Comparison of conventional and molecular techniques to investigate the intestinal microflora of rainbow trout (Oncorhynchus mykiss)

Pond, Michelle J.; Stone, David M.; Alderman, D. J.

doi:10.1016/j.aquaculture.2006.06.037

Cited by 141 publications

(134 citation statements)

References 53 publications

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“…Members of the genus Aeromonas were found mainly in grass carp and crucian carp in this study. This finding is in accordance with a former study that suggested that fish gut may be a reservoir for many opportunistic pathogens [52]. The genus Aeromonas was significantly more abundant in the intestinal mucosa than in the intestinal content.…”

Section: −3supporting

confidence: 82%

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing

et al. 2014

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Gut microbiota is increasingly regarded as an integral component of the host, due to important roles in the modulation of the immune system, the proliferation of the intestinal epithelium and the regulation of the dietary energy intake. Understanding the factors that influence the composition of these microbial communities is essential to health management, and the application to aquatic animals still requires basic investigation. In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. The specimens of the three species were cohabiting in the same pond. Between 6,218 and 10,220 effective sequences were read from each sample, resulting in a total of 110,398 sequences for 13 samples from gut microbiota and pond water. In general, the microbial communities of the three carps were dominated by Fusobacteria, Firmicutes, Proteobacteria and Bacteroidetes, but the abundance of each phylum was significantly different between species. At the genus level, the overwhelming group was Cetobacterium (97.29±0.46 %) in crucian carp, while its abundance averaged c. 40 and 60 % of the sequences read in the other two species. There was higher microbial diversity in the gut of filterfeeding bighead carp than the gut of the two other species, with grazing feeding habits. The composition of intestine microbiota of grass carp and crucian carp shared higher similarity when compared with bighead carp. The principal coordinates analysis (PCoA) with the weighted UniFrac distance and the heatmap analysis suggested that gut microbiota was not a simple reflection of the microbial community in the local habitat but resulted from species-specific selective pressures, possibly dependent on behavioural, immune and metabolic characteristics.

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Section: −3supporting

confidence: 82%

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing

et al. 2014

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“…Previous studies have revealed that the animal digestive tract is a reservoir for many nosocomial pathogens (Donskey 2004;Pond et al 2006), and this may be the same to yellow catfish. In this study, potentially opportunistic pathogens, such as Isolates SC3 (most related to SC53 SM28 SM31 SM8 SC51 SM42 SC37 SC63 SC52 SC20 SC61 SC3 PSC6 SC32 SC12 SM17 SC30 SC34 SC8 SC13 SC22 SC28 SC1 SC26 SC57 SC24 SC38 PSC19 SM13 SM22 SM30 PSC8 SM41 SC39 SM37 SM43 SC7 SM9 SC48 PSC2 PSC15 SC15 PSM3 SC36 SC54 SC21 SC27 PSC20 PSC1 PSM1 SC3 SM5 SM18 SM26 SC58 Chloroflexi SC23 SC4 SC59 SM3 SM20 SM44 SC11 SC42 SC45 SC10 SC49 SC14 SC44 SC60 SC5 Bootstrap values based on 1,000 re-samplings display the significance of the interior nodes, and are shown at branch points.…”

Section: Discussionmentioning

confidence: 99%

Characterization of bacterial community in the stomach of yellow catfish (Pelteobagrus fulvidraco)

Tian

Wang

et al. 2012

World J Microbiol Biotechnol

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In this study, the traditional culture-based technique and the 16S rDNA sequencing method were used to investigate the characterization of bacterial community in the stomach contents and mucus of yellow catfish (Pelteobagrus fulvidraco). The culture-based technique disclosed that the average bacterial numbers in the gastric contents and mucus were 5.79 9 10 7 cfu/g (cfu: colony forming unit) and 1.89 9 10 5 cfu/g, respectively. Several different bacteria were obtained from gastric contents, including species from genera Bradyrhizobium, Phyllobacterium, Plesiomonas, Hafnia, Edwardsiella, Pseudomonas, and Bacillus. However, only two species were isolated from the gastric mucus, including species from genera Plesiomonas and Aeromonas. Forty-five phylotypes were observed from the 65 positive clones from the stomach contents (library SC); nineteen phylotypes were detected from the 45 clones from the stomach mucus (library SM). Further analyses revealed that the fish stomach harbored characteristic microbiota, where Firmicutes was dominant, followed by Proteobacteria and Bacteroidetes and Fusobacteria. This characterization of bacterial community is markedly different from that of the fish intestine, where Proteobacteria is predominant, followed by Fusobacteria and Firmicutes. Chloroflexi (1.5%) was only found in the library SC, while Actinobacteria (4.4%) was only found in the library SM, suggesting that microbiota of GI contents was quite different from that of GI mucus. In addition, several species of bacteria found in the stomach may be potentially opportunistic pathogens, indicating that fish digestive tract is a reservoir for many nosocomial pathogens.

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“…It is generally accepted that the composition of the allochthonous (transient) intestinal tract microbiota is highly variable and is affected by many environmental conditions as salinity, temperature, etc. (Ringo et al 1995;Pond et al 2006;Liu et al 2008), but stable in fish kept in defined conditions (Pond et al 2006). Especially food accessibility, composition, and food changes may affect the bacterial diversity in fish intestine (Ringo and Strom 1994;Ringo et al 2006).…”

Section: Introductionmentioning

confidence: 99%

“…The indigenous microflora of the fish digestive tract has been traditionally investigated by conventional culture-dependent methods including cultivation on selective or non-selective media followed by isolation and phenotypic characterization (Spanggaard et al 2000;Pond et al 2006;Hovda et al 2007;Kim et al 2007). Culture independent methodologies providing information about non-cultivable bacteria (denaturing gradient gel electrophoresis (DGGE), 16S rDNA sequencing) are useful tools and these methodologies have widened the knowledge about the intestinal microbiota in fish as not being simple as believed previously (Pond et al 2006;Hovda et al 2007;Liu et al 2008;Ward et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Composition of cultivable enteric bacteria from the intestine of Antarctic fish (family Nototheniidae)

Sedláček¹,

Staňková²,

Švec³

2016

CZECH J ANIM SCI

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ABSTRACT:In this study, the intestinal bacteria of wild Antarctic fish (family Nototheniidae) were examined using traditional culture-based techniques. Bacterial flora of the gut contents of four marine fish species (Notothenia coriiceps, Trematomus bernacchii, Trematomus hansoni, and Trematomus newnesi) was investigated to describe the allochthonous bacteria inhabiting these Nototheniidae fish. A set of 43 fresh and healthy fish was analyzed and intestinal bacteria were retrieved using the dilution plate technique on selective media Endo agar and XLDA agar. A total of 133 different bacterial isolates were obtained and initially characterized by key phenotypical tests. Notothenoid fish gut microbiota showed low species diversity of isolates and intestines were inhabited by 3 different isolates per fish on average. The bacterial colonization of the intestine content of Trematomus newnesi was poor. Curiously, the Gram-negative non-fermenters, including Pseudomonas sp., Vibrio sp., and Alcaligenes-like isolates represented the majority (59%) of intestine isolates grown on the used selective media for enteric bacteria. Based on preliminary identification, only 54 isolates (41%) were tentatively determined as enteric bacteria. The identification of 54 isolates of Gram-negative fermenting rods to the species level was achieved using biochemical characterization by commercial kits ENTEROtest 24 and Biolog GN2 MicroPlate. Results showed that Enterobacter cloacae phenon and Aeromonas hydrophila were predominant bacterial species in the free-living fish intestine from the group of fermenting Gram-negative rods.

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Comparison of conventional and molecular techniques to investigate the intestinal microflora of rainbow trout (Oncorhynchus mykiss)

Cited by 141 publications

References 53 publications

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing

Characterization of bacterial community in the stomach of yellow catfish (Pelteobagrus fulvidraco)

Composition of cultivable enteric bacteria from the intestine of Antarctic fish (family Nototheniidae)

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