DOCSLIB.ORG

High Variability of Levels of Aliivibrio and Lactic Acid Bacteria in the Intestinal Microbiota of Farmed Atlantic Salmon Salmo Salar L

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
High Variability of Levels of Aliivibrio and Lactic Acid Bacteria in the Intestinal Microbiota of Farmed Atlantic Salmon Salmo Salar L Ann Microbiol (2015) 65:2343–2353 DOI 10.1007/s13213-015-1076-3 ORIGINAL ARTICLE High variability of levels of Aliivibrio and lactic acid bacteria in 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 structure of the intestinal microbiota of farmed Atlantic salm- microbiota of Atlantic salmon (Salmo salar L.) was studied on enabling detection of a minority of taxa not previously using culture and culture-independent methods. Three adult reported as part of the intestinal microbiota of salmonids, in- specimens of S. salar were collected from a commercial salm- cluding the genera Hydrogenophilus, Propionibacterium, on farm in Chile, and their intestinal microbiota were studied Cronobacter, Enhydrobacter, Veillonella, Prevotella,and by partial sequencing of the 16S rRNA gene of pure cultures Atopostipes, as well as to evaluate the health status of farmed as well as of clone libraries. Out of the 74 bacterial isolates, fish when evaluating the dominance of potential pathogenic Pseudomonas was the most predominant genus among cul- species and the incidence of lactic acid bacteria. tured microbiota. In clone libraries, 325 clones were obtained from three adult fish, and a total of 36 operational taxonomic Keywords Aquaculture . Intestinal microbiota . Aliivibrio . units (OTUs) were identified. This indicated that lactic acid Salmon farming . Salmo salar 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 Introduction (99 sequences) of Aliivibrio sp. related to the pathogenic Aliivibrio salmonicida species and the absence of lactic acid Chile is currently a worldwide leading salmon producer and bacteria in the third fish, suggesting a condition of an asymp- the Atlantic salmon Salmo salar L. is one of the main Chilean tomatic non-healthy carrier. It is clear that molecular identifi- salmonid farming products, constituting 182,712 tons from cation of 16S rRNA gene libraries obtained from intestinal January to June of 2014, and comprising 64 % of total salmo- content samples is effective in determining the overall nid exports (SalmonChile 2014). It is well established that the intestinal tract of reared fish harbors a microbiota that fulfill an important role in immunity, nutrition, and disease control of * Félix A. Godoy reared fishes (Trust and Sparrow 1974; Ringø and Birkbeck [email protected]; [email protected] 1999; Moffitt and Mobin 2006). To study the microbiota of the gastrointestinal tract of fish- 1 Centro i ~ mar, Universidad De Los Lagos, Camino Chinquihue km es, the general approach has been the use of conventional 6, Casilla 557, Puerto Montt, Chile culture methods (Ringø et al. 1995). However, it has been 2 Laboratorio de Patobiología Acuática, Departamento de Acuicultura, found that these methods present several disadvantages and Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile usually only detect aerobics and facultative anaerobic bacteria, 3 Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Larrondo but do not detect slow-growing bacteria (Spanggaard et al. 1281, Coquimbo, Chile 2000;Nayak2010). Thus, molecular analysis of DNA extract- 4 Escuela de Ciencias Ambientales, Facultad de Recursos Naturales, ed directly from the sample has rapidly replaced cultivation in Universidad Católica de Temuco, Temuco, Chile the study of the structure of fish intestinal microbiota. 2344 Ann Microbiol (2015) 65:2343–2353 Nonetheless, when some phenotypic properties such as enzy- methods, and to characterize some of the metabolic and enzy- matic activities need to be studied in order to understand the matic capabilities of the isolated strains. potential role of the microbiota in improving fish nutrition, it is more appropriate to study the fish intestinal microbiota composition by culture techniques in combination with Materials and methods culture-independent methods (Bakke-McKellep et al. 2007; Kristiansen et al. 2011;Askarianetal.2012). Sampling The intestinal microbiota composition is known to depend on dietary factors (Gómez and Balcázar 2008;Nayak2010; Three apparently healthy adult specimens of Atlantic salmon Hartviksen et al. 2014). Navarrete et al. (2013), using micro- (Salmo salar L.) with an approximate weight of 2.5 kg were biological analysis, demonstrated that specific bacterial collected from three different rearing cages belonging to a groups were correlated with the administered diet, and commercial salmon farm located at Punta Quilque, X Region, Reveco et al. (2014) reported that intestinal microbiota of Chile (13 °C, water temperature; 32 g L-1, salinity). Samples Salmo salar is sensitive to dietary changes, observing that were packed in sterile bags, placed on ice, immediately the most dominant species were Lactococcus lactis, Weissella transported to the laboratory, and processed within 2 h of confusa,andPhotobacterium phosphoreum.Otherwise, collection. Navarrete et al. (2008) suggested that Atlantic salmon favors Pseudomonas establishment because this species was de- Sample processing and cultured bacterial count tected as the dominant component in most of the samples of juvenile farmed Atlantic salmon. There are other studies Adult salmon were externally washed with sterile deionized that describe the intestinal microbiota of farmed Atlantic water to reduce potential contamination with skin bacteria and salmon; however, the majority of these studies are associ- aseptically eviscerated. Salmon intestines were aseptically re- ated with fingerling or juvenile stages (Bakke-McKellep moved and placed in sterile Petri dishes and were divided into et al. 2007; Navarrete et al. 2008;Cantasetal.2011; proximal intestine (defined as the region between the distal Navarrete et al. 2013; Reveco et al. 2014). pyloric caeca and widening of the intestine and the appearance It has been reported that fish intestinal microbiota have an of transverse luminal folds) and distal intestine (the region important role in regulating nutrient digestion, immune re- from the widening of the intestine and the appearance of trans- sponses, and intestinal differentiation (Bates et al. 2006; verse luminal folds to anus). Then, digesta from proximal and Kanther and Rawls 2010;Merrifieldetal.2010; Nayak distal intestine were gently squeezed out and the two intestinal 2010; Ray et al. 2012), so physiological and biochemical char- segments were thoroughly rinsed three times using 3 mL of acterizations of the intestinal isolates are important in eluci- peptone water in order to collect both adherent and non- dating their functions in the gastrointestinal tract. Several stud- adherent bacteria (Ringø 1993). Culture counts of heterotro- ies reported that freshwater fish reared in warm waters harbor phic bacteria were determined by a spread plate method using proteolytic, amylolytic, and cellulolytic bacteria in their diges- Tryptic soy agar (TSA, Difco Labs). Salmon intestinal con- tive tracts (Bairaigi et al. 2002; Ghosh et al. 2002;Sahaetal. tents samples were aseptically weighed, ground, and added to 2006; Kar et al. 2008), whereas it was reported that an increase 5 mL of sterile physiological saline (0.85 %) (PS) to obtain a in proteolytic enzymes such as trypsin and chymotrypsin in homogenate as previously described by Miranda and salmon induces a better assimilation of proteins, as well as an Zemelman (2001). Appropriate tenfold dilution of the homog- increase in the growth and stimulation of immune and endo- enates in PS was prepared and 0.1 mL aliquots were inoculat- crine systems (Rungruangsak-Torrissen et al. 2009). Addition- ed in triplicate onto agar plates. All plates were incubated at ally, it has been observed that the different bacterial popula- 20 °C for 5–10 days and the bacterial numbers per g of tions composing the intestinal microbiota represent different sample were calculated as described in Miranda and metabolic groups, which can enhance the digestive capacity of Rojas (2007). A group of representative colonies from fish (Ringø and Olsen 1999). Hence, knowledge of the enzy- each sample was selected for purity. matic capacities of the gastrointestinal microbiota of farmed salmon could help regulate the intestinal microbiota enhanc- Bacterial isolation ing nutrition performance of farmed fishes under intensive rearing conditions. However, only a few studies on adult salm- Seventy-four isolates were recovered as a representative sam- on are available, and knowledge of the enzymatic properties ple of the intestinal cultured bacterial community of farmed of the intestinal microbiota of reared salmon is still scarce. salmon. From these, 26 strains were recovered from specimen The main aims of this study were to investigate the com- 1 (17 and nine strains from the proximal and distal intestine, position of intestinal microbiota of adult specimens of farmed respectively), 25 strains from specimen 2 (14 and 11 strains Atlantic salmon, Salmo salar L. by culture and cloning from the proximal and distal intestine, respectively) and 23 Ann Microbiol (2015) 65:2343–2353 2345 strains from specimen 3 (nine and 14 strains from the proximal the color allowed to develop
Load more

Recommended publications
  • A Taxonomic Note on the Genus Lactobacillus
    Taxonomic Description template 1 A taxonomic note on the genus Lactobacillus: 2 Description of 23 novel genera, emended description 3 of the genus Lactobacillus Beijerinck 1901, and union 4 of Lactobacillaceae and Leuconostocaceae 5 Jinshui Zheng1, $, Stijn Wittouck2, $, Elisa Salvetti3, $, Charles M.A.P. Franz4, Hugh M.B. Harris5, Paola 6 Mattarelli6, Paul W. O’Toole5, Bruno Pot7, Peter Vandamme8, Jens Walter9, 10, Koichi Watanabe11, 12, 7 Sander Wuyts2, Giovanna E. Felis3, #*, Michael G. Gänzle9, 13#*, Sarah Lebeer2 # 8 '© [Jinshui Zheng, Stijn Wittouck, Elisa Salvetti, Charles M.A.P. Franz, Hugh M.B. Harris, Paola 9 Mattarelli, Paul W. O’Toole, Bruno Pot, Peter Vandamme, Jens Walter, Koichi Watanabe, Sander 10 Wuyts, Giovanna E. Felis, Michael G. Gänzle, Sarah Lebeer]. 11 The definitive peer reviewed, edited version of this article is published in International Journal of 12 Systematic and Evolutionary Microbiology, https://doi.org/10.1099/ijsem.0.004107 13 1Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key 14 Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, P.R. China. 15 2Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience 16 Engineering, University of Antwerp, Antwerp, Belgium 17 3 Dept. of Biotechnology, University of Verona, Verona, Italy 18 4 Max Rubner‐Institut, Department of Microbiology and Biotechnology, Kiel, Germany 19 5 School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland 20 6 University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy 21 7 Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit 22 Brussel, Brussels, Belgium 23 8 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, 24 Belgium 25 9 Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada 26 10 Department of Biological Sciences, University of Alberta, Edmonton, Canada 27 11 National Taiwan University, Dept.
    [Show full text]
  • Unlocking the Genomic Taxonomy of the Prochlorococcus Collective
    bioRxiv preprint doi: https://doi.org/10.1101/2020.03.09.980698; this version posted March 11, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Unlocking the genomic taxonomy of the Prochlorococcus collective Diogo Tschoeke1#, Livia Vidal1#, Mariana Campeão1, Vinícius W. Salazar1, Jean Swings1,2, Fabiano Thompson1*, Cristiane Thompson1* 1Laboratory of Microbiology. SAGE-COPPE and Institute of Biology. Federal University of Rio de Janeiro. Rio de Janeiro. Brazil. Av. Carlos Chagas Fo 373, CEP 21941-902, RJ, Brazil. 2Laboratory of Microbiology, Ghent University, Gent, Belgium. *Corresponding authors: E-mail: [email protected] , [email protected] Phone no.: +5521981041035, +552139386567 #These authors contributed equally. ABSTRACT 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.09.980698; this version posted March 11, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC.
    [Show full text]
  • Diverse Deep-Sea Anglerfishes Share a Genetically Reduced Luminous
    RESEARCH ARTICLE Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment Lydia J Baker1*, Lindsay L Freed2, Cole G Easson2,3, Jose V Lopez2, Dante´ Fenolio4, Tracey T Sutton2, Spencer V Nyholm5, Tory A Hendry1* 1Department of Microbiology, Cornell University, New York, United States; 2Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States; 3Department of Biology, Middle Tennessee State University, Murfreesboro, United States; 4Center for Conservation and Research, San Antonio Zoo, San Antonio, United States; 5Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States Abstract Deep-sea anglerfishes are relatively abundant and diverse, but their luminescent bacterial symbionts remain enigmatic. The genomes of two symbiont species have qualities common to vertically transmitted, host-dependent bacteria. However, a number of traits suggest that these symbionts may be environmentally acquired. To determine how anglerfish symbionts are transmitted, we analyzed bacteria-host codivergence across six diverse anglerfish genera. Most of the anglerfish species surveyed shared a common species of symbiont. Only one other symbiont species was found, which had a specific relationship with one anglerfish species, Cryptopsaras couesii. Host and symbiont phylogenies lacked congruence, and there was no statistical support for codivergence broadly. We also recovered symbiont-specific gene sequences from water collected near hosts, suggesting environmental persistence of symbionts. Based on these results we conclude that diverse anglerfishes share symbionts that are acquired from the environment, and *For correspondence: that these bacteria have undergone extreme genome reduction although they are not vertically [email protected] (LJB); transmitted.
    [Show full text]
  • Revival and Phylogenetic Analysis of the Luminous Bacterial Cultures of MW Beijerinck
    RESEARCH ARTICLE Historical microbiology: revival and phylogenetic analysis of the luminous bacterial cultures of M. W. Beijerinck Marian J. Figge1, Lesley A. Robertson2, Jennifer C. Ast3 & Paul V. Dunlap3 1The Netherlands Culture Collection of Bacteria, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; 2Department of Biotechnology, Delft University of Technology, Delft, The Netherlands; and 3Department of Ecological and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA Correspondence: Paul V. Dunlap, Abstract Department of Ecology and Evolutionary Biology, University of Michigan, 830 North Luminous bacteria isolated by Martinus W. Beijerinck were sealed in glass University Ave., Ann Arbor, MI 48109-1048, ampoules in 1924 and 1925 and stored under the names Photobacterium phos- USA. Tel.: +1 734 615 9099; fax: +1 734 phoreum and ‘Photobacterium splendidum’. To determine if the stored cultures 763 0544; e-mail: [email protected] were viable and to assess their evolutionary relationship with currently recog- nized bacteria, portions of the ampoule contents were inoculated into culture Present address: Jennifer C. Ast, medium. Growth and luminescence were evident after 13 days of incubation, Evolutionary Biology Centre, Departments of Molecular Evolution and Limnology, Uppsala indicating the presence of viable cells after more than 80 years of storage. The University, Norbyva¨ gen 18C, 752 36, Beijerinck strains are apparently the oldest bacterial cultures to be revived from Uppsala, Sweden. storage. Multi-locus sequence analysis, based on the 16S rRNA, gapA, gyrB, pyrH, recA, luxA, and luxB genes, revealed that the Beijerinck strains are distant Received 3 May 2011; revised 21 July 2011; from the type strains of P.
    [Show full text]
  • (COVIS) Overview
    National Enteric Disease Surveillance: Cholera and Other Vibrio Illness Surveillance (COVIS) Surveillance System Overview: Cholera and Other Vibrio Illness Surveillance (COVIS) Background on infection with species from the family Vibrionaceae Infection with pathogenic species of the family Vibrionaceae can cause two distinct categories of infection: cholera and vibriosis, both of which are nationally notifiable. Cholera is, by definition, caused by infection with toxigenic Vibrio cholerae O1 or O139 and was first reported in the United States in 1832. Infection is characterized by acute, watery diarrhea. An average of 5-10 cases of cholera are reported annually in the United States; most are acquired during international travel, however, on average 1-2 per year are domestically acquired. An increase in the number of cholera cases reported in the United States has occurred when there are cholera outbreaks in the Western Hemisphere, such as Latin America in the 1990s and Haiti in 2010, with almost all attributable to exposures during international travel. CDC annually reports to the World Health Organization all confirmed cholera cases diagnosed in the United States. Vibriosis is caused by infection with any species of the family Vibrionaceae (excluding toxigenic Vibrio cholerae O1 and O139), with an estimated 80,000 cases and 300 deaths annually in the United States (1). The most common clinical manifestations are watery diarrhea, primary septicemia, wound infection, and otitis externa. Risk factors for illness include consumption of shellfish,
    [Show full text]
  • Comparative Genomic Analysis of Carnobacterium Maltaromaticum: Study of Diversity and Adaptation to Different Environments Christelle Iskandar
    Comparative genomic analysis of Carnobacterium maltaromaticum: Study of diversity and adaptation to different environments Christelle Iskandar To cite this version: Christelle Iskandar. Comparative genomic analysis of Carnobacterium maltaromaticum: Study of diversity and adaptation to different environments. Food and Nutrition. Université de Lorraine, 2015. English. NNT : 2015LORR0245. tel-01754646 HAL Id: tel-01754646 https://hal.univ-lorraine.fr/tel-01754646 Submitted on 30 Mar 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. AVERTISSEMENT Ce document est le fruit d'un long travail approuvé par le jury de soutenance et mis à disposition de l'ensemble de la communauté universitaire élargie. Il est soumis à la propriété intellectuelle de l'auteur. Ceci implique une obligation de citation et de référencement lors de l’utilisation de ce document. D'autre part, toute contrefaçon, plagiat, reproduction illicite encourt une poursuite pénale. Contact : [email protected] LIENS Code de la Propriété Intellectuelle. articles L 122. 4
    [Show full text]
  • Characterization of Bacterial Communities of Cold-Smoked Salmon During Storage
    foods Article Characterization of Bacterial Communities of Cold-Smoked Salmon during Storage Aurélien Maillet 1,2,* , Pauline Denojean 2, Agnès Bouju-Albert 2 , Erwann Scaon 1 ,Sébastien Leuillet 1, Xavier Dousset 2, Emmanuel Jaffrès 2,Jérôme Combrisson 1 and Hervé Prévost 2 1 Biofortis Mérieux NutriSciences, 3 route de la Chatterie, 44800 Saint-Herblain, France; [email protected] (E.S.); [email protected] (S.L.); [email protected] (J.C.) 2 INRAE, UMR Secalim, Oniris, Route de Gachet, CS 44307 Nantes, France; [email protected] (P.D.); [email protected] (A.B.-A.); [email protected] (X.D.); [email protected] (E.J.); [email protected] (H.P.) * Correspondence: [email protected] Abstract: Cold-smoked salmon is a widely consumed ready-to-eat seafood product that is a fragile commodity with a long shelf-life. The microbial ecology of cold-smoked salmon during its shelf-life is well known. However, to our knowledge, no study on the microbial ecology of cold-smoked salmon using next-generation sequencing has yet been undertaken. In this study, cold-smoked salmon microbiotas were investigated using a polyphasic approach composed of cultivable methods, V3—V4 16S rRNA gene metabarcoding and chemical analyses. Forty-five cold-smoked salmon products processed in three different factories were analyzed. The metabarcoding approach highlighted 12 dominant genera previously reported as fish spoilers: Firmicutes Staphylococcus, Carnobacterium, Lactobacillus, β-Proteobacteria Photobacterium, Vibrio, Aliivibrio, Salinivibrio, Enterobacteriaceae Serratia, Citation: Maillet, A.; Denojean, P.; Pantoea γ Psychrobacter, Shewanella Pseudomonas Bouju-Albert, A.; Scaon, E.; Leuillet, , -Proteobacteria and .
    [Show full text]
  • Intrahepatic Bacterial Metataxonomic Signature in Non-Alcoholic Fatty Liver
    Hepatology ORIGINAL RESEARCH Intrahepatic bacterial metataxonomic signature in Gut: first published as 10.1136/gutjnl-2019-318811 on 2 January 2020. Downloaded from non- alcoholic fatty liver disease Silvia Sookoian ,1,2 Adrian Salatino,1,3 Gustavo Osvaldo Castaño,4 Maria Silvia Landa,1,3 Cinthia Fijalkowky,1,3 Martin Garaycoechea,5 Carlos Jose Pirola 1,3 ► Additional material is ABSTRact published online only. To view Objective We aimed to characterise the liver tissue Significance of this study please visit the journal online bacterial metataxonomic signature in two independent (http:// dx. doi. org/ 10. 1136/ What is already known on this subject? gutjnl- 2019- 318811). cohorts of patients with biopsy- proven non- alcoholic fatty liver disease (NAFLD) diagnosis, as differences in ► The natural history of non- alcoholic fatty liver For numbered affiliations see disease (NAFLD) is modulated by genetic and end of article. the host phenotypic features—from moderate to severe obesity—may be associated with significant changes in environmental factors. ► Recent discoveries revealed the role of the Correspondence to the microbial DNA profile. Dr Silvia Sookoian, Institute Design and methods Liver tissue samples from 116 gut microbiota in human health and disease, of Medical Research A Lanari, individuals, comprising of 47 NAFLD overweight or including NAFLD. However, the impact of the University of Buenos Aires moderately obese patients, 50 NAFLD morbidly obese liver tissue microbial DNA profiling on the Faculty of Medicine, Buenos disease biology remains unknown. Aires, 10109 CABA, Argentina; patients elected for bariatric surgery and 19 controls, ssookoian@ intramed. net were analysed using high- throughput 16S rRNA gene What are the new findings? Dr Carlos Jose Pirola; sequencing.
    [Show full text]
  • Genomic Taxonomy of Vibrios
    Downloaded from orbit.dtu.dk on: Dec 18, 2017 Genomic taxonomy of vibrios Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.; Vasconcelos, Ana Tereza R.; Vesth, Tammi Camilla; Alves, Nelson Jr; Ussery, David; Iida, Tetsuya; Thompson, FL Published in: B M C Evolutionary Biology Link to article, DOI: 10.1186/1471-2148-9-258 Publication date: 2009 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Thompson, C. C., Vicente, A. C. P., Souza, R. C., Vasconcelos, A. T. R., Vesth, T. C., Alves, N. J., ... Thompson, F. L. (2009). Genomic taxonomy of vibrios. B M C Evolutionary Biology, 9, 258. DOI: 10.1186/1471- 2148-9-258 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. BMC Evolutionary Biology BioMed Central Research article Open Access Genomic taxonomy of vibrios Cristiane C Thompson*1, Ana Carolina P Vicente1, Rangel C Souza2, Ana Tereza R Vasconcelos2, Tammi Vesth3, Nelson Alves Jr4, David W Ussery3, Tetsuya Iida5 and Fabiano L Thompson*4 Address: 1Laboratory of Molecular Genetics of Microrganims, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil, 2National Laboratory for Scientific Computing, Department of Applied and Computational Mathematics, Laboratory of Bioinformatics, Av.
    [Show full text]
  • Sparus Aurata) and Sea Bass (Dicentrarchus Labrax)
    Gut bacterial communities in geographically distant populations of farmed sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax) Eleni Nikouli1, Alexandra Meziti1, Efthimia Antonopoulou2, Eleni Mente1, Konstantinos Ar. Kormas1* 1 Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece 2 Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece * Corresponding author; Tel.: +30-242-109-3082, Fax: +30-242109-3157, E-mail: [email protected], [email protected] Supplementary material 1 Table S1. Body weight of the Sparus aurata and Dicentrarchus labrax individuals used in this study. Chania Chios Igoumenitsa Yaltra Atalanti Sample Body weight S. aurata D. labrax S. aurata D. labrax S. aurata D. labrax S. aurata D. labrax S. aurata D. labrax (g) 1 359 378 558 420 433 448 481 346 260 785 2 355 294 579 442 493 556 516 397 240 340 3 376 275 468 554 450 464 540 415 440 500 4 392 395 530 460 440 483 492 493 365 860 5 420 362 483 479 542 492 406 995 6 521 505 506 461 Mean 380.40 340.80 523.17 476.67 471.60 487.75 504.50 419.67 326.25 696.00 SEs 11.89 23.76 17.36 19.56 20.46 23.85 8.68 21.00 46.79 120.29 2 Table S2. Ingredients of the diets used at the time of sampling. Ingredient Sparus aurata Dicentrarchus labrax (6 mm; 350-450 g)** (6 mm; 450-800 g)** Crude proteins (%) 42 – 44 37 – 39 Crude lipids (%) 19 – 21 20 – 22 Nitrogen free extract (NFE) (%) 20 – 26 19 – 25 Crude cellulose (%) 1 – 3 2 – 4 Ash (%) 5.8 – 7.8 6.2 – 8.2 Total P (%) 0.7 – 0.9 0.8 – 1.0 Gross energy (MJ/Kg) 21.5 – 23.5 20.6 – 22.6 Classical digestible energy* (MJ/Kg) 19.5 18.9 Added vitamin D3 (I.U./Kg) 500 500 Added vitamin E (I.U./Kg) 180 100 Added vitamin C (I.U./Kg) 250 100 Feeding rate (%), i.e.
    [Show full text]
  • Using Oxygen and Biopreservation As Hurdles to Improve Safety Of
    USING OXYGEN AND BIOPRESERVATION AS HURDLES TO IMPROVE SAFETY OF COOKED FOOD DURING STORAGE AT REFRIGERATION TEMPERATURES By NYDIA MUNOZ A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY WASHINGTON STATE UNIVERSITY Department of Biological Systems Engineering MAY 2018 © Copyright by NYDIA MUNOZ, 2018 All Rights Reserved © Copyright by NYDIA MUNOZ, 2018 All Rights Reserved To the Faculty of Washington State University: The members of the Committee appointed to examine the dissertation of NYDIA MUNOZ find it satisfactory and recommend that it be accepted. Shyam Sablani, Ph.D., Chair Juming Tang, Ph.D. Gustavo V. Barbosa-Cánovas, Ph.D. ii ACKNOWLEDGMENT My special gratitude to my advisor Dr. Shyam Sablani for taking me as one his graduate students and supporting me through my Ph.D. study and research. His guidance helped me in all the time of research and writing of this thesis. At the same time, I would like to thank my committee members Dr. Juming Tang and Dr. Gustavo V. Barbosa-Cánovas for their valuable suggestions on my research and allowing me to use their respective laboratories and instruments facilities. I am grateful to Mr. Frank Younce, Mr. Peter Gray and Ms. Tonia Green for training me in the use of relevant equipment to conduct my research, and their technical advice and practical help. Also, the assistance and cooperation of Dr. Helen Joyner, Dr. Barbara Rasco, and Dr. Meijun Zhu are greatly appreciated. I am grateful to Dr. Kanishka Buhnia for volunteering to carry out microbiological counts by my side as well as his contribution and critical inputs to my thesis work.
    [Show full text]
  • View a Copy of This Licence, Visit
    Raimundo et al. Microbiome (2021) 9:43 https://doi.org/10.1186/s40168-020-00970-2 RESEARCH Open Access Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes I. Raimundo1†, R. Silva1†, L. Meunier1,2, S. M. Valente1, A. Lago-Lestón3, T. Keller-Costa1* and R. Costa1,4,5,6* Abstract Background: Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation- dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater. Results: We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated—and biotechnologically versatile—form chitosan.
    [Show full text]