High variability of levels of Aliivibrio.pdf

8/18/2019 High variability of levels of Aliivibrio.pdf

1/13

13

Annals of Microbiology

ISSN 1590-4261

Volume 65

Number 4

Ann Microbiol (2015) 65:2343-2353

DOI 10.1007/s13213-015-1076-3

High variability of levels of Aliivibrioand lactic acid bacteria in the intestinal

microbiota of farmed Atlantic salmonSalmo salar L.

Félix A. Godoy, Claudio D. Miranda,

Geraldine D. Wittwer, Carlos P. Aranda

& Raúl Calderón


2/13

13

Your article is protected by copyright and

all rights are held exclusively by Springer-

Verlag Berlin Heidelberg and the University

of Milan. This e-offprint is for personal

use only and shall not be self-archived inelectronic repositories. If you wish to self-

archive your article, please use the accepted

manuscript version for posting on your own

website. You may further deposit the accepted

manuscript version in any repository,

provided it is only made publicly available 12

months after official publication or later and

provided acknowledgement is given to the

original source of publication and a link is

inserted to the published article on Springer's

website. The link must be accompanied by

the following text: "The final publication is

available at link.springer.com”.


3/13

ORIGINAL ARTICLE

High variability of levels of Aliivibrio and lactic acid bacteriain the intestinal microbiota of farmed Atlantic

salmon Salmo salar L.

Félix A. Godoy1 & Claudio D. Miranda2,3 & Geraldine D. Wittwer1 &

Carlos P. Aranda1 & Raúl Calderón4

Received: 10 November 2014 /Accepted: 11 March 2015 / Published online: 16 April 2015# Springer-Verlag Berlin Heidelberg and the University of Milan 2015

Abstract In the present study, the structure of the intestinal

microbiota of Atlantic salmon (Salmo salar L.) was studiedusing culture and culture-independent methods. Three adult specimens of S. salar were collected from a commercial salm-on farm in Chile, and their intestinal microbiota were studied

by partial sequencing of the 16S rRNA gene of pure culturesas well as of clone libraries. Out of the 74 bacterial isolates,

Pseudomonas was the most predominant genus among cul-tured microbiota. In clone libraries, 325 clones were obtainedfrom three adult fish, and a total of 36 operational taxonomicunits (OTUs) were identified. This indicated that lactic acid

bacteria (Weissella, Leuconostoc, and Lactococcus genera)comprised more than 50 % of identified clones in two fishes.

This was in contrast with the high dominance of a single OTU(99 sequences) of Aliivibrio sp. related to the pathogenic

Aliivibrio salmonicida species and the absence of lactic acid bacteria in the third fish, suggesting a condition of an asymp-tomatic non-healthy carrier. It is clear that molecular identifi-cation of 16S rRNA gene libraries obtained from intestinalcontent samples is effective in determining the overall

structure of the intestinal microbiota of farmed Atlantic salm-

on enabling detection of a minority of taxa not previouslyreported as part of the intestinal microbiota of salmonids, in-cluding the genera Hydrogenophilus, Propionibacterium,Cronobacter , Enhydrobacter , Veillonella, Prevotella, and

Atopostipes, as well as to evaluate the health status of farmedfish when evaluating the dominance of potential pathogenicspecies and the incidence of lactic acid bacteria.

Keywords Aquaculture . Intestinal microbiota . Aliivibrio .

Salmon farming . Salmo salar

Introduction

Chile is currently a worldwide leading salmon producer andthe Atlantic salmon Salmo salar L. is one of the main Chileansalmonid farming products, constituting 182,712 tons fromJanuary to June of 2014, and comprising 64 % of total salmo-nid exports (SalmonChile 2014). It is well established that theintestinal tract of rearedfish harbors a microbiota that fulfill animportant role in immunity, nutrition, and disease control of reared fishes (Trust and Sparrow 1974; Ringø and Birkbeck 1999; Moffitt and Mobin 2006).

To study the microbiota of the gastrointestinal tract of fish-

es, the general approach has been the use of conventionalculture methods (Ringø et al. 1995). However, it has beenfound that these methods present several disadvantages andusually onlydetect aerobics and facultative anaerobic bacteria,

but do not detect slow-growing bacteria (Spanggaard et al.2000; Nayak 2010). Thus,molecular analysis of DNA extract-ed directly from the sample has rapidly replaced cultivation inthe study of the structure of fish intestinal microbiota.

* Félix A. [email protected]; [email protected]

1 Centro i ~ mar, Universidad De Los Lagos, Camino Chinquihue km6, Casilla 557, Puerto Montt, Chile

2 Laboratorio de Patobiología Acuática, Departamento de Acuicultura,Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile

3 Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Larrondo1281, Coquimbo, Chile

4 Escuela de Ciencias Ambientales, Facultad de Recursos Naturales,Universidad Católica de Temuco, Temuco, Chile

Ann Microbiol (2015) 65:2343 – 2353DOI 10.1007/s13213-015-1076-3


4/13

Nonetheless, when some phenotypic properties such as enzy-matic activities need to be studied in order to understand the

potential role of the microbiota in improving fish nutrition, it is more appropriate to study the fish intestinal microbiotacomposition by culture techniques in combination withculture-independent methods (Bakke-McKellep et al. 2007;Kristiansen et al. 2011; Askarian et al. 2012).

The intestinal microbiota composition is known to dependon dietary factors (Gómez and Balcázar 2008; Nayak 2010;Hartviksen et al. 2014). Navarrete et al. (2013), using micro-

biological analysis, demonstrated that specific bacterialgroups were correlated with the administered diet, andReveco et al. (2014) reported that intestinal microbiota of Salmo salar is sensitive to dietary changes, observing that the most dominant species were Lactococcus lactis, Weissellaconfusa, and Photobacterium phosphoreum. Otherwise,

Navarrete et al. (2008) suggested that Atlantic salmon favors Pseudomonas establishment because this species was de-tected as the dominant component in most of the samples

of juvenile farmed Atlantic salmon. There are other studiesthat describe the intestinal microbiota of farmed Atlanticsalmon; however, the majority of these studies are associ-ated with fingerling or juvenile stages (Bakke-McKellepet al. 2007; Navarrete et al. 2008; Cantas et al. 2011;

Navarrete et al. 2013; Reveco et al. 2014).It has been reported that fish intestinal microbiota have an

important role in regulating nutrient digestion, immune re-sponses, and intestinal differentiation (Bates et al. 2006;Kanther and Rawls 2010; Merrifield et al. 2010; Nayak 2010;Rayetal. 2012), so physiological and biochemical char-acterizations of the intestinal isolates are important in eluci-

dating their functions in the gastrointestinal tract. Several stud-ies reported that freshwater fish reared in warm waters harbor

proteolytic, amylolytic, and cellulolytic bacteria in their diges-tive tracts (Bairaigi et al. 2002; Ghosh et al. 2002; Saha et al.2006;Karetal. 2008), whereas it was reported that an increasein proteolytic enzymes such as trypsin and chymotrypsin insalmon induces a better assimilation of proteins, as well as anincrease in the growth and stimulation of immune and endo-crine systems (Rungruangsak-Torrissen et al. 2009). Addition-ally, it has been observed that the different bacterial popula-tions composing the intestinal microbiota represent different metabolic groups, which can enhance the digestive capacity of

fish (Ringø and Olsen 1999). Hence, knowledge of the enzy-matic capacities of the gastrointestinal microbiota of farmedsalmon could help regulate the intestinal microbiota enhanc-ing nutrition performance of farmed fishes under intensiverearing conditions.However, only a few studies on adult salm-on are available, and knowledge of the enzymatic propertiesof the intestinal microbiota of reared salmon is still scarce.

The main aims of this study were to investigate the composition of intestinal microbiota of adult specimens of farmedAtlantic salmon, Salmo salar L. by culture and cloning

methods, and to characterize some of the metabolic and enzy-matic capabilities of the isolated strains.

Materials and methods

Sampling

Three apparently healthy adult specimens of Atlantic salmon(Salmo salar L.) with an approximate weight of 2.5 kg werecollected from three different rearing cages belonging to acommercial salmon farm located at Punta Quilque, X Region,Chile (13 °C, water temperature; 32 g L-1, salinity). Sampleswere packed in sterile bags, placed on ice, immediatelytransported to the laboratory, and processed within 2 h of collection.

Sample processing and cultured bacterial count

Adult salmon were externally washed with sterile deionizedwater to reduce potential contamination with skin bacteria andaseptically eviscerated. Salmon intestines were aseptically re-moved and placed in sterile Petri dishes and were divided into

proximal intestine (defined as the region between the distal pyloric caeca and widening of the intestine and the appearanceof transverse luminal folds) and distal intestine (the regionfrom the widening of the intestine and the appearance of trans-verse luminal folds to anus). Then, digesta from proximal anddistal intestine were gently squeezed out and the two intestinalsegments were thoroughly rinsed three times using 3 mL of

peptone water in order to collect both adherent and non-

adherent bacteria (Ringø 1993). Culture counts of heterotrophic bacteria were determined by a spread plate method usingTryptic soy agar (TSA, Difco Labs). Salmon intestinal con-tents samples were aseptically weighed, ground, and added to5 mL of sterile physiological saline (0.85 %) (PS) to obtain ahomogenate as previously described by Miranda andZemelman (2001). Appropriate tenfold dilution of the homog-enates in PS was prepared and 0.1 mL aliquots were inoculat-ed in triplicate onto agar plates. All plates were incubated at 20 °C for 5 – 10 days and the bacterial numbers per g of sample were calculated as described in Miranda andRojas (2007). A group of representative colonies from

each sample was selected for purity.

Bacterial isolation

Seventy-four isolates were recovered as a representative sample of the intestinal cultured bacterial community of farmedsalmon. From these, 26 strains were recovered from specimen1 (17 and nine strains from the proximal and distal intestine,respectively), 25 strains from specimen 2 (14 and 11 strainsfrom the proximal and distal intestine, respectively) and 23

2344 Ann Microbiol (2015) 65:2343 – 2353


5/13

strains from specimen3 (nine and 14 strains from theproximaland distal intestine, respectively). The strains were randomlyselected from plates with TSA medium and purified threetimes in TSA medium and stored at −85 °C in Tryptic soy

broth (Difco Labs) supplemented with 50 % glycerol (2:1)until use (Gherna 1994).

Bacterial identification by 16S rRNA sequence analysis

Isolates were identified by bacterial 16S rRNA gene sequenceanalysis. For amplification of the 16S rRNA genes, crudeDNA extracts were obtained from pure bacterial isolates usingthe Wizard genomic purification kit (Promega, Madison, WI,USA). The 16S rRNA gene was amplified by the polymerasechain reaction (PCR) using primers 27F 5’-AGAGTTTGATCMTGGCTCAG-3’, 1492R 5’-TACGGYTACCTTGTTACGACTT-3’, and 907R 5’-CCGTCAATTCMTTTGAGTTT-3’ (Lane 1991). PCR products were purified using the Wiz-ard SV Gel kit and PCR Clean-up System (Promega) andsequencing of amplicons was performed by Macrogen (Seoul,Korea). Identification of partial sequences was performedusing the NCBI BLAST (http://www.ncbi.nlm.nih.gov/ ), andstrains were considered to belong to the same genus whensimilarities in their sequences were ≥97 % (Rosselló-Moraand Amman 2001). The partial 16S rRNA gene sequenceswere submitted to the Genbank database and assignedaccession numbers JF743668 to JF767415.

Phenotypic characterization of isolated strains

The phenotypic tests of Gram's stain, cell morphology, andoxidase production were determined according to the proce-dures described in Barrow and Feltham (1993). Additional

phenotypic characteristics were determined by using the API20E system (bioMérieux, Marcy-l’Etoile, France), and strainswere inoculated according to the manufacturer ’s instructions.API 20E strips were incubated at 20 °C for 48 h.

Enzymatic activity of isolated strains

Enzyme production by the salmon intestinal strains were de-terminedutilizing the API ZYM system (bioMérieux), accord-

ing to the manufacturer ’s guidelines. Briefly, isolated colonieswere cultured overnight in Tryptic soy broth, centrifuged at 5000 g at 4 °C and resuspended in sterile 0.8 % (w/v) NaClsolution to obtain a turbidity of 6 McFarland (1.5 – 1.8×109 CFU mL−1). This suspension (65 μ L) was added to eachcapsule, and the test strips were incubated for 8 h at 20 °C.Following incubation, one drop of ZYM A (API; tris-hy-droxymethyl-aminomethane, hydrochloric acid, sodiumlauryl sulphate, H2O) and one drop of ZYM B (API; fast

blue BB, 2-methoxyethanol) were added to each capsule and

the color allowed to develop for 5 min and test strips wereread. All assays were performed twice.

16S rRNA gene library construction and sequencing

From a sample of 200 μ L of the homogenate of the completeintestinal content containing the proximal and distal intestine

(1:1), bacterial DNA was extracted using the QIAMP DNAStool kit (QIAGEN), according to the manufacturer ’s guide-lines. Bacterial DNA was verified by the amplification of afragment of rRNA 16S gene using the 27 F and 907R univer-sal primers, as was previously described and visualized with1 % agarose gels. PCR products were purified from agarosegels with the Wizard SV Gel kit and PCR Clean-up System(Promega) and cloned using the TOPO TA vector according tothe procedures indicated by Invitrogen. Cultures of

Escherichia coli JM 107 strain were made competent usingthe Transform Aid Bacterial Transformation Kit (Fermentas),following the manufacturer ’s guidelines. Each clone was pick-

ed and cultured in LB broth with ampicillin for 16 h. To isolate plasmidic DNA with the insert, 100 μ L of liquid culture wascentrifuged at 6000 g for 30 min, the medium was discarded,and the pellet was resuspended in 100 μ L of sterile water,incubated at 95 °C for 30 min to produce cellular lysis, andthen centrifuged at 6000 g for 30 min. Finally, 5 μ L of thelysate was amplified to detect the occurrence of the insert,using the M13F and M13 R primers. PCR products wereverified in 1 % agarose gels, purified and sequenced byMacrogen (Seoul, Korea).

Sequence analysis

Partial sequences for chimeras using the Chimera Check pro-gram from RPD (Ribosomal Database Project) (http:// fungene.cme.msu.edu/FunGenePipeline/chimera_check/ form.spr ) were analyzed. Clone sequences in this study werealigned using the INFERNAL aligner from RDP, secondary-structure aware aligner (Nawrocki and Eddy 2007). Se-quences with similarities over 97.0 % were defined as one

phylotype, i.e., one operational taxonomic unit (OTU). Thetaxonomic affiliation of the aligned sequences was performedwith Bayesian rRNA Classifier software from the RDP data-

base, using a confidencethreshold of 80 % (Wang et al. 2007).

For phylogenetic tree construction, sequences of clones fromfish 2 classified as Aliivibrio sp. were clustered at 97 % se-quence identity into OTUs, and aligned with 16S rRNA se-quences of the type strains of all species of the genus Aliivibriodeposited in Genbank (NCBI) using Muscle in the MEGA 6software (Tamura et al. 2013). Phylogenetic tree was con-structed by the Maximum Likelihood method based on theTamura-Nei model with 1,000 resampling bootstrap analysesusing MEGA 6 software (Tamura et al. 2013). The partial 16SrRNA gene sequences obtained have been deposited in

Ann Microbiol (2015) 65:2343 – 2353 2345

http://www.ncbi.nlm.nih.gov/http://fungene.cme.msu.edu/FunGenePipeline/chimera_check/form.sprhttp://fungene.cme.msu.edu/FunGenePipeline/chimera_check/form.sprhttp://fungene.cme.msu.edu/FunGenePipeline/chimera_check/form.sprhttp://fungene.cme.msu.edu/FunGenePipeline/chimera_check/form.sprhttp://fungene.cme.msu.edu/FunGenePipeline/chimera_check/form.sprhttp://fungene.cme.msu.edu/FunGenePipeline/chimera_check/form.sprhttp://www.ncbi.nlm.nih.gov/


6/13

GenBank and assigned the accession numbers HQ897283-HQ897612.

Diversity indices

Biodiversity indices were estimated from clone sequences and

isolated strains. Simpson and Shannon indices were calculatedusing software EstimateS 9.1 (http://viceroy.eeb.uconn.edu/ estimates/ ).

Results

Total cultured bacteria

In general, intestinal samples of the studied salmon exhibitedsimilar cultured bacterial levels, with bacterial counts on TSAdecreasing from the foregut to the hindgut. Bacterial counts

from proximal portions were always 1 log higher than those of the distal portions of fish intestine. Proximal portions of fishintestines were >105 CFU g−1, whereas samples from distal

portions of the intestines from all fishes ranged from 103 to104 CFU g−1, as indicated in Table 1.

Diversity of cultured intestinal microbiota

Using culture methods, 74 strains were isolated from intestinalsamples of farmed Atlantic salmon, S. salar . Then the repre-sentative isolates were identified based on 16S rRNA gene

sequencing including Proteobacteria, Actinobacteria, andFirmicutes phyla. Most of the isolated cultured bacteria belonged to the Proteobacteria Phylum, with a high number of representatives of the γ-proteobacteria group. Among the-se, Pseudomonas (31 strains), Acinetobacter (11 strains), and

Psychrobacter (seven strains) were identified as the most important genera among the cultured intestinal microbiota; theywere being detected in all the sampled fishes (Table 2). Nosignificant differences among the three sampled fishes as wellas between bacterial strains isolated from proximal and distal

portions of the intestine were detected, with a noticeable low

incidence of gram-positive organisms, belonging to theStaphylococcus and Bacillus genera (Table 2).

Enzymatic and metabolic properties of cultured intestinal

microbiota

No notable differences in the enzymatic profiles obtained bythe API ZYM tests were observed among the intestinal microbiota strains from the sampled fishes. A high incidence of strains exhibiting the ability to produce the alkaline phospha-tase, esterase (C4), esterase lipase (C8), leucine arylamidase,valine arylamidase, acid phosphatase, and naphthol-AS-BI-

phosphohydrolase enzymes (Table 3) was observed. On theother hand, the production of the β-glucoronidase, N-acetyl-β-glucosaminidase, α -mannosidase, and α -fucosidaseenzymes was rare (Table 3). When salmon intestinal strainswere analyzed for their capacity to assimilate various sub-strates, no notable differences among fish samples as well as

between strains isolated from different intestinal portions weredetected. A high incidence of assimilation of citrate, malate,glucose, and mannose, contrasting with a lower assimilationof phenyl-acetate, adipate, and maltose was observed(Table 4).

Diversity of intestinal microbiota by molecular cloning

When intestinal microbiota were studied by using 16S rRNAcloning, 325 clones were selected and analyzed, mainly fromfishes 1 and 2 (118 and 143 sequences, respectively). Animportant degree of variability in the taxonomic diversity of

clones obtained from intestinal samples of sampled fishes wasdetected (Fig. 1). A significant dominance of Weissella(48.3 %) and Leuconostoc (22.0 %) genera was observedamong the intestinal clones from fish 1, whereas Aliivibrio(81.1 %) was the most dominant genus among the intestinalclones from fish 2. However, no dominance was detectedamong the intestinal clones from fish 3, though Weissella(25.0 %), Aliivibrio (15.6 %), Leuconostoc (12.5 %),

Acinetobacter (10.9 %), and Lactococcus (10.9 %) were themore frequent genera (Fig. 1). Using cloning methodologiesto identify the salmon intestinal microbiota, an important in-cidence of lactic acid bacteria in fish 1 (78.0 %) and 3 (50.0 %)

was observed. I t was comprised of the Weissella, Leuconostoc, Lactococcus, and Enterococcus genera, whereasonly 0.7 % of the intestinal microbiota of fish 2 correspondedto lactic acid bacteria (Fig. 1).

When the number of genera per sample was considered ameasure of richness, it was observed that the not culturedmicrobiota from fishes 1 and 3 exhibited remarkable richnessvalues greater than those of the cultured intestinal microbiota,whereas fish 2 showed the opposite due to the high incidenceof representatives of Aliivibrio genus.

Table 1 Heterotrophic plate counts (Mean±SD of 3 replicates) fromintestinal content samples of farmed salmon Salmo salar L

Sample Intestine section Cultured count±SD (CFU g−1)

Fish 1 Proximal 5.23×105±5.77×103

Distal 3.07×104±3.46×103

Fish 2 Proximal 2.27×105±2.52×104

Distal 7.67×103±1.53×103

Fish 3 Proximal 3.07×105±7.50×104

Distal 1.77×104±2.08×103

2346 Ann Microbiol (2015) 65:2343 – 2353

http://viceroy.eeb.uconn.edu/estimates/http://viceroy.eeb.uconn.edu/estimates/http://viceroy.eeb.uconn.edu/estimates/http://viceroy.eeb.uconn.edu/estimates/


7/13

Table 2 Identification of cultured intestinal microbiota of farmed salmon Salmo salar

Phylum and/or Class Genus similarity (%) Similarity (%) Number of strains

Fish 1 Fish 2 Fish 3

P (n=17) D (n=9) P (n=14) D (n=11) P (n=9) D (n=14)

α -Proteobacteria Agrobacterium 91.3 – 99.4 1 1 2 1

α -Proteobacteria Brevundimonas 100.0 1

γ-Proteobacteria Acinetobacter 98.8 – 100.0 3 2 2 1 3

γ-Proteobacteria Lelliottia 100.0 1

γ-Proteobacteria Luteimonas 98.2 – 98.3 1 1

γ-Proteobacteria Pseudomonas 97.5 – 100.0 9 5 5 6 1 5

γ-Proteobacteria Psychrobacter 98.7 – 100.0 1 1 1 4

γ-Proteobacteria Stenotrophomonas 99.0 – 100.0 2 1 2

Actinobacteria Brachybacterium 99.6 1

Actinobacteria Kocuria 99.8 – 99.9 1 1

Actinobacteria Microbacterium 97.4 1

Actinobacteria Rhodococcus 100.0 1

Firmicutes/Bacilli Bacillus 94.6 –

100.0 1 1Firmicutes/Bacilli Staphylococcus 98.1 – 100.0 2 1

P Proximal section of intestine, D Distal section of intestine

Table 3 Enzymatic activities of intestinal microbiota of farmedsalmon determined using the APIZYM system (bioMérieux)

Activity Percentage of enzymatic activity


P(n=17)

Dn=11)

P(n=10)

D(n=13)

P(n=12)

D(n=12)

Alkaline phosphatase 94.1 100.0 100.0 92.3 100.0 91.7Esterase (C4) 64.7 54.5 60.0 76.9 91.7 83.3

Esterase lipase (C8) 88.2 81.8 90.0 92.3 83.3 66.7

Lipase (C14) 47.1 18.2 20.0 23.1 16.7 0.0

Leucine arylamidase 94.1 100.0 100.0 100.0 100.0 100.0

Valine arylamidase 82.4 45.4 40.0 76.9 66.7 58.3

Cystine arylamidase 17.6 18.2 10.0 30.8 16.7 8.3

Trypsin 64.7 81.8 60.0 76.9 50.0 16.7

α -Chymotrypsin 29.4 18.2 20.0 7.7 33.3 0.0

Acid Phosphatase 100.0 100.0 100.0 100.0 100.0 91.7

Naphthol-AS-BI- phosphohydrolase

94.1 100.0 80.0 100.0 91.7 91.7

α -Galactosidase 11.8 9.1 10.0 7.7 8.3 8.3

β-Galactosidase 23.5 18.2 20.0 30.8 16.7 8.3

β-Glucoronidase 5.9 0.0 0.0 0.0 0.0 8.3

α -Glucosidase 29.4 27.3 30.0 38.5 33.3 16.7

β-Glucosidase 41.2 54.5 30.0 46.2 25.0 8.3

N -Acetyl-β-glucosaminidase 17.6 0.0 0.0 7.7 0.0 0.0

α -Mannosidase 0.0 0.0 0.0 15.4 0.0 0.0

α -Fucosidase 0.0 0.0 0.0 7.7 0.0 0.0

Gelatinase* 35.3 45.4 100.0 69.2 58.3 41.7

P Proximal section of intestine, D Distal section of intestine, * Determined using the API 20NE system

Ann Microbiol (2015) 65:2343 – 2353 2347


8/13

A total of 113 clones classified as Aliivibrio sp.andclusteredinto 14 OTUs were analyzed to provide phylogenetic informa-tion. Phylogenetic analysis shows a dominant OTU (represent-ed by clone NG1) containing 99 sequences (87.6 % of allsequences), which is closely related to pathogenic species

Aliivibrio salmonicida and Aliivibrio logei (Fig. 2).When diversity indices of the salmon intestinal clones were

estimated, fish 3 presented the highest diversity, with Simpsonand Shannon-Wiener diversity indices of 0.86 and 2.22, re-spectively, contrasting with the lowest diversity of intestinalmicrobiota of fish 2 with Simpson and Shannon-Wiener di-

versity indices of 0.32 and 0.68, respectively (Table 5). Oth-erwise, no important differences in the number of genera wereobserved between the fishes 1 and 3 (16 and 14, respectively),

whereas only six genera were detected among the intestinalmicrobiota of fish 3 (Table 5). When diversity indices of clones from intestinal samples were compared to those of the cultured bacteria, the not cultured bacterial diversity indi-ces were slightly higher than the cultured ones of fishes 1 and3, but in fish 2 diversity indices of cultured bacteria weredouble the diversity indices of intestinal clones (Table 5).

Discussion

Most of the currently available information on the intestinalmicrobiota of Atlantic salmon Salmo salar refers to the earlystages of growth, mainly juveniles (Navarrete et al. 2008,

Table 4 Metabolic activities of intestinal microbiota of farmedsalmon determined using the API20NE system (bioMérieux)

Substrate assimilated Percentage of metabolic activity


P (n=17) D (n=9) P (n=12) D (n=14) P (n=10) D (n=11)

Glucose 76.5 100.0 91.7 92.9 90.0 63.6

Arabinose 64.7 88.9 83.3 85.7 70.0 63.6

Mannose 70.6 88.9 83.3 92.9 90.0 81.8

Mannitol 52.9 88.9 83.3 92.9 80.0 45.4

N-acetyl glucosamine 70.6 77.8 83.3 85.7 60.0 45.4

Maltose 29.4 11.1 41.7 35.7 30.0 45.4

Gluconate 64.7 88.9 91.7 85.7 80.0 63.6

Caprate 94.1 77.8 75.0 85.7 60.0 72.7

Adipate 52.9 55.6 25.0 50.0 10.0 9.1

Malate 94.1 100.0 100.0 92.8 90.0 72.7

Citrate 82.4 100.0 100.0 85.7 90.0 81.8

Phenyl-acetate 23.5 22.2 0.0 0.0 10.0 18.2

P Proximal section of intestine, D Distal section of intestine

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

R e l a t i v e a b

u n d a n c e


Acinetobacter Aeromonas

Aliivibrio Atopostipes

Bacillus Citrobacter

Cronobacter Enhydrobacter

Enterobacter Enterococcus

Enterovibrio Hydrogenophilus

Lactococcus Leuconostoc

Photobacterium Prevotella

Propionibacterium Pseudomonas

Stenotrophomonas Streptococcus

Unclassified Veillonella

Vibrio Weissella

Fig. 1 Relative abundance of bacterial genera in 16S rRNAgene clone libraries constructedfrom DNA obtained fromintestinal microbiota of farmedAtlantic salmon (Salmo salar L.).Genus-level classification was based on the Classifier tool of theRibosomal Database Project

(http://rdp.cme.msu.edu/ classifier/classifier.jsp)

2348 Ann Microbiol (2015) 65:2343 – 2353

http://rdp.cme.msu.edu/classifier/classifier.jsphttp://rdp.cme.msu.edu/classifier/classifier.jsphttp://rdp.cme.msu.edu/classifier/classifier.jsphttp://rdp.cme.msu.edu/classifier/classifier.jsp


9/13

2009; Cantas et al. 2011), but knowledge of intestinal microbiota of adults of Atlantic salmon is still scarce. To our knowl-edge, this is the first study of the intestinal microbiota of adult S. salar from intensive farming in Chile.

Most of the previous studies analyzing the cultured fractionof intestinal microbiota of Atlantic salmon using TSA, report-ed similar levels of cultured bacteria as found in this study(Yoshimizu et al. 1976; Huber et al. 2004). Other authorsreported lower levels of cultured counts from salmon intestine

samples such as Navarrete et al. (2008) who found meanvalues ranging from 5.01×102 to 6.31× 103 CFU g−1 of intes-tinal content in juveniles of reared Atlantic salmon, and Ringøet al. (2014) who found mean values of 4.17×102, 1×103 and2.82×102 CFU g−1 of proximal, midintestine and distal intes-tine of S. salar , respectively. In other studies, total viablecounts were determined from adherent and digesta frommidintestine (4.26×103 – 9.77×103 CFU g−1 and 4.07×103 – 1.62×105 CFU g−1, respectively) and distal intestine (8.32×103 – 2.57×104 CFU g−1 and 9.77×103 – 2.63×105 CFU g−1,respectively) of juveniles of S. salar fed with various

experimental diets (Bakke-McKellep et al. 2007), whereasHovda et al. (2007) determined bacterial levels in different sec-tions of the Atlantic salmon gut finding 7.94×103 CFU g−1 inthe foregut, and 5.01×103 CFU g−1 in the midgut.

In this study, the dominant genera identified among thecultured intestinal microbiota isolated using TSA mediumwere Pseudomonas, Acinetobacter, and Psychrobacter (41.89, 14.86, and 9.46 %, respectively). This is in agreement with Navarrete et al. (2008) who reportedthat microbiota from

untreated Atlantic salmon in Chile were mainly composed of Pseudomonas, Acinetobacter , Bacillus, Flavobacterium, Psychrobacter , and Brevundimonas. This also agrees with amore recent study by Cantas et al. (2011), which reported adominance of representatives of the genera Pseudomonas,

Acinetobacter, and Psychrobacter among the gut bacteria of juvenile Salmo salar , identified by bacterial culturing and 16SrRNA PCR techniques. In addition, Pseudomonas sp. and

Acinetobacter sp. have previously been reported as constitut-ing an important part of the intestinal microbiota of salmonids(Cahill 1990; Ringø et al. 2005; Romero and Navarrete 2006;

Fig.2 Phylogenetic tree showingthe relationships between 16SrRNA sequences of classifiedOTUs as Aliivibrio according toRDP from fish 2 and 16S rRNAsequences of thetype strains of allspecies of the genus Aliivibriodeposited in Genbank (NCBI). A bootstrap analysis was performed

with 1,000 repetitions. Sequencesof clones are represented by opencircles and sequencesrepresentatives of the genus

Aliivibrio are represented by filledcircles. Numbers in parenthesesindicate the number of sequences per OTUs

Table 5 Diversity of culturedand not cultured intestinalmicrobiota of farmed salmon


CM UM CM UM CM UM

Number of strains or clones 26 118 25 143 23 64

Number of genera or OTUs 7 16 10 6 9 14

Simpson diversity index 0.66 0.72 0.76 0.32 0.83 0.86

Shannon-Wiener index 1.42 1.77 1.87 0.68 1.96 2.22

CM Cultured microbiota, UM Uncultured microbiota using 16S rRNA clone libraries

Ann Microbiol (2015) 65:2343 – 2353 2349


10/13

Hovda et al. 2007). Furthermore, recent reports have demon-strated the presence of different Psychrobacter species in thealimentary tract of Atlantic salmon (Ringø et al.2006a; 2008),as well as the distal portion of the intestine of Arctic charr (Ringø et al. 2006b).

In this study a high proportion of the isolated bacteria fromthe intestinal content of Atlantic salmon exhibited enzymatic

activities, suggesting a potential role in the degradation andassimilation of nutrients, contributing to the nutrition of rearedsalmon, but the low bacterial counts suggest a poor contribu-tion of bacterial enzymes to the degradation of macronutrients.Furthermore, it is important to note that intestinal transit isshort, and the rearing temperature is much lower than thoseused for in vitro enzymatic assays and the API ZYM profilesare insufficient and other enzymatic assays are required toevaluate the possible contribution to digestion by gut micro-

biota. More research is required to understand the potentialfunction of intestinal microbiota as a source of digestive en-zymes in farmed salmon, and the feasibility of its use in en-

hancing nutrient utilization and growth rate when they are fedwith formulated diets.

As has been noted, when intestinal microbiota were studied by using culture-dependent methods, most of the cultured or-ganisms belonged to the γ-subclasses of the proteobacteria( Pseudomonas sp. and Acinetobacter sp.), in contrast to theintestinal microbiota revealed by the results of direct cloningmethods, that exhibited a predominance of lactic acid bacteria,which comprised more than 36 % of the identified clones.This proportion could have been higher, but for the unexpect-ed high dominance of representatives belonging to the

Aliivibrio genus in fish 2. The fact that lactic acid bacteria

from fish are commonly slow growing, requiring growth con-ditions on agar-media at lowtemperatures for up to four weeks(Ringø and Gatesoupe 1998), would explain why lactic acid

bacteria were only detected from 16S rDNA clones libraries,and not from the intestinal microbiota obtained after culturedon TSA, given that this medium is not suitable for growth of this bacterial group.

It is well established that lactic acid bacteria constitute a part of the native microbiota of fish (Ringø 2004; Hovda et al.2012; Ringø et al. 2014). Our results are in agreement with arecent study, showing the taxonomic affiliation of DGGE

band sequences from the midintestine and distal intestine con-

tent of Atlantic salmon.This study is based on known se-quences of 16S rRNA genes that indicated a high dominanceof lactic acid bacteria mainly composed of the Weissella and

Lactococcus genera, whereas Photobacterium was the most representative of γ-proteobacteria (Reveco et al. 2014). Alongwith this, within the lactic acid bacteria there is a high domi-nance of the genus Weissella from specimens 1 and 3. Variousstrains belonging to this genus have previously been proposedas potential probiotics for various fish species (Cai et al. 1998;Balcázar et al. 2008) However, recent cases of Weissellosis in

salmonids (Liu et al. 2009; Figueiredo et al. 2012), as well asthe experimental development of disease after its inoculation,demonstrated the role of the primary pathogen of some strainsidentified as Weissella sp., confirming Weissellosis as anemerging disease in rainbow trout aquaculture (Marancik et al. 2013; Welch and Good 2013).

When comparing diversity of the intestinal microbiota of

farmed Atlantic salmon obtained by analysis of the 16S rRNAgene of cultured strains and clone libraries, the diversity of clone libraries was higher than those from the cultured micro-

biota, with the exception of fish 2, which exhibited an unex- pectedly high dominance of Aliivibrio representatives whenits clone library was identified. Despite the absence of externaland internal symptoms of vibriosis when fish 2 was sampled,there was a high incidence of Aliivibrio genus in the intestinalmicrobiota, suggesting that the sampled fish was under aninitial stage of infection by this strain. On the other hand, theabsence of Aliivibrio in the cultured microbiota is probablydue to the use of TSA medium without addition of NaCl.

Currently, Aliivibrio genus comprises five species: A. fischeri, A. logei, A. salmonicida, A. wodanis, and A. finisterrensis(Beaz-Hidalgoetal. 2010).Fromthesespecies, A. salmonicida(Egidius et al. 1986), A. wodanis (Lunder et al. 2000), and

A. logei (Benediktsdottir et al. 1998) have been associatedwith disease in Atlantic salmon. Furthermore, it has beendemonstrated that A. salmonicida is able to colonize the fishintestinal tract (Hansen and Olafsen 1999). Further studiesare needed to determine whether high levels of Aliivibriospp. as observed in fish 2, are detrimental to the sanitarystatus of reared salmon under intensive conditions, becausethe increase in the concentration of this genus could be a

response to an infection with a pathogenic Aliivibrio straincausing an imbalance in the structure of the intestinalmicrobiota.

It is important to note that fish 2 not only exhibited aremarkably higher level of Aliivibrio sp. than that ob-served in the other two sampled individuals, but alsoshowed almost an absence of lactic acid bacteria, contrast-ing with the observations in the other sampled fishes. It must be noted that the importance of the interaction be-tween lactic acid bacteria and pathogens in the intestinesof salmon species prevents intestinal cellular damage(Ringø et al. 2010).

In a previous study, it was demonstrated that Vibrio( Aliivibrio) salmonicida can colonize the salmon intestine,which creates healthy carriers (Bjelland et al. 2012), but thisstate only occurs without the bacteria dominating the ubiqui-tous gut microbiota. In this study, the high predominance of

Aliivibrio in the intestinal microbiota of fish 2 suggests that fish 2 was an asymptomatic non-healthy carrier, but the other two sampled individuals were healthy carriers. It is important to note that all sampled fishes had the same origin and rearinghistory. The only difference was that they came from different

2350 Ann Microbiol (2015) 65:2343 – 2353


11/13

cages from adjacent cage blocks belonging to the samecompany.

The use of PCR-based identification of cultured organismsin combination with cloning of 16S rRNA genes, amplifieddirectly from salmon intestinal samples, are necessary to prop-erly study the structure and some functions of salmon intestinalmicrobiota. With this procedure, it must be noted that only the

cultivation-independent analysis could detect a minority taxanot previously reported as part of the intestinal microbiota of salmonids, including the Hydrogenophilus, Propionibacterium,Cronobacter , Enhydrobacter , Veillonella, Prevotella, and

Atopostipes genera, contributing to the knowledge of the mi-crobiota of the digestive tract of farmed Atlantic salmon.

In a previous study, it was found that the microbial intesti-nal community composition varies significantly in individualAtlantic cod specimens caught at a single location, and theauthors suggested that such high variation among specimensis due to a complex combination of factors (Star et al. 2013).The observed high variability is not unexpected, but further

studies are required to understand these variations.In conclusion, this study permitted acquisition of knowl-

edge of the structure of intestinal microbiota of S. salar cul-tured under intensive rearing conditions. There was evidenceof a high variability of levels of Aliivibrio sp. among individ-uals collected from different cages of the same farm. The high

predominance of a single clone of Aliivibrio sp. related to the pathogenic A. salmonicida and A. logei species in a sampledfish suggest its infection by an Aliivibrio strain capable of avoiding fish defense mechanisms and proliferating in theintestinal environment previous to the production of notice-able symptoms of disease. In addition, the absence of lactic

acid bacteria in the intestine of this individual is probablyrelated to its high load of Aliivibrio. It is clear that molecular identification of 16S rRNA gene libraries obtained from intes-tinal content samples is effective in determining the overallstructure of the intestinal microbiota of farmed Atlantic salm-on enabling evaluation of thehealthstatusof farmedfish whenevaluating the dominance of potential pathogenic species aswell as the incidence of lactic acid bacteria.

Acknowledgments The comments and suggestions of one anonymousreviewer are greatly appreciated as they helped to improve the presenta-tion of this work.

References

Askarian F, Zhou Z, Olsen RE, Sperstad S, Ringø E (2012) Culturableautochthonous gut bacteria in Atlantic salmon (Salmo salar L.) feddiets with or without chitin. Characterization by 16S rRNA genesequencing, ability to produce enzymes and in vitro growth inhibi-tion of four fish pathogens. Aquaculture 326 – 329:1 – 8

Bairaigi A, Ghosh K, Sen SK, Ray AK (2002) Enzyme producing bac-terial flora isolated from fish digestive tracts. Aquac Int 10:109 – 121

Bakke-McKellep AM, Penn MH, Salas PM, Refstie S, Sperstad S,Landsverk T, Ringø E, Krogdahl A (2007) Effects of dietarysoyabean meal, inulin and oxytetracycline on intestinal microbiotaand epithelial cell stress, apoptosis and proliferation in the teleost Atlantic salmon (Salmo salar L.). Br J Nutr 97:699 – 713

Balcázar JL, Vendrell D, de Blas I, Ruiz-Zarzuelaa I, Muzquiza JL,Gironesa O (2008) Characterization of probiotic properties of lacticacid bacteria isolated from intestinal microbiota of fish. Aquaculture278:188 – 191

Barrow GH, Feltham RKA (1993) Cowan and steel’s manual for identi-fication of medical bacteria. Cambridge University Press,Cambridge

Bates JM, Mittge E, Kuhlman J, Baden KN, Cheesman SE, Guillemin K (2006) Distinct signals from the microbiota promote different as- pects of zebrafish gut differentiation. Dev Biol 297:374 – 386

Beaz-Hidalgo R, Doce A, Balboa S, Barja JL, Romalde JL (2010) Alii vibr io finisterrens is sp. nov., isolated from Manila clam, Ruditapes philippinarum and emended description of the genus Aliivibrio. Int J Syst Evol Microbiol 60:223 – 228

Benediktsdottir E, Helgason S, Sigurjonsdottir H (1998) Vibrio spp. iso-lated from salmonids with shallow skin lesions and reared at lowtemperature. J Fish Dis 21:19 – 28

Bjelland AM, Johansen R, Brudal E, Hansen H, Winther-Larsen HC,Sørum H (2012) Vibrio salmonicida pathogenesis analyzed by experimental challenge of Atlantic salmon (Salmo salar ). MicrobPathog 52:77 – 84

Cai Y, Benno Y, Nakase T, Oh TK (1998) Specific probiotic characteri-zation of Weissella hellenica DS-12 isolated from flounder intestine.J Gen Appl Microbiol 44:311 – 316

CahillM (1990)Bacterial flora of fishes: a review. Microb Ecol 19:21 – 41Cantas L, Fraser TWK, Fjelldal PG, Mayer I, Sørum H (2011) The

culturable intestinal microbiota of triploid and diploid juvenileAtlantic salmon (Salmo salar ) - a comparison of composition anddrug resistance. BMC Vet Res 7:71. doi:10.1186/1746-6148-7-71

Egidius E, Wiik R, Andersen K, Hoff KA, Hjeltnes B (1986) Vibrio salmonicida sp. nov., a new fish pathogen. Int J Syst Bacteriol 36:518 – 520

Figueiredo HCP, Costa FAA, Leal CAG, Carvalho-Castro GA, Leite RC(2012) Weissella sp. outbreaks in commercial rainbow trout (Oncorhynchus mykiss) farms in Brazil. Vet Microbiol 156:359 – 366

Gherna LR (1994) Culture preservation. In: Gerhardt P, Murray REG,Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp278 – 292

Gómez GD, Balcázar JL (2008) A review onthe interactions between gut microbiota and innate immunity of fish. FEMS Immunol MedMicrobiol 52(2):145 – 154

Ghosh K, Sen SK, Ray AK (2002) Characterization of bacilli isolatedfrom the gut of Rohu, Labeo rohita, fingerlings and its significancein digestion. J Appl Aquac 12:33 – 42

Hansen G, Olafsen J (1999) Bacterial interactions in early life stages of marine cold water fish. Microb Ecol 38:1 – 26

Hartviksen M, Vecino JLG, Ringø E, Bakke A-M, Wadsworth S,

Krogdahl Å, Ruohonen K, Kettunen A (2014) Alternative dietary protein sources for Atlantic salmon (Salmo salar L.) effect on intes-tinal microbiota, intestinal and liver histology and growth. Aquac Nutr 20:381 – 398

Hovda MB, Fontanillas R, McGurk C, Obach O, Rosnes JT (2012)Seasonal variations in the intestinal microbiota of farmed Atlanticsalmon (Salmo salar L.). Aquac Res 43:154 – 159

Hovda MB, Lunestad BT, Fontanillas R, Rosnesa JT (2007) Molecular characterisation of the intestinal microbiota of farmed Atlantic salm-on (Salmo salar L.) by PCR DGGE of conserved 16S rRNA generegions. Aquaculture 272:581 – 588

Huber I, Spanggaard B, Appel KF, Rossen L, Nielsen T, Gram L (2004)Phylogenetic analysis and in situ identification of the intestinal

Ann Microbiol (2015) 65:2343 – 2353 2351

http://dx.doi.org/10.1186/1746-6148-7-71http://dx.doi.org/10.1186/1746-6148-7-71


12/13

microbial community of rainbow trout (Oncorhynchus mykiss,Walbaum). J Appl Microbiol 96:117 – 132

Kanther M, Rawls JF (2010) Host-microbe interactions in the developingzebrafish. Curr Opin Immunol 22:10 – 19

Kar N, Roy RN, Sen SK, Ghosh K (2008) Isolation and characterizationof extracellular enzyme producing bacilli in the digestive tracts of Rohu, Labeo rohita (Hamilton) and murrel, Channa punctatus(Bloch). Asian Fish Sci 21:421 – 434

Kristiansen M, Merrifield DL, Gonzalez Vecino JL, Myklebust R, RingøE (2011) Evaluation of prebiotic and probiotic effects on the intes-tinal gut microbiota and histology of Atlantic salmon (Salmo salar L.). J Aquac Res Dev S1:009. doi:10.4172/2155-9546.S1-009

Lane DJ D1991] 16S/23S rRNA sequencing. In: Stackebrandt E,Goodfellow M Deds] Nucleic acid techniques in bacterial systemat-ics. Wiley, Chichester, pp 115 – 147, 115 – 175

Liu JY, Li AH, Ji C, Yang WM (2009) First description of a novelWeissella species as an opportunistic pathogen for Rainbow Trout Oncorhynchus mykiss(Walbaum) in China. Vet Microbiol 136:314 – 320

Lunder T, Sørum H, Holstad G, Steigerwalt AG, Mowinckel P, Brenner DJ (2000) Phenotypic and genotypic characterization of Vibrioviscosus sp. nov. and Vibrio wodanis sp. nov. isolated fromAtlantic salmon (Salmo salar ) with ‘winter ulcer ’. Int J Syst Evol

Microbiol 50:427 – 450Marancik DP, Welch TJ, Leeds TD, Wiens GD (2013) Acute mortality,

bacterial load, and pathology of select lines of adult rainbow trout challenged with Weissella sp. NC36. J Aquat Anim Health 25:230 – 236

Merrifield DL, Dimitroglou A, Foey A, Daviesa SJ, Bakera RTM,Bøgwaldc J, Castexd M, Ringøc E (2010) The current status andfuture focus of probiotic and prebiotic applications for salmonids.Aquaculture 302:1 – 18

Miranda CD, Rojas R (2007) Occurrence of florfenicol resistance in bacteria associated with two Chilean salmon farms with different history of antibacterial usage. Aquaculture 266:39 – 46

Miranda CD, Zemelman R (2001) Antibiotic resistant bacteria in fishfrom the Concepción Bay, Chile. Mar Pollut Bull 42:1096 – 1102

Moffitt CM, Mobin SMA (2006) Profile of microflora of the posterior intestine of Chinook salmon before, during, and after administrationof rations with andwithout erythromycin. N Am J Aquac68:176 – 185

Navarrete P, Espejo RT, Romero J (2009) Molecular analysis of microbi-otaalongthe digestive tractof juvenile Atlanticsalmón (Salmosalar L). Microb Ecol 57:550 – 561

Navarrete P, Fuentes P, De la Fuente L, Barros L, Magne F, Opazo R,Ibacache C, Espejo RT, Romero J (2013) Short-term effects of die-tary soybean meal and lactic acid bacteria on the intestinal morphol-ogy and microbiota of Atlantic salmon (Salmo salar ). Aquac Nutr 19:827 – 836

Navarrete P, Mardones P, Opazo R, Espejo R, Romero J (2008)Oxytetracycline treatment reduces bacterial diversity of intestinalmicrobiota of Atlantic salmon. J Aquat Anim Health 20:177 – 183

Nawrocki EP, Eddy SR (2007) Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 30(3):540 – 553

Nayak SK (2010) Role of gastrointestinal microbiota in fish. Aquac Res41:1553 – 1573

Ray AK, Ghosh K, Ringø E (2012) Enzyme-producing bacteria isolatedfrom fish gut: a review. Aquac Nutr 18:465 – 492

Reveco FE, Øverland M, Romarheim OH, Mydland LT (2014) Intestinal bacterial community structure differs between healthy and inflamedintestines in Atlantic salmon (Salmo salar L.). Aquaculture 420 – 421:262 – 269

Ringø E (1993) The effect of chromic oxide (Cr 2O3) on aerobic bacterial populations associated with the epithelial mucosa of Arctic charr (Salvelinus alpinus L.). Can J Microbiol 39:1169 – 1173

Ringø E (2004) Lacticacid bacteria in fish and fish farming. In: SalminenS, Ouwehand A, von Wright A (eds) Lactic acid bacteria. MarcelDekker, New York, pp 581 – 610

Ringø E, Birkbeck T (1999) Intestinal microflora of fish larvae and fry.Aquac Res 30:73 – 93

Ringø E, Gatesoupe FJ (1998) Lactic acid bacteria in fish, a review.Aquaculture 160:177 – 203

Ringø E, Løvmo L, Kristiansen M, Bakken Y, Salinas I, Myklebust R,OlsenRE, Mayhew TM (2010) Lactic acid bacteria vs. pathogens inthe gastrointestinal tract of fish: a review. Aquac Res 41:451 – 467

Ringø E, Olsen RE (1999) The effect of diet on aerobic bacterial floraassociated with intestine of Arctic charr (Salvelinus alpinus L.). JAppl Microbiol 86:22 – 28

Ringø E, Schillinger U, Holzapfel W (2005) Antibacterial activities of lacticacid bacteria isolatedfromaquatic animals andthe use of lacticacid bacteria in aquaculture. In: Holzapfel W, Naughton P (eds)Microbial ecology in growing animals. Elsevier, Edinburgh, pp418 – 453

Ringø E, Sperstad S, Kraugerud OF, Krogdahl A (2008) Use of 16SrRNA gene sequencing analysis to characterize culturable intestinal bacteria in Atlantic salmon (Salmo salar ) fed diets with cellulose or non-starch polysaccharides from soy. Aquac Res 39:1087 – 1100

Ringø E, Sperstad S, Myklebust R, Olsen RE, Yao B, Ringø E (2006a)

Characterisation of the microbiota associated with intestine of Atlantic cod (Gadus morhua L.): the effect of fish meal, standardsoybean meal and a bioprocessed soybean meal. Aquaculture 261:829 – 841

Ringø E, Sperstad S, Myklebust R, Mayhew TM, Olsen RE (2006b) Theeffect of dietary inulin on bacteria associated with hindgut of Arcticcharr (Salvelinus alpinus L.). Aquac Res 37:891 – 897

Ringø E, Strøm E, Tabachek J-A (1995) Intestinal microflora of salmo-nids. Aquac Res 26:773 – 789

Ringø E, Zhou Z, He S, Jensen L, Lund V, Mayhew TM, Olsen RE(2014) Effect of stress on intestinal microbiota of Arctic charr,Atlantic salmon, rainbow trout and Atlantic cod: A review. Afr JMicrobiol Rev 8:609 – 618

Romero J, Navarrete P (2006) 16S rDNA-based analysis of dominant

bacterial populations associated with early life stages of coho salm-on (Oncorhynchus kisutch). Microb Ecol 51:422 – 430Rosselló-Mora R, Amman R (2001) The species concept for prokaryotes.

FEMS Microbiol Rev 25:39 – 67Rungruangsak-Torrissen K, Sunde J, Berg AE, Nordgarden U, Fjelldal

PG, Oppedal F (2009) Digestive efficiency, free amino acid poolsand quality of growth performance in Atlantic salmon (Salmo salar L.) affect by light regimes and vaccine types. Fish Physiol Biochem35:255 – 272

Saha S, Roy RN, Sen SK, Ray AR (2006) Characterization of cellulase- producing bacteria from the digestive tract of tilapia, Oreochromismossambica (Peters) and grass carp, Ctenopharyngodon idella(Valenciennes). Aquac Res 37:380 – 388

Salmon C (2014) Asociación de Productores de Salmón y Trucha deChile: Producción mundial de Salmón y Trucha 2014. www.

Salmonchile.cl. Accessed 16 August 2014Spanggaard B, Huber I, Nielsen J, Nielsen T, Appel KF, Gram L (2000)

The microflora of rainbow trout intestine: a comparison of tradition-al and molecular identification. Aquaculture 182:1 – 15

St ar B, Haverkamp THA, Jentoft S, Jakobsen KS (2013) Next generationsequencing shows high variation of the intestinal microbial speciescomposition in Atlantic cod caught at a single location. BMCMicrobiol 13:248

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6:Molecular Evolutionary Genetics Analysis version 6.0. Mol BiolEvol 30:2725 – 2729

2352 Ann Microbiol (2015) 65:2343 – 2353

http://dx.doi.org/10.4172/2155-9546.S1-009http://dx.doi.org/10.4172/2155-9546.S1-009http://www.salmonchile.cl/http://www.salmonchile.cl/http://www.salmonchile.cl/http://www.salmonchile.cl/http://dx.doi.org/10.4172/2155-9546.S1-009


13/13

Trust TJ, Sparrow RAH (1974) The bacterial flora in the alimentary tract of freshwater salmonid fishes. Can J Microbiol 20:1219 – 1228

Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesianclassifier for rapid assignment of rRNA sequences into thenew bacterial taxonomy. Appl Environ Microbiol 73(16):5261 – 5267

Welch TJ, Good CM (2013) Mortality associated with Weissellosis(Weissella sp.) in USA farmed rainbow trout: potential for control by vaccination. Aquaculture 388 – 391:122 – 127

Yoshimizu M, Kimura T, Sakai M (1976) Studies on the intestinal micro-flora of salmonids. The intestinal microflora of fish reared in freshwater and sea water. Bull Jpn Soc Sci Fish 42:91 – 99

Ann Microbiol (2015) 65:2343 – 2353 2353

Documents

High variability of levels of Aliivibrio.pdf