Metabolic Interactions in the Gastrointestinal Tract (GIT): Host, Commensal, Probiotics, and Bacteriophage Influences.
Life on this planet has been intricately associated with bacterial activity at all levels of evolution and bacteria represent the earliest form of autonomous existence. Plants such as those from the Leguminosae family that form root nodules while harboring nitrogen-fixing soil bacteria are a primordial example of symbiotic existence. Similarly, cooperative activities between bacteria and animals can also be observed in multiple domains, including the most inhospitable geographical regions of the planet such as Antarctica and the Lower Geyser Basin of Yellowstone National Park. In humans bacteria are often classified as either beneficial or pathogenic and in this regard we posit that this artificial nomenclature is overly simplistic and as such almost misinterprets the complex activities and inter-relationships that bacteria have with the environment as well as the human host and the plethora of biochemical activities that continue to be identified. We further suggest that in humans there are neither pathogenic nor beneficial bacteria, just bacteria embraced by those that tolerate the host and those that do not. The densest and most complex association exists in the human gastrointestinal tract, followed by the oral cavity, respiratory tract, and skin, where bacteria-pre- and post-birth-instruct the human cell in the fundamental language of molecular biology that normally leads to immunological tolerance over a lifetime. The overall effect of this complex output is the elaboration of a beneficial milieu, an environment that is of equal or greater importance than the bacterium in maintaining homeostasis.
Medlab Clinical Ltd., Sydney 2015 Australia. luis.vitetta@sydney.edu.au.|Sydney Medical School, University of Sydney, Sydney 2006, Australia. luis.vitetta@sydney.edu.au.
Luis
L
Vitetta
Medlab Clinical Ltd., Sydney 2015 Australia. sean_hall@medlab.co.
Sean
S
Hall
Medlab Clinical Ltd., Sydney 2015 Australia. samantha_coulson@medlab.co.|Sydney Medical School, University of Sydney, Sydney 2006, Australia. samantha_coulson@medlab.co.
Samantha
S
Coulson
bacteria; dysbiosis; gastrointestinal tract; metabolite signaling
Nature. 2009 Oct 29;461(7268):1282-6
19865172
Nature. 2013 Dec 19;504(7480):446-50
24226770
Gastroenterology. 2013 Jun;144(7):1394-401, 1401.e1-4
23474283
Nature. 1989 Aug 10;340(6233):467-8
2755508
Nature. 2015 Mar 5;519(7541):92-6
25731162
Hepatobiliary Surg Nutr. 2015 Aug;4(4):289-92
26312245
JAMA Surg. 2013 Jun;148(6):563-9
23571517
Science. 2015 Jul 24;349(6246):1254766
26206939
Nature. 2008 Nov 27;456(7221):507-10
18987631
Nat Med. 2014 Feb;20(2):159-66
24390308
Toxins (Basel). 2013 Nov 07;5(11):2042-57
24212182
Trends Microbiol. 2014 Jul;22(7):399-405
24656964
Free Radic Res. 2013 Nov;47(11):950-7
23937589
Gut. 1987 Oct;28(10 ):1221-7
3678950
Curr Opin Clin Nutr Metab Care. 2002 Nov;5(6):685-94
12394645
Biomarkers. 2011 Nov;16(7):537-52
22022826
Nature. 2013 Dec 19;504(7480):451-5
24226773
Clin Gastroenterol Hepatol. 2007 Mar;5(3):274-84
17368226
ISME J. 2012 May;6(5):915-26
22158393
Am J Physiol Gastrointest Liver Physiol. 2014 Jul 1;307(1):G1-15
24789206
Immunity. 2014 Jan 16;40(1):128-39
24412617
Ann Oncol. 2001;12 Suppl 2:S63-8
11762354
Curr Issues Intest Microbiol. 2007 Sep;8(2):25-43
17542334
Proc Natl Acad Sci U S A. 2011 May 10;108(19):8030-5
21518883
Nat Rev Endocrinol. 2015 Jun;11(6):319-20
25869573
Nature. 2012 Jun 13;486(7402):194-5
22699602
Int J Food Microbiol. 2010 Jul 31;141 Suppl 1:S53-9
20447709
Nature. 2012 Jun 13;486(7402):207-14
22699609
PLoS One. 2011;6(8):e23278
21858054
Nat Rev Gastroenterol Hepatol. 2013 Jun;10(6):352-61
23478383
J Appl Microbiol. 1999 Apr;86(4):615-21
10212407
Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):E1380-9
23520048
Bioessays. 2013 Oct;35(10):913-23
23946088
Infect Immun. 2015 Nov;83(11):4185-93
26259815
Clin Exp Immunol. 2008 Mar;151(3):528-35
18190603
Front Endocrinol (Lausanne). 2014 Jun 05;5:85
24926285
World J Gastroenterol. 2013 Oct 28;19(40):6911-8
24187469
Inflammopharmacology. 2014 Dec;22(6):333-9
25266952
Vet Pathol. 2015 May;52(3):445-55
25428410
FEMS Microbiol Lett. 2007 Jun;271(2):245-50
17451447
Pediatr Allergy Immunol. 2014 Aug;25(5):428-38
24899389
Mol Microbiol. 2014 May;92(3):543-56
24593252
Nat Rev Microbiol. 2013 Apr;11(4):227-38
23435359
World J Gastroenterol. 2005 Feb 28;11(8):1131-40
15754393
J Biol Chem. 2007 Jan 19;282(3):1830-7
17099249
Curr Opin Clin Nutr Metab Care. 2012 Nov;15(6):580-5
23037903
Science. 2011 May 20;332(6032):974-7
21512004
Am J Respir Cell Mol Biol. 2016 Feb;54(2):161-9
26473323
J Physiol Pharmacol. 2001 Dec;52(4 Pt 1):505-21
11787755
Microbiol Mol Biol Rev. 2000 Mar;64(1):69-114
10704475
Ann Nutr Metab. 2012;61(2):160-74
23037511
Nature. 2013 Jul 4;499(7456):97-101
23803760
Int J Med Microbiol. 2010 Jan;300(1):57-62
19783474
Gut Microbes. 2013 Jan-Feb;4(1):4-16
23022738
Science. 2011 Jan 21;331(6015):337-41
21205640
Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2058-9
24434557
Front Cell Infect Microbiol. 2014 Oct 15;4:143
25360420
Nutrients. 2015 Apr 14;7(4):2839-49
25875123
J Allergy Clin Immunol. 2013 Aug;132(2):253-62; quiz 263
23905915
Res Microbiol. 2006 Apr;157(3):241-7
16266797
J Gastrointest Surg. 2010 Mar;14 (3):449-61
20033346
Diabetes. 2012 Feb;61(2):364-71
22190648
Gut Pathog. 2013 Aug 13;5(1):23
23941657
Infect Immun. 1978 Aug;21(2):532-9
357289
Horm Mol Biol Clin Investig. 2014 Jan;17(1):53-61
25372730
Autoimmun Rev. 2016 Jan;15(1):1-8
26299984
Anim Health Res Rev. 2008 Jun;9(1):101-10
18541076
PLoS One. 2013 Nov 20;8(11):e80604
24278294
Front Med (Lausanne). 2014 Aug 25;1:24
25593900
J Bacteriol. 2004 Jun;186(12):3677-86
15175280
Gut. 2016 Apr;65(4):575-83
26511795
Nature. 2013 Aug 8;500(7461):232-6
23842501
Microbiology. 2013 Feb;159(Pt 2):402-10
23397453
FEBS Lett. 2012 May 21;586(10):1547-54
22673524
Nature. 2010 Jul 15;466(7304):334-8
20631792
Cell. 2008 May 30;133(5):775-87
18510923
J Biol Chem. 2003 Jul 11;278(28):25481-9
12711604
Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):228-33
19966295
Nat Immunol. 2013 Jul;14(7):685-90
23778796
J Clin Invest. 2014 Oct;124(10):4162-5
25271724
Curr Protoc Immunol. 2015 Apr 01;109:14.12.1-10
25845562
Pharmaceuticals (Basel). 2014 Sep 19;7(9):954-89
25244509
Cell. 2005 Jul 15;122(1):107-18
16009137
FEMS Microbiol Rev. 1992 Jun;8(3-4):165-80
1515159
Cell Metab. 2011 May 4;13(5):517-26
21531334
Nat Immunol. 2013 Jul;14(7):676-84
23778795
Nat Med. 2013 May;19(5):576-85
23563705
ISME J. 2013 Mar;7(3):615-21
23151642
Prog Brain Res. 2000;122:159-72
10737056
Trends Genet. 2013 Jan;29(1):51-8
23140990
Mucosal Immunol. 2010 May;3(3):247-59
20404811
Annu Rev Med. 1990;41:447-55
2184742
Cell Host Microbe. 2008 Oct 16;4(4):337-49
18854238
Nephrology (Carlton). 2016 Mar;21(3):170-7
26239363
Mol Nutr Food Res. 2013 May;57(5):824-32
23450842
Dis Mon. 2015 Jul;61(7):259-90
25921792
Viruses. 2013 Mar 11;5(3):806-23
23478639
Curr Opin Microbiol. 2013 Jun;16(3):246-54
23880135
Res Microbiol. 2008 Jun;159(5):367-73
18541415
Cell. 2014 Jan 16;156(1-2):84-96
24412651
Exp Mol Med. 2014 Dec 19;46:e127
25523099
FEMS Microbiol Rev. 2004 May;28(2):127-81
15109783
Nature. 2011 Jan 27;469(7331):543-7
21270894
Curr Opin Infect Dis. 2009 Jun;22(3):292-301
19352175
Nat Chem Biol. 2014 Jun;10(6):416-24
24838170
Mucosal Immunol. 2009 Mar;2(2):166-72
19129752
Sci Transl Med. 2012 Jun 6;4(137):137rv7
22674557
Probiotics Antimicrob Proteins. 2015 Sep;7(3):222-31
26093857
Immunol Rev. 2014 May;259(1):60-74
24712459
Int J Food Microbiol. 2014 Mar 3;173:30-5
24412414
Trends Pharmacol Sci. 2009 Nov;30(11):557-62
19837462