A new view of the fish gut microbiome: Advances from next-generation sequencing

Ghanbari, Mahdi; Kneifel, Wolfgang; Domig, Konrad J.

doi:10.1016/j.aquaculture.2015.06.033

Cited by 515 publications

(430 citation statements)

References 89 publications

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“…During the past three decades, an increasing attention was paid to studying the versatile role of microbes in the nutrition of fishes Nayak, 2010;Ray et al, 2012;Ghanbari et al, 2015). Microorganisms may contribute to fish nutrition either directly as part of the ingested and digested food Matĕna et al, 1995;Kamjunke and Mehner, 2001) or indirectly by colonizing their digestive tracts and participating in digestion processes, influencing absorption and synthesis of important nutrients (Ray et al, 2012;Li et al, 2013;Clements et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

“…In addition, the importance of this food resource often seems to be marginal Matĕna et al, 1995;Kamjunke and Mehner, 2001). However, all fish species have specific microbe communities thriving in their digestive tracts (Ghanbari et al, 2015). Composition and functioning of these intestinal microbes change along sections of the digestive tract and vary among fish species and across habitats (Sullam et al, 2012;Li et al, 2014;Ni et al, 2014;Li et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Gut content microbiota of introduced bigheaded carps ( Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

Borsodi

Krett

Felföldi

et al. 2017

Microbiological Research

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Studying the microbiota in the alimentary tract of bigheaded carps (Hypophthalmichthys spp.) gained special interest recently, as these types of investigations on non-native fish species may lead to a better understanding of their ecological role and feeding habits in an invaded habitat. For microbiological examinations, bigheaded carp gut contents and water column samples from Lake Balaton (Hungary) were collected from spring to autumn in 2013.Denaturing Gradient Gel Electrophoresis (DGGE) and pyrosequencing of the 16S rRNA gene were performed to reveal the composition. According to the DGGE patterns, bacterial communities of water samples separated clearly from that of the intestines. Moreover, the bacterial communities in the foreguts and hindguts were also strikingly dissimilar. Based on pyrosequencing, both foregut and hindgut samples were predominated by the fermentative genus Cetobacterium (Fusobacteria). The presence of some phytoplankton taxa and the high relative abundance of cellulose-degrading bacteria in the guts suggest that intestinal microbes may have an important role in digesting algae and making them utilizable for bigheaded carps that lack cellulase enzyme. In turn, the complete absence of typical heterotrophic freshwater bacteria in all studied sections of the intestines indicated that bacterioplankton probably has a negligible role in the nutrition of bigheaded carps.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Gut content microbiota of introduced bigheaded carps ( Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

Borsodi

Krett

Felföldi

et al. 2017

Microbiological Research

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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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“…The potential reason for differentiation in spoilage pattern when dietary FM and FO are replaced can be possibly attributed to microbiota alterations in the intestine and mucus. It has been clearly indicated that fish gut microbiota is highly affected by a number of environmental parameters including diet [51]. Changes of intestinal microbiota have been indicated in rainbow trout when fed with plant-based diets and these include both the increase in numbers and the alteration of predominant microbe genera [52,53].…”

Section: Days In Icementioning

confidence: 99%

Impact of Diets Containing Plant Raw Materials as Fish Meal and Fish Oil Replacement on Rainbow Trout (Oncorhynchus mykiss), Gilthead Sea Bream (Sparus aurata), and Common Carp (Cyprinus carpio) Freshness

Grigorakis

Kogiannou

Corraze

et al. 2018

Journal of Food Quality

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The present study aimed to evaluate whether the total or high substitution of fish meal (FM) and fish oil (FO) by sustainable plant raw materials (plant meal and oils) in long-term feeding for rainbow trout, gilthead sea bream, and common carp can result in spoilage alterations during ice storage. These three species were fed throughout their whole rearing cycle with plant-based diets and compared to counterparts that received FM/FO-based diets or commercial-like diets. Sensory QIM schemes adopted for these species and ATP breakdown products ( -value and components) were used to evaluate the freshness. Sensory acceptability of 14, 15, and 12 days was found for rainbow trout, gilthead sea bream, and common carp, respectively. This corresponded to -values of approximately 80%, 35%, and 65% for rainbow trout, gilthead sea bream, and common carp, respectively. No major effect of dietary history on postmortem shelf life was shown for gilthead sea bream and common carp; neither sensory-perceived nor chemical freshness showed diet-related differences. Rainbow trout fed with the plant-based diet exhibited slightly worse sensory freshness than fish fed with FM/FO-based diets, at the end of shelf life. These findings imply that FM and FO can be successfully substituted without major impacts on shelf life of fish.

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A new view of the fish gut microbiome: Advances from next-generation sequencing

Cited by 515 publications

References 89 publications

Gut content microbiota of introduced bigheaded carps ( Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

Gut content microbiota of introduced bigheaded carps ( Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

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

Impact of Diets Containing Plant Raw Materials as Fish Meal and Fish Oil Replacement on Rainbow Trout (Oncorhynchus mykiss), Gilthead Sea Bream (Sparus aurata), and Common Carp (Cyprinus carpio) Freshness

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