title: Impact of genomics on the field of probiotic research: historical perspectives to modern paradigms.
abstract: For thousands of years, humans have safely consumed microorganisms through fermented foods. Many of these bacteria are considered probiotics, which act through diverse mechanisms to confer a health benefit to the host. However, it was not until the availability of whole-genome sequencing and the era of genomics that mechanisms of probiotic efficacy could be discovered. In this review, we explore the history of the probiotic concept and the current standard of integrated genomic techniques to discern the complex, beneficial relationships between probiotic microbes and their hosts.
authors.affiliation: Department of Microbiology, North Carolina State University, Raleigh, NC, USA.
authors.forename: Brant R
authors.initials: BR
authors.lastname: Johnson
authors.forename: Todd R
authors.initials: TR
authors.lastname: Klaenhammer
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D035843:Biomedical Research / Q000266:history*; D016644:Canthaxanthin / Q000266:history; D023281:Genomics / Q000266:history; D049672:History, 19th Century; D049673:History, 20th Century; D049674:History, 21st Century; D006801:Humans; D019936:Probiotics / Q000737:chemistry / Q000266:history*
chemical_list: D016644:Canthaxanthin
references.citation: Nat Rev Microbiol. 2005 Oct;3(10):777-88
references.pmid: 16205711
references.citation: J Bacteriol. 2004 Dec;186(23):7829-35
references.pmid: 15547253
references.citation: Pediatrics. 2009 Aug;124(2):e172-9
references.pmid: 19651563
references.citation: J Biol Chem. 2001 Jan 19;276(3):1772-9
references.pmid: 11038353
references.citation: Nature. 1988 May 19;333(6170):276-8
references.pmid: 2835685
references.citation: Appl Environ Microbiol. 2012 Jan;78(1):1-6
references.pmid: 22038602
references.citation: Appl Environ Microbiol. 2008 Aug;74(15):4711-8
references.pmid: 18539797
references.citation: J Nutr. 2007 Mar;137(3 Suppl 2):830S-7S
references.pmid: 17311983
references.citation: Antonie Van Leeuwenhoek. 1996 Feb;69(2):193-202
references.pmid: 8775979
references.citation: Microbiology (Reading). 2005 Dec;151(Pt 12):3881-3894
references.pmid: 16339934
references.citation: Clin Vaccine Immunol. 2012 Sep;19(9):1374-81
references.pmid: 22761297
references.citation: FEMS Microbiol Rev. 2004 Oct;28(4):405-40
references.pmid: 15374659
references.citation: Microbiol Mol Biol Rev. 2008 Dec;72(4):728-64, Table of Contents
references.pmid: 19052326
references.citation: Appl Environ Microbiol. 2009 Sep;75(18):6013-6
references.pmid: 19633113
references.citation: Nat Rev Microbiol. 2010 Mar;8(3):171-84
references.pmid: 20157338
references.citation: J Gen Microbiol. 1970 Aug;62(2):223-39
references.pmid: 4321864
references.citation: J Gastroenterol Hepatol. 2003 Aug;18(8):986-91
references.pmid: 12859730
references.citation: Microb Ecol. 2012 Apr;63(3):651-73
references.pmid: 22031452
references.citation: Clin Vaccine Immunol. 2011 Nov;18(11):1834-44
references.pmid: 21900526
references.citation: Int J Syst Evol Microbiol. 2006 Dec;56(Pt 12):2783-2792
references.pmid: 17158978
references.citation: Proc Natl Acad Sci U S A. 2007 May 1;104(18):7617-21
references.pmid: 17456596
references.citation: Int J Food Microbiol. 1998 May 5;41(1):45-51
references.pmid: 9631336
references.citation: J Bacteriol. 2009 Jul;191(13):4144-51
references.pmid: 19376856
references.citation: J Med Microbiol. 2009 May;58(Pt 5):663-670
references.pmid: 19369530
references.citation: J Bacteriol. 2009 Aug;191(15):5020-1
references.pmid: 19465650
references.citation: Microbiology (Reading). 2010 Mar;156(Pt 3):603-608
references.pmid: 20093288
references.citation: J Appl Microbiol. 2006 Apr;100(4):728-38
references.pmid: 16553727
references.citation: Neurogastroenterol Motil. 2012 May;24(5):405-13
references.pmid: 22404222
references.citation: Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19474-9
references.pmid: 19047644
references.citation: Infect Immun. 1985 Jan;47(1):84-9
references.pmid: 3917428
references.citation: Infect Immun. 1985 Aug;49(2):320-4
references.pmid: 3926645
references.citation: Int Microbiol. 2004 Mar;7(1):59-62
references.pmid: 15179608
references.citation: Can Fam Physician. 2009 Feb;55(2):143-8
references.pmid: 19221071
references.citation: J Bacteriol. 2010 May;192(10):2647-8
references.pmid: 20348264
references.citation: Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11217-22
references.pmid: 21690406
references.citation: BMC Genomics. 2013 May 10;14:312
references.pmid: 23663691
references.citation: Appl Environ Microbiol. 2005 Oct;71(10):6008-13
references.pmid: 16204515
references.citation: Science. 1999 Dec 17;286(5448):2361-4
references.pmid: 10600751
references.citation: Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2371-6
references.pmid: 19190178
references.citation: Appl Environ Microbiol. 2005 Dec;71(12):8344-51
references.pmid: 16332821
references.citation: Br J Nutr. 2010 Aug;104 Suppl 2:S1-63
references.pmid: 20920376
references.citation: J Med Microbiol. 2009 Aug;58(Pt 8):996-1005
references.pmid: 19528183
references.citation: J Nutr. 2007 Mar;137(3 Suppl 2):791S-3S
references.pmid: 17311976
references.citation: FEMS Microbiol Lett. 2008 Jun;283(2):210-5
references.pmid: 18435747
references.citation: Antonie Van Leeuwenhoek. 1999 Jul-Nov;76(1-4):293-315
references.pmid: 10532385
references.citation: J Bacteriol. 2004 Sep;186(17):5721-9
references.pmid: 15317777
references.citation: Nat Rev Microbiol. 2011 Jan;9(1):27-38
references.pmid: 21113182
references.citation: Pediatr Allergy Immunol. 2005 Feb;16(1):65-71
references.pmid: 15693914
references.citation: Curr Opin Microbiol. 2013 Jun;16(3):284-92
references.pmid: 23866974
references.citation: Curr Pharm Des. 2009;15(13):1528-36
references.pmid: 19442170
references.citation: J Appl Microbiol. 2009 Jul;107(1):269-79
references.pmid: 19302300
references.citation: J Appl Microbiol. 2003;95(1):86-91
references.pmid: 12807457
references.citation: Proc Natl Acad Sci U S A. 2005 Mar 15;102(11):3906-12
references.pmid: 15671160
references.citation: Ann N Y Acad Sci. 2009 May;1165:183-9
references.pmid: 19538305
references.citation: Appl Environ Microbiol. 2012 Jul;78(14):5028-32
references.pmid: 22562992
references.citation: J Bacteriol. 1999 Nov;181(21):6670-8
references.pmid: 10542168
references.citation: FEMS Microbiol Rev. 2010 Mar;34(2):199-230
references.pmid: 20088967
references.citation: Nat Med. 2007 Jan;13(1):35-7
references.pmid: 17159985
references.citation: Antonie Van Leeuwenhoek. 2002 Aug;82(1-4):29-58
references.pmid: 12369195
references.citation: J Bacteriol. 2007 Jul;189(13):4624-34
references.pmid: 17449631
references.citation: Appl Environ Microbiol. 2002 Jan;68(1):219-26
references.pmid: 11772630
references.citation: Appl Environ Microbiol. 1996 Jun;62(6):1958-63
references.pmid: 8787394
references.citation: Gut. 2013 May;62(5):787-96
references.pmid: 23474420
references.citation: Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17193-8
references.pmid: 19805152
references.citation: Nat Rev Immunol. 2012 Oct;12(10):728-34
references.pmid: 23007572
references.citation: Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4623-30
references.pmid: 21282652
references.citation: Mol Microbiol. 2002 Oct;46(2):381-94
references.pmid: 12406216
references.citation: Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2512-7
references.pmid: 14983040
references.citation: Antonie Van Leeuwenhoek. 1996 Oct;70(2-4):113-28
references.pmid: 8879403
references.citation: Appl Environ Microbiol. 2009 May;75(10):3153-60
references.pmid: 19304838
references.citation: FEMS Microbiol Lett. 2004 Sep 15;238(2):291-5
references.pmid: 15358413
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6718-23
references.pmid: 16617113
references.citation: J Gen Microbiol. 1992 Aug;138 Pt 8:1689-96
references.pmid: 1527509
references.citation: J Clin Microbiol. 2012 Mar;50(3):1134-6
references.pmid: 22205802
references.citation: Nat Rev Microbiol. 2008 May;6(5):349-62
references.pmid: 18345021
references.citation: Appl Environ Microbiol. 2005 Oct;71(10):5794-804
references.pmid: 16204490
references.citation: Mol Microbiol. 2013 Sep;89(6):1187-200
references.pmid: 23879596
references.citation: Appl Environ Microbiol. 2011 Sep;77(18):6587-96
references.pmid: 21784918
references.citation: J Exp Med. 1915 Apr 1;21(4):365-88
references.pmid: 19867878
references.citation: Cochrane Database Syst Rev. 2011 Sep 07;(9):CD006895
references.pmid: 21901706
references.citation: Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10462-7
references.pmid: 22689992
references.citation: PLoS One. 2012;7(9):e44409
references.pmid: 23028535
references.citation: FEMS Microbiol Rev. 1993 Sep;12(1-3):39-85
references.pmid: 8398217
references.citation: Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14422-7
references.pmid: 12381787
references.citation: Ann Nutr Metab. 2009;54(1):22-7
references.pmid: 19229114
references.citation: Appl Environ Microbiol. 2008 Mar;74(6):1812-9
references.pmid: 18245259
references.citation: FEMS Microbiol Rev. 2013 Nov;37(6):915-35
references.pmid: 23488471
references.citation: BMC Genomics. 2010 Nov 23;11:651
references.pmid: 21092245
references.citation: Pediatrics. 2010 May;125(5):921-30
references.pmid: 20403939
references.citation: Aliment Pharmacol Ther. 2013 Oct;38(8):864-86
references.pmid: 23981066
references.citation: J Gen Microbiol. 1970 Aug;62(2):241-50
references.pmid: 4321865
references.citation: Nat Rev Microbiol. 2011 Nov 21;10(1):66-78
references.pmid: 22101918
references.citation: Neurogastroenterol Motil. 2011 Mar;23(3):187-92
references.pmid: 21303428
references.citation: Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4562-9
references.pmid: 20823239
references.citation: Annu Rev Food Sci Technol. 2010;1:397-414
references.pmid: 22129342
references.citation: Science. 1995 Jul 28;269(5223):496-512
references.pmid: 7542800
references.citation: Antonie Van Leeuwenhoek. 2008 Jun;94(1):35-50
references.pmid: 18338233
references.citation: Am J Gastroenterol. 2010 Jul;105(7):1636-41
references.pmid: 20145608
references.citation: Am J Clin Nutr. 2007 Feb;85(2):488-96
references.pmid: 17284748
references.citation: Am J Gastroenterol. 2011 Jan;106(1):130-8
references.pmid: 20859264
references.citation: J Med Microbiol. 2003 Oct;52(Pt 10):925-930
references.pmid: 12972590
references.citation: FEMS Microbiol Lett. 2007 Nov;276(2):140-8
references.pmid: 17888009
references.citation: Appl Environ Microbiol. 2006 Jun;72(6):4143-53
references.pmid: 16751526
references.citation: Appl Environ Microbiol. 2010 Aug;76(15):5005-12
references.pmid: 20562289
references.citation: Microbiology (Reading). 2010 Nov;156(Pt 11):3360-3367
references.pmid: 20829293
references.citation: Microbiology (Reading). 2013 Nov;159(Pt 11):2269-2282
references.pmid: 24002751
references.citation: Cell Microbiol. 2009 May;11(5):703-9
references.pmid: 19191786
references.citation: Appl Environ Microbiol. 2014 Jan;80(2):730-40
references.pmid: 24242237
references.citation: J Bacteriol. 2009 Dec;191(24):7630-1
references.pmid: 19820099
references.citation: Microbiol Immunol. 2001;45(3):259-62
references.pmid: 11345536
references.citation: Microbiology (Reading). 2007 Jan;153(Pt 1):291-9
references.pmid: 17185558
references.citation: Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9274-9
references.pmid: 16754859
references.citation: J Allergy Clin Immunol. 2005 Jun;115(6):1260-7
references.pmid: 15940144
references.citation: Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10321-6
references.pmid: 15985548
references.citation: Infect Immun. 2002 Dec;70(12):7169-71
references.pmid: 12438404
references.citation: J Clin Gastroenterol. 2011 Jul;45(6):518-25
references.pmid: 21436726