Skip to main content

Human microbiome versus food-borne pathogens: friend or foe

Abstract

As food safety advances, there is a great need to maintain, distribute, and provide high-quality food to a much broader consumer base. There is also an ever-growing “arms race” between pathogens and humans as food manufacturers. The human microbiome is a collective organ of microbes that have found community niches while associating with their host and other microorganisms. Humans play an important role in modifying the environment of these organisms through their life choices, especially through individual diet. The composition of an individual’s diet influences the digestive system—an ecosystem with the greatest number and largest diversity of organisms currently known. Organisms living on and within food have the potential to be either friends or foes to the consumer. Maintenance of this system can have multiple benefits, but lack of maintenance can lead to a host of chronic and preventable diseases. Overall, this dynamic system is influenced by intense competition from food-borne pathogens, lifestyle, overall diet, and presiding host-associated microbiota.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2

References

  1. Adams M, Mitchell R (2002) Fermentation and pathogen control: a risk assessment approach. Int J Food Microbiol 79:75–83

  2. Altekruse SF, Stern NJ, Fields PI, Swerdlow DL (1999) Campylobacter jejuni—an emerging foodborne pathogen. Emerg Infect Dis 5:28–35

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  3. Argyri AA, Zoumpopoulou G, Karatzas KA, Tsakalidou E, Nychas GJ, Panagou EZ, Tassou CC (2013) Selection of potential probiotic lactic acid bacteria from fermented olives by in vitro tests. Food Microbiol 33:282–291

    CAS  PubMed  Article  Google Scholar 

  4. Auclair J, Frappier M, Millette M (2015) Lactobacillus acidophilus CL1285, Lactobacillus casei LBC80R, and Lactobacillus rhamnosus CLR2 (Bio-K): characterization, manufacture, mechanisms of action, and quality control of a specific probiotic combination for primary prevention of Clostridium difficile infection. Clin Infect Dis 60:S135–S143

    PubMed  Article  Google Scholar 

  5. Aydin F, Atabay HI, Akan M (2001) The isolation and characterization of Campylobacter jejuni subsp. jejuni from domestic geese (Anser anser). J Appl Microbiol 90:637–642

    CAS  PubMed  Article  Google Scholar 

  6. Bacciarini LN, Boerlin P, Straub R, Frey J, Grone A (2003) Immunohistochemical localization of Clostridium perfringens β2-toxin in the gastrointestinal tract of horses. Vet Pathol 40:376–381

    CAS  PubMed  Article  Google Scholar 

  7. Backhed F (2011) Programming of host metabolism by the gut microbiota. Ann Nutr Metab 58:44–52

    PubMed  Article  CAS  Google Scholar 

  8. Bai L, Guo Y, Lan R, Dong Y, Wang W, Hu Y, Gan X, Yan S, Fu P, Pei X, Xu J, Liu X, Li F (2015) Genotypic characterization of Shiga toxin-producing Escherichia coli O157:H7 isolates in food products from China between 2005 and 2010. Food Control 50:209–214

    Article  Google Scholar 

  9. Barbosa MS, Todorov SD, Ivanova IV, Belguesmia Y, Choiset Y, Rabesona H, Chobert J-M, Haertle T, Franco BDGM (2016) Characterization of a two-peptide plantaricin produced by Lactobacillus plantarum MBSa4 isolated from Brazilian salami. Food Control 60:103–112

    CAS  Article  Google Scholar 

  10. Bartosch S, Fite A, Macfarlane GT, Mcmurdo MET (2004) Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota. Appl Environ Microbiol 70:3575–3581

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  11. Bedani R, Pauly-Silveira ND, Roselino MN, de Valdez GF, Rossi EA (2010) Effect of fermented soy product on the fecal microbiota of rats fed on a beef-based animal diet. J Sci Food Agric 90:233–238

    CAS  PubMed  Article  Google Scholar 

  12. Bennett SD, Walsh KA, Gould LH (2013) Foodborne disease outbreaks caused by Bacillus cereus, Clostridium perfringens, and Staphylococcus aureus—United States, 1998–2008. Clin. Infect Dis 57:425–433

    Article  Google Scholar 

  13. Bennik M, Van Overbeek W, Smid E, Gorris L (1999) Biopreservation in modified atmosphere stored mungbean sprouts: the use of vegetable associated bacteriocinogenic lactic acid bacteria to control the growth of Listeria monocytogenes. Lett Appl Microbiol 28:226–232

  14. Benno Y, Endo K, Mizutani T, Namba Y, Komori T, Mitsuoka T (1989) Comparsion of fecal microflora of elderly persons in rural and urban areas of Japan. Appl Environ Microbiol 55:1100–1105

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Berg AM, Kelly CP, Farraye FA (2012) Clostridium difficile infection in the inflammatory bowel disease patient. Inflamm Bowel Dis 19:194–204

    Article  Google Scholar 

  16. Bergonier D, Sobral D, Febler AT, Jacquet E, Gilbert FB, Schwarz S, Treilles M, Bouloc P, Pourcel C, Vergnaud G (2014) Staphylococcus aureus from 152 cases of bovine, ovine and caprine mastitis investigated by multiple-locus variable number of tandem repeat analysis (MLVA). Vet Res 45:97

    PubMed  PubMed Central  Article  Google Scholar 

  17. Berry ED, Wells JE (2010) Escherichia coli O157:H7: recent advances in research on occurrence, transmission, and control in cattle and the production environment. Adv Food Nut Res 60:67–117

    CAS  Article  Google Scholar 

  18. Biagi E, Nylund L, Candela M, Ostan R, Bucci L, Pini E, Nikkila J, Monti D, Satokari R, Franceschi C, Brigidi P, De Vos W (2010) Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS ONE 5:e10667

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  19. Biotechnology and Food Safety: proceedings of the Second International Symposium. 2014. Elsevier https://books.google.com/books?hl=en&lr=&id=d4qjBQAAQBAJ&pgis=1.

  20. Bogaert D, Keijser B, Huse S, Rossen J, Veenhoven R, van Gils E, Bruin J, Montijn R, Bonten M, Sanders E (2011) Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PLoS One 6:e17035

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  21. Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch GD, Fonstein M, Overbeek R, Kyprides N, Purnelle B, Prozzi D, Ngui K, Masuy D, Hancy F, Burteau S, Boutry M, Delcour J, Goffeau A, Hols P (2004) Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol 22:1554–1558

    CAS  PubMed  Article  Google Scholar 

  22. Bostanci N, Belibasakis GN (2012) Porphyromonas gingivalis: an invasive and evasive opportunistic oral pathogen. FEMS Microbiol Lett 333:1–9

    CAS  PubMed  Article  Google Scholar 

  23. Bourdichon F, Casaregola S, Farrokh C, Frisvad JC, Gerds ML, Hammes WP, Harnett J, Huys G, Laulund S, Ouwehand A, Powell IB, Prajapati JB, Seto Y, Ter Schure E, Van Boven A, Vankerckhoven V, Zgoda A, Tuijtelaars S, Hansen EB (2012) Food fermentations: microorganisms with technological beneficial use. Int J Food Microbiol 154:87–97

    CAS  PubMed  Article  Google Scholar 

  24. Bovee-Oudenhoven IM, ten Bruggencate SJ, Lettink-Wissink ML, van der Meer R (2003) Dietary fructo-oligosaccharides and lactulose inhibit intestinal colonisation but stimulate translocation of Salmonella in rats. Gut 52:1572–1578

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  25. Bowey E, Adlercreutz H, Rowland I (2003) Metabolism of isoflavones and lignans by the gut microflora: a study in germ-free and human flora associated rats. Food Chem Toxicol 41:631–636

    CAS  PubMed  Article  Google Scholar 

  26. Brown K, DeCoffe D, Molcan E, Gibson DL (2012) Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients 4:1095–1119

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  27. Bungay AAC, de Los Reyes CS, Estacio MJ (2005) The zoonotic potential of campylobacteriosis and its implications to human health. Philippine J Sci 134:69–77

    Google Scholar 

  28. Caminero A, Herran AR, Nistal E, Perez-Andres J, Vaquero L, Vivas S, Ruiz de Morales JM, Albillos SM, Casqueiro J (2014) Diversity of the cultivable human gut microbiome involved in gluten metabolism: isolation of microorganisms with potential interest for coeliac disease. FEMS Microbiol Ecol 88:309–319

    CAS  PubMed  Article  Google Scholar 

  29. Carbonero F, Gaskins HR (2013) Sulfate-reducing bacteria in the human gut microbiome. Encyclopedia of Metagenomics:617–619

  30. Cardona F, Andrés-Lacueva C, Tulipani S, Tinahones FJ, Queipo-Ortuno MI (2013) Benefits of polyphenols on gut microbiota and implications in human health. J Nutr Biochem 24:1415–1422

    CAS  PubMed  Article  Google Scholar 

  31. Carriere J, Bretin A, Barnich N, Nguyen HTT (2015) Crohn’s disease-associated adherent-invasive Escherichia coli induce secretion of exosomes with pro-inflammatory activity by intestinal epithelial cells. Gastroenterology 148:S-710

    Article  Google Scholar 

  32. Casaburi A, Piombino P, Nychas G-J, Villani F, Ercolini D (2015) Bacterial populations and the volatilome associated to meat spoilage. Food Microbiol 45:83–102

    CAS  PubMed  Article  Google Scholar 

  33. Casaburi A, Di Martino V, Ferranti P, Picariello L, Villani F (2016) Technological properties and bacteriocins production by Lactobacillus curvatus 54M16 and its use as starter culture for fermented sausage manufacture. Food Control 59:31–45

    CAS  Article  Google Scholar 

  34. Chakchouk-Mtibaa A, Elleuch L, Smaoui S, Najah S, Sellem I, Abdelkafi S, Mellouli L (2014) An antilisterial bacteriocin BacFL31 produced by Enterococcus faecium FL31 with a novel structure containing hydroxyproline residues. Anaerobe 27:1–6

    CAS  PubMed  Article  Google Scholar 

  35. Charalampopoulos D, Wang R, Pandiella SS, Webb C (2002) Application of cereals and cereal components in functional foods: a review. Int J Food Microbiol 79:131–141

    CAS  PubMed  Article  Google Scholar 

  36. Chauret C (2011) Survival and control of Escherichia coli O157:H7 in foods, beverages, soil and water. Virulence 2:593–601

    PubMed  Article  Google Scholar 

  37. Chiang BL, Sheih YH, Wang LH, Liao CK, Gill HS (2000) Enhancing immunity by dietary consumption of a probiotic lactic acid bacterium (Bifidobacterium lactis HN019): optimization and definition of cellular immune responses. Eur J Clin Nutr 54:849–855

    CAS  PubMed  Article  Google Scholar 

  38. Chou LS, Weimer B (1999) Isolation and characterization of acid- and bile-tolerant isolates from strains of Lactobacillus acidophilus. J Dairy Sci 82:23–31

    CAS  PubMed  Article  Google Scholar 

  39. Clemente JC, Ursell LK, Parfrey LW, Knight R (2012) The impact of the gut microbiota on human health: an integrative view. Cell 148:1258–1270

    CAS  PubMed  Article  Google Scholar 

  40. Cornejo-Juarez P, Vilar-Compte D, Perez-Jimenez C, Namendys-Silva SA, Sandoval-Hernandez S, Volkow-Fernandez P (2015) The impact of hospital-acquired infections with multidrug-resistant bacteria in an oncology intensive care unit. Int J Infect Dis 31:31–34

    CAS  PubMed  Article  Google Scholar 

  41. Cossart P (2011) Illuminating the landscape of host-pathogen interactions with the bacterium Listeria monocytogenes. Proc Nat Acad Sci USA 108:19484–19491

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  42. Croxen MA, Finlay BB (2010) Molecular mechanisms of Escherichia coli pathogenicity. Nat. Rev Microbiol 8:26–38

    CAS  Google Scholar 

  43. Croxen MA, Law RJ, Scholz R, Keeney KM, Wlodarska M, Finlay BB (2013) Recent advances in understanding enteric pathogenic Escherichia coli. Clin Microbiol Rev 26:822–880

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  44. Dahlsten E, Lindstrom M, Korkeala H (2015) Mechanisms of food processing and storage-related stress tolerance in Clostridium botulinum. Res Microbiol 166:344–352

    CAS  PubMed  Article  Google Scholar 

  45. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559–563

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  46. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 107:14691–14696

    PubMed  PubMed Central  Article  Google Scholar 

  47. de Kraker MEA, Davey PG, Grundmann H (2011) Mortality and hospital stay associated with resistant Staphylococcus aureus and Escherichia coli bacteremia: estimating the burden of antibiotic resistance in Europe. PLoS Med 8:e1001104

    PubMed  PubMed Central  Article  Google Scholar 

  48. de La Serre CB, Ellis CL, Lee J, Hartman AL, Rutledge JC, Raybould HE (2010) Propensity to high-fat diet-induced obesity in rats is associated with changes in the gut microbiota and gut inflammation. Am J Physiol Gastrointest Liver Physiol 299:G440–G448

    Article  CAS  Google Scholar 

  49. de Vrese M, Schrezenmeir J (2008) Probiotics, prebiotics, and synbiotics. Adv Biochem Eng Biotechnol 111:1–66

    PubMed  Google Scholar 

  50. de Vrese M, Laue C, Offick B, Soeth E, Repenning F, Thob A, Schrezenmeir J (2015) A combination of acid lactase from Aspergillus oryzae and yogurt bacteria improves lactose digestion in lactose maldigesters synergistically: a randomized, controlled, double-blind cross-over trial. Clin Nutr 34:394–399

    PubMed  Article  CAS  Google Scholar 

  51. Derrien M, van Hylckama VJET (2015) Fate, activity, and impact of ingested bacteria within the human gut microbiota. Trends Microbiol 23:354–366

    CAS  PubMed  Article  Google Scholar 

  52. Dong H, Rowland I, Tuohy KM, Thomas LV, Yaqoob P (2010) Selective effects of Lactobacillus casei shirota on T cell activation, natural killer cell activity and cytokine production. Clin Exp Immunol 161:378–388

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Douillard FP, de Vos WM (2014) Functional genomics of lactic acid bacteria: from food to health. Microb Cell Factories S8. doi:10.1186/1475-2859-13-S1-S8

  54. Douillard FP, Ribbera A, Jarvinen HM, Kant R, Pietila TE, Randazzo C, Paulin L, Laine PK, Caggia C, von Ossowski I, Reunanen J, Satokari R, Salminen S, Palva A, de Vos WM (2013) Comparative genomic and functional analysis of Lactobacillus casei and Lactobacillus rhamnosus strains marketed as probiotics. Appl Environ Microbiol 79:1923–1933

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  55. Doulgeraki AI, Ercolini D, Villani F, Nychas GJ (2012) Spoilage microbiota associated to the storage of raw meat in different conditions. Int J Food Microbiol 157:130–141

    PubMed  Article  Google Scholar 

  56. Doyle MP, Erickson MC, Alali W, Cannon J, Deng X, Ortega Y, Smith MA, Zhao T (2015) The food industry’s current and future role in preventing microbial foodborne illness within the United States. Clin Infect Dis 61:252–259

    PubMed  Article  Google Scholar 

  57. Dykes GA, Sampathkumar B, Korber DR (2003) Planktonic or biofilm growth effects survival, hydrophobicity and protein expression patterns of a pathogenic Campylobacter jejuni strain. Int J Food Microbiol 89:1–10

    CAS  PubMed  Article  Google Scholar 

  58. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638

    PubMed  PubMed Central  Article  Google Scholar 

  59. El-Demerdash M, Abdien H, Mansour D, Elfeil W, Abdallah MS (2014) Protective efficacy of synbiotics in the prevention of Salmonella typhimurium in chickens. Global Anim Sci J 2:78–85

    Google Scholar 

  60. Erturk-Hasdemir D, Kasper DL (2013) Resident commensals shaping immunity. Curr Opin Immunol 25:450–455

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  61. Estrada-Garcia T, Navarro-Garcia F (2012) Enteroaggregative Escherichia coli pathotype: a genetically heterogeneous emerging foodborne enteropathogen. FEMS Immunol Med Microbiol 66:281–298

    CAS  PubMed  Article  Google Scholar 

  62. Evans CT, Safdar N (2015) Current trends in the epidemiology and outcomes of Clostridium difficile infection. Clin Infect Dis 60(Suppl 2):S66–S71

    PubMed  Article  Google Scholar 

  63. Food Safety and Inspection Service, USDA (2015). FSIS-2014 Recall Summary. Data Collection and Reports. 24 Mar

  64. Frank DN, Feazel LM, Bessesen MT, Price CS, Janoff EN, Pace NR (2010) The human nasal microbiota and Staphylococcus aureus carriage. PLoS One 5:e10598. doi:10.1371/journal.pone.0010598

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  65. Freitag NE, Port GC, Miner MD (2009) Listeria monocytogenes—from saprophyte to intracellular pathogen. Nat Rev Microbiol 7:623–628

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  66. Garcia AB, Vigre H, Josefsen MH (2015) Towards the production of reliable quantitative microbiological data for risk assessment: direct quantification of Campylobacter in naturally infected chicken fecal samples using selective culture and real-time PCR. Food Control 55:133–140

    CAS  Article  Google Scholar 

  67. García-Cañas V, Simó C, Herrero M, Ibáñez E, Cifuentes A (2012) Present and future challenges in food analysis: foodomics. Anal Chem 84:10150–10159

  68. Gharst G, Oyarzabal OA, Hussain SK (2013) Review of current methodologies to isolate and identify Campylobacter spp. from foods. J Microbiol Methods 95:84–92

    CAS  PubMed  Article  Google Scholar 

  69. Gibson GR, Probert HM, Loo JV, Rastall RA, Roberfroid MB (2004) Dietary modulation of the human colonic microbiota: updating the concept of prebiotics. Nutr Res Rev 17:259–275

    CAS  PubMed  Article  Google Scholar 

  70. Gilchrist MJ, Greko C, Wallinga DB, Beran GW, Riley DG, Thorne PS (2007) The potential role of concentrated animal feeding operations in infectious disease epidemics and antibiotic resistance. Environ Health Perspect 115:313–316

    PubMed  PubMed Central  Article  Google Scholar 

  71. Gill HS, Rutherfurd KJ, Cross ML (2001) Dietary probiotic supplementation enhances natural killer cell activity in the elderly: an investigation of age-related immunological changes. J Clin Immunol 21:264–271

    CAS  PubMed  Article  Google Scholar 

  72. Goerges S, Aigner U, Silakowski B, Scherer S (2006) Inhibition of Listeria monocytogenes by food-borne yeasts. Appl Environ Microbiol 72:313–318

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  73. Guandalini S (2011) Probiotics for prevention and treatment of diarrhea. J Clin Gastroenterol 45:S149–S153

    PubMed  Article  Google Scholar 

  74. Guran HS, Vural A, Erkan ME (2014) The prevalence and molecular typing of Clostridium perfringens in ground beef and sheep meats. J Verbr Lebensm 9:121–128

    Article  Google Scholar 

  75. Hadimli HH, Erganis O, Sayin Z, Aras Z (2012) Toxinotyping of Clostridium perfringens isolates by ELISA and PCR from lambs suspected of enterotoxemia. Turkish J Vet Anim Sci 36:409–415

    CAS  Google Scholar 

  76. Hamon M, Bierne H, Cossart P (2006) Listeria monocytogenes: a multifaceted model. Nat Rev Microbiol 4:423–434

    CAS  PubMed  Article  Google Scholar 

  77. Hatoum R, Labrie S, Fliss I (2012) Identification and partial characterization of antilisterial compounds produced by dairy yeasts. Probiotics Antimicrob Prot 5:8–17

    Article  CAS  Google Scholar 

  78. Hattori M, Taylor TD (2009) The human intestinal microbiome: a new frontier of human biology. DNA Res 16:1–12

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  79. Helms M, Simonsen J, Molbak K (2004) Quinolone resistance is associated with increased risk of invasive illness or death during infection with Salmonella serotype typhimurium. J Infect Dis 190:1652–1654

    PubMed  Article  Google Scholar 

  80. Holzapfel WH, Wood BJB (2014) Introduction to the LAB in Lactic acid bacteria: biodiversity and taxonomy by Holzapfel WH, Wood BJB (Eds), pp 1–12, ISBN: 9781444333831, Willy press

  81. Hooton TM (2012) Uncomplicated urinary tract infection. N Engl J Med 366:1028–1037

    CAS  PubMed  Article  Google Scholar 

  82. Hopkins M, Sharp R, Macfarlane G (2001) Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles. Gut 48:198–205

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  83. Hsiao WWL, Li KL, Liu Z, Jones C, Fraser-Liggett CM, Fouad AF (2012) Microbial transformation from normal oral microbiota to acute endodontic infections. BMC Genomics 13:345

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  84. Huang H, Brooks BW, Lowman R, Carrillo CD (2015) Campylobacter species in animal, food, and environmental sources, and relevant testing programs in Canada. Can J Microbiol 61:701–721

    CAS  PubMed  Article  Google Scholar 

  85. Iyer R, Tomar SK, Maheswari TU, Singh R (2010) Streptococcus thermophilus strains: multifunctional lactic acid bacteria. Inter Dairy J 20:133–141

    CAS  Article  Google Scholar 

  86. Jacob ME, Callaway TR, Nagaraja TG (2009) Dietary interactions and interventions affecting Escherichia coli O157 colonization and shedding in cattle. Foodborne Pathog Dis 6:785–792

    PubMed  Article  Google Scholar 

  87. Jacobs DM, Gaudier E, van Duynhoven J, Vaughan EE (2009) Non-digestible food ingredients, colonic microbiota and the impact on gut health and immunity: a role for metabolomics. Curr Drug Metab 10:41–45

    CAS  PubMed  Article  Google Scholar 

  88. Jakobsson HE, Jernberg C, Andersson AF, Sjolund-Karlsson M, Jansson JK, Engstrand L (2010) Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One 5:e9836

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  89. Jeffery IB, O’toole PW (2013) Diet-microbiota interactions and their implications for healthy living. Nutrients 5:234–252

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  90. Kailasapathy K, Chin J (2000) Survival and therapeutic potential of probiotic organisms with reference to Lactobacillus acidophilus and Bifidobacterium spp. Immunol Cell Biol 78:80–88

    CAS  PubMed  Article  Google Scholar 

  91. Kanjee U, Houry WA (2013) Mechanisms of acid resistance in Escherichia coli. Annu Rev Microbiol 67:65–81

    CAS  PubMed  Article  Google Scholar 

  92. Kaur N, Chen CC, Luther J, Kao JY (2011) Intestinal dysbiosis in inflammatory bowel disease. Gut Microbes 2:211–216

    PubMed  Article  Google Scholar 

  93. Kiers J, Meijer JC, Nout MJR, Rombouts FM, Nabuurs MJA, Van Der Meulen J (2003) Effect of fermented soya beans on diarrhoea and feed efficiency in weaned piglets. J Appl Microbiol 95:545–552

    CAS  PubMed  Article  Google Scholar 

  94. Kim J, Jung MY, Chang YH, Kim S, Kim SJ, Park YH (2007) Probiotic properties of Lactobacillus and Bifidobacterium strains isolated from porcine gastrointestinal tract. Appl Microbiol Biotechnol 74:1103–1111

    CAS  PubMed  Article  Google Scholar 

  95. Kim JY, Young JA, Gunther NW, Lee JL (2014) Inhibition of Salmonella by bacteriocin-producing lactic acid bacteria derived from U.S. kimchi and broiler chicken. J Food Safety 35:1–12

    CAS  Article  Google Scholar 

  96. Klaenhammer TR, Kleerebezem M, Kopp MV, Rescigno M (2012) The impact of probiotics and prebiotics on the immune system. Nat Rev Immunol 12:728–734

    CAS  PubMed  Article  Google Scholar 

  97. Koreen L, Ramaswamy SV, Graviss EA, Naidich S, Musser JM, Kreiswirth BN (2004) Spa typing method for discriminating among Staphylococcus aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation. J Clin Microbiol 42:792–799

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  98. Krych L, Hansen CHF, Hansen AK, van den Berg FWJ, Nielsen DS (2013) Quantitatively different, yet qualitatively alike: a meta-analysis of the mouse core gut microbiome with a view towards the human gut microbiome. PLoS ONE 8:e62578

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  99. Kurakawa T, Ogata K, Matsuda K, Tsuji H, Kubota H, Takada T, Kado Y, Asahara T, Takahashi T, Nomoto K (2015a) Diversity of intestinal Clostridium coccoides group in the Japanese population, as demonstrated by reverse transcription-quantitative PCR. PLoS One 10:e0126226

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  100. Kurakawa T, Ogata K, Tsuji H, Kado Y, Takahashi T, Kida Y, Ito M, Okada N, Nomoto K (2015b) Establishment of a sensitive system for analysis of human vaginal microbiota on the basis of rRNA-targeted reverse transcription-quantitative PCR. J Microbiol Methods 111:93–104

    CAS  PubMed  Article  Google Scholar 

  101. Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sorensen SJ, Hansen LH, Jakobsen M (2010) Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS ONE 5:e9085

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  102. Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Dore J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, Bork P, Wang J, Ehrlich SD, Pedersen O (2013) Richness of human gut microbiome correlates with metabolic markers. Nature 500:541–546

    PubMed  Article  CAS  Google Scholar 

  103. Le Loir Y, Baron F, Gautier M (2003) Staphylococcus aureus and food poisoning. Genet Mol Res 2:63–76

    PubMed  Google Scholar 

  104. Leahy SC, Higgins DG, Fitzgerald GF, Van Sinderen D (2005) Getting better with Bifidobacteria. J Appl Microbiol 98:1303–1315

    CAS  PubMed  Article  Google Scholar 

  105. Lee HY, Chai LC, Pui CF, Mustafa S, Cheah YK, Nishibuchi M, Radu S (2013) Formation of biofilm by Listeria monocytogenes ATCC 19112 at different incubation temperatures and concentrations of sodium chloride. Brazilian J Microbiol 44:51–55

    CAS  Article  Google Scholar 

  106. Leverentz B, Conway WS, Janisiewicz W, Abadias M, Kurtzman CP, Camp MJ (2006) Biocontrol of the food-borne pathogens Listeria monocytogenes and Salmonella enterica serovar poona on fresh-cut apples with naturally occurring bacterial and yeast antagonists. Appl Environ Microbiol 72:1135–1140

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  107. Levri KM, Ketvertis K, Deramo M, Merenstein JH, D’Amico F (2005) Do probiotics reduce adult lactose intolerance? A systematic review. J Fam Pract 54:613–620

    PubMed  Google Scholar 

  108. Ley RE, Peterson DA, Gordon JI (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124:837–848

    CAS  PubMed  Article  Google Scholar 

  109. Li J, Zhang W, Wang C, Yu Q, Dai R, Pei X (2012) Lactococcus lactis expressing food-grade β-galactosidase alleviates lactose intolerance symptoms in post-weaning Balb/c mice. Appl Microbiol Biotechnol 96:1499–1506

    CAS  PubMed  Article  Google Scholar 

  110. Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Dore J, Ehrlich SD, Bork P, Wang J (2014) An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 32:834–841

    CAS  PubMed  Article  Google Scholar 

  111. Liato V, Labrie S, Viel C, Benali M, Aider M (2015) Study of the combined effect of electro-activated solutions and heat treatment on the destruction of spores of Clostridium sporogenes and Geobacillus stearothermophilus in model solution and vegetable puree. Anaerobe 35(Pt B):11–21

    CAS  PubMed  Article  Google Scholar 

  112. Lin CS, Chang CJ, Lu CC, Martel J, Ojcius DM, Ko YF, Young JD, Lai HC (2014) Impact of the gut microbiota, prebiotics, and probiotics on human health and disease. Biomed J 37:259–268

    PubMed  Article  Google Scholar 

  113. Lindstrom M, Heikinheimo A, Lahti P, Korkeala H (2011) Novel insights into the epidemiology of Clostridium perfringens type A food poisoning. Food Microbiol 28:192–198

    PubMed  Article  Google Scholar 

  114. Ling Z, Liu X, Chen X, Zhu H, Nelson KE, Xia Y, Li L, Xiang C (2011) Diversity of cervicovaginal microbiota associated with female lower genital tract infections. Microb Ecol 61:704–714

    PubMed  Article  Google Scholar 

  115. Looney WJ, Narita M, Muhlemann K (2009) Stenotrophomonas maltophilia: an emerging opportunist human pathogen. Lancet Infect Dis 9:312–323

    CAS  PubMed  Article  Google Scholar 

  116. Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG (2014) Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ Health Perspect 122:284–291

    PubMed  PubMed Central  Google Scholar 

  117. Ma K, Maeda T, You H, Shirai Y (2014) Open fermentative production of L-lactic acid with high optical purity by thermophilic Bacillus coagulans using excess sludge as nutrient. Bioresour Technol 151:28–35

    CAS  PubMed  Article  Google Scholar 

  118. Mahenthiralingam E, Baldwin A, Drevinek P, Vanlaere E, Vandamme P, LiPuma JJ, Dowson CG (2006) Multilocus sequence typing breathes life into a microbial metagenome. PLoS One 1:e17

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  119. Maiden MCJ (2006) Multilocus sequence typing of bacteria. Annu Rev Microbiol 60:561–588

    CAS  PubMed  Article  Google Scholar 

  120. Majowicz SE, Scallan E, Jones-Bitton A, Sargeant JM, Stapleton J, Angulo FJ, Yeung DH, Kirk MD (2014) Global incidence of human shiga toxin-producing Escherichia coli infections and deaths: a systematic review and knowledge synthesis. Foodborne Pathog Dis 11:447–455

    PubMed  PubMed Central  Article  Google Scholar 

  121. Makarova KS, Koonin EV (2006) Evolutionary genomics of lactic acid bacteria. J Bacteriol 189:1199–1208

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  122. Malinen E, Rinttila T, Kajander K, Matto J, Kassinen A, Krogius L, Saarela M, Korpela R, Palva A (2005) Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Am J Gastroenterology 100:373–382

    CAS  Article  Google Scholar 

  123. Marlow G, Ellett S, Ferguson IR, Zhu S, Karunasinghe N, Jesuthasan AC, Han DY, Fraser AG, Ferguson LR (2013) Transcriptomics to study the effect of a mediterranean-inspired diet on inflammation in Crohn’s disease patients. Hum Genomics 7:24

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  124. Martín R, Langa S, Reviriego C, Jimínez E, Marín ML, Xaus J, Fernandez L, Rodríguez JM (2003) Human milk is a source of lactic acid bacteria for the infant gut. J Pediatr 143:754–758

    PubMed  Article  Google Scholar 

  125. Martinez-Medina M, Aldeguer X, Gonzalez-Huix F, Acero D, Garcia-Gil LJ (2006) Abnormal microbiota composition in the ileocolonic mucosa of Crohn’s disease patients as revealed by polymerase chain reaction-denaturing gradient gel electrophoresis. Inflamm Bowel Dis 12:1136–1145

    PubMed  Article  Google Scholar 

  126. Matijasic BB, Obermajer T, Lipoglavsek L, Grabnar I, Avgustin G, Rogelj I (2014) Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia. Eur J Nutr 53:1051–1064

    CAS  PubMed  Article  Google Scholar 

  127. Matto J, Fonden R, Tolvanen T, von Wright A, Vilpponen-Salmela T, Satokari R, Saarela M (2006) Intestinal survival and persistence of probiotic Lactobacillus and Bifidobacterium strains administered in triple-strain yoghurt. Int Dairy J 16:1174–1118

    Article  CAS  Google Scholar 

  128. Mauldin PD, Salgado CD, Hansen IS, Durup DT, Bosso JA (2010) Attributable hospital cost and length of stay associated with health care-associated infections caused by antibiotic-resistant gram-negative bacteria. Antimicrob Agents Chemother 54:109–115

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  129. McFarland LV (2015) From yaks to yogurt: the history, development, and current use of probiotics. Clin Infect Dis 60(Suppl 2):S85–S90

    PubMed  Article  Google Scholar 

  130. Miwa N, Masuda T, Terai K, Kawamura A, Otani K, Miyamoto H (1999) Bacteriological investigation of an outbreak of Clostridium perfringens food poisoning caused by Japanese food without animal protein. Int J Food Microbiol 49:103–106

    CAS  PubMed  Article  Google Scholar 

  131. Moretro T, Langsrud S (2004) Listeria monocytogenes: biofilm formation and persistence in food-processing environments. Biofilms 1:107–121

    Article  Google Scholar 

  132. Murillo N, Raoult D (2013) Skin microbiota: overview and role in the skin diseases acne vulgaris and rosacea. Future Microbiol 8:209–222

    CAS  PubMed  Article  Google Scholar 

  133. Murphy TF, Parameswaran GI (2009) Moraxella catarrhalis, a human respiratory tract pathogen. Clin Infect Dis 49:124–131

    PubMed  Article  Google Scholar 

  134. Nakayama J, Hoshiko H, Fukuda M, Tanaka H, Sakamoto N, Tanaka S, Ohue K, Sakai K, Sonomoto K (2007) Molecular monitoring of bacterial community structure in long-aged nukadoko: pickling bed of fermented rice bran dominated by slow-growing lactobacilli. J Biosci Bioeng 104:481–489

    CAS  PubMed  Article  Google Scholar 

  135. Nes IF, Johnsborg O (2004) Exploration of antimicrobial potential in LAB by genomics. Curr Opin Biotechnol 15:100–104

    CAS  PubMed  Article  Google Scholar 

  136. Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S (2012) Host-gut microbiota metabolic interactions. Science 336:1262–1267

    CAS  PubMed  Article  Google Scholar 

  137. Nishio, Y., E. Noguchi, S. Ito, E. Ichikawa, Y. Umebayashi, F. Otsuka, and T. Arinami (2001) Mutation and association analysis of the interferon regulatory factor 2 gene (IRF2) with atopic dermatitis. Journal of Human Genetics: 664–67. Web

  138. Noor R, Hasan Md F, Munna MS, Rahman MM (2015) Demonstration of virulent genes within Listeria and Klebsiella isolates contaminating the export quality frozen shrimps. Int Aquat Res 7:157–161

    Article  Google Scholar 

  139. Nutrition Center for Food Safety and Applied. 2015. Laboratory methods—BAM: diarrheagenic Escherichia coli. Center for Food Safety and Applied Nutrition. http://www.fda.gov/food/foodscienceresearch/laboratorymethods/ucm070080.htm

  140. O’Keefe, Stephen (2008) Nutrition and colonic health: the critical role of the microbiota. Curr Opin Gastroenterol: 51-58

  141. O’Loughlin JL, Samuelson DR, Braundmeier-Fleming AG, White BA, Haldorson GJ, Stone JB, Lessmann JJ, Eucker TP, Konkel ME (2015) The intestinal microbiota influences Campylobacter jejuni colonization and extraintestinal dissemination in mice. Appl Environ Microbiol 81:4642–4650

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  142. Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M, Oshima K, Kodama T, Abe H, Nakayama K, Kurokawa K, Tobe T, Hattori M, Hayashi T (2009) Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Nat Acad Sci USA 106:17939–17944

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  143. Olaoye OA (2011) Meat: an overview of its composition, biochemical changes and associated microbial agents. Int Food Res J 18:877–885

    CAS  Google Scholar 

  144. Oliver SP, Patel DA, Callaway TR, Torrence ME (2009) ASAS centennial paper: developments and future outlook for preharvest food safety. J Anim Sci 87:419–4437

    CAS  PubMed  Article  Google Scholar 

  145. Olszak T, An D, Zeissig S, Vera MP, Richter R, Franke A, Glickman JN, Siebert R, Baron RM, Kasper DL, Blumberg RS (2012) Microbial exposure dung early life has persistent effects on natural killer T cell function. Science 336:489–493

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  146. Onda T, Yanagida F, Tsuji M, Shinohara T, Yokotsuka K (2003) Production and purification of a bacteriocin peptide produced by Lactococcus sp. strain GM005, isolated from miso-paste. Int J Food Microbiol 87:153–159

    CAS  PubMed  Article  Google Scholar 

  147. Ono H, Nishio S, Tsurii J, Kawamoto T, Sonomoto K, Nakayama J (2015) Effects of Japanese pepper and red pepper on the microbial community during nukadoko fermentation. Biosci Microbiota Food Health 34: 1–9.

  148. Ortega E, Abriouel H, Lucas R, Galvez A (2010) Multiple roles of Staphylococcus aureus enterotoxins: pathogenicity, superantigenic activity, and correlation to antibiotic resistance. Toxins 2:2117–2131

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  149. Packey CD, Sartor RB (2009) Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Curr Opin Infect Dis 22:292–301

    PubMed  PubMed Central  Article  Google Scholar 

  150. Palaria A, Johnson-Kanda I, O’sullivan DJ (2012) Effect of a synbiotic yogurt on levels of fecal Bifidobacteria, Clostridia, and Enterobacteria. Appl Environ Microbiol 78:933–940

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  151. Park KY, Jeong JK, Lee YE, Daily JW 3rd (2014) Health benefits of kimchi (Korean fermented vegetables) as a probiotic food. J Med Food 17:6–20

    CAS  PubMed  Article  Google Scholar 

  152. Parkhill J, Wren BW, Mungall K, Ketley JM (2000) The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403:665–668

    CAS  PubMed  Article  Google Scholar 

  153. Patel R, DuPont HL (2015) New approaches for bacteriotherapy: prebiotics, new-generation probiotics, and synbiotics. Clin Infect Dis 60(Suppl 2):S108–S121

    PubMed  Article  Google Scholar 

  154. Pearce RA, Wallace FM, Call JE, Dudley RL, Oser A (2003) Prevalence of Campylobacter within a swine slaughter and processing facility. J Food Prot 66:1550–1556

    CAS  PubMed  Google Scholar 

  155. Pielsticker C, Glunder G, Rautenschlein S (2012) Colonization properties of Campylobacter jejuni in chickens. Eur J Microbiol Immuno 2:61–65

    CAS  Article  Google Scholar 

  156. Purim K, Bordignon G, Queiroz-Telles F (2005) Fungal infection of the feet in soccer players and non-athlete individuals. Rev Iberoam Micol 22:34–38

    PubMed  Article  Google Scholar 

  157. Qaisrani SN, van Krimpen MM, Kwakkel RP, Verstegen MWA, Hendriks WH (2015) Diet structure, butyric acid, and fermentable carbohydrates influence growth performance, gut morphology, and cecal fermentation characteristics in broilers. Poultry Sci 94:2152–2164

    CAS  Article  Google Scholar 

  158. Rhee S, Lee JE, Lee CH (2011) Importance of lactic acid bacteria in asian fermented foods. Microb Cell Factories 10:S5

    Article  Google Scholar 

  159. Rinttila T, Lyra A, Krogius-Kurikka L, Palva A (2011) Real-time PCR analysis of enteric pathogens from fecal samples of irritable bowel syndrome subjects. Gut Pathog 3:6

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  160. Robinson CJ, Bohannan BJM, Young VB (2010) From structure to function: the ecology of host-associated microbial communities. Microbiol Mol Biol Rev 74:453–476

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  161. Rodriguez E, Calzada J, Arques J, Rodriguez JM, Nunez M, Medina M (2005) Antimicrobial activity of pediocin-producing Lactococcus lactis on Listeria monocytogenes, Staphylococcus aureus and Escherichia coli O157:H7 in cheese. Int Dairy J 15:51–57

    CAS  Article  Google Scholar 

  162. Rodriguez-Beltran J, Tourret J, Tenaillon O, Lopez E, Bourdelier E, Costas C, Matic I, Denamur E, Blazquez J (2015) High recombinant frequency in extraintestinal pathogenic Escherichia coli strains. Mol Biol Evol 32:1708–1716

    PubMed  Article  Google Scholar 

  163. Rodriguez-Pazo N, Vazquez-Araujo L, Perez-Rodríguez N, Cortes-Dieguez S, Dominguez JM (2013) Cell-free supernatants obtained from fermentation of cheese whey hydrolyzates and phenylpyruvic acid by Lactobacillus plantarum as a source of antimicrobial compounds, bacteriocins, and natural aromas. Appl Biochem Biotechnol 171:1042–1060

    CAS  PubMed  Article  Google Scholar 

  164. Rosales RS, Churchward CP, Schnee C, Sachse K, Lysnyansky I, Catania S, Iob L, Ayling RD, Nicholas RAJ (2015) Global multilocus sequence typing analysis of Mycoplasma bovis isolates reveals two main population clusters. J Clin Microbiol 53:789–794

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  165. Rosendale DI, Maddox IS, Miles MC, Rodier M, Skinner M, Sutherland J (2008) High-throughput microbial bioassays to screen potential New Zealand functional food ingredients intended to manage the growth of probiotic and pathogenic gut bacteria. Int J Food Sci Technol 43:2257–2267

    CAS  Article  Google Scholar 

  166. Rupnik M, Wilcox MH, Gerding DN (2009) Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Micro 7:526–536

    CAS  Article  Google Scholar 

  167. Saez-Lara MJ, Gomez-Llorente C, Plaza-Diaz J, Gil A (2015) The role of probiotic lactic acid bacteria and Bifidobacteria in the prevention and treatment of inflammatory bowel disease and other related diseases: a systematic review of randomized human clinical trials Biomed Res Int Article ID 505878

  168. Sahin O, Kassem II, Shen Z, Lin J, Rajashekara G, Zhang Q (2015) Campylobacter in poultry: ecology and potential interventions. Avian Dis 59:185–200

    PubMed  Article  Google Scholar 

  169. Sakaridis I, Soultos N, Dovas CI, Papavergou E, Ambrosiadis I, Koidis P (2012) Lactic acid bacteria from chicken carcasses with inhibitory activity against Salmonella spp. and Listeria monocytogenes. Czech J Food Sci 18:62–66

    CAS  Google Scholar 

  170. Sanders ME, Guarner F, Guerrant R, Holt PR, Quigley EM, Sartor RB, Sherman PM, Mayer EA (2013) An update on the use and investigation of probiotics in health and disease. Gut 62:787–796

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  171. Satin M (2008) Food alert!: the ultimate sourcebook for food safety. 2nd ed. New York, NY

  172. Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, Griffin PM (2011) Foodborne illness acquired in the United States—major pathogens. Emerg Infect Dis 17:7–15

    PubMed  PubMed Central  Article  Google Scholar 

  173. Scanlan PD, Shanahan F, Clune Y, Collins JK, O’sullivan GC, O’riordan M, Holmes E, Wang Y, Marchesi JR (2008) Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol 10:789–798

    CAS  PubMed  Article  Google Scholar 

  174. Schroeter J, Klaenhammer T (2009) Genomics of lactic acid bacteria. FEMS Microbiol Lett 292:1–6

    CAS  PubMed  Article  Google Scholar 

  175. Shim J (2013) Gut microbiota in inflammatory bowel disease. Pediatr Gastroenterol Hepatol Nutr 16(1):17–21

  176. Simpson PJ, Ross RP, Fitzgerald GF, Stanton C (2004) Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum. Int J Syst Evol Microbiol 54:401–406

    CAS  PubMed  Article  Google Scholar 

  177. Singh OV, Nagaraj NS, Gabani P (2011) Systems biology: integrating ‘-omics’-oriented approaches to determine foodborne microbial toxins. Handbook of systems toxicology. Ed. Casciano DA and Sahu SC. Wily Press, ISBN 978–0–470-68401-6

  178. Sobel J (2008) Botulism. Clin Infect Dis 41:1167–1173

    Article  Google Scholar 

  179. Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R (2013) Cohabiting family members share microbiota with one another and with their dogs. E Life 2:e00458

    PubMed  PubMed Central  Google Scholar 

  180. Spor A, Koren O, Ley R (2011) Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 9:279–290

    CAS  PubMed  Article  Google Scholar 

  181. Spratt BG (1999) Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet. Curr Opin Microbiol 2:312–316

    CAS  PubMed  Article  Google Scholar 

  182. Srimark N, Khunajakr N (2015) Characterization of the bacteriocin-like substance from Lactococcus lactis subsp. lactis WX153 against swine pathogen Streptococcus suis. J Health Res 29:259–267

    CAS  Google Scholar 

  183. Stanley D, Wu SB, Rodgers N, Swick RA, Moore RJ (2014) Differential responses of cecal microbiota to fishmeal, Eimeria and Clostridium perfringens in a necrotic enteritis challenge model in chickens. PLoS One 9:e104739

    PubMed  PubMed Central  Article  Google Scholar 

  184. Stecher B, Hardt WD (2011) Mechanisms controlling pathogen colonization of the gut. Curr Opin Microbiol 14:82–91

    CAS  PubMed  Article  Google Scholar 

  185. Stenfors ALP, Fagerlund A, Granum PE (2008) From soil to gut: Bacillus cereus and its food poisoning toxins. FEMS Microbiol Rev 32:579–606

    Article  CAS  Google Scholar 

  186. Stewart EJ (2012) Growing unculturable bacteria. J Bacteriol 194:4151–4160

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  187. Suo C, Yin Y, Wang X, Lou X, Song D, Wang X, Gu Q (2012) Effects of Lactobacillus plantarum ZJ316 on pig growth and pork quality. BMC Vet Res 8:89

    PubMed  Article  Google Scholar 

  188. Suskovic J, Kos B, Goreta J, Matosic S (2001) Role of lactic acid bacteria and Bifidobacteria in synbiotic effect. Food Technol Biotechnol 39:227–235

    CAS  Google Scholar 

  189. Taylor AD, Yu Q, Chen S, Homola J, Jiang S (2005) Comparison of E. coli O157:H7 preparation methods used for detection with surface plasmon resonance sensor. Sensors Actuators B: Chem 107:202–208

    CAS  Article  Google Scholar 

  190. Teh AHT, Lee SM, Dykes GA (2014) Does Campylobacter jejuni form biofilm in food-related environments? Appl Environ Microbiol 80:5154–5160

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  191. Tejero-Sarinena S, Barlow J, Costabile A, Gibson GR, Rowland I (2012) In vitro evaluation of the antimicrobial activity of a range of probiotics against pathogens: evidence for the effects of organic acids. Anaerobe 18:530–538

    CAS  PubMed  Article  Google Scholar 

  192. Titilawo Y, Obi L, Okoh A (2015) Occurrence of virulence gene signatures associated with diarrhoeagenic and non-diarrhoeagenic pathovars of Escherichia coli isolates from some selected rivers in south-western Nigeria. BMC Microbiol 15:204

    PubMed  PubMed Central  Article  Google Scholar 

  193. Todd ECD, Greig JD, Bartleson CA, Michaels BS (2008) Outbreaks where food workers have been implicated in the spread of foodborne disease. Part 4. Infective doses and pathogen carriage. J Food Prot 71:2239–2373

    Google Scholar 

  194. Tulini FL, Hymery N, Haertle T, Le Blay G, De Martinis EC (2015) Screening for antimicrobial and proteolytic activities of lactic acid bacteria isolated from cow, buffalo and goat milk and cheeses marketed in the southeast region of Brazil. J Dairy Res, 1–10. doi:10.1017/S0022029915000606

  195. Vaishampayan PA, Kuehl JV, Froula JL, Morgan JL, Ochman H, Francino MP (2010) Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol 2:53–66

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  196. Vandamme P, De Bruyne K, Pot B (2014) Phylogenetics and systematics in lactic acid bacteria: biodiversity and taxonomy. In: Holzapfel, WH, Wood BJB (eds), pp 31–44, ISBN: 9781444333831, Willy Press

  197. Varsaki A, Murphy C, Barczynska A, Jordan K, Carroll C (2015) The acid adaptive tolerance response in Campylobacter jejuni induces a global response, as suggested by proteomics and microarrays. Microbial Biotechnol 8:974–988

    CAS  Article  Google Scholar 

  198. Waters AE, Contente-Cuomo T, Buchhagen J, Liu CM, Watson L, Pearce K, Foster JT, Bowers J, Driebe EM, Engelthaler DM, Keim PS, Price LB (2011) Multidrug-resistant Staphylococcus aureus in US meat and poultry. Clin Infect Dis 52:1227–1230

    PubMed  PubMed Central  Article  Google Scholar 

  199. Wisener LV, Sargeant JM, O’Connor AM, Faires MC, Glass-Kaastra SK (2015) The use of direct-fed microbials to reduce shedding of Escherichia coli O157 in beef cattle: a systematic review and meta-analysis. Zoonoses Pub Health 62:75–89

    CAS  Article  Google Scholar 

  200. Woappi Y, Gabani P, Singh OV (2013) Emergence of antibiotic-producing microorganisms in residential versus recreational microenvironments. Br Microbiol Res J 3:280–294

    PubMed  PubMed Central  Article  Google Scholar 

  201. Woappi Y, Gabani P, Singh A, Singh OV (2014) Antibiotrophs: the complexity of antibiotic-subsisting and antibiotic-resistant microorganisms. Crit Rev Microbiol. doi:10.3109/1040841X.2013.875982

    PubMed  Google Scholar 

  202. Wollowski I, Rechkemmer G, Beatrice BL (2001) Protective role of probiotics and prebiotics in colon cancer. Am J Clin Nutr 73:451S–455S

    CAS  PubMed  Google Scholar 

  203. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y-Y, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334:105–108

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  204. Xu J (2006) Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15:1713–1731

    CAS  PubMed  Article  Google Scholar 

  205. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI (2012) Human gut microbiome viewed across age and geography. Nature 486:222–227

    CAS  PubMed  PubMed Central  Google Scholar 

  206. Zalan Z, Hudacek J, Stetina J, Chumchalova J, Halasz A (2009) Production of organic acids by Lactobacillus strains in three different media. Eur Food Res Technol 230:395–404

    Article  CAS  Google Scholar 

  207. Zhang C, Zhang M, Wang S, Han R, Cao Y, Hua W, Mao Y, Zhang X, Pang X, Wei C, Zhao G, Chen Y, Zhao L (2009) Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. ISME J 4:232–241

    PubMed  Article  CAS  Google Scholar 

  208. Zhang X, Zhang S, Shi Y, Shen F, Wang H (2014) A new high phenyl lactic acid-yielding Lactobacillus plantarum IMAU10124 and a comparative analysis of lactate dehydrogenase gene. FEMS Microbiol Lett 356:89–96

    CAS  PubMed  Article  Google Scholar 

  209. Zimmer J, Lange B, Frick JS, Sauer H, Zimmermann K, Schwiertz A, Rusch K, Klosterhalfen S, Enck P (2012) A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. Eur J Clin Nutr 66:53–60

    CAS  PubMed  Article  Google Scholar 

Download references

Acknowledgments

The authors are thankful for the institutional assistance. The authors also acknowledge the valuable studies conducted in this field not being cited in this article due to space limitation.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Om V. Singh.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animal rights and informed consent

This article does not contain any studies with human participants or animals performed by any of the authors.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Josephs-Spaulding, J., Beeler, E. & Singh, O.V. Human microbiome versus food-borne pathogens: friend or foe. Appl Microbiol Biotechnol 100, 4845–4863 (2016). https://doi.org/10.1007/s00253-016-7523-7

Download citation

Keywords

  • Microbiome
  • Human
  • Food
  • Diet
  • Nutrition
  • Pathogen
  • Probiotic