Skip to main content Accessibility help

The microbiome of the soft palate of swine

  • Shaun Kernaghan (a1), Adina R. Bujold (a1) and Janet I. MacInnes (a1)


The tonsil of the soft palate in pigs is a secondary lymphoid tissue that provides a first line of defense against foreign antigens entering by the mouth or nares. It has been known for a long time to be the site of colonization of important swine and zoonotic bacterial pathogens. Initially our understanding of microbes present at this site came from culture-based studies. Very recently, sequence-based approaches have been used to identify the core microbiome of the swine tonsil. Although animal to animal and herd to herd variation was detected in these studies, >90 of the organisms detected belonged to the phyla Proteobacteria and Firmicutes. Members of the family Pasteurellaceae appeared to be predominate in the tonsil; however, the relative proportions of Actinobacillus, Haemophilus, and Pasteurella varied. Members of the families Moraxellaceae, Fusobacteriaceae, Veillonellaceae, and Neisseriaceae were also seen as frequent residents of the tonsil.


Corresponding author

*Corresponding author. E-mail:


Hide All
Aas, JA, Paster, BJ, Stokes, LN, Olsen, I and Dewhirst, FE (2005). Defining the normal bacterial flora of the oral cavity. Journal of Clinical Microbiology 43: 57215732.
Aas, JA, Griffen, AL, Dardis, SR, Lee, AM, Olsen, I, Dewhirst, FE, Leys, EJ and Paster, BJ (2008). Bacteria of dental caries in primary and permanent teeth in children and young adults. Journal of Clinical Microbiology 46: 14071417.
Autio, T, Markkula, A, Hellstrom, S, Niskanen, T, Lunden, J and Korkeala, H (2004). Prevalence and genetic diversity of Listeria monocytogenes in the tonsils of pigs. Journal of Food Protection 67: 805808.
Avila, M, Ojcius, DM and Yilmaz, O (2009). The oral microbiota: living with a permanent guest. DNA and Cell Biology 28: 405411.
Baele, M, Chiers, K, Devriese, LA, Smith, HE, Wisselink, HJ, Vaneechoutte, M and Haesebrouck, F (2001). The Gram-positive tonsillar and nasal flora of piglets before and after weaning. Journal of Applied Microbiology 91: 997–1003.
Belz, GT and Heath, TJ (1996). Tonsils of the soft palate of young pigs: crypt structure and lymphoepithelium. Anatomical Record 245: 102113.
Brandtzaeg, P (2003). Immunology of tonsils and adenoids: everything the ENT surgeon needs to know. International Journal of Pediatric Otorhinolaryngology 67: S69S76.
Brandtzaeg, P, Baekkevold, ES, Farstad, IN, Jahnsen, FL, Johansen, FE, Nilsen, EM and Yamanaka, T (1999). Regional specialization in the mucosal immune system: what happens in the microcompartments? Immunology Today 20: 141151.
Casteleyn, C, Breugelmans, S, Simoens, P and Van den Broeck, W (2011a). The tonsils revisited: review of the anatomical localization and histological characteristics of the tonsils of domestic and laboratory animals. Clinical and Developmental Immunology 2011: 472460.
Casteleyn, C, Simoens, P and Van den Broeck, W (2011b). Terminology of the tonsils. Anatomia, Histologia, Embryologia 40: 204209.
Chen, T, Yu, WH, Izard, J, Baranova, OV, Lakshmanan, A and Dewhirst, FE (2010). The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database: The Journal of Biological Databases and Curation 2010: baq013.
Chiers, K, Haesebrouck, F, Mateusen, B, Van Overbeke, I and Ducatelle, R (2001). Pathogenicity of Actinobacillus minor, Actinobacillus indolicus and Actinobacillus porcinus strains for gnotobiotic piglets. Journal of Veterinary Medicine B, Infectious Diseases and Veterinary Public Health 48: 127131.
Devriese, LA, Hommez, J, Pot, B and Haesebrouck, F (1994). Identification and composition of the streptococcal and enterococcal flora of tonsils, intestines and faeces of pigs. Journal of Applied Bacteriology 77: 3136.
Ellsworth, S, Kirkbride, CA and Johnson, DD (1980). Excretion of Mycobacterium avium from lesions in the intestine and tonsils of infected swine. American Journal of Veterinary Research 41: 15261530.
FAO/WHO (2002). Report of a joint FAO/WHO expert consultation on guidelines for the evaluation of probiotics in food. London, Ontario, Canada: World Health Organization and Food and Agriculture Organization of the United Nations.
Fredriksson-Ahomaa, M, Wacheck, S, Koenig, M, Stolle, A and Stephan, R (2009). Prevalence of pathogenic Yersinia enterocolitica and Yersinia pseudotuberculosis in wild boars in Switzerland. International Journal of Food Microbiology 135: 199202.
Guglielmetti, S, Taverniti, V, Minuzzo, M, Arioli, S, Stuknyte, M, Karp, M and Mora, D (2010). Oral bacteria as potential probiotics for the pharyngeal mucosa. Applied and Environmental Microbiology 76: 39483958.
Horter, DC, Yoon, KJ and Zimmerman, JJ (2003). A review of porcine tonsils in immunity and disease. Animal Health Research Reviews/Conference of Research Workers in Animal Diseases 4: 143155.
Huyghebaert, G, Ducatelle, R and Van Immerseel, F (2011). An update on alternatives to antimicrobial growth promoters for broilers. Veterinary Journal 187: 182188.
Jahnsen, FL and Brandtzaeg, P (1999). Antigen presentation and stimulation of the immune system in human airways. Allergy 54(Suppl. 57): 3749.
Jamin, A, Gorin, S, Le Potier, M and Kuntz-Simon, G (2006). Characterization of conventional and plasmacytoid dendritic cells in swine secondary lymphoid organs and blood. Veterinary Immunology and Immunopathology 114: 224237.
Jensen, TK, Møller, K, Lindecrona, R and Jorsal, SE (2000). Detection of Lawsonia intracellularis in the tonsils of pigs with proliferative enteropathy. Research in Veterinary Science 68: 2326.
Kasenõmm, P, Kull, M and Mikelsaar, M (2002). Association between tonsillar core microflora and post-tonsillectomy bacteremia. Microbial Ecology in Health and Disease 14: 122127.
Kenny, M, Smidt, H, Mengheri, E and Miller, B (2011). Probiotics – do they have a role in the pig industry? Animal: An International Journal of Animal Bioscience 5: 462470.
Kernaghan, S, Ojha, S, Slavic, D, Chen, S, Poljak, Z and MacInnes, JI (2011). Bacterial community profiling of tonsils from diseased pigs using terminal restriction fragment length polymorphism analysis. In 92nd AGM Conference of Research Workers in Animal Diseases, 92nd AGM Conference of Research Workers in Animal Diseases, Chicago, Illinois, December 4–6, 2011.
Lomonaco, S, Decastelli, L, Bianchi, DM, Nucera, D, Grassi, MA, Sperone, V and Civera, T (2009). Detection of Salmonella in finishing pigs on farm and at slaughter in Piedmont, Italy. Zoonoses and Public Health 56: 137144.
Lowe, BA, Marsh, TL, Isaacs-Cosgrove, N, Kirkwood, RN, Kiupel, M and Mulks, MH (2011). Microbial communities in the tonsils of healthy pigs. Veterinary Microbiology 147: 346357.
Lowe, BA, Marsh, TL, Isaacs-Cosgrove, N, Kirkwood, RN, Kiupel, M and Mulks, MH (2012). Defining the “core microbiome” of the microbial communities in the tonsils of healthy pigs. BMC Microbiology 12: 20.
MacInnes, JI, Gottschalk, M, Lone, AG, Metcalf, DS, Ojha, SS, Rosendal, T, Watson, SB and Friendship, RM (2008). Prevalence of Actinobacillus pleuropneumoniae, Actinobacillus suis, Haemophilus parasuis, Pasteurella multocida, and Streptococcus suis in representative Ontario swine herds. Canadian Journal of Veterinary Research 72: 242248.
Makhanon, M, Tummaruk, P, Thongkamkoon, P, Thanawongnuwech, R and Prapasarakul, N (2012). Comparison of detection procedures of Mycoplasma hyopneumoniae, Mycoplasma hyosynoviae, and Mycoplasma hyorhinis in lungs, tonsils, and synovial fluid of slaughtered pigs and their distributions in Thailand. Tropical Animal Health and Production 44: 313318.
Marois, C, Le Carrou, J, Kobisch, M and Gautier-Bouchardon, AV (2007). Isolation of Mycoplasma hyopneumoniae from different sampling sites in experimentally infected and contact SPF piglets. Veterinary Microbiology 120: 96–104.
Marois, C, Cariolet, R, Morvan, H and Kobisch, M (2008). Transmission of pathogenic respiratory bacteria to specific pathogen free pigs at slaughter. Veterinary Microbiology 129: 325332.
Moller, K, Andersen, LV, Christensen, G and Kilian, M (1993). Optimalization of the detection of NAD dependent Pasteurellaceae from the respiratory tract of slaughterhouse pigs. Veterinary Microbiology 36: 261271.
Mulder, IE, Schmidt, B, Stokes, CR, Lewis, M, Bailey, M, Aminov, RI, Prosser, JI, Gill, BP, Pluske, JR, Mayer, CD, Musk, CC and Kelly, D (2009). Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces. BMC Biology 7: 79.
Ngo, TH, Tran, TB, Tran, TT, Nguyen, VD, Campbell, J, Pham, HA, Huynh, HT, Nguyen, VV, Bryant, JE, Tran, TH, Farrar, J and Schultsz, C (2011). Slaughterhouse pigs are a major reservoir of Streptococcus suis serotype 2 capable of causing human infection in southern Vietnam. PloS One 6: e17943.
Opriessnig, T, Gimenez-Lirola, LG and Halbur, PG (2011). Polymicrobial respiratory disease in pigs. Animal Health Research Reviews/Conference of Research Workers in Animal Diseases 12: 133148.
Ortiz Martinez, P, Mylona, S, Drake, I, Fredriksson-Ahomaa, M, Korkeala, H and Corry, JE (2010). Wide variety of bioserotypes of enteropathogenic Yersinia in tonsils of English pigs at slaughter. International Journal of Food Microbiology 139: 6469.
O'Sullivan, T, Friendship, R, Blackwell, T, Pearl, D, McEwen, B, Carman, S, Slavic, D and Dewey, C (2011). Microbiological identification and analysis of swine tonsils collected from carcasses at slaughter. Canadian Journal of Veterinary Research 75: 106111.
Pennisi, E (2005). A mouthful of microbes. Science 307: 18991901.
Prakash, S, Tomaro-Duchesneau, C, Saha, S and Cantor, A (2011). The gut microbiota and human health with an emphasis on the use of microencapsulated bacterial cells. Journal of Biomedicine and Biotechnology 2011: 981214.
Pride, DT, Salzman, J, Haynes, M, Rohwer, F, Davis-Long, C, White, RA III, Loomer, P, Armitage, GC and Relman, DA (2011). Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME Journal 6: 915–26.
Quince, C, Lanzen, A, Curtis, TP, Davenport, RJ, Hall, N, Head, IM, Read, LF and Sloan, WT (2009). Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods 6: 639641.
Quince, C, Lanzen, A, Davenport, RJ and Turnbaugh, PJ (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12: 38.
Sallusto, F, Lanzavecchia, A and Mackay, C (1998). Chemokines and chemokine receptors in T-cell priming and Th1/Th2-mediated responses. Immunology Today 19: 568574.
Santagati, M, Scillato, M, Patane, F, Aiello, C and Stefani, S (2012). Bacteriocin-producing oral streptococci and inhibition of respiratory pathogens. FEMS Immunology and Medical Microbiology 65: 2331.
Schutte, UM, Abdo, Z, Bent, SJ, Shyu, C, Williams, CJ, Pierson, JD and Forney, LJ (2008). Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Applied Microbiology and Biotechnology 80: 365380.
Shan, T, Li, L, Simmonds, P, Wang, C, Moeser, A and Delwart, E (2011). The fecal virome of pigs on a high-density farm. Journal of Virology 85: 1169711708.
Staats, JJ, Feder, I, Okwumabua, O and Chengappa, MM (1997). Streptococcus suis: past and present. Veterinary Research Communications 21: 381407.
Takahashi, T, Sunama, P, Satra, J, Cholsindhu, N, Kongthon, S, Jitnupong, W, Yamamoto, K, Kijima, M and Furuuchi, S (1999). Serotyping and pathogenicity of Erysipelothrix strains isolated from tonsils of slaughter pigs in Thailand. Journal of Veterinary Medical Science/The Japanese Society of Veterinary Science 61: 10071011.
Tonpitak, W, Rohde, J and Gerlach, GF (2007). Prevalence of “Actinobacillus porcitonsillarum” in porcine tonsils and development of a diagnosis duplex PCR differentiating between “Actinobacillus porcitonsillarum” and Actinobacillus pleuropneumoniae. Veterinary Microbiology 122: 157165.
Vouloumanou, EK, Makris, GC, Karageorgopoulos, DE and Falagas, ME (2009). Probiotics for the prevention of respiratory tract infections: a systematic review. International Journal of Antimicrobial Agents 34: 197.e1–197.10.
Wohlgemuth, S, Loh, G and Blaut, M (2010). Recent developments and perspectives in the investigation of probiotic effects. International Journal of Medical Microbiology 300: 3–10.
Zhang, CP, Ning, YB, Zhang, ZQ, Song, L, Qiu, HS, Gao, HY and Fan, XZ (2009). Distributions of pathogenic capsular types and in vitro antimicrobial susceptibility of different serotypes of Streptococcus suis isolated from clinically healthy sows from 10 provinces in China. Zhonghua Liu Xing Bing Xue Za Zhi 30: 235238.
Zuckermann, FA (1999). Extrathymic CD4/CD8 double positive T cells. Veterinary Immunology and Immunopathology 72: 5566.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Animal Health Research Reviews
  • ISSN: 1466-2523
  • EISSN: 1475-2654
  • URL: /core/journals/animal-health-research-reviews
Please enter your name
Please enter a valid email address
Who would you like to send this to? *



Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed