Table 1.
Studies evaluating the diversity of teleost-associated microbial communities.
| Study | Fish species | Fish origina | Organ | Sequences derived (approx.) | Target/technique | Phyla (order of abundance) | Notable genera/findings |
|---|---|---|---|---|---|---|---|
| Di Maiuta et al., 2013 | Panaque sp. (catfish) | A | Faeces samples externally | 143,670 | 16S/454 pyroseqeuncing | Fusobacteria, Cyanobacteria, Beta-proteobacteria, Flavobacteria, Clostridia + other minor groups | Putative cellulolytic bacteria identified Aeromonas sp., Flavobacterium sp., Bacteroides sp., Clostridium sp., and Pseudomonas sp. |
| Desai et al., 2012 | Oncorhynchus mykiss | A | Intestinal contents | 99,568 | 16S/454 pyroseqeuncing + DGGE | Proteobacteria, Firmicutes, Actinobacteria, Bacteriodetes | NA |
| Ye et al., 2014 | Dorosoma cepedianum | W | Intestinal mucosa and contents | 400,000+ | 16S/454 pyroseqeuncing | Cyanobacteria/Cholorplast, Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Fusobatceria, Planctomycetes, Chloroflexi, Crenarchaeota | Significant differences between foregut and hindgut microbiota, but not between species |
| Ye et al., 2014 | Hypophthalmichthys molitrix | W | Intestinal mucosa and contents | 400,000+ | 16S/454 pyroseqeuncing | Cyanobacteria/Chloroplast, Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Fusobatceria, Planctomycetes, Chloroflexi, Crenarchaeota | Significant differences between foregut and hindgut microbiota, but not between species |
| Geraylou et al., 2013 | Acipenser baerii | A | Hindgut contents | 29,318 | 16S/454 pyroseqeuncing | Fusobacteria/Firmicutes, Chlamydiae, Bacteriodetes, Actinobacteria | Arabinoxylan oligosaccharide prebuiotics modulate hindgut microbiome composition |
| Star et al., 2013 | Gadus morhua | W | Intestinal contents | 280,447 | 16S/454 pyroseqeuncing | Proteobacteria (mostly Vibrionacae), Bacteriodetes, Firmicutes, other minor groups | Large inter-indivudual differences in community composition for fish captured at the same site |
| Li et al., 2013 | Cyprinus carpio (transgenic) | A | Intestinal mucosa and contents | 621,110 | 16S/454 pyroseqeuncing + DGGE | Proteobacteria, Fusobacteria, Bacteroidetes, Firmicutes | Differential abundance of bacterial phyla between fast growing transgenic and wild type. Firmicutes: Bacteriodetes ratio differences between transgenic and wild type |
| Semova et al., 2012 | Dario rerio | A | Hindgut | 10,000+ (data not shown) | 16S/454 Pyrosequencing | Firmicutes, Proteobatceria, Bacteriodetes + minor phyla | Microfolora enhance fatty acid uptake in the zebrafish intestine |
| Wu et al., 2012b | Ctenopharyngodon idellus | A | Intestinal mucosa | 93,991 | 16S/454 Pyrosequencing | Firmicutes, Baceriodes, Proteobatceria, Spirochaetes | Cellulose digesting genera present—Anoxybacillus, Leuconostoc, Clostridium, Actinomyces, Citrobacter |
| Wu et al., 2012b | Ctenopharyngodon idellus | A | Intestinal contents | 93,991 | 16S/454 Pyrosequencing | Firmicutes, Cyanobacteria, Proteobacteria, Bacteriodetes | Cellulose digesting genera present—Anoxybacillus, Leuconostoc, Clostridium, Actinomyces, Citrobacter |
| Roeselers et al., 2011 | Dario rerio | A/Wild | Intestinal mucosa and contents | 22,980 | 16S/454 Pyrosequencing, Sanger sequence, TRFLP profiling | Proteobacteria, Fusobacteria, Firmicutes, Actinobateria | Core microbiome: γ-Proteobacteria, β-Proteobacteria, Fusobacteria, Bacilli, Flavobacteria, Actinobacteria classes, Aeromonas, Shewanella |
| Martin-Antonio et al., 2007 | Solea senegalensis | A | Intestinal mucosa and contents | 176 | 16S/Culture + Sanger Sequencing | alpha-proteobacteria, gamma-proteobacteria, firmicutes | Temperature and diet both influence microbiota present |
| Sun et al., 2009 | Epinephelus coioides | A | Intestinal contents | 17 | 16S/Culture + Sanger Sequencing | Beta -proteobacteria, Gamma-proteobacteria, Firmicutes | Species unequally dispersed beween fast and slow growing phenotypes (e.g., Bacillus pumilis super-abundant in fast growers) |
| Huber et al., 2004 | Oncorhynchus mykiss | A | Intestinal contents | 146 | 16S/Culture + Sanger Sequencing | Beta -proteobacteria, Gamma-proteobacteria | DAPI staining and FISH analysis demoastrate large number of unculturable bacterial species present |
| Skrodenyte-Arbaciauskiene et al., 2008 | Salmo salar (juvenile, freshwater) | W | Intestinal contents | 52 | 16S/Culture + Sanger Sequencing | Gamma-proteobacteria, firmicutes | Principal differences were present between S. trutta and S. salmo were at bacterial species level |
| Skrodenyte-Arbaciauskiene et al., 2008 | Salmo trutta (juvenile, freshwater) | W | Intestinal contents | 47 | 16S/Culture + Sanger Sequencing | Gamma-proteobacteria | Principal differences were present between S. trutta and S. salmo were at bacterial species level |
| Skrodenyte-Arbaciauskiene et al., 2006 | Salmo trutta fario | W | Intestinal contents | 100 | 16S/Culture + Sanger Sequencing | Gamma-proteobacteria | Multiple differences at family and species level between populations isolated from two different river systems |
| Wu et al., 2012a | Pelteobagrus fulvidraco | A | Midgut contents, midgut mucus | 74 | 16S/Culture + Sanger Sequencing | Firmicutes, Proteobacteria, Bacteriodetes, Fusobacteria | Different bacterial genera between gut contents and mucosa. Stomach contents conatained Chloroflexi, while mucous Actinobacteria |
| Cantas et al., 2011 | Salmo salar (juvenile) | A | Intestinal mucosa and contents | 18 | 16S/Culture + Sanger Sequencing | Gamma-proteobacteria, firmicutes, actinobacteria | Differences between dilpoid and triploid individuals non-significant |
| Valdenegro-Vega et al., 2013 | Thunnus maccoyii | Ranched | Gills, Spleen, Kidneys | 24 | 16S/Culture + Sanger Sequencing | (no order) Vibrio and Photobacterium sp. predominate | – |
| Cantas et al., 2012 | Dario rerio | A | Intestinal contents | 13 | 16S/Culture + Sanger Sequencing | Gamma-proteobacteria, beta-proteobatceria, alpha-proteobatceria, firmicutes | – |
| Tetlock et al., 2012 | Petromyzon marinus | A | Intestinal contents | 682 | 16S/DGGE + Sanger sequencing | Proteobacteria | Dominated by Aeromonas species |
| Shiina et al., 2006 | Takifugu niphobles | W | Intestinal contents | 24 | 16S/DGGE + Sanger sequencing | Firmicutes, Gamma-proteobacteria, Spirochaetes | Cultivable species restricted in greater part to Vibrio species |
| Tetlock et al., 2012 | Petromyzon marinus | A | Intestinal mucosa and contents | 682 | 16S/DGGE + Sanger sequencing | Proteobacteria, Bacteriodetes, Tenericutes, + minor phyla | Hugely diverse environment, multiple genera and species |
| He et al., 2010 | Oreochromis sp. | A | Intestinal contents | 19 | 16S/DGGE + Sanger sequencing | Cyanobacteria. Proteobacteria, Firmicutes, Actinobacteria, Fusobacterium | Significant influence on antibiotics on gut microbiota |
| Silva et al., 2011 | Carassius auratus | A | Intestinal mucosa and contents | 60 | 16S/DGGE + Culture + Sanger Sequencing | Gamma-proteobacteria, Firmicutes | Dominated by Aeromonas species |
| Svanevik and Lunestad, 2011 | Scomber scombrus | W | Gills/skin/inestine contents | 99 | 16S/DGGE + Culture + Sanger Sequencing | Gamma-proteobacteria, Firmicutes | Vibrio, Pscrobatcer immobilis, Oceanisphaera and some Shewanella species only present in the gut (samples direct from purse seine onlu included) |
| Kühlwein et al., 2013 | Cyprinus carpio L. | A | Intestinal contents | 27 | 16S/DGGE + Culture + Sanger Sequencing | (no order) Proteobacteria, Firmicutes, Fusobacteria | Dietary β-(1,3)(1,6)-D-glucan supplementation impacts gut microbiota |
| Kim et al., 2007 | Oncorhynchus mykiss | A | Intestinal mucosa and contents | 199 | 16S/DGGE + Culture + Sanger Sequencing | Proteobacteria, Fusobacteria | Differences between intestinal mucosa and contents. e.g., Gut contents—Enterobacter, Bacteroides, Flavobacteria, Pasteurellacae. Mucosa =- Enterobacter, Aeromonadacae, Pseudomonadacae, Mycoplasmatacae |
| Silva et al., 2011 | Sparus aurata | A | Intestinal mucosa and contents | 160 | 16S/DGGE + Culture + Sanger Sequencing | Gamma-proteobacteria, Bacteroidetes, Firmicutes | Dominated by Photobacterium sp. |
| Navarrete et al., 2012 | Oncorhynchus kisutch (juvenile) | A | Eggs + Juvenile intestinal contents | 14 | 16S/DGGE + Sanger sequencing | Egg—Bacteriodetes (flavobacteria), Beta-proteobacteria; Juvemiles—Gamma-proteobatceria, firmicutes | – |
| Merrifield et al., 2013 | Dario rerio | A | Hindgut | 8 | 16S/DGGE + Sanger sequencing | (no order) Fusobacteria, Gammaproteobacteria | Nanoparticles included in diet disrupt communty structure |
| Ni et al., 2012 | Ctenopharyngodon idellus | A/W | Intestinal mucosa and contents | 75 | 16S/DGGE + Sanger sequencing | (no order) Cetobacterium. Aeromonas, Plesiomonas, Sporacetigenium, Enterobacter | – |
| Tapia-Paniagua et al., 2010 | Solea senegalensis | A | Intestinal contents | 7 | 16S/DGGE + Sanger sequencing | Gamma-proteobacteria | Dominated by Vibrio species, enhanced by prebiotics |
| Zhou et al., 2012 | Gadus morhua | A | Intestinal mucosa and contents | 34 | 16S/DGGE + Sanger sequencing | Proteobacteria, Firmicutes, Actinobacteria, Bacteriodetes, Deinococci | Genera associated with chitin-rich diet: Escherichia, Erwinia, Thermus |
| Geraylou et al., 2012 | Acipenser baerii | A | Hindgut | 36 | 16S/DGGE + Sanger Sequencing | Proteobacteria, Firmicutes, Fusobacteria | Comparison of different diets on hind gut fermentation |
| Liu et al., 2012 | Carassius auratus | A | Intestinal contents | ND | 16S/DGGE + Sanger Sequencing | Actinobacteria, Firmicutes, Proteobacteria | Antibiotic treatment disrupts microbiota of healthy fish more significantly than those with disease. |
| Li et al., 2012 | Ctenopharyngodon idellus | A | Intestinal mucosa and contents | 41 | 16S/DGGE + Sanger Sequencing | (no order) alpha, beta and gamma-proteobacteria, Actinobacteria | – |
| Li et al., 2012 | Hypophthalmichthys molitrix | A | Intestinal mucosa and contents | 41 | 16S/DGGE + Sanger Sequencing | (no order) Actinobacteria, Firmicutes, alpha and gamma-proteobacteria | – |
| Li et al., 2012 | Hypophthalmichthys nobilis | A | Intestinal mucosa and contents | 41 | 16S/DGGE + Sanger Sequencing | (no order) alpha, beta and gamma-proteobacteria, Actinobacteria | – |
| Li et al., 2012 | Megalobrama amblycephala | A | Intestinal mucosa and contents | 41 | 16S/DGGE + Sanger Sequencing | Beta and Gamma-proteobacteria | – |
| Navarrete et al., 2010 | Salmo salar | A (marine) | Intestinal mucosa and contents | 700 | 16S/RFLP + Sanger sequencing | Gamma-proteobacteria, Firmicutes, Bacterioidetes | Pseudomonas, Acinetobacter, Flavobacterium, Psychrobacter, Brevundimonas, Caulobacter, Mycoplana, Aeromonas, Haemophilus, Aeromonas salmonicida, Bacillus, Micrococcus/Kocuria. Reduction in diversity among tetracyclin treated indiividuals |
| Moran et al., 2005 | Kyphosus sydneyanus | W | Intestinal contents | 12 | 16S/T-RFLP, Sanger Sequencing | (no order) Closteridium species | Putative inviolvement in short chain fatty acid metabolism |
| Smriga et al., 2010 | Acanthurus nigricans | W | Intestinal contents | 48 | 16S/TA cloning, Sanger sequencing | Bacteriodetes, Firmicutes Proteobacteria (Vibrionacae ijn minority), Bacteriodete, Spirochaetes | – |
| Smriga et al., 2010 | Chlorurus sordidus | W | Intestinal contents | 44 | 16S/TA cloning, Sanger sequencing | Proteobacteria (mostly Vibrionacae), Bacteriodetes + other minor groups | – |
| Ward et al., 2009 | Chaenocephalus aceratus | W | Intestinal contents | 303 | 16S/TA cloning, Sanger sequencing | Gamma-proteobatceria | Photobacterium |
| Smriga et al., 2010 | Lutjanus bohar | W | Intestinal contents | 46 | 16S/TA cloning, Sanger sequencing | Proteobacteria (Vibrionacae), Firmicutes | – |
| Ward et al., 2009 | Notothenia coriiceps | W | Intestinal contents | 194 | 16S/TA cloning, Sanger sequencing | Gamma-proteobatceria | Photobacterium/Vibrio |
| Green et al., 2013 | Salmo salar | A (marine) | Intestinal contents | 30 | 16S/TA cloning, Sanger sequencing | (no order) Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Verrucomicrobi | Addition of soyabean derived protein resulted in dysbiotic changes in intestinal microbiota and presence of genera not normally associated with the marine environment |
| Larsen et al., 2013 | Cynoscion arenarius, | W | Skin mucosa | 69 | 16S/TA cloning, Sanger sequencing | Proteobacteria, Firmicutes, Bacteriodetes | Fish species, capture locality and capture date all influence skin microbiota |
| Larsen et al., 2013 | Cynoscion nebulosus | W | Skin mucosa | 69 | 16S/TA cloning, Sanger sequencing | Proteobacteria, Firmicutes, Bacteriodetes | Fish species, capture locality and capture date all influence skin microbiota |
| Larsen et al., 2013 | Lagodon rhomboides | W | Skin mucosa | 69 | 16S/TA cloning, Sanger sequencing | Proteobacteria, Firmicutes, Actinobacteria | Fish species, capture locality and capture date all influence skin microbiota |
| Larsen et al., 2013 | Lutjanus campechanus | W | Skin mucosa | 69 | 16S/TA cloning, Sanger sequencing | Proteobacteria, Firmicutes, Actinobacteria, Bacteriodetes, Cyanobacteria | Fish species, capture locality and capture date all influence skin microbiota |
| Larsen et al., 2013 | Micropogonias undulatus | W | Skin mucosa | 69 | 16S/TA cloning, Sanger sequencing | Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria, Bacteriodetes | Fish species, capture locality and capture date all influence skin microbiota |
| Larsen et al., 2013 | Mugil cephalus | W | Skin mucosa | 69 | 16S/TA cloning, Sanger sequencing | Proteobacteria, Firmicutes, Actinobacteria, Bacteriodetes, Cyanobacteria | Fish species, capture locality and capture date all influence skin microbiota |
| Navarrete et al., 2009 | Salmo salar (juvenile) | A | Intestinal mucosa and contents | 80 | 16S&ITS/TTGE and Sanger sequencing | Proteobacteria | Differences between gut compartments by TGGE |
| Arias et al., 2013 | Lutjanus campechanus | W | Anterior Kidney | 43 | 16S/Culture + Sanger Sequencing | Proteobacteria, Firmicutes, Actinobacteria | Firmicultes and Actinobatceria more common on the skin than in the kidney |
| Ringø et al., 2006 | Gadus morhua | A | Intestinal mucosa and contents | 425 | 16S/Culture + Sanger Sequencing | (no order) Firmicutes, Bacteriodetes, Actinobacteria, Proteobacteria | Dietary differences in microbiota. Bacteriodetes preferentially adherent. Anthrobacter absent from foregut |
| Arias et al., 2013 | Lutjanus campechanus | W | Skin mucosa | 179 | 16S/Culture + Sanger Sequencing | Proteobacteria, Firmicutes, Actinobacteria | Firmicultes and Actinobatceria are more common on the skin than in the kidney |
| Mansfield et al., 2010 | Oncorhynchus mykiss | A | Ground intestinal tissue | 3357 | HSP60/Sanger clones libraries | Firmicutes, gamma-proteobacteria, alpha-proteobacteria, actinobacteria | – |
| Boutin et al., 2013a | Salvelinus fontinalis | A | Skin mucosa | 117,260 | 16S/454 pyroseqeuncing | Proteobacteria (Alpha, Gamma, Beta and Delta), Actinobacteria, Bacteroidetes, Firmicutes, TM7, Chlorobi | Probiotic treatment by an indigenous strain does not disturb the natural microbiota of Salvelinus fontinalis |
| Boutin et al., 2014 | Salvelinus fontinalis | A | Skin mucosa | 87,940 | 16S/454 pyroseqeuncing | Proteobacteria (Alpha, Gamma), Bacteroidetes | Salvelinus fontinalis presents three QTL region linked to the abundance of three commensal genera |
| Boutin et al., 2013b | Salvelinus fontinalis | A | Skin mucosa | 678,211 | 16S/454 pyroseqeuncing | Proteobacteria (Beta, Alpha, Gamma), Actinobacteria, Bacteroidetes | Host’ stress influences the skin microbiota. Commensals strains abundance decreases and favors growth of opportunistic pathogens |
a
Aquaculture, A; Wild, W.