Gut microbiota disturbance during antibiotic therapy: A multi-omic approach

Gut Microbes

Volumn 5, Issue 1, 2013, Pages

  Ferrer, Manuel ^a   dos Santos, Vitor A P Martins ^b,c   Ott, Stephan J ^d,e   Moya, Andrés ^f,g,h  

^a CSIC   (Spain)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c LIFEGLIMMER GMBH   (Germany)

^d UNIVERSITY OF KIEL   (Germany)

^e UNIVERSITY HOSPITAL SCHLESWIG HOLSTEIN   (Germany)

^f Centro Superior de Investigación en Salud Pública CSISP   (Spain)

^g UNIVERSITY OF VALENCIA   (Spain)

^h CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

Author keywords

Antibiotic therapy; Human gut microbiota; Metabolomic; Metagenomic; Metaproteomic; Metatranscriptomic

Indexed keywords

AMOXICILLIN; AMPICILLIN; CEFAZOLIN; CHLORTETRACYCLINE; CIPROFLOXACIN; IMIPENEM; METRONIDAZOLE; PENICILLIN DERIVATIVE; RNA 16S; STREPTOMYCIN; SULBACTAM; SULFADIMIDINE; VANCOMYCIN;

AMINO ACID METABOLISM; ANTIBIOTIC THERAPY; ARTICLE; BACTERIAL COLONIZATION; BACTERIAL OVERGROWTH; CARBOHYDRATE METABOLISM; CELL RESPIRATION; ENERGY YIELD; ENTEROCOCCUS; FAECALIBACTERIUM; GENE EXPRESSION; GENETIC VARIABILITY; HUMAN; INTESTINE FLORA; MASS SPECTROMETRY; NONHUMAN; PROTEIN DEGRADATION;

EID: 84892527790     PISSN: 19490976     EISSN: 19490984     Source Type: Journal    
DOI: None     Document Type: Article

References (50)

1. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, et al. Evolution of mammals and their gut microbes. Science 2008; 320:1647-51; PMID:18497261; http://dx.doi. org/10.1126/science.1155725
2. Tschöp MH, Hugenholtz P, Karp CL. Getting to the core of the gut microbiome. Nat Biotechnol 2009; 27:344-6; PMID:19352371; http://dx.doi. org/10.1038/nbt0409-344
3. Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R. Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology 2011; 140:1713-9; PMID:21530737; http://dx.doi.org/10.1053/j. gastro.2011.02.011
4. Kinross JM, Darzi AW, Nicholson JK. Gut microbiome-host interactions in health and disease. Genome Med 2011; 3:14; PMID:21392406; http:// dx.doi.org/10.1186/gm228
5. Baquero F, Nombela C. The microbiome as a human organ. Clin Microbiol Infect 2012; 18(Suppl 4):2-4; PMID:22647038; http://dx.doi. org/10.1111/j.1469-0691.2012.03916.x
6. Feeney A, Sleator RD. The human gut microbiome: the ghost in the machine. Future Microbiol 2012; 7:1235-7; PMID:23075440; http://dx.doi. org/10.2217/fmb.12.105
7. Strader AD, Woods SC. Gastrointestinal hormones and food intake. Gastroenterology 2005; 128:175-91; PMID:15633135; http://dx.doi.org/10.1053/j. gastro.2004.10.043
8. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, et al. A core gut microbiome in obese and lean twins. Nature 2009; 457:480-4; PMID:19043404; http://dx.doi.org/10.1038/ nature07540
9. Kelly P. Nutrition, intestinal defence and the microbiome. Proc Nutr Soc 2010; 69:261-8; PMID:20202280; http://dx.doi.org/10.1017/ S0029665110000108
10. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al.; MetaHIT Consortium. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464:59-65; PMID:20203603; http://dx.doi.org/10.1038/ nature08821
11. Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI. Human nutrition, the gut microbiome and the immune system. Nature 2011; 474:327-36; PMID:21677749; http://dx.doi.org/10.1038/ nature10213
12. Brüls T, Weissenbach J. The human metagenome: our other genome? Hum Mol Genet 2011; 20(R2):R142-8; PMID:21840927; http://dx.doi.org/10.1093/ hmg/ddr353
13. Noverr MC, Huffnagle GB. Does the microbiota regulate immune responses outside the gut? Trends Microbiol 2004; 12:562-8; PMID:15539116; http:// dx.doi.org/10.1016/j.tim.2004.10.008
14. Mai V, Draganov PV. Recent advances and remaining gaps in our knowledge of associations between gut microbiota and human health. World J Gastroenterol 2009; 15:81-5; PMID:19115471; http://dx.doi. org/10.3748/wjg.15.81
15. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 2009; 9:313-23; PMID:19343057; http://dx.doi.org/10.1038/nri2515
16. Hwang JS, Im CR, Im SH. Immune disorders and its correlation with gut microbiome. Immune Netw 2012; 12:129-38; PMID:23091436; http://dx.doi. org/10.4110/in.2012.12.4.129
17. Nyangale EP, Mottram DS, Gibson GR. Gut microbial activity, implications for health and disease: the potential role of metabolite analysis. J Proteome Res 2012; 11:5573-85; PMID:23116228
18. Shen D, Liu C, Xu R, Zhang F. Human gut microbiota: dysbiosis and manipulation. Front Cell Infect Microbiol 2012; 2:123; PMID:23061053; http://dx.doi.org/10.3389/fcimb.2012.00123
19. Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 2008; 6:e280; PMID:19018661; http:// dx.doi.org/10.1371/journal.pbio.0060280
20. Antonopoulos DA, Huse SM, Morrison HG, Schmidt TM, Sogin ML, Young VB. Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect Immun 2009; 77:2367-75; PMID:19307217; http:// dx.doi.org/10.1128/IAI.01520-08
21. Preidis GA, Versalovic J. Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Gastroenterology 2009; 136:2015-31; PMID:19462507; http://dx.doi.org/10.1053/j. gastro.2009.01.072
22. Jakobsson HE, Jernberg C, Andersson AF, Sjölund-Karlsson M, Jansson JK, Engstrand L. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One 2010; 5:e9836; PMID:20352091; http://dx.doi. org/10.1371/journal.pone.0009836
23. Jernberg C, Löfmark S, Edlund C, Jansson JK. Longterm impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 2010; 156:3216-23; PMID:20705661; http://dx.doi.org/10.1099/ mic.0.040618-0
24. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 2011; 108(Suppl 1):4554-61; PMID:20847294; http://dx.doi.org/10.1073/ pnas.1000087107
25. Flint HJ. Obesity and the gut microbiota. J Clin Gastroenterol 2011; 45(Suppl):S128-32; PMID:21992951; http://dx.doi.org/10.1097/ MCG.0b013e31821f44c4
26. Willing BP, Russell SL, Finlay BB. Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat Rev Microbiol 2011; 9:233-43; PMID:21358670; http://dx.doi.org/10.1038/ nrmicro2536
27. Cotter PD, Stanton C, Ross RP, Hill C. The impact of antibiotics on the gut microbiota as revealed by high throughput DNA sequencing. Discov Med 2012; 13:193-9; PMID:22463795
28. Flint HJ. The impact of nutrition on the human microbiome. Nutr Rev 2012; 70(Suppl 1):S10-3; PMID:22861801; http://dx.doi. org/10.1111/j.1753-4887.2012.00499.x
29. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, et al. Human gut microbiome viewed across age and geography. Nature 2012; 486:222-7; PMID:22699611
30. Pérez-Cobas AE, Gosalbes MJ, Friedrichs A, Knecht H, Artacho A, Eismann K, Otto W, Rojo D, Bargiela R, von Bergen M, et al. Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut 2013; 62:1591-601; PMID:23236009; http:// dx.doi.org/10.1136/gutjnl-2012-303184
31. Ferrer M, Ruiz A, Lanza F, Haange SB, Oberbach A, Till H, Bargiela R, Campoy C, Segura MT, Richter M, et al. Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure. Environ Microbiol 2013; 15:211-26; PMID:22891823; http://dx.doi. org/10.1111/j.1462-2920.2012.02845.x
32. Montoliu I, Genick U, Ledda M, Collino S, Martin FP, le Coutre J, Rezzi S. Current status on genomemetabolome-wide associations: an opportunity in nutrition research. Genes Nutr 2013; 8:19-27; PMID:23065485; http://dx.doi.org/10.1007/ s12263-012-0313-7
33. Cho I, Yamanishi S, Cox L, Methé BA, Zavadil J, Li K, Gao Z, Mahana D, Raju K, Teitler I, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 2012; 488:621-6; PMID:22914093; http://dx.doi.org/10.1038/ nature11400
34. Russell SL, Gold MJ, Willing BP, Thorson L, McNagny KM, Finlay BB. Perinatal antibiotic treatment affects murine microbiota, immune responses and allergic asthma. Gut Microbes 2013; 4:158-64; PMID:23333861; http://dx.doi. org/10.4161/gmic.23567
35. Looft T, Allen HK. Collateral effects of antibiotics on mammalian gut microbiomes. Gut Microbes 2012; 3:463-7; PMID:22825498; http://dx.doi. org/10.4161/gmic.21288
36. Antunes LC, Han J, Ferreira RB, Lolic P, Borchers CH, Finlay BB. Effect of antibiotic treatment on the intestinal metabolome. Antimicrob Agents Chemother 2011; 55:1494-503; PMID:21282433; http://dx.doi.org/10.1128/AAC.01664-10
37. Pélissier MA, Vasquez N, Balamurugan R, Pereira E, Dossou-Yovo F, Suau A, Pochart P, Magne F. Metronidazole effects on microbiota and mucus layer thickness in the rat gut. FEMS Microbiol Ecol 2010; 73:601-10; PMID:20579100
38. Manichanh C, Reeder J, Gibert P, Varela E, Llopis M, Antolin M, Guigo R, Knight R, Guarner F. Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res 2010; 20:1411-9; PMID:20736229; http://dx.doi. org/10.1101/gr.107987.110
39. Ladero V, Linares DM, Del Rio B, Fernandez M, Martin MC, Alvarez MA. Draft genome sequence of the tyramine producer Enterococcus durans strain IPLA 655. Genome Announc 2013; 1:e00265-13; PMID:23682153
40. Fernández de Palencia P, Fernández M, Mohedano ML, Ladero V, Quevedo C, Alvarez MA, López P. Role of tyramine synthesis by food-borne Enterococcus durans in adaptation to the gastrointestinal tract environment. Appl Environ Microbiol 2011; 77:699-702; PMID:21097601; http://dx.doi.org/10.1128/ AEM.01411-10
41. Murri M, Leiva I, Gomez-Zumaquero JM, Tinahones FJ, Cardona F, Soriguer F, Queipo-Ortuño MI. Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study. BMC Med 2013; 11:46; PMID:23433344; http:// dx.doi.org/10.1186/1741-7015-11-46
42. Wrzosek L, Miquel S, Noordine ML, Bouet S, Joncquel Chevalier-Curt M, Robert V, Philippe C, Bridonneau C, Cherbuy C, Robbe-Masselot C, et al. Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent. BMC Biol 2013; 11:61; PMID:23692866; http://dx.doi. org/10.1186/1741-7007-11-61
43. Raouf AH, Tsai HH, Parker N, Hoffman J, Walker RJ, Rhodes JM. Sulphation of colonic and rectal mucin in inflammatory bowel disease: reduced sulphation of rectal mucus in ulcerative colitis. Clin Sci (Lond) 1992; 83:623-6; PMID:1335401
44. Nakano V, Nascimento e Silva Ad, Merino VR, Wexler HM, Avila-Campos MJ. Antimicrobial resistance and prevalence of resistance genes in intestinal Bacteroidales strains. Clinics (Sao Paulo) 2011; 66:543-7; PMID:21655744; http://dx.doi. org/10.1590/S1807-59322011000400004
45. Zhao Y, Wu J, Li JV, Zhou NY, Tang H, Wang Y. Gut microbiota composition modifies fecal metabolic profiles in mice. J Proteome Res 2013; 12:2987-99; PMID:23631562; http://dx.doi.org/10.1021/ pr400263n
46. Sakamoto M, Benno Y. Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov. Int J Syst Evol Microbiol 2006; 56:1599-605; PMID:16825636; http://dx.doi.org/10.1099/ijs.0.64192-0
47. Winter SE, Lopez CA, Bäumler AJ. The dynamics of gut-associated microbial communities during inflammation. EMBO Rep 2013; 14:319-27; PMID:23478337; http://dx.doi.org/10.1038/ embor.2013.27
48. Hernández E, Bargiela R, Diez MS, Friedrichs A, Pérez-Cobas AE, Gosalbes MJ, Knecht H, Martínez-Martínez M, Seifert J, von Bergen M, et al. Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity. Gut Microbes 2013; 4:306-15; PMID:23782552; http://dx.doi.org/10.4161/ gmic.25321
49. Ganesh BP, Klopfleisch R, Loh G, Blaut M. Commensal Akkermansia muciniphila exacerbates Gut inflammation in Salmonella typhimuriuminfected gnotobiotic Mice. PLoS One 2013; 8:e74963; PMID:24040367; http://dx.doi.org/10.1371/ journal.pone.0074963
50. Mizrahi I, Biran D, Ron EZ. Requirement for the acetyl phosphate pathway in Escherichia coli ATP-dependent proteolysis. Mol Microbiol 2006; 62:201-11; PMID:16987178; http://dx.doi. org/10.1111/j.1365-2958.2006.05360.x