Microbiomes in the context of developing sustainable intensified aquaculture

Abstract

With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining sustainable in terms of environmental impact and promoting good welfare and health in farmed species. Microbiomes fundamentally underpin animal health, being a key part of their digestive, metabolic and defense systems, in the latter case protecting against opportunistic pathogens in the environment. The potential to manipulate the microbiome to the advantage of enhancing health, welfare and production is an intriguing prospect that has gained considerable traction in recent years. In this review we first set out what is known about the role of the microbiome in aquaculture production systems across the phylogenetic spectrum of cultured animals, from invertebrates to finfish. With a view to reducing environmental footprint and tightening biological and physical control, investment in “closed” aquaculture systems is on the rise, but little is known about how the microbial systems of these closed systems affect the health of cultured organisms. Through comparisons of the microbiomes and their dynamics across phylogenetically distinct animals and different aquaculture systems, we focus on microbial communities in terms of their functionality in order to identify what features within these microbiomes need to be harnessed for optimizing healthy intensified production in support of a sustainable future for aquaculture.

Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus

“…The HBW samples all have similar microbiomes, and therefore may be considered as an indicator of a standard microbial membership and composition for healthy sea urchins in our aquarium. However, it should be noted that a single “healthy” microbiome likely does not exist, as a major characteristic of a healthy microbiome is its ability to be dynamic [ 23 ]. Nonetheless, because the microbiomes of the DBW samples differ from those of the HBW samples (regions of non-lesioned tissue) from sea urchins in the same aquarium, this indicates that the spotting disease infection affects surface areas of the sea urchin that are outside of the observable lesions.…”

“…Although previous studies have focused on identifying the causative agent underlying spotting disease, which suggests a wide array of pathogenic bacteria, few studies have reported an analysis of microbiomes of tissues from sea urchins infected with spotting disease [ 5 ]. Furthermore, none report the microbiome of tissues from sea urchins housed in a closed aquarium system, which have distinct properties and dynamics compared to open aquarium systems, leading to direct impacts on the host microbiome [ 23 ]. Because the microbiome on sea urchins shifts when transferred from the ocean to a closed aquarium [ 24 ], sampling sea urchins housed in the same aquarium system allows direct comparisons among the microbiome samples.…”

Genetics and Genomics of Infectious Diseases in Key Aquaculture Species

“…This study is not intended to offer an exhaustive review of the existing literature on these subjects. A more comprehensive exploration of these themes can be found in recent review articles [35,36]. The current paper aims to emphasize the key discoveries derived from our research employing genetic and genomics methodologies to enhance disease resistance, focusing on three principal aquaculture species: white leg shrimp (Litopenaeus vannamei), striped catfish (Pangasianodon hypophthalmus), and yellowtail kingfish (Seriola lalandi).…”

Comparative analysis of the structural and compositional change of spotted sea bass (Lateolabrax maculatus) gut microflora following Aeromonas veronii infection and the effects of Lactobacillus plantarum on these changes

“…It plays an increasingly important role in the global food supply. [2][3][4] Infectious diseases caused by viruses, bacteria, and other pathogens are common occurrences in the aquaculture industry, resulting in substantial economic losses and significantly im-pacting its sustainable development. 5 As aquaculture plays a vital role in global food security, understanding and managing the factors influencing fish health, such as gut microbiota dynamics during infections, contribute to ensuring a stable and secure food supply.…”