Human microbiome versus food-borne pathogens: friend or foe

Applied Microbiology and Biotechnology

Volumn 100, Issue 11, 2016, Pages 4845-4863

  Josephs Spaulding, Jonathan ^a   Beeler, Erik ^a   Singh, Om V ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Diet; Food; Human; Microbiome; Nutrition; Pathogen; Probiotic

Indexed keywords

BIOLOGY; DIGESTIVE SYSTEM; FOOD PRODUCTS; FOOD SAFETY; MICROORGANISMS; NUTRITION; PATHOGENS;

FOOD MANUFACTURERS; FOOD-BORNE PATHOGENS; HIGH QUALITY; HUMAN; HUMAN MICROBIOME; MICROBIOME; MICROBIOTAS; PROBIOTICS;

FOOD MICROBIOLOGY;

BACTERIAL PROTEIN; BACTERIAL RNA; PREBIOTIC AGENT; PROBIOTIC AGENT; RNA 16S;

DIET; DIGESTIBILITY; FOOD QUALITY; FOOD SAFETY; HUMAN ACTIVITY; MICROBIAL ACTIVITY; PATHOGENICITY; PROBIOTICS;

ADAPTATION; BACILLUS CEREUS; BACTERIAL METABOLISM; BACTERIAL TRANSMISSION; BACTERIUM; BIFIDOBACTERIUM BREVE; BIFIDOBACTERIUM INFANTIS; BIFIDOBACTERIUM LONGUM; CAMPYLOBACTER; CLOSTRIDIUM BOTULINUM; CLOSTRIDIUM PERFRINGENS; COMMENSALISM; COMPETITION; DENATURING GRADIENT GEL ELECTROPHORESIS; DIET; DYSBIOSIS; ENTEROTOXIGENIC ESCHERICHIA COLI; FERMENTED PRODUCT; FOOD BORNE PATHOGEN; FOOD INTAKE; HOMEOSTASIS; HOST PATHOGEN INTERACTION; HUMAN; INHERITANCE; INTESTINE FLORA; INVASIVE SPECIES; LACTIC ACID BACTERIUM; LACTOBACILLUS CRISPATUS; LACTOBACILLUS CURVATUS; LACTOBACILLUS PARACASEI; LACTOBACILLUS PLANTARUM; LACTOBACILLUS RHAMNOSUS; LACTOCOCCUS LACTIS; LACTOCOCCUS LACTIS SUBSP. LACTIS; LISTERIA MONOCYTOGENES; MEAT; METABOLIC REGULATION; METABOLOMICS; METAGENOMICS; MICROBIAL DIVERSITY; MULTILOCUS SEQUENCE TYPING; MULTIPLE LOCUS VARIABLE NUMBER OF TANDEM REPEAT ASSAY; NONHUMAN; OMNIVORE; PROTEOMICS; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SALMONELLA; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; SHIGELLA; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS; SYMBIOSIS; SYSTEMS BIOLOGY; TRANSCRIPTOMICS; VARIABLE NUMBER OF TANDEM REPEAT; VEGETARIAN; VERTICAL TRANSMISSION; VIBRIO CHOLERAE; YERSINIA ENTEROCOLITICA; FERMENTATION; FOODBORNE DISEASES; MICROBIOLOGY; MICROFLORA;

DIET; FERMENTATION; FOODBORNE DISEASES; HUMANS; METAGENOMICS; MICROBIOTA; MULTILOCUS SEQUENCE TYPING; PROBIOTICS; SYMBIOSIS;

EID: 85027943007     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-016-7523-7     Document Type: Review

References (209)

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
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
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
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
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
7. Backhed F (2011) Programming of host metabolism by the gut microbiota. Ann Nutr Metab 58:44–52
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
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
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
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
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
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
15. Berg AM, Kelly CP, Farraye FA (2012) Clostridium difficile infection in the inflammatory bowel disease patient. Inflamm Bowel Dis 19:194–204
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
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
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
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
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
22. Bostanci N, Belibasakis GN (2012) Porphyromonas gingivalis: an invasive and evasive opportunistic oral pathogen. FEMS Microbiol Lett 333:1–9
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
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
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
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
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
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
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
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
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
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
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
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
36. Chauret C (2011) Survival and control of Escherichia coli O157:H7 in foods, beverages, soil and water. Virulence 2:593–601
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
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
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
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
41. Cossart P (2011) Illuminating the landscape of host-pathogen interactions with the bacterium Listeria monocytogenes. Proc Nat Acad Sci USA 108:19484–19491
42. Croxen MA, Finlay BB (2010) Molecular mechanisms of Escherichia coli pathogenicity. Nat. Rev Microbiol 8:26–38
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
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
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
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
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
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
49. de Vrese M, Schrezenmeir J (2008) Probiotics, prebiotics, and synbiotics. Adv Biochem Eng Biotechnol 111:1–66
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
51. Derrien M, van Hylckama VJET (2015) Fate, activity, and impact of ingested bacteria within the human gut microbiota. Trends Microbiol 23:354–366
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
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
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
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
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
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
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
60. Erturk-Hasdemir D, Kasper DL (2013) Resident commensals shaping immunity. Curr Opin Immunol 25:450–455
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
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
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
65. Freitag NE, Port GC, Miner MD (2009) Listeria monocytogenes—from saprophyte to intracellular pathogen. Nat Rev Microbiol 7:623–628
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
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
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
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
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
72. Goerges S, Aigner U, Silakowski B, Scherer S (2006) Inhibition of Listeria monocytogenes by food-borne yeasts. Appl Environ Microbiol 72:313–318
73. Guandalini S (2011) Probiotics for prevention and treatment of diarrhea. J Clin Gastroenterol 45:S149–S153
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
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
76. Hamon M, Bierne H, Cossart P (2006) Listeria monocytogenes: a multifaceted model. Nat Rev Microbiol 4:423–434
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
78. Hattori M, Taylor TD (2009) The human intestinal microbiome: a new frontier of human biology. DNA Res 16:1–12
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
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
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
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
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
85. Iyer R, Tomar SK, Maheswari TU, Singh R (2010) Streptococcus thermophilus strains: multifunctional lactic acid bacteria. Inter Dairy J 20:133–141
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
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
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
89. Jeffery IB, O’toole PW (2013) Diet-microbiota interactions and their implications for healthy living. Nutrients 5:234–252
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
91. Kanjee U, Houry WA (2013) Mechanisms of acid resistance in Escherichia coli. Annu Rev Microbiol 67:65–81
92. Kaur N, Chen CC, Luther J, Kao JY (2011) Intestinal dysbiosis in inflammatory bowel disease. Gut Microbes 2:211–216
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
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
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
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
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
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
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
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
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
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
103. Le Loir Y, Baron F, Gautier M (2003) Staphylococcus aureus and food poisoning. Genet Mol Res 2:63–76
104. Leahy SC, Higgins DG, Fitzgerald GF, Van Sinderen D (2005) Getting better with Bifidobacteria. J Appl Microbiol 98:1303–1315
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
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
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
108. Ley RE, Peterson DA, Gordon JI (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124:837–848
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
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
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
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
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
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
115. Looney WJ, Narita M, Muhlemann K (2009) Stenotrophomonas maltophilia: an emerging opportunist human pathogen. Lancet Infect Dis 9:312–323
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
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
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
119. Maiden MCJ (2006) Multilocus sequence typing of bacteria. Annu Rev Microbiol 60:561–588
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
121. Makarova KS, Koonin EV (2006) Evolutionary genomics of lactic acid bacteria. J Bacteriol 189:1199–1208
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
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
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
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
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
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
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
129. McFarland LV (2015) From yaks to yogurt: the history, development, and current use of probiotics. Clin Infect Dis 60(Suppl 2):S85–S90
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
131. Moretro T, Langsrud S (2004) Listeria monocytogenes: biofilm formation and persistence in food-processing environments. Biofilms 1:107–121
132. Murillo N, Raoult D (2013) Skin microbiota: overview and role in the skin diseases acne vulgaris and rosacea. Future Microbiol 8:209–222
133. Murphy TF, Parameswaran GI (2009) Moraxella catarrhalis, a human respiratory tract pathogen. Clin Infect Dis 49:124–131
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
135. Nes IF, Johnsborg O (2004) Exploration of antimicrobial potential in LAB by genomics. Curr Opin Biotechnol 15:100–104
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
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
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
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
143. Olaoye OA (2011) Meat: an overview of its composition, biochemical changes and associated microbial agents. Int Food Res J 18:877–885
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
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
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
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
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
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
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
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
153. Patel R, DuPont HL (2015) New approaches for bacteriotherapy: prebiotics, new-generation probiotics, and synbiotics. Clin Infect Dis 60(Suppl 2):S108–S121
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
155. Pielsticker C, Glunder G, Rautenschlein S (2012) Colonization properties of Campylobacter jejuni in chickens. Eur J Microbiol Immuno 2:61–65
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
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
158. Rhee S, Lee JE, Lee CH (2011) Importance of lactic acid bacteria in asian fermented foods. Microb Cell Factories 10:S5
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
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
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
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
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
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
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
166. Rupnik M, Wilcox MH, Gerding DN (2009) Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Micro 7:526–536
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
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
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
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
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
174. Schroeter J, Klaenhammer T (2009) Genomics of lactic acid bacteria. FEMS Microbiol Lett 292:1–6
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
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
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
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
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
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
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
184. Stecher B, Hardt WD (2011) Mechanisms controlling pathogen colonization of the gut. Curr Opin Microbiol 14:82–91
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
186. Stewart EJ (2012) Growing unculturable bacteria. J Bacteriol 194:4151–4160
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
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
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
190. Teh AHT, Lee SM, Dykes GA (2014) Does Campylobacter jejuni form biofilm in food-related environments? Appl Environ Microbiol 80:5154–5160
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
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
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
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
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
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
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
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
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
202. Wollowski I, Rechkemmer G, Beatrice BL (2001) Protective role of probiotics and prebiotics in colon cancer. Am J Clin Nutr 73:451S–455S
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
204. Xu J (2006) Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15:1713–1731
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
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
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
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
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