in the innate immune response (e.g., de Bruijn, Liu, Wiegertjes, & Raaijmakers, ; Gómez & Balcázar, ; Tarnecki et al, 2017). Disentangling the links between microbiome and fish health is a hot topic, particularly given the growth of the aquaculture industry.…”

“…The monocultural and relatively sterile conditions of aquaculture tend to produce fish unable to appropriately cope with novel and complex (natural) environments. The lack of previous exposure to predators limits individual recognition which may become fatal (Brown & Warburton, 1999). 4.…”