Fish Gut Microbiome: Current Approaches and Future Perspectives

Talwar, Chandni; Nagar, Shekhar; Lal, Rup; Negi, Ram Krishan

doi:10.1007/s12088-018-0760-y

Cited by 162 publications

(110 citation statements)

References 132 publications

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“…Despite this known biological importance, the composition of the intestinal microbiome in wild fish populations remains poorly understood. To date, studies of the fish intestinal microbiome have revealed a limited phylogenetic diversity, with genera from Proteobacteria, Firmicutes, and Bacteroidetes constituting up to 90% of the sequence reads across different species (Verner-Jeffreys et al, 2003;Ward et al, 2009;Ghanbari et al, 2015;Givens et al, 2015;Riiser et al, 2018;Talwar et al, 2018). Apart from this relatively low bacterial diversity, several studies have reported a limited geographical differentiation between intestinal bacterial communities, indicating a strong influence of host-associated factors on the composition of the gut microbiome (Ye et al, 2014;Llewellyn et al, 2016;Riiser et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

Riiser

Haverkamp

Varadharajan

et al. 2019

Environmental Microbiology

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Summary Atlantic cod (Gadus morhua) is an ecologically important species with a wide‐spread distribution in the North Atlantic Ocean, yet little is known about the diversity of its intestinal microbiome in its natural habitat. No geographical differentiation in this microbiome was observed based on 16S rRNA amplicon analyses, yet such finding may result from an inherent lack of power of this method to resolve fine‐scaled biological complexity. Here, we use metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway–located 470 km apart. Resolving the species community to unprecedented resolution, we identify two abundant species, Photobacterium iliopiscarium and Photobacterium kishitanii, which comprise over 50% of the classified reads. Interestingly, the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution.

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Section: Introductionmentioning

confidence: 99%

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

Riiser

Haverkamp

Varadharajan

et al. 2019

Environmental Microbiology

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“…), and the emerging importance of understanding the functional profiles of gut microbial communities through metagenomic analyses (Talwar et al. ). This review seeks to briefly touch on overarching themes of fish gut microbiome research, while highlighting numerous potential real‐world applications of fish gut microbiome research across sub‐disciplines in the aquatics and fisheries fields.…”

Section: The Gut Microbiotamentioning

confidence: 99%

Fish Gut Microbiome: A Primer to an Emerging Discipline in the Fisheries Sciences

2020

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High throughput next generation sequencing has propelled advances in genomic inquiry, including discoveries on the composition of the host gut microbiota. Research on mammals has demonstrated critical ways through which the gut microbiota influences host health and fitness, but applications involving fisheries are in their infancy. Given the breadth of research interests and importance of hatcheries in fisheries management and aquaculture in food production, studies investigating the gut microbiome of fish will play an integral role in promoting fish growth and health in all settings. This perspective highlights what is currently known about the fish gut microbiome, and how research can apply next generation sequencing and related methods to address emerging questions in fisheries and aquaculture. With continuing advances in sequencing technologies, gut microbiome research will change our understanding of the microbiota's role in fisheries and aquaculture through inquiry into the mutualistic relationship between microbes and fish hosts.

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“…The gill microbiome, and the interaction with N. perurans, may thus shape the host's immunological machinery and response to infection [12]. As in the case of other sh pathologies associated with microbiomes [35], AGD is thus a multifactorial gill disease [4], requiring complex interactions between environmental factors (temperature, salinity, etc. ), the sh microbiome, the host's metabolism, and pathogens.…”

Section: Freshwater Bathing Appears To Regulate Response Of N Peruramentioning

confidence: 99%

Dynamic Gill and Mucous Microbiomes Track an Amoebic Gill Disease Episode in Farmed Atlantic Salmon

Birlanga¹,

McCormack²,

Ijaz³

et al. 2020

Preprint

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Background Amongst gill disorders in Atlantic salmon, amoebic gill disease (AGD) is currently one of the most common and virulent, resulting in large losses for the aquaculture industry. However, our understanding of the role of the gill microbiome during AGD development is limited. Thus, we undertook a longitudinal study with the main objective of characterising the microbiome of gill, and mucous, samples from farmed Atlantic salmon before, and during, an AGD episode. Using a newly optimised DNA extraction protocol, we sequenced rRNA genes from 90 Atlantic salmon gill microbiomes from a fish farm (West coast of Ireland) over the course of a summer season. The first aetiological agent of AGD, Neoparamoeba perurans , was quantified using PCR targeting 18S rRNA genes. The same analyses were done using mucous samples as suitable, non-lethal alternatives to gill samples. Microbiome features across the sampling campaign were distinguished, focusing on patterns before and during the AGD episode. Results The richness and balance of the prokaryotic community on gills were trending upwards prior to the first appearance of AGD symptoms. The microbiome changed significantly, with reduced diversity and balance, after the AGD episode was confirmed, and the changing bacterial community was driven by competitive exclusion. However, this trend was reversed with the application of a first, and a second, freshwater bath treatment. Mucous samples behaved similarly. The variance of the entire prokaryotic community from both gill and mucous samples was significantly affected by the abundance of N. perurans . Rubritalea sp. were abundant in every gill and mucous sample; however, other genera ( Dyadobacter, Shewanella and Pedobacter ) were maximally abundant in gill and mucous samples 12 days prior to the first detection of AGD symptoms. Conclusions Gill and mucous microbiomes changed significantly after the first AGD symptoms were evident, correlating with N. perurans concentrations and supporting a connection between the development of the AGD and the gill microbiome. Those changes, however, were reversed by the application of multiple freshwater treatments, which returned gills to a more healthy state. Despite differences between microbiome features from gill and mucous samples, the data establish mucous scrapings as suitable, non-lethal substitutes for partial characterisation of the whole prokaryotic community from fish gills. The genus Shewanella was widely present, and significantly more abundant, immediately before the first AGD symptoms than during the AGD episode, marking this out as a feasible, putative target in identifying proxies for early detection of AGD.

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Fish Gut Microbiome: Current Approaches and Future Perspectives

Cited by 162 publications

References 132 publications

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

Fish Gut Microbiome: A Primer to an Emerging Discipline in the Fisheries Sciences

Dynamic Gill and Mucous Microbiomes Track an Amoebic Gill Disease Episode in Farmed Atlantic Salmon

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