Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics.
TLDR
This review aims to summarize the available knowledge on fish gastrointestinal communities obtained from metagenomics, including biases from sample processing, factors influencing assemblage structure, intestinal microbiology of important aquaculture species and description of the teleostean core microbiome.Abstract:
The gut microbiome of vertebrates plays an integral role in host health by stimulating development of the immune system, aiding in nutrient acquisition and outcompeting opportunistic pathogens. Development of next-generation sequencing technologies allows researchers to survey complex communities of microorganisms within the microbiome at great depth with minimal costs, resulting in a surge of studies investigating bacterial diversity of fishes. Many of these studies have focused on the microbial structure of economically significant aquaculture species with the goal of manipulating the microbes to increase feed efficiency and decrease disease susceptibility. The unravelling of intricate host-microbe symbioses and identification of core microbiome functions is essential to our ability to use the benefits of a healthy microbiome to our advantage in fish culture, as well as gain deeper understanding of bacterial roles in vertebrate health. This review aims to summarize the available knowledge on fish gastrointestinal communities obtained from metagenomics, including biases from sample processing, factors influencing assemblage structure, intestinal microbiology of important aquaculture species and description of the teleostean core microbiome.read more
Citations
More filters
Journal ArticleDOI
The Gut Microbiota of Marine Fish.
Sian Egerton,Sarah C. Culloty,Jason Whooley,Catherine Stanton,Catherine Stanton,R. Paul Ross,R. Paul Ross +6 more
TL;DR: The factors shaping marine fish gut microbiota are reviewed and gaps in the research are highlighted and a clear understanding of the role that specific gut microbiota play is still lacking.
Journal ArticleDOI
Gut Microbiota and Energy Homeostasis in Fish.
Robyn Lisa Butt,Hélène Volkoff +1 more
TL;DR: Current knowledge on the possible effects of microbiota on feeding, digestive processes, growth, and energy homeostasis in fish is described, with emphasis on the influence of brain and gut hormones, environmental factors, and inter-specific differences.
Journal ArticleDOI
Lactic Acid Bacteria in Finfish—An Update
TL;DR: Results indicate that LAB may vary in their immunological effects depending on the species and hosts, which includes their impacts on finfish aquaculture, possible routes for treatment and their interaction with fish immune responses.
References
More filters
Journal ArticleDOI
EFFECTS OF PLANT-BASED DIETS ON THE DISTAL GUT MICROBIOME OF RAINBOW TROUT (Oncorhynchus mykiss).
Atul R. Desai,Matthew G. Links,Stephanie A. Collins,Graeme S. Mansfield,M. D. Drew,Andrew G. Van Kessel,Janet E. Hill +6 more
TL;DR: It is demonstrated that changes in the intestinal microbiome that may contribute to negative health outcomes when diets contain plant meal proteins can be minimized with additional processing of plant ingredients.
Journal ArticleDOI
Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.).
TL;DR: Deep sequencing approach using the Illumina MiSeq approach shows differences in rearing conditions of Atlantic salmon, 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.
Journal ArticleDOI
The biogeography of the atlantic salmon (Salmo salar) gut microbiome
Martin S. Llewellyn,Philip McGinnity,Melanie Dionne,Justine Letourneau,Florian Thonier,Gary R. Carvalho,Simon Creer,Nicolas Derome +7 more
TL;DR: Patterns of Mycoplasmataceae phylotype recruitment to the intestinal microbial community among sites and life-cycle stages support a dual role for deterministic and stochastic processes in defining the composition of the S. salar gut microbiome.
Journal ArticleDOI
Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota
Chris C. R. Smith,Lisa K. Snowberg,J. Gregory Caporaso,J. Gregory Caporaso,Rob Knight,Daniel I. Bolnick +5 more
TL;DR: The results suggest that population level differences in stickleback gut microbiota may depend more on internal sorting processes (host genotype) than on colonization processes (transient environmental effects), which are associated with multiple covarying ecological variables.
Journal ArticleDOI
The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing
Nicholas A. Kennedy,Alan W. Walker,Susan H. Berry,Sylvia H. Duncan,Freda M. Farquarson,Petra Louis,John M. Thomson,Jack Satsangi,Harry J. Flint,Julian Parkhill,Charlie W. Lees,Georgina L. Hold +11 more
TL;DR: Significant differences in DNA yield and bacterial DNA composition when comparing DNA extracted from the same fecal sample with different extraction kits are demonstrated, highlighting the importance of ensuring that samples in a study are prepared with the same method, and the need for caution when cross-comparing studies that use different methods.