A primer on metagenomics and next‐generation sequencing in fish gut microbiome research

Abstract

Fishes constitute a vital component of the aquatic ecosystem, that interacts with physical, chemical, and biological components of the ecosystem. They are found in almost all aquatic environments ranging from high mountain streams to the abyssal and hadal zones of the deepest oceans. With an origin dating back to 600 million years and an estimate of 34,600 species described till date (FishBase, 2021), fishes comprise nearly half of the total vertebrate diversity (Nelson, 2007).Fishes are associated with complex assemblages of microorganisms, comprising bacteria, archaea, viruses, yeasts, and protists, collectively known as 'microbiota' or 'microbiome' (Merrifield & Rodiles, 2015). The characteristic microbial community inhabiting a particular environment along with their genomes and theatre of activity is referred to as the 'microbiome' (Gilbert et al., 2016;Prescott, 2017). However, in certain contexts, the term 'microbiota' is used to define the collection of microorganisms and the term 'microbiome' to refers to the collection of microbial genomes (Burokas et al., 2015).Microorganisms take residence in almost every organ of the fish such as skin, gills, digestive tract, internal organs like the liver, kidney, spleen, and light-emitting organs (Austin, 2002). However, fish gut microflora is often acclaimed as an 'extra organ' owing to its significant contribution to important physiological functions of the host such as digestion, metabolism, reproduction, development, and immune response (Butt & Volkoff, 2019). Further, the composition of the gut microflora is affected by a plethora of factors such as habitat salinity, temperature, trophic level, taxonomy, feeding habits and host selective pressures within the gut, leading to the development of a unique and diverse microflora (Bevins & Salzman, 2011;Sullam et al., 2012). Therefore, it may be safely presumed that the fish gut microbiome, representing 'worlds within worlds' (Butt & Volkoff, 2019) is a biodiversity hotspot and a promising source for bioprospecting applications.

Research Progress of the Gut Microbiome in Hybrid Fish

“…Fish comprise nearly 50% of the total vertebrate diversity, and more than 34,000 species have been described to date, constituting a crucial part of the aquatic ecosystem [ 15 , 16 ]. Microorganisms exist in almost every fish organ, including the skin, digestive tract, internal organs, and luminous organs [ 17 ].…”

“…The gastrointestinal microbiota of fish mainly consist of aerobic or facultative anaerobic microorganisms and facultative and obligate anaerobes [ 20 , 22 , 23 , 24 ]. Among them, Proteobacteria, Firmicutes, and Bacteroidetes constitute 90% of the gut microbiome of most fish [ 15 ]. In addition, Actinobacteria, Fusobacteria, Bacilli, Clostridia, and Verrucomicrobia are the dominant bacterial phyla in fish gut microorganisms [ 15 , 25 , 26 , 27 , 28 , 29 ].…”

“…Among them, Proteobacteria, Firmicutes, and Bacteroidetes constitute 90% of the gut microbiome of most fish [ 15 ]. In addition, Actinobacteria, Fusobacteria, Bacilli, Clostridia, and Verrucomicrobia are the dominant bacterial phyla in fish gut microorganisms [ 15 , 25 , 26 , 27 , 28 , 29 ]. The gut microbiota of fish participate in various physiological functions.…”

“…The gut microbiota of fish participate in various physiological functions. There are several beneficial effects on the host, such as reproduction, development, nutrition, immunity, and stress responses, and the gut microbiota are often referred to as an ‘extra organ’ [ 15 , 30 ]. Nayak has described the role of fish gastrointestinal microbiota in nutrition, immunity, and health management [ 20 ].…”

“…These new research methods have led to a better understanding of the connections between the microorganisms and their respective hosts. The Illumina system, Roche 454 system, and Ion Torrent Personal Genome Machine (PGM) are the primary next-generation sequencing (NGS) platforms used in fish gut microbiome research, and the Illumina system is the most commonly used [ 15 ].…”