Potential effects of horizontal gene exchange in the human gut

Frontiers in Immunology

Volumn 8, Issue NOV, 2017, Pages

  Lerner, Aaron ^a,b   Matthias, Torsten ^b   Aminov, Rustam ^c,d  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b Mikroforum Ring   (Germany)

^c KAZAN FEDERAL UNIVERSITY   (Russian Federation)

^d UNIVERSITY OF ABERDEEN   (United Kingdom)

Author keywords

Biofilm; Dysbiome; Environment; Gut; Horizontal gene transfer; Intestine; Microbiome; Probiotics

Indexed keywords

PROBIOTIC AGENT;

ALPHAPROTEOBACTERIA; ANTIBIOTIC RESISTANCE; ARTICLE; AUTOIMMUNE DISEASE; BACTERIUM CONJUGATION; ESCHERICHIA COLI; GENETIC TRANSDUCTION; GENETIC TRANSFORMATION; HORIZONTAL GENE TRANSFER; HUMAN; INTESTINE FLORA; LACTOBACILLUS DELBRUECKII; LIVESTOCK; NONHUMAN; SALMONELLA; TETRAHYMENA PYRIFORMIS;

EID: 85035020911     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2017.01630     Document Type: Article

References (182)

1. Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, et al. Toward a predictive understanding of earth's microbiomes to address 21st century challenges. mBio (2016) 7:e714-6. doi:10.1128/mBio.00714-16
2. Juhas M. Horizontal gene transfer in human pathogens. Crit Rev Microbiol (2015) 41:101-8. doi:10.3109/1040841X.2013.804031
3. Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet (2012) 13:260-70. doi:10.1038/nrg3182
4. Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, et al. A higher level classification of all living organisms. PLoS One (2015) 10:e0119248. doi:10.1371/journal.pone.0119248
5. Aminov RI. Horizontal gene exchange in environmental microbiota. Front Microbiol (2011) 2:158. doi:10.3389/fmicb.2011.00158
6. Aminov RI. The extent and regulation of lateral gene transfer in natural microbial ecosystems. In: Francino MP, editor. Horizontal Gene Transfer in Microorganisms. (Chap. 6), Norwich, UK: Horizon Scientific Press (2012). p. 93-100
7. Hotopp JCD. Horizontal gene transfer between bacteria and animals. Trends in Genetics (2011) 27:157-63. doi:10.1016/j.tig.2011.01.005
8. Robinson KM, Sieber KB, Hotopp JCD. A review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer. PLoS Genet (2013) 9:e1003877. doi:10.1371/journal.pgen.1003877
9. Gyles C, Boerlin P. Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease. Vet Pathol (2014) 51:328-40. doi:10.1177/0300985813511131
10. Yue J, Hu X, Sun H, Yang Y, Huang J. Widespread impact of horizontal gene transfer on plant colonization of land. Nat Commun (2012) 3:1152. doi:10.1038/ncomms2148
11. Yang Z, Liu L, Fang H, Li P, Xu S, Cao W, et al. Origin of the plant Tm-1-like gene via two independent horizontal transfer events and one gene fusion event. Sci Rep (2016) 6:33691. doi:10.1038/srep33691
12. Durzynska J, Gozdzicka-Józefiak A. Viruses and cells intertwined since the dawn of evolution. Virol J (2015) 12:169. doi:10.1186/s12985-015-0400-7
13. Caetano-Anollés G, Nasir A, Zhou K, Caetano-Anollés D, Mittenthal JE, Sun FJ, et al. Archaea: the first domain of diversified life. Archaea (2014) 2014:590214. doi:10.1155/2014/590214
14. Qiu H, Cai G, Luo J, Bhattacharya D, Zhang N. Extensive horizontal gene transfers between plant pathogenic fungi. BMC Biol (2016) 14:41. doi:10.1186/s12915-016-0264-3
15. Fitzpatrick DA. Horizontal gene transfer in fungi. FEMS Microbiol Lett (2012) 329:1-8. doi:10.1111/j.1574-6968.2011.02465.x
16. Gladyshev EA, Meselson M, Arkhipova IR. Massive horizontal gene transfer in bdelloid rotifers. Science (2008) 2008(320):1210-3. doi:10.1126/science.1156407
17. Koonin EV. Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions. F1000Res (2016) 5:1805. doi:10.12688/f1000research.8737.1
18. Aminov RI. A brief history of the antibiotic era: lessons learned and challenges for the future. Front Microbiol (2010) 1:134. doi:10.3389/fmicb.2010.00134
19. Treangen TJ, Rocha EP. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet (2011) 7:e1001284. doi:10.1371/journal.pgen.1001284
20. McDaniel LD, Young E, Delaney J, Ruhnau F, Ritchie KB, Paul JH. High frequency of horizontal gene transfer in the oceans. Science (2010) 330:50. doi:10.1126/science.1192243
21. Panaud O. Horizontal transfers of transposable elements in eukaryotes: the flying genes. C R Biol (2016) 339:296-9. doi:10.1016/j.crvi.2016.04.013
22. Schroeder M, Brooks BD, Brooks AE. The complex relationship between virulence and antibiotic resistance. Genes (Basel) (2017) 8:E39. doi:10.3390/genes8010039
23. Babic A, Berkmen MB, Lee CA, Grossman AD. Efficient gene transfer in bacterial cell chains. MBio (2011) 2:e27-11. doi:10.1128/mBio.00027-11
24. Lopatkin AJ, Huang S, Smith RP, Srimani JK, Sysoeva TA, Bewick S, et al. Antibiotics as a selective driver for conjugation dynamics. Nat Microbiol (2016) 1:16044. doi:10.1038/nmicrobiol.2016.44
25. Crisp A, Boschetti C, Perry M, Tunnacliffe A, Micklem G. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. Genome Biol (2015) 16:50. doi:10.1186/s13059-015-0607-3
26. Lurie-Weinberger MN, Peeri M, Gophna U. Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen. Genomics (2012) 2012(99):52-8. doi:10.1016/j.ygeno.2011.10.005
27. Gielda LM, DiRita VJ. Zinc competition among the intestinal microbiota. mBio (2012) 3(4):171-12. doi:10.1128/mBio.00171-12
28. Hansen EE, Lozupone CA, Rey FE, Wu M, Guruge JL, Narra A, et al. Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proc Natl Acad Sci U S A (2011) 108(Suppl 1):4599-606. doi:10.1073/pnas.1000071108
29. Zaneveld JR, Lozupone C, Gordon JI, Knight R. Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives. Nucleic Acids Res (2010) 38:3869-79. doi:10.1093/nar/gkq066
30. Shterzer N, Mizrahi I. The animal gut as a melting pot for horizontal gene transfer. Can J Microbiol (2015) 61:603-5. doi:10.1139/cjm-2015-0049
31. Liu L, Chen X, Skogerbø G, Zhang P, Chen R, He S, et al. The human microbiome: a hot spot of microbial horizontal gene transfer. Genomics (2012) 100:265-70. doi:10.1016/j.ygeno.2012.07.012
32. Coyne MJ, Zitomersky NL, McGuire AM, Earl AM, Comstock LE. Evidence of extensive DNA transfer between bacteroidales species within the human gut. MBio (2014) 5:e1305-14. doi:10.1128/mBio.01305-14
33. Ma H, Bryers JD. Non-invasive determination of conjugative transfer of plasmids bearing antibiotic-resistance genes in biofilm-bound bacteria: effects of substrate loading and antibiotic selection. Appl Microbiol Biotechnol (2013) 97:317-28. doi:10.1007/s00253-012-4179-9
34. Yosef I, Manor M, Qimron U. Counteracting selection for antibiotic-resistant bacteria. Bacteriophage (2016) 6:e1096996. doi:10.1080/21597081.2015.1096996
35. Long H, Miller SF, Strauss C, Zhao C, Cheng L, Ye Z, et al. Antibiotic treatment enhances the genome-wide mutation rate of target cells. Proc Natl Acad Sci U S A (2016) 113:E2498-505. doi:10.1073/pnas.1601208113
36. Koike S, Mackie R, Aminov R. Agricultural use of antibiotics and antibiotic resistance. In: Mirete S, Pérez ML, editors. Antibiotic Resistance Genes in Natural Environments and Long-Term Effects. (Chap. 8), Hauppauge, NY: Nova Science Publishers. Inc (2017). p. 217-50
37. Salyers AA, Gupta A, Wang Y. Human intestinal bacteria as reservoirs for antibiotic resistance genes. Trends Microbiol (2004) 12:412-6. doi:10.1016/j.tim.2004.07.004
38. Schjørring S, Krogfel KA. Assessment of bacterial antibiotic resistance transfer in the gut. Int J Microbiol (2011) 2011:312956. doi:10.1155/2011/312956
39. Huddleston JR. Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes. Infect Drug Resist (2014) 7:167-76. doi:10.2147/IDR.S48820
40. Francino MP. Antibiotics and the human gut microbiome: dysbioses and accumulation of resistances. Front Microbiol (2016) 6:1543. doi:10.3389/fmicb.2015.01543
41. Kazimierczak KA, Scott KP, Kelly D, Aminov RI. Tetracycline resistome of the organic pig gut. Appl Environ Microbiol (2009) 75:1717-22. doi:10.1128/AEM.02206-08
42. van Schaik W. The human gut resistome. Philos Trans R Soc Lond B Biol Sci (2015) 370:20140087. doi:10.1098/rstb.2014.0087
43. Perry JA, Wright GD. The antibiotic resistance 'mobilome': searching for the link between environment and clinic. Front Microbiol (2013) 4:138. doi:10.3389/fmicb.2013.00138
44. Gosalbes MJ, Vallès Y, Jiménez-Hernández N, Balle C, Riva P, Miravet-Verde S, et al. High frequencies of antibiotic resistance genes in infants' meconium and early fecal samples. J Dev Orig Health Dis (2016) 7:35-44. doi:10.1017/S2040174415001506
45. Aminov RI, Mackie RI. Evolution and ecology of antibiotic resistance genes. FEMS Microbiol Lett (2007) 271:147-61. doi:10.1111/j.1574-6968.2007.00757.x
46. Aminov RI. The role of antibiotics and antibiotic resistance in nature. Environ Microbiol (2009) 11:2970-88. doi:10.1111/j.1462-2920.2009.01972.x
47. Verraes C, Van Boxstael S, Van Meervenne E, Van Coillie E, Butaye P, Catry B, et al. Antimicrobial resistance in the food chain: a review. Int J Environ Res Public Health (2013) 10:2643-69. doi:10.3390/ijerph10072643
48. Flórez AB, Campedelli I, Delgado S, Alegría á, Salvetti E, Felis GE, et al. Antibiotic susceptibility profiles of dairy Leuconostoc, analysis of the genetic basis of atypical resistances and transfer of genes in vitro and in a food matrix. PLoS One (2016) 11:e0145203. doi:10.1371/journal.pone.0145203
49. Hu Y, Yang X, Li J, Lv N, Liu F, Wu J, et al. The bacterial mobile resistome transfer network connecting the animal and human microbiomes. Appl Environ Microbiol (2016) 82:6672-81. doi:10.1128/AEM.01802-16
50. Aviv G, Rahav G, Gal-Mor O. Horizontal transfer of the Salmonella enterica serovar infantis resistance and virulence plasmid pESI to the gut microbiota of warm-blooded hosts. MBio (2016) 7:e1395-1316. doi:10.1128/mBio.01395-16
51. Frye JG, Lindsey RL, Meinersmann RJ, Berrang ME, Jackson CR, Englen MD, et al. Related antimicrobial resistance genes detected in different bacterial species co-isolated from swine fecal samples. Foodborne Pathog Dis (2011) 8:663-79. doi:10.1089/fpd.2010.0695
52. Barondess JJ, Beckwith J. A bacterial virulence determinant encoded by lysogenic coliphage lambda. Nature (1990) 346:871-4. doi:10.1038/346871a0
53. Brabban AD, Hite E, Callaway TR. Evolution of foodborne pathogens via temperate bacteriophage-mediated gene transfer. Foodborne Pathog Dis (2005) 2:287-303. doi:10.1089/fpd.2005.2.287
54. Broaders E, Gahan CG, Marchesi JR. Mobile genetic elements of the human gastrointestinal tract: potential for spread of antibiotic resistance genes. Gut Microbes (2013) 4:271-80. doi:10.4161/gmic.24627
55. Jiang X, Ellabaan MMH, Charusanti P, Munck C, Blin K, Tong Y, et al. Dissemination of antibiotic resistance genes from antibiotic producers to pathogens. Nat Commun (2017) 8:15784. doi:10.1038/ncomms15784
56. Johnsen PJ, Simonsen GS, Olsvik O, Midtvedt T, Sundsfjord A. Stability, persistence, and evolution of plasmid-encoded VanA glycopeptide resistance in enterococci in the absence of antibiotic selection in vitro and in gnotobiotic mice. Microb Drug Resist (2002) 8:161-70. doi:10.1089/107662902760326869
57. Dahl KH, Mater DD, Flores MJ, Johnsen PJ, Midtvedt T, Corthier G, et al. Transfer of plasmid and chromosomal glycopeptide resistance determinants occurs more readily in the digestive tract of mice than in vitro and exconjugants can persist stably in vivo in the absence of glycopeptide selection. J Antimicrob Chemother (2007) 59:478-86. doi:10.1093/jac/dkl530
58. Thimm T, Hoffmann A, Fritz I, Tebbe CC. Contribution of the earthworm Lumbricus rubellus (Annelida, Oligochaeta) to the establishment of plasmids in soil bacterial communities. Microb Ecol (2001) 41:341-51. doi:10.1007/s002480000115
59. Matsuo J, Oguri S, Nakamura S, Hanawa T, Fukumoto T, Hayashi Y, et al. Ciliates rapidly enhance the frequency of conjugation between Escherichia coli strains through bacterial accumulation in vesicles. Res Microbiol (2010) 161:711-9. doi:10.1016/j.resmic.2010.07.004
60. Oguri S, Matsuo J, Hayashi Y, Nakamura S, Hanawa T, Fukumoto T, et al. Ciliates promote the transfer of the gene encoding the extended-spectrum ß-lactamase CTX-M-27 between Escherichia coli strains. J Antimicrob Chemother (2011) 66:527-30. doi:10.1093/jac/dkq487
61. Poole T, Crippen T. Conjugative plasmid transfer between Salmonella enterica NEWPORT and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle, Alphitobius diaperinus (Coleoptera: Tenebrionidae). Poult Sci (2009) 88:1553-8. doi:10.3382/ps.2008-00553
62. Dionisio F, Matic I, Radman M, Rodrigues OR, Taddei F. Plasmids spread very fast in heterogeneous bacterial communities. Genetics (2002) 162:1525-32
63. Sperandio V, Torres AG, Jarvis B, Nataro JP, Kaper JB. Bacteria-host communication: the language of hormones. Proc Natl Acad Sci U S A (2003) 100:8951-6. doi:10.1073/pnas.1537100100
64. Clarke MB, Hughes DT, Zhu C, Boedeker EC, Sperandio V. The QseC sensor kinase: a bacterial adrenergic receptor. Proc Natl Acad Sci U S A (2006) 103:10420-5. doi:10.1073/pnas.0604343103
65. Karavolos MH, Spencer H, Bulmer DM, Thompson A, Winzer K, Williams P, et al. Adrenaline modulates the global transcriptional profile of Salmonella revealing a role in the antimicrobial peptide and oxidative stress resistance responses. BMC Genomics (2008) 9:458. doi:10.1186/1471-2164-9-458
66. Spencer H, Karavolos MH, Bulmer DM, Aldridge P, Chhabra SR, Winzer K, et al. Genome-wide transposon mutagenesis identifies a role for host neuroendocrine stress hormones in regulating the expression of virulence genes in Salmonella. J Bacteriol (2010) 192:714-24. doi:10.1128/JB.01329-09
67. Peterson G, Kumar A, Gart E, Narayanan S. Catecholamines increase conjugative gene transfer between enteric bacteria. Microb Pathog (2011) 51:1-8. doi:10.1016/j.micpath.2011.03.002
68. Patterson AM, Mulder IE, Travis AJ, Lan A, Cerf-Bensussan N, Gaboriau-Routhiau V, et al. Human gut symbiont Roseburia hominis promotes and regulates innate immunity. Front Immunol (2017) 8:1166. doi:10.3389/fimmu.2017.01166
69. Aggarwala V, Liang G, Bushman FD. Viral communities of the human gut: metagenomic analysis of composition and dynamics. Mob DNA (2017) 8:12. doi:10.1186/s13100-017-0095-y
70. Costerton JW, Cheng KJ, Geesey GG, Ladd TI, Nickel JC, Dasgupta M, et al. Bacterial biofilms in nature and disease. Annu Rev Microbiol (1987) 41:435-64. doi:10.1146/annurev.mi.41.100187.002251
71. Watters C, Fleming D, Bishop D, Rumbaugh KP. Host responses to biofilm. Prog Mol Biol Transl Sci (2016) 142:193-239. doi:10.1016/bs.pmbts.2016.05.007
72. Lerner A, Aminov R, Matthias T. Dysbiosis may trigger autoimmune diseases via inappropriate posttranslational modification of host proteins. Front Microbiol (2016) 7:84. doi:10.3389/fmicb.2016.00084
73. Lerner A, Aminov R, Matthias T. Intestinal dysbiotic transglutaminases are potential environmental drivers of systemic autoimmunogenesis. Front Microbiol (2017) 8:66. doi:10.3389/fmicb.2017.00066
74. Bollinger RR, Everett ML, Palestrant D, Love SD, Lin SS, Parker W. Human secretory immunoglobulin A may contribute to biofilm formation in the gut. Immunology (2003) 109:580-7. doi:10.1046/j.1365-2567.2003.01700.x
75. Rakoff-Nahoum S, Foster KR, Comstock LE. The evolution of cooperation within the gut microbiota. Nature (2016) 533:255-9. doi:10.1038/nature17626
76. MetchnikoffE. In: Chalmers Mitchell P, editor. Essais Optimistes. The Prolongation of Life. Optimistic Studies. Paris/London: Heinemann (1907). 1907 p
77. Transparency Market Research. Probiotics Market (Dietary Supplements, Animal Feed, Foods & Beverages)-Global Industry Size, Share, Trends, Analysis, Growth and Forecast 2012-2018. (2013). Available from: http://www.transparencymarketresearch.com/probiotics-market.html
78. Lilly DM, Stillwell RH. Probiotics: growth-promoting factors produced by microorganisms. Science (1965) 147:747-8. doi:10.1126/science.147.3659.747
79. Fuller R. Probiotics in man and animals. J Appl Bacteriol (1989) 66:365-78. doi:10.1111/j.1365-2672.1989.tb05105.x
80. Wong A, Ngu DY, Dan LA, Ooi A, Lim RL. Detection of antibiotic resistance in probiotics of dietary supplements. Nutr J (2015) 14:95. doi:10.1186/s12937-015-0084-2
81. Zheng M, Zhang R, Tian X, Zhou X, Pan X, Wong A. Assessing the risk of probiotic dietary supplements in the context of antibiotic resistance. Front Microbiol (2017) 8:908. doi:10.3389/fmicb.2017.00908
82. van Reenen CA, Dicks LM. Horizontal gene transfer amongst probiotic lactic acid bacteria and other intestinal microbiota: what are the possibilities? A review. Arch Microbiol (2011) 193:157-68. doi:10.1007/s00203-010-0668-3
83. Ceapa C, Davids M, Ritari J, Lambert J, Wels M, Douillard FP, et al. The variable regions of Lactobacillus rhamnosus genomes reveal the dynamic evolution of metabolic and host-adaptation repertoires. Genome Biol Evol (2016) 8:1889-905. doi:10.1093/gbe/evw123
84. Baugher JL, Durmaz E, Klaenhammer TR. Spontaneously induced prophages in Lactobacillus gasseri contribute to horizontal gene transfer. Appl Environ Microbiol (2014) 80:3508-17. doi:10.1128/AEM.04092-13
85. Mercanti DJ, Rousseau GM, Capra ML, Quiberoni A, Tremblay DM, Labrie SJ, et al. Genomic diversity of phages infecting probiotic strains of Lactobacillus paracasei. Appl Environ Microbiol (2015) 82:95-105. doi:10.1128/AEM.02723-15
86. Tannock GW, Luchansky JB, Miller L, Connell H, Thode-Andersen S, Mercer AA, et al. Molecular characterization of a plasmid-borne (pGT633) erythromycin resistance determinant (ermGT) from Lactobacillus reuteri 100-63. Plasmid (1994) 31:60-71. doi:10.1006/plas.1994.1007
87. Lin CF, Fung ZF, Wu CL, Chung TC. Molecular characterization of a plasmid-borne (pTC82) chloramphenicol resistance determinant (cat-TC) from Lactobacillus reuteri G4. Plasmid (1996) 36:116-24. doi:10.1006/plas.1996.0039
88. Egervärn M, Roos S, Lindmark H. Identification and characterization of antibiotic resistance genes in Lactobacillus reuteri and Lactobacillus plantarum. J Appl Microbiol (2009) 107:1658-68. doi:10.1111/j.1365-2672.2009.04352.x
89. Courvalin P. Predictable and unpredictable evolution of antibiotic resistance. J Intern Med (2008) 264:4-16. doi:10.1111/j.1365-2796.2008.01940.x
90. Doron S, Snydman DR. Risk and safety of probiotics. Clin Infect Dis (2015) 60(Suppl 2):S129-34. doi:10.1093/cid/civ085
91. Dessart SR, Steenson LR. High frequency intergeneric and intrageneric transfer conjugal transfer of drug resistance plasmids in Leuconostoc mesenteroides ssp. cremoris. J Dairy Sci (1991) 74:2912-9. doi:10.3168/jds. S0022-0302(91)78474-9
92. Morelli L, Sarra PG, Bottazzi V. In vivo transfer of pAM beta 1 from Lactobacillus reuteri to Enterococcus faecalis. J Appl Bacteriol (1988) 65:371-5. doi:10.1111/j.1365-2672.1988.tb01905.x
93. Kristensen NB, Bryrup T, Allin KH, Nielsen T, Hansen TH, Pedersen O. Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials. Genome Med (2016) 8:52. doi:10.1186/s13073-016-0300-5
94. Egervärn M, Lindmark H, Olsson J, Roos S. Transferability of a tetracycline resistance gene from probiotic Lactobacillus reuteri to bacteria in the gastrointestinal tract of humans. Antonie Van Leeuwenhoek (2010) 97:189-200. doi:10.1007/s10482-009-9401-0
95. Rosander A, Connolly E, Roos S. Removal of antibiotic resistance gene-carrying plasmids from Lactobacillus reuteri ATCC 55730 and characterization of the resulting daughter strain, L. reuteri DSM 17938. Appl Environ Microbiol (2008) 74:6032-40. doi:10.1128/AEM.00991-08
96. Duranti S, Lugli GA, Mancabelli L, Turroni F, Milani C, Mangifesta M, et al. Prevalence of antibiotic resistance genes among human gut-derived bifidobacteria. Appl Environ Microbiol (2017) 83:e2894-2816. doi:10.1128/AEM.02894-16
97. Fittipaldi N, Segura M, Grenier D, Gottschalk M. Virulence factors involved in the pathogenesis of the infection caused by the swine pathogen and zoonotic agent Streptococcus suis. Future Microbiol (2012) 7:259-79. doi:10.2217/fmb.11.149
98. Lerner A, Matthias T. Changes in intestinal tight junction permeability associated with industrial food additives explain the rising incidence of autoimmune disease. Autoimmun Rev (2015) 14:479-89. doi:10.1016/j.autrev.2015.01.009
99. Lerner A, Matthias T. Possible association between celiac disease and bacterial transglutaminase in food processing: a hypothesis. Nutr Rev (2015) 73:544-52. doi:10.1093/nutrit/nuv011
100. Matthias T, Jeremias P, Neidhöfer S, Lerner A. The industrial food additive microbial transglutaminase, mimics the tissue transglutaminase and is immunogenic in celiac disease patients. Autoimmun Rev (2016) 15:1111-9. doi:10.1016/j.autrev.2016.09.011
101. Yu J, Pian Y, Ge J, Guo J, Zheng Y, Jiang H, et al. Functional and structural characterization of the antiphagocytic properties of a novel transglutaminase from Streptococcus suis. J Biol Chem (2015) 290:19081-92. doi:10.1074/jbc. M115.643338
102. Imperial IC, Ibana JA. Addressing the antibiotic resistance problem with probiotics: reducing the risk of its double-edged sword effect. Front Microbiol (2016) 7:1983. doi:10.3389/fmicb.2016.01983
103. Gueimonde M, Sánchez B, G de Los Reyes-Gavilán C, Margolles A. Antibiotic resistance in probiotic bacteria. Front Microbiol (2013) 4:202. doi:10.3389/fmicb.2013.00202
104. Drago L, Mattina R, De Vecchi E, Toscano M. Phenotypic and genotypic antibiotic resistance in some probiotics proposed for medical use. Int J Antimicrob Agents (2013) 41:396-7. doi:10.1016/j.ijantimicag.2012.11.015
105. Jennings JC, Kolwyck DC, Kays SB, Whetsell AJ, Surber JB, Cromwell GL, et al. Determining whether transgenic and endogenous plant DNA and transgenic protein are detectable in muscle from swine fed Roundup Ready soybean meal. J Anim Sci (2003) 81:1447-55. doi:10.2527/2003.8161447x
106. Netherwood T, Martín-Orúe SM, O'Donnell AG, Gockling S, Graham J, Mathers JC, et al. Assessing the survival of transgenic plant DNA in the human gastrointestinal tract. Nat Biotechnol (2004) 22:204-9. doi:10.1038/nbt934
107. Zhu Y, Li D, Wang F, Yin J, Jin H. Nutritional assessment and fate of DNA of soybean meal from roundup ready or conventional soybeans using rats. Arch Anim Nutr (2004) 58:295-310. doi:10.1080/00039420412331273277
108. Phipps RH, Jones AK, Tingey AP, Abeyasekera S. Effect of corn silage from an herbicide-tolerant genetically modified variety on milk production and absence of transgenic DNA in milk. J Dairy Sci (2005) 88:2870-8. doi:10.3168/jds. S0022-0302(05)72968-4
109. Wilcks A, Jacobsen BB. Lack of detectable DNA uptake by transformation of selected recipients in mono-associated rats. BMC Res Notes (2010) 3:49. doi:10.1186/1756-0500-3-49
110. Deni J, Message B, Chioccioli M, Tepfer D. Unsuccessful search for DNA transfer from transgenic plants to bacteria in the intestine of the tobacco horn worm, Manduca sexta. Transgenic Res (2005) 14:207-15. doi:10.1007/s11248-004-6701-z
111. Mohr KI, Tebbe CC. Field study results on the probability and risk of a horizontal gene transfer from transgenic herbicide-resistant oilseed rape pollen to gut bacteria of bees. Appl Microbiol Biotechnol (2007) 75:573-82. doi:10.1007/s00253-007-0846-7
112. Wang HH, Manuzon M, Lehman M, Wan K, Luo H, Wittum TE, et al. Food commensal microbes as a potentially important avenue in transmitting antibiotic resistance genes. FEMS Microbiol Lett (2006) 254:226-31. doi:10.1111/j.1574-6968.2005.00030.x
113. Flórez AB, Ammor MS, Mayo B. Identification of tet(M) in two Lactococcus lactis strains isolated from a Spanish traditional starter-free cheese made of raw milk and conjugative transfer of tetracycline resistance to lactococci and enterococci. Int J Food Microbiol (2008) 121:189-94. doi:10.1016/j.ijfoodmicro.2007.11.029
114. Bernardeau M, Vernoux JP, Henri-Dubernet S, Guéguen M. Safety assessment of dairy microorganisms: the Lactobacillus genus. Int J Food Microbiol (2008) 126:278-85. doi:10.1016/j.ijfoodmicro.2007.08.015
115. Börjesson S, Ny S, Egervärn M, Bergström J, Rosengren Å, Englund S, et al. Limited dissemination of extended-spectrum ß-lactamase-and plasmid-encoded Ampc-producing Escherichia coli from food and farm animals, Sweden. Emerg Infect Dis (2016) 22:634-40. doi:10.3201/eid2204.151142
116. Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science (2011) 332:970-4. doi:10.1126/science.1198719
117. Ewers C, Bethe A, Semmler T, Guenther S, Wieler LH. Extended-spectrum ß-lactamase-producing and AmpC-producing Escherichia coli from livestock and companion animals, and their putative impact on public health: a global perspective. Clin Microbiol Infect (2012) 18:646-55. doi:10.1111/j.1469-0691.2012.03850.x
118. Guenther S, Wuttke J, Bethe A, Vojtech J, Schaufler K, Semmler T, et al. Is fecal carriage of extended-spectrum-ß-lactamase-producing Escherichia coli in urban rats a risk for public health? Antimicrob Agents Chemother (2013) 57:2424-5. doi:10.1128/AAC.02321-12
119. Dierikx C, van der Goot J, Fabri T, van Essen-Zandbergen A, Smith H, Mevius D. Extended-spectrum-ß-lactamase-and AmpC-ß-lactamase-producing Escherichia coli in Dutch broilers and broiler farmers. J Antimicrob Chemother (2013) 68:60-7. doi:10.1093/jac/dks349
120. Ljungquist O, Ljungquist D, Myrenås M, Rydén C, Finn M, Bengtsson B. Evidence of household transfer of ESBL-/pAmpC-producing Enterobacteriaceae between humans and dogs-a pilot study. Infect Ecol Epidemiol (2016) 6:31514. doi:10.3402/iee.v6.31514
121. Ewers C, Grobbel M, Bethe A, Wieler LH, Guenther S. Extended-spectrum beta-lactamases-producing gram-negative bacteria in companion animals: action is clearly warranted! Berl Munch Tierarztl Wochenschr (2011) 124:94-101
122. Lazarus B, Paterson DL, Mollinger JL, Rogers BA. Do human extraintestinal Escherichia coli infections resistant to expanded-spectrum cephalosporins originate from food-producing animals? A systematic review. Clin Infect Dis (2015) 60:439-52. doi:10.1093/cid/ciu785
123. Ciechonska M, Grob A, Isalan M. From noise to synthetic nucleoli: can synthetic biology achieve new insights? Integr Biol (Camb) (2016) 8:383-93. doi:10.1039/c5ib00271k
124. Piñero-Lambea C, Ruano-Gallego D, Fernández Lá. Engineered bacteria as therapeutic agents. Curr Opin Biotechnol (2015) 35:94-102. doi:10.1016/j.copbio.2015.05.004
125. Escoll P, Mondino S, Rolando M, Buchrieser C. Targeting of host organelles by pathogenic bacteria: a sophisticated subversion strategy. Nat Rev Microbiol (2016) 14:5-19. doi:10.1038/nrmicro.2015.1
126. Moos WH, Faller DV, Harpp DN, Kanara I, Pernokas J, Powers WR, et al. Microbiota and neurological disorders: a gut feeling. Biores Open Access (2016) 5:137-45. doi:10.1089/biores.2016.0010
127. Holmgren L. Horizontal gene transfer: you are what you eat. Biochem Biophys Res Commun (2010) 396:147-51. doi:10.1016/j.bbrc.2010.04.026
128. Eisenstein M. Living factories of the future. Nature (2016) 531:401-3. doi:10.1038/531401a
129. Garber K. Drugging the gut microbiome. Nat Biotechnol (2015) 33:228-31. doi:10.1038/nbt.3161
130. Madhusoodanan J. Viral soldiers. Scientist (2016) 30:27-33
131. Abedon ST, García P, Mullany P, Aminov R. Editorial: phage therapy: past, present and future. Front Microbiol (2017) 8:981. doi:10.3389/fmicb.2017.00981
132. Haegeman A, Jones JT, Danchin EG. Horizontal gene transfer in nematodes: a catalyst for plant parasitism? Mol Plant Microbe Interact (2011) 24:879-87. doi:10.1094/MPMI-03-11-0055
133. Danchin EGJ, Guzeeva EA, Mantelin S, Berepiki A, Jones JT. Horizontal gene transfer from bacteria has enabled the plant-parasitic nematode Globodera pallida to feed on host-derived sucrose. Mol Biol Evol (2016) 33:1571-9. doi:10.1093/molbev/msw041
134. Wybouw N, Pauchet Y, Heckel DG, Leeuwen TV. Horizontal gene transfer contributes to the evolution of arthropod herbivory. Genome Biol Evol (2016) 8:1785-801. doi:10.1093/gbe/evw119
135. Boto L. Horizontal gene transfer in the acquisition of novel traits by metazoans. Proc Biol Sci (2014) 281:20132450. doi:10.1098/rspb.2013.2450
136. Ivancevic AM, Walsh AM, Kortschak RD, Adelson DL. Jumping the fine LINE between species: horizontal transfer of transposable elements in animals catalyses genome evolution. Bioessays (2013) 35:1071-82. doi:10.1002/bies.201300072
137. Huang W, Tsai L, Li Y, Hua N, Sun C, Wei C. Widespread of horizontal gene transfer in the human genome. BMC Genomics (2017) 18:274. doi:10.1186/s12864-017-3649-y
138. McCarthy CG, Fitzpatrick DA. Systematic search for evidence of interdomain horizontal gene transfer from prokaryotes to oomycete lineages. mSphere (2016) 1:e195-116. doi:10.1128/mSphere.00195-16
139. Huang J. Horizontal gene transfer in eukaryotes: the weak-link model. Bioessays (2013) 35:868-75. doi:10.1002/bies.201300007
140. Salzberg SL, White O, Peterson J, Eisen JA. Microbial genes in the human genome: lateral transfer or gene loss? Science (2001) 292:1903-6. doi:10.1126/science.1061036
141. Salzberg SL. Horizontal gene transfer is not a hallmark of the human genome. Genome Biol (2017) 18:85. doi:10.1186/s13059-017-1214-2
142. Stanhope MJ, Lupas A, Italia MJ, Koretke KK, Volker C, Brown JR. Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature (2001) 411:940-4. doi:10.1038/35082058
143. Genereux DP, Logsdon JM Jr. Much ado about bacteria-to-vertebrate lateral gene transfer. Trends Genet (2003) 19:191-5. doi:10.1016/S0168-9525(03)00055-6
144. Dupont PY, Cox MP. Genomic data quality impacts automated detection of lateral gene transfer in fungi. G3 (Bethesda) (2017) 7:1301-14. doi:10.1534/g3.116.038448
145. Willerslev E, Mourier T, Hansen AJ, Christensen B, Barnes I, Salzberg SL. Contamination in the draft of the human genome masquerades as lateral gene transfer. DNA Seq (2002) 13:75-6. doi:10.1080/10425170290023392
146. Arakawa K. No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci U S A (2016) 113:E3057. doi:10.1073/pnas.1602711113
147. Sieber KB, Bromley RE, Dunning Hotopp JC. Lateral gene transfer between prokaryotes and eukaryotes. Exp Cell Res (2017) 358(2):421-6. doi:10.1016/j.yexcr.2017.02.009
148. Riley DR, Sieber KB, Robinson KM, White JR, Ganesan A, Nourbakhsh S, et al. Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples. PLoS Comput Biol (2013) 9:e1003107. doi:10.1371/journal.pcbi.1003107
149. Danchin EG. Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube? BMC Biol (2016) 14:101. doi:10.1186/s12915-016-0330-x
150. Lerner A, Jeremias P, Matthias T. The world incidence and prevalence of autoimmune diseases is increasing: a review. Internat J Celiac Disease (2015) 3:151-5. doi:10.12691/ijcd-3-4-8
151. Arleevskaya MI, Manukyan G, Inoue R, Aminov R. Editorial: microbial and environmental factors in autoimmune and inflammatory diseases. Front Immunol (2017) 8:243. doi:10.3389/fimmu.2017.00243
152. Braidwood RJ, Howe B, Reed CA. The Iranian Prehistoric Project: new problems arise as more is learned of the first attempts at food production and settled village life. Science (1961) 133:2008-10. doi:10.1126/science.133.3469.2008
153. Cordain L, Eaton SB, Sebastian A, Mann N, Lindeberg S, Watkins BA, et al. Origins and evolution of the Western diet: health implications for the 21st century. Am J Clin Nutr (2005) 81:341-54
154. Oelzea VM, Munster A, Nicklisch N, Meller H, Dresely V, Alt KW. Early neolithic diet and animal husbandry: stable isotope evidence from three Linearbandkeramik (LBK) sites in Central Germany. J Archaeol Sci (2011) 38:270-9. doi:10.1016/j.jas.2010.08.027
155. Moeller AH. The shrinking human gut microbiome. Curr Opin Microbiol (2017) 38:30-5. doi:10.1016/j.mib.2017.04.002
156. Mancabelli L, Milani C, Lugli GA, Turroni F, Ferrario C, van Sinderen D, et al. Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations. Environ Microbiol (2017) 19:1379-90. doi:10.1111/1462-2920.13692
157. Øyri SF, Muzes G, Sipos F. Dysbiotic gut microbiome: a key element of Crohn's disease. Comp Immunol Microbiol Infect Dis (2015) 43:36-49. doi:10.1016/j.cimid.2015.10.005
158. Levy M, Kolodziejczyk AA, Thaiss CA, Elinav E. Dysbiosis and the immune system. Nat Rev Immunol (2017) 17:219-32. doi:10.1038/nri.2017.7
159. Ipci K, Altintoprak N, Muluk NB, Senturk M, Cingi C. The possible mechanisms of the human microbiome in allergic diseases. Eur Arch Otorhinolaryngol (2017) 274:617-26. doi:10.1007/s00405-016-4058-6
160. Schmidt B, Mulder IE, Musk CC, Aminov RI, Lewis M, Stokes CR, et al. Establishment of normal gut microbiota is compromised under excessive hygiene conditions. PLoS One (2011) 6(12):e28284. doi:10.1371/journal.pone.0028284
161. Mulder IE, Schmidt B, Lewis M, Delday M, Stokes CR, Bailey M, et al. Restricting microbial exposure in early life negates the immune benefits associated with gut colonization in environments of high microbial diversity. PLoS One (2011) 6:e28279. doi:10.1371/journal.pone.0028279
162. Riley LW, Raphael E, Faerstein E. Obesity in the United States-dysbiosis from exposure to low-dose antibiotics? Front Publ Health (2013) 1:69. doi:10.3389/fpubh.2013.00069
163. Molina V, Shoenfeld Y. Infection, vaccines and other environmental triggers of autoimmunity. Autoimmunity (2005) 38:235-45. doi:10.1080/08916930500050277
164. Floreani A, Leung PS, Gershwin ME. Environmental basis of autoimmunity. Clin Rev Allergy Immunol (2016) 50:287-300. doi:10.1007/s12016-015-8493-8
165. Proal AD, Albert PJ, Marshall TG. The human microbiome and autoimmunity. Curr Opin Rheumatol (2013) 25:234-40. doi:10.1097/BOR.0b013e32835cedbf
166. RuffWE, Kriegel MA. Autoimmune host-microbiota interactions at barrier sites and beyond. Trends Mol Med (2015) 21:233-44. doi:10.1016/j.molmed.2015.02.006
167. Christen U. Editorial: pathogen infection and autoimmunity. Int Rev Immunol (2014) 33:261-5. doi:10.3109/08830185.2014.897345
168. Magira EE, Pitsolis T, Delimpasi S, Vourlakou C, Vlachoyiannopoulos P, Zakynthinos S. Virus infection and autoimmunity: is there a cause-and-effect relationship? J Clin Virol (2014) 59:137-40. doi:10.1016/j.jcv.2013.08.002
169. Cooke A. Infection and autoimmunity. Blood Cells Mol Dis (2009) 42:105-7. doi:10.1016/j.bcmd.2008.10.004
170. Kivity S, Agmon-Levin N, Blank M, Shoenfeld Y. Infections and autoimmunity-friends or foes? Trends Immunol (2009) 30:409-14. doi:10.1016/j.it.2009.05.005
171. Lerner A, Matthias T. GUT-the Trojan horse in remote organs' autoimmunity. J Clin Cell Immunol (2016) 7:401. doi:10.4172/2155-9899.1000401
172. Moeller AH, Caro-Quintero A, Mjungu D, Georgiev AV, Lonsdorf EV, Muller MN, et al. Cospeciation of gut microbiota with hominids. Science (2016) 353:380-2. doi:10.1126/science.aaf3951
173. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalog established by metagenomic sequencing. Nature (2010) 464:59-65. doi:10.1038/nature08821
174. Lacroix B, Citovsky V. Transfer of DNA from bacteria to eukaryotes. mBio (2016) 7:e863-816. doi:10.1128/mBio.00863-16
175. Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature (2010) 464(7290):908-12. doi:10.1038/nature08937
176. Hehemann JH, Kelly AG, Pudlo NA, Martens EC, Boraston AB. Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Proc Natl Acad Sci U S A (2012) 109:19786-91. doi:10.1073/pnas.1211002109
177. Aminov RI. History of antimicrobial drug discovery-major classes and health impact. Biochem Pharmacol (2017) 133:4-19. doi:10.1016/j.bcp.2016.10.001
178. Ravi A, Avershina E, Foley SL, Ludvigsen J, Storrø O, Øien T, et al. The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons. Sci Rep (2015) 5:15317. doi:10.1038/srep15317
179. Giraud E, Rychlik I, Cloeckaert A. Editorial: antimicrobial resistance and virulence common mechanisms. Front Microbiol (2017) 8:310. doi:10.3389/fmicb.2017.00310
180. Lange A, Beier S, Steimle A, Autenrieth IB, Huson DH, Frick J-S. Extensive mobilome-driven genome diversification in mouse gut-associated Bacteroides vulgatus mpk. Genome Biol Evol (2016) 8:1197-207. doi:10.1093/gbe/evw070
181. Alderuccio F, Toh BH. Tackling autoimmunity with gene therapy. Chimerism (2012) 3:1-4. doi:10.4161/chim.22061
182. Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Nishimura EO, et al. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci U S A (2015) 112:15976-81. doi:10.1073/pnas.1510461112