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Chapter 4 : Sociomicrobiology and Pathogenic Bacteria

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Sociomicrobiology and Pathogenic Bacteria, Page 1 of 2

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Abstract:

Microbiology has gathered much attention in recent years in part thanks to major scientific advancements in the microbiome field. Large-scale projects such as the NIH-funded Human Microbiome Project ( ) provide extensive catalogues of the microbes that live in and on the human body. Statements like “the human body is home to bacteria that outnumber human cells by more than 10:1” or “the genetic content of these bacteria can be 100x that of the human genome” are often used by mainstream media and are known to the general public. Vast explorations of the human and nonhuman microbiomes are to a large extent boosted by recent breakthroughs in DNA sequencing and community metagenomics ( ), and the many studies that have emerged reveal an expanding role of multispecies host-associated microbial communities in several host functions ( ). Arguably, one of the most notable functions of commensal microbiota, i.e., nonpathogenic microbes, is protecting the host from colonization by other microbes ( ). This is an exciting area of research that aims to address open questions in pathogenesis such as why individuals exposed to the same pathogen can differ in their levels of infection. It can also explain why patients can have increased risk of infections after antibiotic therapy destroys the commensal microbiota that would naturally protect against pathogen invasion.

Citation: Xavier J. 2016. Sociomicrobiology and Pathogenic Bacteria, p 89-101. In Kudva I, Cornick N, Plummer P, Zhang Q, Nicholson T, Bannantine J, Bellaire B (ed),

Virulence Mechanisms of Bacterial Pathogens, Fifth Edition

. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.VMBF-0019-2015
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Figures

Image of Figure 1
Figure 1

A model of biofilm development and life cycle proposed in reference 18. Planktonic bacteria attach to surfaces, initiate expression of biofilm genes such as synthesis of extracellular polymeric matrices, and grow a biofilm. A cell can detach from a mature biofilm and go back to the planktonic state, closing the biofilm life cycle.

Citation: Xavier J. 2016. Sociomicrobiology and Pathogenic Bacteria, p 89-101. In Kudva I, Cornick N, Plummer P, Zhang Q, Nicholson T, Bannantine J, Bellaire B (ed),

Virulence Mechanisms of Bacterial Pathogens, Fifth Edition

. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.VMBF-0019-2015
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Image of Figure 2
Figure 2

Siderophore production as a cooperative trait ( ). Some bacterial pathogens like secrete siderophores to scavenge iron the in iron-limited environments of host tissues (panel 1). Siderophores have high affinity to iron and can be taken up by bacteria including non–siderophore producers that still have the siderophore receptors (panel 2). Non–siderophore producers exploit wild-type producers by not paying the cost of siderophore production, but this cheating behavior can lead to the extinction of siderophore production in the population (panel 3).

Citation: Xavier J. 2016. Sociomicrobiology and Pathogenic Bacteria, p 89-101. In Kudva I, Cornick N, Plummer P, Zhang Q, Nicholson T, Bannantine J, Bellaire B (ed),

Virulence Mechanisms of Bacterial Pathogens, Fifth Edition

. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.VMBF-0019-2015
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Image of Figure 3
Figure 3

Laboratory experiments reveal the hallmarks of cheating. Siderophore-producing grow reasonably well in iron-depleted media by increasing iron uptake thanks to siderophore scavenging ( Fig. 2 ). Non–siderophore producers (cheaters) grow poorly in the same environment when alone but do better when mixed with producers by not paying the cost of siderophore production. The advantage of nonproducers comes at the expense of the whole population ( ). The competitive advantage of cheaters decreases as their frequency increases because there are fewer cooperators to exploit in the population. This example is taken from a study of type III secretion systems in where mutants lacking the type III system could cheat over wild-type bacteria (WT), but their measured competitive index decreased as cheater numbers increased in the population ( ).

Citation: Xavier J. 2016. Sociomicrobiology and Pathogenic Bacteria, p 89-101. In Kudva I, Cornick N, Plummer P, Zhang Q, Nicholson T, Bannantine J, Bellaire B (ed),

Virulence Mechanisms of Bacterial Pathogens, Fifth Edition

. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.VMBF-0019-2015
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Colonization resistance by the gut microbiota can be harmed by antibiotic therapy. (Panel 1) The gut microbiota can resist colonization by pathogens such as . (Panel 2) Antibiotics disrupt the ecology of the commensal microbiota. (Panel 3) Antibiotic-challenged microbiota open the way to colonization.

Citation: Xavier J. 2016. Sociomicrobiology and Pathogenic Bacteria, p 89-101. In Kudva I, Cornick N, Plummer P, Zhang Q, Nicholson T, Bannantine J, Bellaire B (ed),

Virulence Mechanisms of Bacterial Pathogens, Fifth Edition

. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.VMBF-0019-2015
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555819286.chap4
1. Peterson J,, Garges S,, Giovanni M,, McInnes P,, Wang L,, Schloss JA,, Bonazzi V,, McEwen JE,, Wetterstrand KA,, Deal C . 2009. The NIH human microbiome project. Genome Res 19 : 23172323.[PubMed] [CrossRef]
2. Turnbaugh PJ,, Ley RE,, Hamady M,, Fraser-Liggett CM,, Knight R,, Gordon JI . 2007. The human microbiome project. Nature 449 : 804810.[PubMed] [CrossRef]
3. The Human Microbiome Project Consortium . 2012. A framework for human microbiome research. Nature 486 : 215221.[PubMed] [CrossRef]
4. 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 : 16351638.[PubMed] [CrossRef]
5. Turnbaugh PJ,, Hamady M,, Yatsunenko T,, Cantarel BL,, Duncan A,, Ley RE,, Sogin ML,, Jones WJ,, Roe BA,, Affourtit JP . 2009. A core gut microbiome in obese and lean twins. Nature 457 : 480484.[PubMed] [CrossRef]
6. Ley RE,, Bäckhed F,, Turnbaugh P,, Lozupone CA,, Knight RD,, Gordon JI . 2005. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102 : 1107011075.[PubMed] [CrossRef]
7. Cho I,, Blaser MJ . 2012. The human microbiome: at the interface of health and disease. Nat Rev Genet 13 : 260270.[PubMed] [CrossRef]
8. Morgan XC,, Tickle TL,, Sokol H,, Gevers D,, Devaney KL,, Ward DV,, Reyes JA,, Shah SA,, LeLeiko N,, Snapper SB . 2012. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 13 : R79. [PubMed] [CrossRef]
9. Taur Y,, Pamer EG . 2013. The intestinal microbiota and susceptibility to infection in immunocompromised patients. Curr Opin Infect Dis 26 : 332337.[PubMed] [CrossRef]
10. Parsek MR,, Greenberg EP . 2005. Sociomicrobiology: the connections between quorum sensing and biofilms. Trends Microbiol 13 : 2733.[PubMed] [CrossRef]
11. Costerton J,, Stewart PS,, Greenberg E . 1999. Bacterial biofilms: a common cause of persistent infections. Science 284 : 13181322.[PubMed] [CrossRef]
12. Ashby M,, Neale J,, Knott S,, Critchley I . 1994. Effect of antibiotics on non-growing planktonic cells and biofilms of Escherichia coli . J Antimicrob Chemother 33 : 443452.[PubMed] [CrossRef]
13. Ledeboer NA,, Jones BD . 2005. Exopolysaccharide sugars contribute to biofilm formation by Salmonella enterica serovar Typhimurium on HEp-2 cells and chicken intestinal epithelium. J Bacteriol 187 : 32143226.[PubMed] [CrossRef]
14. Anderl JN,, Franklin MJ,, Stewart PS . 2000. Role of antibiotic penetration limitation in Klebsiella pneumoniae biofilm resistance to ampicillin and ciprofloxacin. Antimicrob Agents Chemother 44 : 18181824.[PubMed] [CrossRef]
15. Drescher K,, Nadell CD,, Stone HA,, Wingreen NS,, Bassler BL . 2014. Solutions to the public goods dilemma in bacterial biofilms. Curr Biol 24 : 5055.[PubMed] [CrossRef]
16. Nadell CD,, Drescher,, Wingreen NS,, Bassler BL . 2015. Extracellular matrix structure governs invasion resistance in bacterial biofilms. ISME J 9 : 17001709.[PubMed] [CrossRef]
17. Dapa T,, Unnikrishnan M . 2013. Biofilm formation by Clostridium difficile . Gut Microbes 4 : 397402.[PubMed] [CrossRef]
18. O’Toole G,, Kaplan HB,, Kolter R . 2000. Biofilm formation as microbial development. Annu Rev Microbiol 54 : 4979.[PubMed] [CrossRef]
19. Stewart PS,, Costerton JW . 2001. Antibiotic resistance of bacteria in biofilms. Lancet 358 : 135138.[PubMed] [CrossRef]
20. Characklis W,, Cooksey K . 1983. Biofilms and microbial fouling. Adv Appl Microbiol 29 : 93138.[CrossRef]
21. Henze M,, Harremoës P . 1983. Anaerobic treatment of wastewater in fixed film reactors: a literature review. Water Sci Technol 15 : 1101.
22. Davies DG,, Parsek MR,, Pearson JP,, Iglewski BH,, Costerton J,, Greenberg E . 1998. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science 280 : 295298.[PubMed] [CrossRef]
23. Parsek MR,, Greenberg E . 2005. Sociomicrobiology: the connections between quorum sensing and biofilms. Trends Microbiol 13 : 2733.[PubMed] [CrossRef]
24. O’Toole GA,, Kolter R . 1998. Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol Microbiol 30 : 295304.[PubMed] [CrossRef]
25. O’Toole GA,, Pratt LA,, Watnick PI,, Newman DK,, Weaver VB,, Kolter R . 1999. Genetic approaches to study of biofilms. Methods Enzymol 310 : 91109.[PubMed] [CrossRef]
26. O’Toole G,, Kaplan HB,, Kolter R . 2000. Biofilm formation as microbial development. Annu Rev Microbiol 54 : 4979.[PubMed] [CrossRef]
27. Hentzer M,, Riedel K,, Rasmussen TB,, Heydorn A,, Andersen JB,, Parsek MR,, Rice SA,, Eberl L,, Molin S,, Høiby N,, Kjelleberg S,, Givskov M . 2002. Inhibition of quorum sensing in Pseudomonas aeruginosa biofilm bacteria by a halogenated furanone compound. Microbiology 148 : 87102.[PubMed] [CrossRef]
28. Boyle KE,, Heilmann S,, van Ditmarsch D,, Xavier JB . 2013. Exploiting social evolution in biofilms. Curr Opin Microbiol 16 : 207212.[PubMed] [CrossRef]
29. Jenal U,, Malone J . 2006. Mechanisms of cyclic-di-GMP signaling in bacteria. Annu Rev Genet 40 : 385407.[PubMed] [CrossRef]
30. Güvener ZT,, Harwood CS . 2007. Subcellular location characteristics of the Pseudomonas aeruginosa GGDEF protein, WspR, indicate that it produces cyclic-di-GMP in response to growth on surfaces. Mol Microbiol 66 : 14591473.[PubMed] [CrossRef]
31. Hickman JW,, Harwood CS . 2008. Identification of FleQ from Pseudomonas aeruginosa as a c-di-GMP-responsive transcription factor. Mol Microbiol 69 : 376389.[PubMed] [CrossRef]
32. Baraquet C,, Murakami K,, Parsek MR,, Harwood CS . 2012. The FleQ protein from Pseudomonas aeruginosa functions as both a repressor and an activator to control gene expression from the pel operon promoter in response to c-di-GMP. Nucleic Acids Res 40 : 72077218.[PubMed] [CrossRef]
33. Dasgupta N,, Arora SK,, Ramphal R . 2000. fleN, a gene that regulates flagellar number in Pseudomonas aeruginosa . J Bacteriol 182 : 357364.[PubMed] [CrossRef]
34. van Ditmarsch D,, Boyle KE,, Sakhtah H,, Oyler JE,, Nadell CD,, Deziel E,, Dietrich LE,, Xavier JB . 2013. Convergent evolution of hyperswarming leads to impaired biofilm formation in pathogenic bacteria. Cell Rep 4 : 697708.[PubMed] [CrossRef]
35. Kuchma SL,, Brothers KM,, Merritt JH,, Liberati NT,, Ausubel FM,, O’Toole GA . 2007. BifA, a cyclic-di-GMP phosphodiesterase, inversely regulates biofilm formation and swarming motility by Pseudomonas aeruginosa PA14. J Bacteriol 189 : 81658178.[PubMed] [CrossRef]
36. Kearns DB . 2013. You get what you select for: better swarming through more flagella. Trends Microbiol 21 : 508509.[PubMed] [CrossRef]
37. Watnick P,, Kolter R . 2000. Biofilm, city of microbes. J Bacteriol 182 : 26752679.[PubMed] [CrossRef]
38. Pennisi E . 2005. How did cooperative behavior evolve? Science 309 : 93. [PubMed] [CrossRef]
39. Griffin AS,, West SA,, Buckling A . 2004. Cooperation and competition in pathogenic bacteria. Nature 430 : 10241027.[PubMed] [CrossRef]
40. Keller L,, Surette MG . 2006. Communication in bacteria: an ecological and evolutionary perspective. Nat Rev Microbiol 4 : 249258.[PubMed] [CrossRef]
41. West SA,, Griffin AS,, Gardner A,, Diggle SP . 2006. Social evolution theory for microorganisms. Nat Rev Microbiol 4 : 597607.[PubMed] [CrossRef]
42. Hamilton WD . 1964. Genetical evolution of social behaviour. I. J Theor Biol 7 : 116.[CrossRef]
43. Hamilton WD . 1964. The genetical evolution of social behaviour. II. J Theor Biol 7 : 1752.[CrossRef]
44. Dawkins R . 2006. The Selfish Gene. Oxford University Press, Oxford, UK.
45. Visca P,, Ciervo A,, Orsi N . 1994. Cloning and nucleotide sequence of the pvdA gene encoding the pyoverdin biosynthetic enzyme L-ornithine N5-oxygenase in Pseudomonas aeruginosa . J Bacteriol 176 : 11281140.[PubMed]
46. Xavier JB,, Foster KR . 2007. Cooperation and conflict in microbial biofilms. Proc Natl Acad Sci USA 104 : 876881.[PubMed] [CrossRef]
47. Nadell CD,, Bassler BL . 2011. A fitness trade-off between local competition and dispersal in Vibrio cholerae biofilms. Proc Natl Acad Sci USA 108 : 1418114185.[PubMed] [CrossRef]
48. Kim W,, Racimo F,, Schluter J,, Levy SB,, Foster KR . 2014. Importance of positioning for microbial evolution. Proc Natl Acad Sci USA 111 : E1639E1647.[PubMed] [CrossRef]
49. Köhler T,, Curty LK,, Barja F,, Van Delden C,, Pechère JC . 2000. Swarming of Pseudomonas aeruginosa is dependent on cell-to-cell signaling and requires flagella and pili. J Bacteriol 182 : 59905996.[PubMed] [CrossRef]
50. Rashid MH,, Kornberg A . 2000. Inorganic polyphosphate is needed for swimming, swarming, and twitching motilities of Pseudomonas aeruginosa . Proc Natl Acad Sci USA 97 : 48854890.[PubMed] [CrossRef]
51. Xavier JB,, Kim W,, Foster KR . 2011. A molecular mechanism that stabilizes cooperative secretions in Pseudomonas aeruginosa . Mol Microbiol 79 : 166179.[PubMed] [CrossRef]
52. de Vargas Roditi L,, Boyle KE,, Xavier JB . 2013. Multilevel selection analysis of a microbial social trait. Mol Syst Biol 9 : 684. [PubMed] [CrossRef]
53. Czechowska K,, McKeithen-Mead S,, Al Moussawi K,, Kazmierczak BI . 2014. Cheating by type 3 secretion system-negative Pseudomonas aeruginosa during pulmonary infection. Proc Natl Acad Sci USA 111 : 78017806.[PubMed] [CrossRef]
54. van Ditmarsch D,, Xavier JB . 2014. Seeing is believing: what experiments with microbes reveal about evolution. Trends Microbiol 22 : 24.[PubMed] [CrossRef]
55. Brown SP,, West SA,, Diggle SP,, Griffin AS . 2009. Social evolution in micro-organisms and a Trojan horse approach to medical intervention strategies. Philos Trans R Soc Lond B Biol Sci 364 : 31573168.[PubMed] [CrossRef]
56. Mitri S,, Xavier JB,, Foster KR . 2011. Social evolution in multispecies biofilms. Proc Natl Acad Sci USA 108(Suppl 2): 1083910846.[PubMed] [CrossRef]
57. Grice EA,, Kong HH,, Conlan S,, Deming CB,, Davis J,, Young AC,, Bouffard GG,, Blakesley RW,, Murray PR,, Green ED,, Turner ML,, Segre JA,, Progra NCS . 2009. Topographical and temporal diversity of the human skin microbiome. Science 324 : 11901192.[PubMed] [CrossRef]
58. Dewhirst FE,, Chen T,, Izard J,, Paster BJ,, Tanner ACR,, Yu W-H,, Lakshmanan A,, Wade WG . 2010. The human oral microbiome. J Bacteriol 192 : 50025017.[PubMed] [CrossRef]
59. Kau AL,, Ahern PP,, Griffin NW,, Goodman AL,, Gordon JI . 2011. Human nutrition, the gut microbiome and the immune system. Nature 474 : 327336.[PubMed] [CrossRef]
60. 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 : 105108.[PubMed] [CrossRef]
61. Ezenwa VO,, Gerardo NM,, Inouye DW,, Medina M,, Xavier JB . 2012. Microbiology. Animal behavior and the microbiome. Science 338 : 198199.[PubMed] [CrossRef]
62. Taur Y,, Xavier JB,, Lipuma L,, Ubeda C,, Goldberg J,, Gobourne A,, Lee YJ,, Dubin KA,, Socci ND,, Viale A,, Perales MA,, Jenq RR,, van den Brink MR,, Pamer EG . 2012. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis 55 : 905914.[PubMed] [CrossRef]
63. Bucci V,, Bradde S,, Biroli G,, Xavier JB . 2012. Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota. PLoS Comput Biol 8 : e1002497. doi:10.1371/journal.pcbi.1002497. [PubMed] [CrossRef]
64. Ubeda C,, Taur Y,, Jenq RR,, Equinda MJ,, Son T,, Samstein M,, Viale A,, Socci ND,, van den Brink MR,, Kamboj M,, Pamer EG . 2010. Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J Clin Invest 120 : 43324341.[PubMed] [CrossRef]
65. Buffie CG,, Jarchum I,, Equinda M,, Lipuma L,, Gobourne A,, Viale A,, Ubeda C,, Xavier J,, Pamer EG . 2012. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect Immun 80 : 6273.[PubMed] [CrossRef]
66. Marino S,, Baxter NT,, Huffnagle GB,, Petrosino JF,, Schloss PD . 2014. Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci USA 111 : 439444.[PubMed] [CrossRef]
67. Stein RR,, Bucci V,, Toussaint NC,, Buffie CG,, Ratsch G,, Pamer EG,, Sander C,, Xavier JB . 2013. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput Biol 9 : e1003388. doi:10.1371/journal.pcbi.1003388. [PubMed] [CrossRef]
68. Fisher CK,, Mehta P . 2014. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PloS One 9 : e102451. doi:10.1371/journal.pone.0102451. [PubMed] [CrossRef]
69. Buffie CG,, Bucci V,, Stein RR,, McKenney PT,, Ling L,, Gobourne A,, No D,, Liu H,, Kinnebrew M,, Viale A,, Littmann E,, van den Brink MR,, Jenq RR,, Taur Y,, Sander C,, Cross J,, Toussaint NC,, Xavier JB,, Pamer EG . 2014. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile . Nature. [Epub ahead of print.] [PubMed] [CrossRef]
70. Nadell CD,, Xavier JB,, Foster KR . 2009. The sociobiology of biofilms. FEMS Microbiol Rev 33 : 206224.[PubMed] [CrossRef]
71. Goodman AL,, Kallstrom G,, Faith JJ,, Reyes A,, Moore A,, Dantas G,, Gordon JI . 2011. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci USA 108 : 62526257.[PubMed] [CrossRef]
72. Cullen TW,, Schofield WB,, Barry NA,, Putnam EE,, Rundell EA,, Trent MS,, Degnan PH,, Booth CJ,, Yu H,, Goodman AL . 2015. Gut microbiota. Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation. Science 347 : 170175.[PubMed] [CrossRef]
73. Bucci V,, Xavier JB . 2014. Towards predictive models of the human gut microbiome. J Mol Biol. [Epub ahead of print.] [PubMed] [CrossRef]
74. Griffin AS,, West SA,, Buckling A . 2004. Cooperation and competition in pathogenic bacteria. Nature 430 : 10241027.[PubMed] [CrossRef]

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