Microbial Ecology

, Volume 60, Issue 2, pp 320–330 | Cite as

Ecological Characterisation of the Colonic Microbiota in Arctic and Sub-Arctic Seals

  • Trine GladEmail author
  • Vibeke Fam Kristiansen
  • Kaare M. Nielsen
  • Lorenzo Brusetti
  • André-Denis G. Wright
  • Monica A. Sundset
Environmental Microbiology


Dominant colonic bacteria in wild hooded (n = 9), harbour (n = 1) and grey (n = 1) seals were identified using 16S rRNA gene clone libraries (313 clones), revealing 52.7% Bacteroidetes, 41.5% Firmicutes, 4.5% Proteobacteria and 1.0% Fusobacteria. Thirty (77%) of the 39 phylotypes identified were novel, showing <97% sequence similarity to their nearest cultivated relatives. Mean colonic bacterial cell density, determined by real-time PCR, was high (12.8 log10 cells/g wet wt) for the hooded seals, while the number of methanogenic Archea was low (4.0 log10 cells/g wet wt). The level of ampicillin (ampr) and tetracycline-resistant (tetr) isolates was investigated by cultivation. Aerobic ampr isolates were only detected in colon contents from four hooded seals, whereas aerobic tetr isolates were found in seven of the nine hooded seals. These data provide novel insight to the gut microbiota of Arctic and sub-Arctic seals living in the wild.


Methane Emission Polar Bear Harbour Seal Methanogenic Archaea Grey Seal 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors wish to thank Prof. Arnoldus Schytte Blix, Prof. Lars P. Folkow and Prof. Karl-Arne Stokkan at the Department of Arctic and Marine Biology, University of Tromsø, for the possibility to take part in the expedition to the Greenland Sea and for their advice and help throughout the expedition. We also thank Prof. Stokkan for sampling the harbour and grey seals at the coast of Northern Norway. We are grateful to Dr. Lise Norgård (GenØk-Centre for Biosafety, Tromsø) for assistance in the field collecting the hooded seal samples and Korinne Northwood at CSIRO (Brisbane, Australia) for assistance with real-time PCR. This study was funded by the Norwegian Research Council and the Roald Amundsen Centre for Arctic Research (University of Tromsø, Norway).


  1. 1.
    Achá SJ, Kühn I, Mbazima G, Colque-Navarro P, Möllby R (2005) Changes of viability and composition of the Escherichia coli flora in faecal samples during long time storage. J Microbiol Meth 63:229–238CrossRefGoogle Scholar
  2. 2.
    Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169PubMedGoogle Scholar
  3. 3.
    Berg I, Haug T, Nilssen KT (2002) Harbour Seal (Phoca vitulina) diet in Vesterålen, North Norway. Sarsia 87:451–461CrossRefGoogle Scholar
  4. 4.
    Bigg MA (1981) Harbour seal. In: Ridgeway SH, Harrison RJ (eds) Handbook of marine mammals, vol. 2. Academic Press, London, pp 1–27Google Scholar
  5. 5.
    Bjerrum L, Engberg RM, Leser TD, Jensen BB, Finster K, Pedersen K (2006) Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques. Poult Sci 85:1151–1164PubMedGoogle Scholar
  6. 6.
    Bogomolni AL, Gast RJ, Ellis JC, Dennett M, Pugliares KR, Lentell BJ, Moore MJ (2008) Victims or vectors: a survey of marine vertebrate zoonoses from coastal waters of the Northwest Atlantic. Dis Aquat Organ 81:13–38CrossRefPubMedGoogle Scholar
  7. 7.
    Bonner WN (1981) Grey seal. In: Ridgeway SH, Harrison RJ (eds) Handbook of marine mammals, vol. 2. Academic Press, London, pp 111–144Google Scholar
  8. 8.
    Brusetti L, Glad T, Borin S, Myren P, Rizzi A, Johnsen PJ, Carter P, Daffonchio D, Nielsen KM (2008) Low prevalence of bla TEM genes in Arctic environments and agricultural soil and rhizosphere. Microb Ecol Health Dis 20:27–36CrossRefGoogle Scholar
  9. 9.
    Carattoli A, Lovari S, Franco A, Cordaro G, Di Matteo P, Battisti A (2005) Extended-spectrum beta-lactamases in Escherichia coli isolated from dogs and cats in Rome, Italy, from 2001 to 2003. Antimicrob Agents Chemother 49:833–835CrossRefPubMedGoogle Scholar
  10. 10.
    Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucl Acids Res 35:D169–D172CrossRefPubMedGoogle Scholar
  11. 11.
    Costa D, Poeta P, Saenz Y, Vinue L, Rojo-Bezares B, Jouini A, Zarazaga M, Rodrigues J, Torres C (2006) Detection of Escherichia coli harbouring extended-spectrum beta-lactamases of the CTX-M, TEM and SHV classes in faecal samples of wild animals in Portugal. J Antimicrob Chemother 58:1311–1312CrossRefPubMedGoogle Scholar
  12. 12.
    Denman S, McSweeney C (2006) Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Microbiol Ecol 58:572–582CrossRefPubMedGoogle Scholar
  13. 13.
    Denman S, Tomkins N, McSweeney C (2007) Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiol Ecol 62:313–322CrossRefPubMedGoogle Scholar
  14. 14.
    Ehlers B, Strauch E, Goltz M, Kubsch D, Wagner H, Maidhof H, Bendiek J, Appel B, Buhk HJ (1997) Nachweis gentechnischer Veränderungen in Mais mittels PCR. Bundesgesundheitsbl 40:118–121CrossRefGoogle Scholar
  15. 15.
    Folkow LP, Martensson PE, Blix AS (1996) Annual distribution of hooded seals (Cystophora cristata) in the Greenland and Norwegian Seas. Polar Biol 16:179–189CrossRefGoogle Scholar
  16. 16.
    Forster PM, Ramaswamy V (2007) Changes in atmospheric constituents and in radiative forcing. In: Solomon S, Qin D, Manning M, Chen Z, Marquis M, Averyt KB, Tignor M, Miller HL (eds) Climate change 2007: the physical science basis: contribution of working group I to the fourth assessment report of the intergovernmental panel on climate change. Cambridge University Press, CambridgeGoogle Scholar
  17. 17.
    Furushita M, Shiba T, Maeda T, Yahata M, Kaneoka A, Takahashi Y, Torii K, Hasegawa T, Ohta M (2003) Similarity of tetracycline resistance genes isolated from fish farm bacteria to those from clinical isolates. Appl Environ Microbiol 69:5336–5342CrossRefPubMedGoogle Scholar
  18. 18.
    Gilliver MA, Bennett M, Begon M, Hazel SM, Hart CA (1999) Enterobacteria: antibiotic resistance found in wild rodents. Nature 401:233–234CrossRefPubMedGoogle Scholar
  19. 19.
    Glad T, Bernhardsen P, Nielsen KM, Brusetti L, Andersen M, Aars J, Sundset MA (2010) Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard. BMC Microbiol 10:10. doi: 10.1186/1471-2180-1110-1110 CrossRefPubMedGoogle Scholar
  20. 20.
    Glad T, Klingenberg C, Flaegstad T, Ericson JU, Olsvik Ø (2001) Rapid detection of the methicillin-resistance gene, mecA, in coagulase-negative staphylococci. Scand J Infect Dis 33:502–506CrossRefPubMedGoogle Scholar
  21. 21.
    Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika Trust 40:237–264Google Scholar
  22. 22.
    Guglielmetti E, Korhonen JM, Heikkinen J, Morelli L, Wright Av (2009) Transfer of plasmid-mediated resistance to tetracycline in pathogenic bacteria from fish and aquaculture environments. FEMS Microbiol Lett 293:28–34CrossRefPubMedGoogle Scholar
  23. 23.
    Hammond PS, Hall AJ, Prime JH (1994) The diet of grey seals around Orkney and other islands and mainland sites in north-eastern Scotland. J Appl Ecol 31:340–350CrossRefGoogle Scholar
  24. 24.
    Haug T, Nilssen KT, Lindblom L (2000) First independent feeding of harp (Phoca groenlandica) and hooded seals (Cystophora cristata) pups in the Greenland Sea. NAMMCO Sci Publ 2:29–39Google Scholar
  25. 25.
    Henriksen G, Gjertz I, Kondakov A (1997) A review of the distribution and abundance of harbour seals (Phoca vitulina), on Svalbard, Norway, and in the Barents Sea. Mar Mammal Sci 13:157–163CrossRefGoogle Scholar
  26. 26.
    Henriksen G, Moen K (1997) Interaction between seal and salmon fisheries in Tana River and Tanafjord, Finnmark, north Norway, and possible consequences for the harbour seal Phoca vitulina. Fauna Norvegica Serie A 18:21–31Google Scholar
  27. 27.
    Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317–2319CrossRefPubMedGoogle Scholar
  28. 28.
    Jensen BB (1996) Methanogenesis in monogastric animals. Environ Monit Assess 42:99–112CrossRefGoogle Scholar
  29. 29.
    Kim S-R, Nonaka L, Suzuki S (2004) Occurrence of tetracycline resistance genes tet(M) and tet(S) in bacteria from marine aquaculture sites. FEMS Microbiol Lett 237:147–156CrossRefPubMedGoogle Scholar
  30. 30.
    Kozak GK, Boerlin P, Janecko N, Reid-Smith RJ, Jardine C (2009) Antimicrobial resistance in Escherichia coli isolates from swine and wild small mammals in the proximity of swine farms and in natural environments in Ontario, Canada. Appl Environ Microbiol 75:559–566CrossRefPubMedGoogle Scholar
  31. 31.
    Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics. In: Stackebrandt E, Goodfellow M (eds) Modern microbiological methods. Wiley, Chichester, p 133Google Scholar
  32. 32.
    Lapierre L, Cornejo J, Borie C, Toro C, San Martin B (2008) Genetic characterization of antibiotic resistance genes linked to class 1 and class 2 integrons in commensal strains of Escherichia coli isolated from poultry and swine. Microb Drug Resist 14:265–272CrossRefPubMedGoogle Scholar
  33. 33.
    Leser TD, Amenuvor JZ, Jensen TK, Lindecrona RH, Boye M, Moller K (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol 68:673–690CrossRefPubMedGoogle Scholar
  34. 34.
    Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI (2008) Evolution of mammals and their gut microbes. Science 320:1647–1651CrossRefPubMedGoogle Scholar
  35. 35.
    Livermore DM (1995) Beta-lactamases in laboratory and clinical resistance. Clin Microbiol Rev 8:557–584PubMedGoogle Scholar
  36. 36.
    Mazel D, Davies J (1999) Antibiotic resistance in microbes. Cell Mol Life Sci 56:742–754CrossRefPubMedGoogle Scholar
  37. 37.
    Mikkelsen B, Haug T, Nilssen KT (2002) Summer diet of grey seals (Halichoerus grypus) in Faroese waters. Sarsia 87:462–471CrossRefGoogle Scholar
  38. 38.
    Mortensson PE, Nordoy ES, Messelt EB, Blix AS (1998) Gut length, food transit time and diving habit in phocid seals. Polar Biol 20:213–217CrossRefGoogle Scholar
  39. 39.
    Nilssen KT, Haug T (2007) Status of grey seals (Halichoerus grypus) in Norway. NAMMCO Sci Publ 6:23–31Google Scholar
  40. 40.
    Olsen MA, Nilssen KT, Mathiesen SD (1996) Gross anatomy of the gastrointestinal system of harp seals (Phoca groenlandica). J Zool 238:581–589CrossRefGoogle Scholar
  41. 41.
    Olsen MA, Aagnes TH, Mathiesen SD (1994) Digestion of herring by indigenous bacteria in the minke whale forestomach. Appl Environ Microbiol 60:4445–4455PubMedGoogle Scholar
  42. 42.
    Osterblad M, Norrdahl K, Korpimaki E, Huovinen P (2001) Antibiotic resistance: how wild are wild mammals? Nature 409:37–38CrossRefPubMedGoogle Scholar
  43. 43.
    Potelov V, Nilssen KT, Svetochev V, Haug T (2000) Feeding habits of harp (Phoca groenlandica) and hooded seals (Cystophora cristata) during late winter, spring and early summer in the Greenland Sea. NAMMCO Sci Publ 2:40–49Google Scholar
  44. 44.
    Rizzotti L, La Gioia F, Dellaglio F, Torriani S (2009) Molecular diversity and transferability of the tetracycline resistance gene tet (M), carried on Tn916-1545 family transposons, in enterococci from a total food chain. Antonie Leeuwenhoek 96:43–52CrossRefPubMedGoogle Scholar
  45. 45.
    Saengkerdsub S, Anderson RC, Wilkinson HH, Kim W-K, Nisbet DJ, Ricke SC (2007) Identification and quantification of methanogenic archaea in adult chicken ceca. Appl Environ Microbiol 73:353–356CrossRefPubMedGoogle Scholar
  46. 46.
    Saenz Y, Brinas L, Dominguez E, Ruiz J, Zarazaga M, Vila J, Torres C (2004) Mechanisms of resistance in multiple-antibiotic-resistant Escherichia coli strains of human, animal, and food origins. Antimicrob Agents Chemother 48:3996–4001CrossRefPubMedGoogle Scholar
  47. 47.
    Seveno N, Smalla K, van Elsas JD, Collard J-M, Karagouni A, Kallifidas D, Wellington E (2002) Occurrence and reservoirs of antibiotic resistance genes in the environment. Rev Med Microbiol 13:15–27Google Scholar
  48. 48.
    Singh G (2004) β-Lactams in the new millennium. Part-I: monobactams and carbapenems. Mini Rev Med Chem 4:69–92CrossRefPubMedGoogle Scholar
  49. 49.
    Skillman LC, Toovey AF, Williams AJ, Wright A-DG (2006) Development and validation of a real-time PCR method to quantify rumen protozoa and examination of variability between Entodinium populations in sheep offered a hay-based diet. Appl Environ Microbiol 72:200–206CrossRefPubMedGoogle Scholar
  50. 50.
    Sundset MA, Edwards J, Cheng Y, Senosiain R, Fraile M, Northwood KS, Præsteng K, Glad T, Mathiesen S, Wright A-DG (2009) Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture. Microb Ecol 57:335–348CrossRefPubMedGoogle Scholar
  51. 51.
    Sundset MA, Edwards JE, Cheng YF, Senosiain RS, Fraile MN, Northwood KS, Præsteng KE, Glad T, Mathiesen SD, Wright A-DG (2009) Rumen microbial diversity in Svalbard reindeer, with particular emphasis on methanogenic archaea. FEMS Microb Ecol 70:553–562CrossRefGoogle Scholar
  52. 52.
    Sundset MA, Præsteng K, Cann I, Mathiesen SD, Mackie RI (2007) Novel rumen bacterial diversity in two geographically separated sub-species of reindeer. Microb Ecol 54:424–438CrossRefPubMedGoogle Scholar
  53. 53.
    Sørum H (1999) Antibiotic resistance in aquaculture. Acta veterinaria Scand Suppl 92:29–36Google Scholar
  54. 54.
    Wang GC, Wang Y (1997) Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl Environ Microbiol 63:4645–4650PubMedGoogle Scholar
  55. 55.
    Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian Classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267CrossRefPubMedGoogle Scholar
  56. 56.
    Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposals for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci 87:4576–4579CrossRefPubMedGoogle Scholar
  57. 57.
    Wright A-DG, Northwood KS, Obispo NE (2009) Rumen-like methanogens identified from the crop of the folivorous South American bird, the hoatzin (Opisthocomus hoazin). ISME J 3:1120–1126CrossRefPubMedGoogle Scholar
  58. 58.
    Yang S, Ma S, Chen J, Mao H, He Y, Xi D, Yang L, He T, Deng W (2009) Bacterial diversity in the rumen of Gayals (Bos frontalis), Swamp buffaloes (Bubalus bubalis) and Holstein cow as revealed by cloned 16S rRNA gene sequences. Mol Biol Rep 37:2063–2073CrossRefPubMedGoogle Scholar
  59. 59.
    Zhu R, Liu Y, Xu H, Ma J, Gong Z, Zhao S (2008) Methane emissions from three seal animal colonies in the maritime Antarctic. Atmos Environ 42:1197–1205CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Trine Glad
    • 1
    • 2
    Email author
  • Vibeke Fam Kristiansen
    • 1
    • 2
  • Kaare M. Nielsen
    • 1
    • 3
  • Lorenzo Brusetti
    • 4
  • André-Denis G. Wright
    • 5
  • Monica A. Sundset
    • 2
  1. 1.Department of PharmacyUniversity of TromsøTromsøNorway
  2. 2.Department of Arctic and Marine BiologyUniversity of TromsøTromsøNorway
  3. 3.GenØk-Center for Biosafety, Research ParkTromsøNorway
  4. 4.Faculty of Science and TechnologyFree University of Bozen/BolzanoBolzanoItaly
  5. 5.Department of Animal ScienceUniversity of VermontBurlingtonUSA

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