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EcoSal Plus

Domain 9: Life in Communities and the Environment

Residency in the Gut of Healthy Human Adults

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  • Authors: Jonathan N. V. Martinson1, and Seth T. Walk2
  • Editor: Edward G. Dudley3
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717; 2: Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717; 3: Penn State University, University Park, PA
  • Received 14 January 2020 Accepted 10 August 2020 Published 25 September 2020
  • Address correspondence to Seth T. Walk, [email protected]
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  • Abstract:

    is one of the most well-studied bacterial species, but several significant knowledge gaps remain regarding its ecology and natural history. Specifically, the most important factors influencing its life as a member of the healthy human gut microbiome are either underevaluated or currently unknown. Distinct population dynamics have been observed over the past century from a handful of temporal studies conducted in healthy human adults. Early studies using serology up to the most recent studies using genotyping and DNA sequencing approaches have all identified long-lived residents and short-lived transients. This review summarizes these discoveries and other studies that focused on the underlying mechanisms that lead to establishment and maintenance of residency in healthy human adults. Many fundamental knowledge gaps remain and are highlighted with the hope of facilitating future studies in this exciting research area.

  • Citation: Martinson J, Walk S. 2020. Residency in the Gut of Healthy Human Adults, EcoSal Plus 2020; doi:10.1128/ecosalplus.ESP-0003-2020

References

1. Escherich T. 1988. The intestinal bacteria of the neonate and breast-fed infant. 1884. Rev Infect Dis 10:1220–1225 http://dx.doi.org/10.1093/clinids/10.6.1220. [PubMed]
2. Zimmer C. 2008. Microcosm: E. coli and the New Science of Life. Knopf Doubleday Publishing Group, New York, NY.
3. Castellani A, Chambers AJ. 1919. Manual of Tropical Medicine. William Wood, New York, NY. http://dx.doi.org/10.5962/bhl.title.84653 [PubMed]
4. Méric G, Hitchings MD, Pascoe B, Sheppard SK. 2016. From Escherich to the Escherichia coli genome. Lancet Infect Dis 16:634–636 http://dx.doi.org/10.1016/S1473-3099(16)30066-4.
5. Martinson JNV, Pinkham NV, Peters GW, Cho H, Heng J, Rauch M, Broadaway SC, Walk ST. 2019. Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults. ISME J 13:2306–2318 http://dx.doi.org/10.1038/s41396-019-0435-7. [PubMed]
6. Nowrouzian F, Hesselmar B, Saalman R, Strannegard IL, Aberg N, Wold AE, Adlerberth I. 2003. Escherichia coli in infants’ intestinal microflora: colonization rate, strain turnover, and virulence gene carriage. Pediatr Res 54:8–14 http://dx.doi.org/10.1203/01.PDR.0000069843.20655.EE. [PubMed]
7. Tenaillon O, Skurnik D, Picard B, Denamur E. 2010. The population genetics of commensal Escherichia coli. Nat Rev Microbiol 8:207–217 http://dx.doi.org/10.1038/nrmicro2298. [PubMed]
8. Mueller NT, Bakacs E, Combellick J, Grigoryan Z, Dominguez-Bello MG. 2015. The infant microbiome development: mom matters. Trends Mol Med 21:109–117 http://dx.doi.org/10.1016/j.molmed.2014.12.002. [PubMed]
9. Suvarna K, Stevenson D, Meganathan R, Hudspeth MES. 1998. Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menA gene from Escherichia coli. J Bacteriol 180:2782–2787 http://dx.doi.org/10.1128/JB.180.10.2782-2787.1998. [PubMed]
10. Richter TKS, Michalski JM, Zanetti L, Tennant SM, Chen WH, Rasko DA. 2018. Responses of the human gut Escherichia coli population to pathogen and antibiotic disturbances. mSystems 3:e00047-18 http://dx.doi.org/10.1128/mSystems.00047-18. [PubMed]
11. Blount ZD. 2015. The unexhausted potential of E. coli. eLife 4:e05826 http://dx.doi.org/10.7554/eLife.05826. [PubMed]
12. Abia ALK, Ubomba-Jaswa E. 2019. Dirty money on holy ground: isolation of potentially pathogenic bacteria and fungi on money collected from church offerings. Iran J Public Health 48:849–857 http://dx.doi.org/10.18502/ijph.v48i5.1801. [PubMed]
13. Akoachere J-FTK, Gaelle N, Dilonga HM, Nkuo-Akenji TK. 2014. Public health implications of contamination of Franc CFA (XAF) circulating in Buea (Cameroon) with drug resistant pathogens. BMC Res Notes 7:16 http://dx.doi.org/10.1186/1756-0500-7-16. [PubMed]
14. Nwankwo EO, Ekwunife N, Mofolorunsho KC. 2014. Nosocomial pathogens associated with the mobile phones of healthcare workers in a hospital in Anyigba, Kogi state, Nigeria. J Epidemiol Glob Health 4:135–140 http://dx.doi.org/10.1016/j.jegh.2013.11.002. [PubMed]
15. Pal S, Juyal D, Adekhandi S, Sharma M, Prakash R, Sharma N, Rana A, Parihar A. 2015. Mobile phones: reservoirs for the transmission of nosocomial pathogens. Adv Biomed Res 4:144 http://dx.doi.org/10.4103/2277-9175.161553. [PubMed]
16. Bodhidatta L, Pitisuttithum P, Chamnanchanant S, Chang KT, Islam D, Bussaratid V, Venkatesan MM, Hale TL, Mason CJ. 2012. Establishment of a Shigella sonnei human challenge model in Thailand. Vaccine 30:7040–7045 http://dx.doi.org/10.1016/j.vaccine.2012.09.061. [PubMed]
17. Tannock GW, Tiong IS, Priest P, Munro K, Taylor C, Richardson A, Schultz M. 2011. Testing probiotic strain Escherichia coli Nissle 1917 (Mutaflor) for its ability to reduce carriage of multidrug-resistant E. coli by elderly residents in long-term care facilities. J Med Microbiol 60:366–370 http://dx.doi.org/10.1099/jmm.0.025874-0. [PubMed]
18. Johnson JR, Clabots C. 2006. Sharing of virulent Escherichia coli clones among household members of a woman with acute cystitis. Clin Infect Dis 43:e101–e108 http://dx.doi.org/10.1086/508541. [PubMed]
19. Johnson JR, Clabots C, Kuskowski MA. 2008. Multiple-host sharing, long-term persistence, and virulence of Escherichia coli clones from human and animal household members. J Clin Microbiol 46:4078–4082 http://dx.doi.org/10.1128/JCM.00980-08. [PubMed]
20. Fratamico PM, DebRoy C, Liu Y, Needleman DS, Baranzoni GM, Feng P. 2016. Advances in molecular serotyping and subtyping of Escherichia coli. Front Microbiol 7:644.
21. Caugant DA, Levin BR, Orskov I, Orskov F, Svanborg Eden C, Selander RK. 1985. Genetic diversity in relation to serotype in Escherichia coli. Infect Immun 49:407–413 http://dx.doi.org/10.1128/IAI.49.2.407-413.1985. [PubMed]
22. Shooter RA, Bettleheim KA, Lennox-King SMJ, O’Farrell S. 1977. Escherichia coli serotypes in the faeces of healthy adults over a period of several months. J Hyg (Lond) 78:95–98 http://dx.doi.org/10.1017/S0022172400055972. [PubMed]
23. Beasley DE, Koltz AM, Lambert JE, Fierer N, Dunn RR. 2015. The evolution of stomach acidity and its relevance to the human microbiome. PLoS One 10:e0134116 http://dx.doi.org/10.1371/journal.pone.0134116. [PubMed]
24. Ridlon JM, Kang DJ, Hylemon PB, Bajaj JS. 2014. Bile acids and the gut microbiome. Curr Opin Gastroenterol 30:332–338 http://dx.doi.org/10.1097/MOG.0000000000000057. [PubMed]
25. Macconkey A. 1905. Lactose-fermenting bacteria in faeces. J Hyg (Lond) 5:333–379 http://dx.doi.org/10.1017/S002217240000259X. [PubMed]
26. Macconkey AT. 1908. Bile salt media and their advantages in some bacteriological examinations. J Hyg (Lond) 8:322–334 http://dx.doi.org/10.1017/S0022172400003375. [PubMed]
27. Totsuka K. 1902. Studien uber Bacterium coli. Z Hyg Infektionskr 45:115–124.
28. Wallick H, Stuart CA. 1943. Antigenic relationships of Escherichia coli isolated from one individual. J Bacteriol 45:121–126 http://dx.doi.org/10.1128/JB.45.2.121-126.1943. [PubMed]
29. Smith HL. 1899. Zur Kenntnis der Colibacillen des Säuglingsstuhles. Zentr Bakt Parasitenk I Orig 25:689–693.
30. Kauffmann F, Perch B. 1943. Uber die Coliflora des gesunden Menschen. Acta Pathol Microbiol Scand 20:201–220.
31. Sears HJ, Brownlee I, Uchiyama JK. 1950. Persistence of individual strains of Escherichia coli in the intestinal tract of man. J Bacteriol 59:293–301 http://dx.doi.org/10.1128/JB.59.2.293-301.1950. [PubMed]
32. Sears HJ, Brownlee I. 1952. Further observations on the persistence of individual strains of Escherichia coli in the intestinal tract of man. J Bacteriol 63:47–57 http://dx.doi.org/10.1128/JB.63.1.47-57.1952. [PubMed]
33. Halbert SP. 1948. The antagonism of coliform bacteria against Shigellae. J Immunol 58:153–167.
34. Robinet HG. 1962. Relationship of host antibody to fluctuations of Escherichia coli serotypes in the human intestine. J Bacteriol 84:896–901 http://dx.doi.org/10.1128/JB.84.5.896-901.1962. [PubMed]
35. Branche WC Jr, Young VM, Robinet HG, Massey ED. 1963. Effect of colicine production on Escherichia coli in the normal human intestine. Proc Soc Exp Biol Med 114:198–201 http://dx.doi.org/10.3181/00379727-114-28624. [PubMed]
36. Anantham S. 2013. Analysis of persistent and antibiotic resistant commensal Escherichia coli from healthy adults. Available from: http://ses.library.usyd.edu.au/bitstream/2123/10399/1/Anantham_SA_Thesis.pdf.
37. Caugant DA, Levin BR, Selander RK. 1981. Genetic diversity and temporal variation in the E. coli population of a human host. Genetics 98:467–490.
38. Milkman R. 1973. Electrophoretic variation in Escherichia coli from natural sources. Science 182:1024–1026 http://dx.doi.org/10.1126/science.182.4116.1024. [PubMed]
39. Milkman R. 1997. Recombination and population structure in Escherichia coli. Genetics 146:745–750.
40. Selander RK, Levin BR. 1980. Genetic diversity and structure in Escherichia coli populations. Science 210:545–547 http://dx.doi.org/10.1126/science.6999623. [PubMed]
41. Whittam TS. 1989. Clonal dynamics of Escherichia coli in its natural habitat. Antonie van Leeuwenhoek 55:23–32 http://dx.doi.org/10.1007/BF02309616. [PubMed]
42. Tzabar Y, Pennington TH. 1991. The population structure and transmission of Escherichia coli in an isolated human community; studies on an Antarctic base. Epidemiol Infect 107:537–542 http://dx.doi.org/10.1017/S0950268800049232. [PubMed]
43. Whittam TS, Ochman H, Selander RK. 1983. Multilocus genetic structure in natural populations of Escherichia coli. Proc Natl Acad Sci USA 80:1751–1755 http://dx.doi.org/10.1073/pnas.80.6.1751. [PubMed]
44. Herzer PJ, Inouye S, Inouye M, Whittam TS. 1990. Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. J Bacteriol 172:6175–6181 http://dx.doi.org/10.1128/JB.172.11.6175-6181.1990. [PubMed]
45. Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140–3145 http://dx.doi.org/10.1073/pnas.95.6.3140. [PubMed]
46. Reid SD, Herbelin CJ, Bumbaugh AC, Selander RK, Whittam TS. 2000. Parallel evolution of virulence in pathogenic Escherichia coli. Nature 406:64–67 http://dx.doi.org/10.1038/35017546. [PubMed]
47. Eisen JA, Kaiser D, Myers RM. 1997. Gastrogenomic delights: a movable feast. Nat Med 3:1076–1078 http://dx.doi.org/10.1038/nm1097-1076. [PubMed]
48. Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J. 2008. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190:6881–6893 http://dx.doi.org/10.1128/JB.00619-08. [PubMed]
49. Clermont O, Bonacorsi S, Bingen E. 2000. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol 66:4555–4558 http://dx.doi.org/10.1128/AEM.66.10.4555-4558.2000. [PubMed]
50. Clermont O, Christenson JK, Denamur E, Gordon DM. 2013. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep 5:58–65 http://dx.doi.org/10.1111/1758-2229.12019. [PubMed]
51. Higgins CF, Ames GF-L, Barnes WM, Clement JM, Hofnung M. 1982. A novel intercistronic regulatory element of prokaryotic operons. Nature 298:760–762. [PubMed]
52. Stern MJ, Ames GF-L, Smith NH, Robinson EC, Higgins CF. 1984. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37:1015–1026 http://dx.doi.org/10.1016/0092-8674(84)90436-7.
53. Versalovic J, Koeuth T, Lupski JR. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19:6823–6831 http://dx.doi.org/10.1093/nar/19.24.6823. [PubMed]
54. Qian Z, Adhya S. 2017. DNA repeat sequences: diversity and versatility of functions. Curr Genet 63:411–416 http://dx.doi.org/10.1007/s00294-016-0654-7. [PubMed]
55. Mohapatra BR, Mazumder A. 2008. Comparative efficacy of five different rep-PCR methods to discriminate Escherichia coli populations in aquatic environments. Water Sci Technol 58:537–547 http://dx.doi.org/10.2166/wst.2008.424. [PubMed]
56. Hulton CSJ, Higgins CF, Sharp PM. 1991. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol 5:825–834 http://dx.doi.org/10.1111/j.1365-2958.1991.tb00755.x. [PubMed]
57. Burge C, Campbell AM, Karlin S. 1992. Over- and under-representation of short oligonucleotides in DNA sequences. Proc Natl Acad Sci USA 89:1358–1362 http://dx.doi.org/10.1073/pnas.89.4.1358. [PubMed]
58. Versalovic J, Lupski JR. 1998. Interspersed repetitive sequences in bacterial genomes, p 38–48. In de Bruijn FJ, Lupski JR, Weinstock GM (ed), Bacterial Genomes: Physical Structure and Analysis. Springer, US, Boston, MA. http://dx.doi.org/10.1007/978-1-4615-6369-3_5
59. Johnson JR, O’Bryan TT. 2000. Improved repetitive-element PCR fingerprinting for resolving pathogenic and nonpathogenic phylogenetic groups within Escherichia coli. Clin Diagn Lab Immunol 7:265–273 http://dx.doi.org/10.1128/CDLI.7.2.265-273.2000. [PubMed]
60. Clermont O, Gordon D, Denamur E. 2015. Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes. Microbiology 161:980–988 http://dx.doi.org/10.1099/mic.0.000063. [PubMed]
61. Qi W, Lacher DW, Bumbaugh AC, Hyma KE, Ouellette LM, Large TM, Tarr CL, Whittam TS. 2004. EcMLST: an online database for multi locus sequence typing of pathogenic Escherichia coli, p. 520–521. In Proceedings 2004 IEEE Computational Systems Bioinformatics Conference, 2004 CSB 2004. IEEE;
62. Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, Karch H, Reeves PR, Maiden MC, Ochman H, Achtman M. 2006. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol 60:1136–1151 http://dx.doi.org/10.1111/j.1365-2958.2006.05172.x. [PubMed]
63. Jaureguy F, Landraud L, Passet V, Diancourt L, Frapy E, Guigon G, Carbonnelle E, Lortholary O, Clermont O, Denamur E, Picard B, Nassif X, Brisse S. 2008. Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. BMC Genomics 9:560 http://dx.doi.org/10.1186/1471-2164-9-560. [PubMed]
64. Chen Y, Son I. 2014. Polymerase chain reaction-based subtyping methods, p 1–26. In Oyarzabal OA, Kathariou S (ed), DNA Methods in Food Safety: Molecular Typing of Foodborne and Waterborne Bacterial Pathogens. Wiley Blackwell, Hoboken, NJ.
65. Ray M, Schwartz DC. 2014. Pulsed-field gel electrophoresis and the molecular epidemiology of foodborne pathogens, p 27–46. In Oyawzabal OA, Kathariou S (ed), DNA Methods in Food Safety: Molecular Typing of Foodborne and Waterborne Bacterial Pathogens. Wiley Blackwell, Hoboken, NJ. http://dx.doi.org/10.1002/9781118278666.ch2 [PubMed]
66. Johnson JR, Clabots C. 2006. Sharing of virulent Escherichia coli clones among household members of a woman with acute cystitis. Clin Infect Dis 43:e101–e108 http://dx.doi.org/10.1086/508541. [PubMed]
67. Damborg P, Nielsen SS, Guardabassi L. 2009. Escherichia coli shedding patterns in humans and dogs: insights into within-household transmission of phylotypes associated with urinary tract infections. Epidemiol Infect 137:1457–1464 http://dx.doi.org/10.1017/S095026880900226X. [PubMed]
68. McBurney WT. 1999. Perturbation of the enterobacterial microflora detected by molecular analysis. Microb Ecol Health Dis 11:175–179.
69. Tchesnokova V, Avagyan H, Billig M, Chattopadhyay S, Aprikian P, Chan D, Pseunova J, Rechkina E, Riddell K, Scholes D, Fang FC, Johnson JR, Sokurenko EV. 2016. A novel 7-single nucleotide polymorphism-based clonotyping test allows rapid prediction of antimicrobial susceptibility of extraintestinal Escherichia coli directly from urine specimens. Open Forum Infect Dis 3:ofw002 http://dx.doi.org/10.1093/ofid/ofw002. [PubMed]
70. Rogers BA, Kennedy KJ, Sidjabat HE, Jones M, Collignon P, Paterson DL. 2012. Prolonged carriage of resistant E. coli by returned travellers: clonality, risk factors and bacterial characteristics. Eur J Clin Microbiol Infect Dis 31:2413–2420 http://dx.doi.org/10.1007/s10096-012-1584-z. [PubMed]
71. Blyton MDJ, Banks SC, Peakall R, Gordon DM. 2013. High temporal variability in commensal Escherichia coli strain communities of a herbivorous marsupial. Environ Microbiol 15:2162–2172 http://dx.doi.org/10.1111/1462-2920.12088. [PubMed]
72. Nielsen KL, Stegger M, Kiil K, Godfrey PA, Feldgarden M, Lilje B, Andersen PS, Frimodt-Møller N. 2017. Whole-genome comparison of urinary pathogenic Escherichia coli and faecal isolates of UTI patients and healthy controls. Int J Med Microbiol 307:497–507 http://dx.doi.org/10.1016/j.ijmm.2017.09.007. [PubMed]
73. Matsui Y, Hu Y, Rubin J, de Assis RS, Suh J, Riley LW. 2020. Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community. MicrobiologyOpen 9:1225–1233 http://dx.doi.org/10.1002/mbo3.1032. [PubMed]
74. Jernberg C, Löfmark S, Edlund C, Jansson JK. 2007. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1:56–66 http://dx.doi.org/10.1038/ismej.2007.3. [PubMed]
75. Liu H, Han M, Li SC, Tan G, Sun S, Hu Z, Yang P, Wang R, Liu Y, Chen F, Peng J, Peng H, Song H, Xia Y, Chu L, Zhou Q, Guan F, Wu J, Bu D, Ning K. 2019. Resilience of human gut microbial communities for the long stay with multiple dietary shifts. Gut 68:2254–2255 http://dx.doi.org/10.1136/gutjnl-2018-317298. [PubMed]
76. Pereira FC, Berry D. 2017. Microbial nutrient niches in the gut. Environ Microbiol 19:1366–1378 http://dx.doi.org/10.1111/1462-2920.13659. [PubMed]
77. Granato ET, Meiller-Legrand TA, Foster KR. 2019. The evolution and ecology of bacterial warfare. Curr Biol 29:R521–R537 http://dx.doi.org/10.1016/j.cub.2019.04.024. [PubMed]
78. Hardin G. 1960. The competitive exclusion principle. Science 131:1292–1297 http://dx.doi.org/10.1126/science.131.3409.1292. [PubMed]
79. Ghoul M, Mitri S. 2016. The ecology and evolution of microbial competition. Trends Microbiol 24:833–845 http://dx.doi.org/10.1016/j.tim.2016.06.011. [PubMed]
80. Freter R, Brickner H, Fekete J, Vickerman MM, Carey KE. 1983. Survival and implantation of Escherichia coli in the intestinal tract. Infect Immun 39:686–703 http://dx.doi.org/10.1128/IAI.39.2.686-703.1983. [PubMed]
81. Freter R, Brickner H, Botney M, Cleven D, Aranki A. 1983. Mechanisms that control bacterial populations in continuous-flow culture models of mouse large intestinal flora. Infect Immun 39:676–685 http://dx.doi.org/10.1128/IAI.39.2.676-685.1983. [PubMed]
82. Freter R. 1956. Experimental enteric Shigella and Vibrio infections in mice and guinea pigs. J Exp Med 104:411–418 http://dx.doi.org/10.1084/jem.104.3.411. [PubMed]
83. Conway T, Cohen PS. 2015. Commensal and pathogenic Escherichia coli metabolism in the gut. Microbiol Spectr 3. [PubMed]
84. Hutchinson GE. 1991. Population studies: animal ecology and demography. Bull Math Biol 53:193–213 http://dx.doi.org/10.1007/BF02464429.
85. Hutchinson GE. 1978. An Introduction to Population Biology. Yale University Press, New Haven, CT.
86. Faber F, Tran L, Byndloss MX, Lopez CA, Velazquez EM, Kerrinnes T, Nuccio SP, Wangdi T, Fiehn O, Tsolis RM, Bäumler AJ. 2016. Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion. Nature 534:697–699 http://dx.doi.org/10.1038/nature18597. [PubMed]
87. Olsan EE, Byndloss MX, Faber F, Rivera-Chávez F, Tsolis RM, Bäumler AJ. 2017. Colonization resistance: the deconvolution of a complex trait. J Biol Chem 292:8577–8581 http://dx.doi.org/10.1074/jbc.R116.752295. [PubMed]
88. Bachmann BJ. 1996. Derivations and genotypes of some mutant derivatives of Escherichia coli K-12, p 2460–2488. In Neidhardt FC (ed), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed. ASM Press, Washington, DC.
89. Naas T, Blot M, Fitch WM, Arber W. 1994. Insertion sequence-related genetic variation in resting Escherichia coli K-12. Genetics 136:721–730.
90. Jensen KF. 1993. The Escherichia coli K-12 “wild types” W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J Bacteriol 175:3401–3407 http://dx.doi.org/10.1128/JB.175.11.3401-3407.1993. [PubMed]
91. Deriu E, Liu JZ, Pezeshki M, Edwards RA, Ochoa RJ, Contreras H, Libby SJ, Fang FC, Raffatellu M. 2013. Probiotic bacteria reduce Salmonella Typhimurium intestinal colonization by competing for iron. Cell Host Microbe 14:26–37 http://dx.doi.org/10.1016/j.chom.2013.06.007. [PubMed]
92. Stecher B. 2015. The Roles of inflammation, nutrient availability and the commensal microbiota in enteric pathogen infection. Microbiol Spectr 3:10.1128/microbiolspec.MBP-0008-2014.
93. Pi H, Jones SA, Mercer LE, Meador JP, Caughron JE, Jordan L, Newton SM, Conway T, Klebba PE. 2012. Role of catecholate siderophores in Gram-negative bacterial colonization of the mouse gut. PLoS One 7:e50020 http://dx.doi.org/10.1371/journal.pone.0050020. [PubMed]
94. Nowrouzian F, Adlerberth I, Wold AE. 2001. P fimbriae, capsule and aerobactin characterize colonic resident Escherichia coli. Epidemiol Infect 126:11–18 http://dx.doi.org/10.1017/S0950268801005118. [PubMed]
95. Helander HF, Fändriks L. 2014. Surface area of the digestive tract: revisited. Scand J Gastroenterol 49:681–689 http://dx.doi.org/10.3109/00365521.2014.898326. [PubMed]
96. Spaulding CN, Klein RD, Ruer S, Kau AL, Schreiber HL, Cusumano ZT, Dodson KW, Pinkner JS, Fremont DH, Janetka JW, Remaut H, Gordon JI, Hultgren SJ. 2017. Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist. Nature 546:528–532 http://dx.doi.org/10.1038/nature22972. [PubMed]
97. Branda SS, Vik S, Friedman L, Kolter R. 2005. Biofilms: the matrix revisited. Trends Microbiol 13:20–26 http://dx.doi.org/10.1016/j.tim.2004.11.006. [PubMed]
98. Tytgat HLP, Nobrega FL, van der Oost J, de Vos WM. 2019. Bowel biofilms: tipping points between a healthy and compromised gut? Trends Microbiol 27:17–25 http://dx.doi.org/10.1016/j.tim.2018.08.009. [PubMed]
99. Randal Bollinger R, Barbas AS, Bush EL, Lin SS, Parker W. 2007. Biofilms in the large bowel suggest an apparent function of the human vermiform appendix. J Theor Biol 249:826–831 http://dx.doi.org/10.1016/j.jtbi.2007.08.032. [PubMed]
100. Deplancke B, Gaskins HR. 2001. Microbial modulation of innate defense: goblet cells and the intestinal mucus layer. Am J Clin Nutr 73:1131S–1141S http://dx.doi.org/10.1093/ajcn/73.6.1131S. [PubMed]
101. Johansson MEV, Phillipson M, Petersson J, Velcich A, Holm L, Hansson GC. 2008. The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc Natl Acad Sci USA 105:15064–15069 http://dx.doi.org/10.1073/pnas.0803124105. [PubMed]
102. Johansson MEV, Gustafsson JK, Holmén-Larsson J, Jabbar KS, Xia L, Xu H, Ghishan FK, Carvalho FA, Gewirtz AT, Sjövall H, Hansson GC. 2014. Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis. Gut 63:281–291 http://dx.doi.org/10.1136/gutjnl-2012-303207. [PubMed]
103. Jakobsson HE, Rodríguez-Piñeiro AM, Schütte A, Ermund A, Boysen P, Bemark M, Sommer F, Bäckhed F, Hansson GC, Johansson ME. 2015. The composition of the gut microbiota shapes the colon mucus barrier. EMBO Rep 16:164–177 http://dx.doi.org/10.15252/embr.201439263. [PubMed]
104. Johansson MEV, Jakobsson HE, Holmén-Larsson J, Schütte A, Ermund A, Rodríguez-Piñeiro AM, Arike L, Wising C, Svensson F, Bäckhed F, Hansson GC. 2015. Normalization of host intestinal mucus layers requires long-term microbial colonization. Cell Host Microbe 18:582–592 http://dx.doi.org/10.1016/j.chom.2015.10.007. [PubMed]
105. Bokranz W, Wang X, Tschäpe H, Römling U. 2005. Expression of cellulose and curli fimbriae by Escherichia coli isolated from the gastrointestinal tract. J Med Microbiol 54:1171–1182 http://dx.doi.org/10.1099/jmm.0.46064-0. [PubMed]
106. Flament-Simon S-C, Duprilot M, Mayer N, García V, Alonso MP, Blanco J, Nicolas-Chanoine MH. 2019. Association between kinetics of early biofilm formation and clonal lineage in Escherichia coli. Front Microbiol 10:1183 http://dx.doi.org/10.3389/fmicb.2019.01183. [PubMed]
107. White AP, Sibley KA, Sibley CD, Wasmuth JD, Schaefer R, Surette MG, Edge TA, Neumann NF. 2011. Intergenic sequence comparison of Escherichia coli isolates reveals lifestyle adaptations but not host specificity. Appl Environ Microbiol 77:7620–7632 http://dx.doi.org/10.1128/AEM.05909-11. [PubMed]
108. Li X-Y, Lachnit T, Fraune S, Bosch TCG, Traulsen A, Sieber M. 2017. Temperate phages as self-replicating weapons in bacterial competition. J R Soc Interface 14:20170563 http://dx.doi.org/10.1098/rsif.2017.0563. [PubMed]
109. García-Bayona L, Comstock LE. 2018. Bacterial antagonism in host-associated microbial communities. Science 361:eaat2456 http://dx.doi.org/10.1126/science.aat2456. [PubMed]
110. Manrique P, Dills M, Young MJ. 2017. The human gut phage community and its implications for health and disease. Viruses 9:141 http://dx.doi.org/10.3390/v9060141. [PubMed]
111. Gordon DM. 2016. The natural history of bacteriocins, p 1–10. In Dorit RL, Roy SM, Riley MA (ed), The Bacteriocins: Current Knowledge and Future Prospects. Caister, Poole, UK.
112. Rebuffat S. 2012. Microcins in action: amazing defence strategies of Enterobacteria. Biochem Soc Trans 40:1456–1462 http://dx.doi.org/10.1042/BST20120183. [PubMed]
113. Gratia A. 1925. Sur un remarquable exemple d’antagonisme entre deux souches de coilbacille. C R Seances Soc Biol Fil 93:1040–1041.
114. Cascales E, Buchanan SK, Duché D, Kleanthous C, Lloubès R, Postle K, Riley M, Slatin S, Cavard D. 2007. Colicin biology. Microbiol Mol Biol Rev 71:158–229 http://dx.doi.org/10.1128/MMBR.00036-06. [PubMed]
115. Gratia A, Fredericq P. 1946. Diversite des souches antibiotiques de b-coli et etendue variable de leur champ daction. C R Seances Soc Biol Fil 140:1032–1033.
116. Gordon DM, O’Brien CL. 2006. Bacteriocin diversity and the frequency of multiple bacteriocin production in Escherichia coli. Microbiology 152:3239–3244 http://dx.doi.org/10.1099/mic.0.28690-0. [PubMed]
117. Sassone-Corsi M, Nuccio SP, Liu H, Hernandez D, Vu CT, Takahashi AA, Edwards RA, Raffatellu M. 2016. Microcins mediate competition among Enterobacteriaceae in the inflamed gut. Nature 540:280–283 http://dx.doi.org/10.1038/nature20557. [PubMed]
118. Brown SP, Fredrik Inglis R, Taddei F. 2009. Evolutionary ecology of microbial wars: within-host competition and (incidental) virulence. Evol Appl 2:32–39 http://dx.doi.org/10.1111/j.1752-4571.2008.00059.x. [PubMed]
119. Chao L, Levin BR. 1981. Structured habitats and the evolution of anticompetitor toxins in bacteria. Proc Natl Acad Sci USA 78:6324–6328 http://dx.doi.org/10.1073/pnas.78.10.6324. [PubMed]
120. Kortright KE, Chan BK, Koff JL, Turner PE. 2019. Phage therapy: a renewed approach to combat antibiotic-resistant bacteria. Cell Host Microbe 25:219–232 http://dx.doi.org/10.1016/j.chom.2019.01.014. [PubMed]
121. Twort FW. 1915. An investigation on the nature of ultra-microscopic viruses. Lancet 186:1241–1243 http://dx.doi.org/10.1016/S0140-6736(01)20383-3.
122. D’Herelle MF. 1917. Sur un microbe invisible antagoniste des bacilles dysenteriques. CR Acad Sci Paris 165:373–375.
123. Summers WC. 1999. Félix d’Herelle and the Origins of Molecular Biology. Yale University Press, New Haven, CT.
124. Furuse K, Osawa S, Kawashiro J, Tanaka R, Ozawa A, Sawamura S, Yanagawa Y, Nagao T, Watanabe I. 1983. Bacteriophage distribution in human faeces: continuous survey of healthy subjects and patients with internal and leukaemic diseases. J Gen Virol 64:2039–2043 http://dx.doi.org/10.1099/0022-1317-64-9-2039. [PubMed]
125. Battesti A, Majdalani N, Gottesman S. 2011. The RpoS-mediated general stress response in Escherichia coli. Annu Rev Microbiol 65:189–213 http://dx.doi.org/10.1146/annurev-micro-090110-102946. [PubMed]
126. King T, Ishihama A, Kori A, Ferenci T. 2004. A regulatory trade-off as a source of strain variation in the species Escherichia coli. J Bacteriol 186:5614–5620 http://dx.doi.org/10.1128/JB.186.17.5614-5620.2004. [PubMed]
127. MacArthur RH. 1959. On the breeding distribution pattern of North American migrant birds. Auk 76:318–325 http://dx.doi.org/10.2307/4081809.
128. Lack D. 1954. The Natural Regulation of Animal Numbers. Oxford University Press, New York, NY.
129. Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM, Groussin M, Xavier RJ, Alm EJ. 2019. Adaptive evolution within gut microbiomes of healthy people. Cell Host Microbe 25:656–667.e8 http://dx.doi.org/10.1016/j.chom.2019.03.007. [PubMed]
130. Robinson CD, Bohannan BJ, Britton RA. 2019. Scales of persistence: transmission and the microbiome. Curr Opin Microbiol 50:42–49 http://dx.doi.org/10.1016/j.mib.2019.09.009. [PubMed]
131. Reeves PR, Liu B, Zhou Z, Li D, Guo D, Ren Y, Clabots C, Lan R, Johnson JR, Wang L. 2011. Rates of mutation and host transmission for an Escherichia coli clone over 3 years. PLoS One 6:e26907 http://dx.doi.org/10.1371/journal.pone.0026907. [PubMed]
132. Ghalayini M, Launay A, Bridier-Nahmias A, Clermont O, Denamur E, Lescat M, Tenaillon O. 2018. Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size. Appl Environ Microbiol 84:e02377-17 http://dx.doi.org/10.1128/AEM.02377-17. [PubMed]
133. Nowrouzian FL, Adlerberth I, Wold AE. 2006. Enhanced persistence in the colonic microbiota of Escherichia coli strains belonging to phylogenetic group B2: role of virulence factors and adherence to colonic cells. Microbes Infect 8:834–840 http://dx.doi.org/10.1016/j.micinf.2005.10.011. [PubMed]
134. Wold AE, Caugant DA, Lidin-Janson G, de Man P, Svanborg C. 1992. Resident colonic Escherichia coli strains frequently display uropathogenic characteristics. J Infect Dis 165:46–52 http://dx.doi.org/10.1093/infdis/165.1.46. [PubMed]
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/content/journal/ecosalplus/10.1128/ecosalplus.ESP-0003-2020
2020-09-25
2021-04-19

Abstract:

is one of the most well-studied bacterial species, but several significant knowledge gaps remain regarding its ecology and natural history. Specifically, the most important factors influencing its life as a member of the healthy human gut microbiome are either underevaluated or currently unknown. Distinct population dynamics have been observed over the past century from a handful of temporal studies conducted in healthy human adults. Early studies using serology up to the most recent studies using genotyping and DNA sequencing approaches have all identified long-lived residents and short-lived transients. This review summarizes these discoveries and other studies that focused on the underlying mechanisms that lead to establishment and maintenance of residency in healthy human adults. Many fundamental knowledge gaps remain and are highlighted with the hope of facilitating future studies in this exciting research area.

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