Comparison of the gut microbiomes of 12 bony fish and 3 shark species

Givens, Carrie E.; Ransom, Briana; Bano, Nasreen; Hollibaugh, James T.

doi:10.3354/meps11034

Cited by 274 publications

(294 citation statements)

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“…As intestinal microbiota of fish play a key role in health, understanding the interactions between fish and gut microbiota is an important research field for fish health and aquaculture (van Kessel et al, 2011). Initial studies have shown that fish harbour a diverse microbiota, dependent on host species (Sullam et al, 2012, Li et al, 2014, Givens et al, 2015), life cycle stage (Giatsis et al, 2014, Ingerslev et al, 2014a, Zarkasi et al, 2014, Zarkasi et al, 2016) and diet (Navarrete et al, 2013, Wong et al, 2013, Ingerslev et al, 2014b). Fish present a unique case among vertebrates with microorganisms from environmental sources potentially having a much higher influence on bacterial composition and health status due to constant contact with water (Austin, 2006, Ringø et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

“…The fish intestine can harbour 10 7 to 10 11 bacteria/g intestinal content, with aerobes and facultative anaerobes being more abundant than obligate anaerobes, and can be split between the autochthonous species that are attached to the intestinal mucosa and the allochthonous that do not attach either due to lack of ability or outcompetition by mucous attached bacteria (Nayak, 2010, Navarrete et al, 2012, Llewellyn et al, 2014, Givens et al, 2015). …”

Section: Introductionmentioning

confidence: 99%

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Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.)

2017

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Gut microbes are key players in host immune system priming, protection and development, as well as providing nutrients to the host that would be otherwise unavailable. Due to this importance, studies investigating the link between host and microbe are being initiated in farmed fish. The establishment, maintenance and subsequent changes of the intestinal microbiota are central to define fish physiology and nutrition in the future. In fish, unlike mammals, acquiring intestinal microbes is believed to occur around the time of first feeding mainly from the water surrounding them and their microbial composition over time is shaped therefore by their habitat.Here we compare the distal intestine microbiota of Atlantic salmon parr reared in a recirculating laboratory aquarium with that of age matched parr maintained in cage culture in an open freshwater loch environment of a commercial fish farm to establish the microbial profiles in the gut at the freshwater stage and investigate if there is a stable subset of bacteria present regardless of habitat type. We used deep sequencing across two variable regions of the 16S rRNA gene, with a mean read depth of 180,144 ± 12,096 raw sequences per sample. All individual fish used in this study had a minimum of 30,000 quality controlled reads, corresponding to an average of 342 ± 19 Operational Taxonomic Units (OTUs) per sample, which predominantly mapped to the phyla Firmicutes, Proteobacteria, and Tenericutes.The results indicate that species richness is comparable between both treatment groups, however, significant differences were found in the compositions of the gut microbiota between the rearing groups. Furthermore, a core microbiota of 19 OTUs was identified, shared by all samples regardless of treatment group, mainly consisting of members of the phyla Proteobacteria, Bacteroidetes and Firmicutes. Core microbiotas of the individual rearing groups were determined (aquarium fish: 19 + 4 (total 23) OTUs, loch fish: 19 + 13 (total 32) OTUs), indicating that microbe acquisition or loss is occurring differently in the two habitats, but also that selective forces are acting within the host, offering niches to specific bacterial taxa.The new information gathered in this study by the Illumina MiSeq approach will be useful to understand and define the gut microbiota of healthy Atlantic salmon in freshwater and expand on previous studies using DGGE, TGGE and T-RFPL. Monitoring deviations from these profiles, especially the core microbes which are present regardless of habitat type, might be used in the future as early indicator for intestinal health issues caused by sub optimal feed or infectious diseases in the farm setting.Statement of relevanceThe Microbiome is central to gut health, local immune function and nutrient up take. We have used deep sequencing approach to show differences in rearing conditions of Atlantic salmon. This work is of interest to aquaculture nutritionists.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.)

2017

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“…The microbiomes of diverse marine animals are currently under study, from simplistic organisms including sponges (e.g., Webster et al, 2010) and ctenophores (Daniels and Breitbart, 2012) to more complex organisms such as sea squirts (Blasiak et al, 2014) and sharks (Givens et al, 2015). Below I present some of the current study systems that represent a diverse cross-section of marine animal phyla, and trends of research in these systems including focus on symbiosis and dysbiosis.…”

Section: Overview Of Diverse and Emerging Animal-microbiome Study Sysmentioning

confidence: 99%

Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean

2017

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All animals on Earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal-microbial relationships were historically explored in single host-symbiont systems. However, new explorations into the diversity of microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and a more multi-member microbiome. The potential for microbiomes to influence the health, physiology, behavior, and ecology of marine animals could alter current understandings of how marine animals adapt to change, and especially the growing climate-related and anthropogenic-induced changes already impacting the ocean environment. This review explores the nature of marine animal-microbiome relationships and interactions, and possible factors that may shift associations from symbiotic to dissociated states. I present a brief review of current microbiome research and opportunities, using examples of select marine animals that span diverse phyla within the Animalia, including systems that are more and less developed for symbiosis research, including two represented in my own research program. Lastly, I consider challenges and emerging solutions for moving these and other study systems into a more detailed understanding of host-microbiome interactions within a changing ocean.

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“…BOX FIGURE 1 | Depiction of a coral reef and associated microbiomes with organismal hosts [i.e., invertebrates Tianero et al, 2014;Hakim et al, 2016), seagrass (Ettinger et al, 2017;Fahimipour et al, 2017), fish (Ghanbari et al, 2015;Givens et al, 2015;Parris et al, 2016), corals (Barott et al, 2011;Blackall et al, 2015;Hester et al, 2016), macroalgae (Barott et al, 2011;Burke et al, 2011;Egan et al, 2013;Brodie et al, 2016), sponges Blackall et al, 2015), turf algae (Hester et al, 2016)] and environmental parameters [i.e., reef water (McCliment et al, 2012), sediment (Ettinger et al, 2017)]. The size of the bubble indicates a more species rich microbiome (based on OTUs).…”

Section: Overview Of the Beneficial Roles That Bacteria Play In Coralsmentioning

confidence: 99%

Responses of Coral-Associated Bacterial Communities to Local and Global Stressors

et al. 2017

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The microbial contribution to ecological resilience is still largely overlooked in coral reef ecology. Coral-associated bacteria serve a wide variety of functional roles with reference to the coral host, and thus, the composition of the overall microbiome community can strongly influence coral health and survival. Here, we synthesize the findings of recent studies (n = 45) that evaluated the impacts of the top three stressors facing coral reefs (climate change, water pollution and overfishing) on coral microbiome community structure and diversity. Contrary to the species losses that are typical of many ecological communities under stress, here we show that microbial richness tends to be higher rather than lower for stressed corals (i.e., in ∼60% of cases), regardless of the stressor. Microbial responses to stress were taxonomically consistent across stressors, with specific taxa typically increasing in abundance (e.g

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Comparison of the gut microbiomes of 12 bony fish and 3 shark species

Cited by 274 publications

References 57 publications

Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.)

Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.)

Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean

Responses of Coral-Associated Bacterial Communities to Local and Global Stressors

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