메뉴 건너뛰기




Volumn 174, Issue 6, 2018, Pages 1406-1423.e16

Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

Author keywords

antibiotics; microbiome; Probiotics

Indexed keywords

CIPROFLOXACIN; CIPROFLOXACIN PLUS DEXAMETHASONE; METRONIDAZOLE; PROBIOTIC AGENT; SUPHERB BIO 25; TRANSCRIPTOME; ANTIINFECTIVE AGENT; RNA 16S;

EID: 85052739697     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2018.08.047     Document Type: Article
Times cited : (781)

References (61)
  • 2
    • 84887390865 scopus 로고    scopus 로고
    • Lactobacilli and bifidobacteria in the prevention of antibiotic-associated diarrhoea and Clostridium difficile diarrhoea in older inpatients (PLACIDE): a randomised, double-blind, placebo-controlled, multicentre trial
    • Allen, S.J., Wareham, K., Wang, D., Bradley, C., Hutchings, H., Harris, W., Dhar, A., Brown, H., Foden, A., Gravenor, M.B., Mack, D., Lactobacilli and bifidobacteria in the prevention of antibiotic-associated diarrhoea and Clostridium difficile diarrhoea in older inpatients (PLACIDE): a randomised, double-blind, placebo-controlled, multicentre trial. Lancet 382 (2013), 1249–1257.
    • (2013) Lancet , vol.382 , pp. 1249-1257
    • Allen, S.J.1    Wareham, K.2    Wang, D.3    Bradley, C.4    Hutchings, H.5    Harris, W.6    Dhar, A.7    Brown, H.8    Foden, A.9    Gravenor, M.B.10    Mack, D.11
  • 3
    • 84923879507 scopus 로고    scopus 로고
    • Repeated exposure to antibiotics in infancy: a predisposing factor for juvenile idiopathic arthritis or a sign of this group's greater susceptibility to infections?
    • Arvonen, M., Virta, L.J., Pokka, T., Kröger, L., Vähäsalo, P., Repeated exposure to antibiotics in infancy: a predisposing factor for juvenile idiopathic arthritis or a sign of this group's greater susceptibility to infections?. J. Rheumatol. 42 (2015), 521–526.
    • (2015) J. Rheumatol. , vol.42 , pp. 521-526
    • Arvonen, M.1    Virta, L.J.2    Pokka, T.3    Kröger, L.4    Vähäsalo, P.5
  • 4
    • 85051960349 scopus 로고    scopus 로고
    • Harms Reporting in Randomized Controlled Trials of Interventions Aimed at Modifying Microbiota: A Systematic Review
    • Published online July 17, 2018
    • Bafeta, A., Koh, M., Riveros, C., Ravaud, P., Harms Reporting in Randomized Controlled Trials of Interventions Aimed at Modifying Microbiota: A Systematic Review. Ann. Intern. Med., 2018, 10.7326/M18-0343 Published online July 17, 2018.
    • (2018) Ann. Intern. Med.
    • Bafeta, A.1    Koh, M.2    Riveros, C.3    Ravaud, P.4
  • 5
    • 0037204196 scopus 로고    scopus 로고
    • Clinical practice. Antibiotic-associated diarrhea
    • Bartlett, J.G., Clinical practice. Antibiotic-associated diarrhea. N. Engl. J. Med. 346 (2002), 334–339.
    • (2002) N. Engl. J. Med. , vol.346 , pp. 334-339
    • Bartlett, J.G.1
  • 6
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: a flexible trimmer for Illumina sequence data
    • Bolger, A.M., Lohse, M., Usadel, B., Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 (2014), 2114–2120.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 9
    • 84872488958 scopus 로고    scopus 로고
    • Bacteriocins - a viable alternative to antibiotics?
    • Cotter, P.D., Ross, R.P., Hill, C., Bacteriocins - a viable alternative to antibiotics?. Nat. Rev. Microbiol. 11 (2013), 95–105.
    • (2013) Nat. Rev. Microbiol. , vol.11 , pp. 95-105
    • Cotter, P.D.1    Ross, R.P.2    Hill, C.3
  • 10
    • 79952756960 scopus 로고    scopus 로고
    • Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
    • Dethlefsen, L., Relman, D.A., Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl. Acad. Sci. USA 108:Suppl 1 (2011), 4554–4561.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 4554-4561
    • Dethlefsen, L.1    Relman, D.A.2
  • 11
    • 56849106496 scopus 로고    scopus 로고
    • The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
    • Dethlefsen, L., Huse, S., Sogin, M.L., Relman, D.A., The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol., 6, 2008, e280.
    • (2008) PLoS Biol. , vol.6 , pp. e280
    • Dethlefsen, L.1    Huse, S.2    Sogin, M.L.3    Relman, D.A.4
  • 13
    • 60849139395 scopus 로고    scopus 로고
    • GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
    • Eden, E., Navon, R., Steinfeld, I., Lipson, D., Yakhini, Z., GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics, 10, 2009, 48.
    • (2009) BMC Bioinformatics , vol.10 , pp. 48
    • Eden, E.1    Navon, R.2    Steinfeld, I.3    Lipson, D.4    Yakhini, Z.5
  • 15
    • 84923915405 scopus 로고    scopus 로고
    • Gut microbiota disturbance during antibiotic therapy: a multi-omic approach
    • Ferrer, M., Martins dos Santos, V.A., Ott, S.J., Moya, A., Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut Microbes 5 (2014), 64–70.
    • (2014) Gut Microbes , vol.5 , pp. 64-70
    • Ferrer, M.1    Martins dos Santos, V.A.2    Ott, S.J.3    Moya, A.4
  • 16
    • 0017392876 scopus 로고
    • Bacteriocin from Actinomyces odontolyticus with temperature-dependent killing properties
    • Franker, C.K., Herbert, C.A., Ueda, S., Bacteriocin from Actinomyces odontolyticus with temperature-dependent killing properties. Antimicrob. Agents Chemother. 12 (1977), 410–417.
    • (1977) Antimicrob. Agents Chemother. , vol.12 , pp. 410-417
    • Franker, C.K.1    Herbert, C.A.2    Ueda, S.3
  • 17
    • 34047114842 scopus 로고    scopus 로고
    • Diversity of enterococcal bacteriocins and their grouping in a new classification scheme
    • Franz, C.M., van Belkum, M.J., Holzapfel, W.H., Abriouel, H., Gálvez, A., Diversity of enterococcal bacteriocins and their grouping in a new classification scheme. FEMS Microbiol. Rev. 31 (2007), 293–310.
    • (2007) FEMS Microbiol. Rev. , vol.31 , pp. 293-310
    • Franz, C.M.1    van Belkum, M.J.2    Holzapfel, W.H.3    Abriouel, H.4    Gálvez, A.5
  • 18
    • 8344249371 scopus 로고    scopus 로고
    • Molecular quantification of lactic acid bacteria in fermented milk products using real-time quantitative PCR
    • Furet, J.-P., Quénée, P., Tailliez, P., Molecular quantification of lactic acid bacteria in fermented milk products using real-time quantitative PCR. Int. J. Food Microbiol. 97 (2004), 197–207.
    • (2004) Int. J. Food Microbiol. , vol.97 , pp. 197-207
    • Furet, J.-P.1    Quénée, P.2    Tailliez, P.3
  • 19
    • 33644893604 scopus 로고    scopus 로고
    • The effect of a probiotic drink with Lactobacillus plantarum 299v on the bacterial composition in faeces and mucosal biopsies of rectum and ascending colon
    • Goossens, D.A., Jonkers, D.M., Russel, M.G., Stobberingh, E.E., Stockbrügger, R.W., The effect of a probiotic drink with Lactobacillus plantarum 299v on the bacterial composition in faeces and mucosal biopsies of rectum and ascending colon. Aliment. Pharmacol. Ther. 23 (2006), 255–263.
    • (2006) Aliment. Pharmacol. Ther. , vol.23 , pp. 255-263
    • Goossens, D.A.1    Jonkers, D.M.2    Russel, M.G.3    Stobberingh, E.E.4    Stockbrügger, R.W.5
  • 20
    • 84961214408 scopus 로고    scopus 로고
    • Impact of probiotic supplements on microbiome diversity following antibiotic treatment of mice
    • Grazul, H., Kanda, L.L., Gondek, D., Impact of probiotic supplements on microbiome diversity following antibiotic treatment of mice. Gut Microbes 7 (2016), 101–114.
    • (2016) Gut Microbes , vol.7 , pp. 101-114
    • Grazul, H.1    Kanda, L.L.2    Gondek, D.3
  • 21
    • 18444399939 scopus 로고    scopus 로고
    • Quantitative real-time PCR assays to identify and quantify fecal Bifidobacterium species in infants receiving a prebiotic infant formula
    • Haarman, M., Knol, J., Quantitative real-time PCR assays to identify and quantify fecal Bifidobacterium species in infants receiving a prebiotic infant formula. Appl. Environ. Microbiol. 71 (2005), 2318–2324.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 2318-2324
    • Haarman, M.1    Knol, J.2
  • 22
    • 84860708876 scopus 로고    scopus 로고
    • Probiotics for the prevention and treatment of antibiotic-associated diarrhea: a systematic review and meta-analysis
    • Hempel, S., Newberry, S.J., Maher, A.R., Wang, Z., Miles, J.N., Shanman, R., Johnsen, B., Shekelle, P.G., Probiotics for the prevention and treatment of antibiotic-associated diarrhea: a systematic review and meta-analysis. JAMA 307 (2012), 1959–1969.
    • (2012) JAMA , vol.307 , pp. 1959-1969
    • Hempel, S.1    Newberry, S.J.2    Maher, A.R.3    Wang, Z.4    Miles, J.N.5    Shanman, R.6    Johnsen, B.7    Shekelle, P.G.8
  • 24
    • 84890310958 scopus 로고    scopus 로고
    • Antibiotic exposure in the first two years of life and development of asthma and other allergic diseases by 7.5 yr: a dose-dependent relationship
    • Hoskin-Parr, L., Teyhan, A., Blocker, A., Henderson, A.J., Antibiotic exposure in the first two years of life and development of asthma and other allergic diseases by 7.5 yr: a dose-dependent relationship. Pediatr. Allergy Immunol. 24 (2013), 762–771.
    • (2013) Pediatr. Allergy Immunol. , vol.24 , pp. 762-771
    • Hoskin-Parr, L.1    Teyhan, A.2    Blocker, A.3    Henderson, A.J.4
  • 27
    • 34248152283 scopus 로고    scopus 로고
    • Long-term ecological impacts of antibiotic administration on the human intestinal microbiota
    • Jernberg, C., Löfmark, S., Edlund, C., Jansson, J.K., Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 1 (2007), 56–66.
    • (2007) ISME J. , vol.1 , pp. 56-66
    • Jernberg, C.1    Löfmark, S.2    Edlund, C.3    Jansson, J.K.4
  • 28
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa, M., Goto, S., KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28 (2000), 27–30.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 29
    • 33746702149 scopus 로고    scopus 로고
    • Adhesion of the probiotic bacterium Lactobacillus plantarum 299v onto the gut mucosa in critically ill patients: a randomised open trial
    • Klarin, B., Johansson, M.L., Molin, G., Larsson, A., Jeppsson, B., Adhesion of the probiotic bacterium Lactobacillus plantarum 299v onto the gut mucosa in critically ill patients: a randomised open trial. Crit. Care 9 (2005), R285–R293.
    • (2005) Crit. Care , vol.9 , pp. R285-R293
    • Klarin, B.1    Johansson, M.L.2    Molin, G.3    Larsson, A.4    Jeppsson, B.5
  • 31
    • 84867306721 scopus 로고    scopus 로고
    • Snakemake–a scalable bioinformatics workflow engine
    • Köster, J., Rahmann, S., Snakemake–a scalable bioinformatics workflow engine. Bioinformatics 28 (2012), 2520–2522.
    • (2012) Bioinformatics , vol.28 , pp. 2520-2522
    • Köster, J.1    Rahmann, S.2
  • 32
    • 84867173210 scopus 로고    scopus 로고
    • Antibiotic exposure and IBD development among children: a population-based cohort study
    • Kronman, M.P., Zaoutis, T.E., Haynes, K., Feng, R., Coffin, S.E., Antibiotic exposure and IBD development among children: a population-based cohort study. Pediatrics 130 (2012), e794–e803.
    • (2012) Pediatrics , vol.130 , pp. e794-e803
    • Kronman, M.P.1    Zaoutis, T.E.2    Haynes, K.3    Feng, R.4    Coffin, S.E.5
  • 33
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B., Salzberg, S.L., Fast gapped-read alignment with Bowtie 2. Nat. Methods 9 (2012), 357–359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 34
  • 35
    • 84957935234 scopus 로고    scopus 로고
    • Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases
    • Lichtman, J.S., Ferreyra, J.A., Ng, K.M., Smits, S.A., Sonnenburg, J.L., Elias, J.E., Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases. Cell Rep. 14 (2016), 1049–1061.
    • (2016) Cell Rep. , vol.14 , pp. 1049-1061
    • Lichtman, J.S.1    Ferreyra, J.A.2    Ng, K.M.3    Smits, S.A.4    Sonnenburg, J.L.5    Elias, J.E.6
  • 36
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love, M.I., Huber, W., Anders, S., Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 2014, 550.
    • (2014) Genome Biol. , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 38
    • 85015820719 scopus 로고    scopus 로고
    • Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome
    • Manor, O., Borenstein, E., Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome. Microbiome, 5, 2017, 19.
    • (2017) Microbiome , vol.5 , pp. 19
    • Manor, O.1    Borenstein, E.2
  • 39
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • Martin, M., Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet 17 (2011), 10–12.
    • (2011) EMBnet , vol.17 , pp. 10-12
    • Martin, M.1
  • 40
    • 0032152205 scopus 로고    scopus 로고
    • Epidemiology, risk factors and treatments for antibiotic-associated diarrhea
    • McFarland, L.V., Epidemiology, risk factors and treatments for antibiotic-associated diarrhea. Dig. Dis. 16 (1998), 292–307.
    • (1998) Dig. Dis. , vol.16 , pp. 292-307
    • McFarland, L.V.1
  • 41
    • 84924590652 scopus 로고    scopus 로고
    • Use of probiotics to correct dysbiosis of normal microbiota following disease or disruptive events: a systematic review
    • McFarland, L.V., Use of probiotics to correct dysbiosis of normal microbiota following disease or disruptive events: a systematic review. BMJ Open, 4, 2014, e005047.
    • (2014) BMJ Open , vol.4 , pp. e005047
    • McFarland, L.V.1
  • 42
    • 85018653355 scopus 로고    scopus 로고
    • Efficacy and Safety of Lactobacillus plantarum DSM 9843 (LP299V) in the Prevention of Antibiotic-Associated Gastrointestinal Symptoms in Children-Randomized, Double-Blind, Placebo-Controlled Study
    • Olek, A., Woynarowski, M., Ahrén, I.L., Kierkuś, J., Socha, P., Larsson, N., Önning, G., Efficacy and Safety of Lactobacillus plantarum DSM 9843 (LP299V) in the Prevention of Antibiotic-Associated Gastrointestinal Symptoms in Children-Randomized, Double-Blind, Placebo-Controlled Study. J. Pediatr. 186 (2017), 82–86.
    • (2017) J. Pediatr. , vol.186 , pp. 82-86
    • Olek, A.1    Woynarowski, M.2    Ahrén, I.L.3    Kierkuś, J.4    Socha, P.5    Larsson, N.6    Önning, G.7
  • 43
    • 84861760530 scopus 로고    scopus 로고
    • IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
    • Peng, Y., Leung, H.C., Yiu, S.-M., Chin, F.Y., IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28 (2012), 1420–1428.
    • (2012) Bioinformatics , vol.28 , pp. 1420-1428
    • Peng, Y.1    Leung, H.C.2    Yiu, S.-M.3    Chin, F.Y.4
  • 45
    • 79251477530 scopus 로고    scopus 로고
    • Antibiotic exposure by 6 months and asthma and allergy at 6 years: Findings in a cohort of 1,401 US children
    • Risnes, K.R., Belanger, K., Murk, W., Bracken, M.B., Antibiotic exposure by 6 months and asthma and allergy at 6 years: Findings in a cohort of 1,401 US children. Am. J. Epidemiol. 173 (2011), 310–318.
    • (2011) Am. J. Epidemiol. , vol.173 , pp. 310-318
    • Risnes, K.R.1    Belanger, K.2    Murk, W.3    Bracken, M.B.4
  • 46
    • 84919371813 scopus 로고    scopus 로고
    • Detection and viability of Lactococcus lactis throughout cheese ripening
    • Ruggirello, M., Dolci, P., Cocolin, L., Detection and viability of Lactococcus lactis throughout cheese ripening. PLoS ONE, 9, 2014, e114280.
    • (2014) PLoS ONE , vol.9 , pp. e114280
    • Ruggirello, M.1    Dolci, P.2    Cocolin, L.3
  • 47
    • 84930943859 scopus 로고    scopus 로고
    • Development of a quantitative PCR assay for rapid detection of Lactobacillus plantarum and Lactobacillus fermentum in cocoa bean fermentation
    • Schwendimann, L., Kauf, P., Fieseler, L., Gantenbein-Demarchi, C., Miescher Schwenninger, S., Development of a quantitative PCR assay for rapid detection of Lactobacillus plantarum and Lactobacillus fermentum in cocoa bean fermentation. J. Microbiol. Methods 115 (2015), 94–99.
    • (2015) J. Microbiol. Methods , vol.115 , pp. 94-99
    • Schwendimann, L.1    Kauf, P.2    Fieseler, L.3    Gantenbein-Demarchi, C.4    Miescher Schwenninger, S.5
  • 48
    • 85025664354 scopus 로고    scopus 로고
    • Antibiotic Exposure in Early Life Increases Risk of Childhood Obesity: A Systematic Review and Meta-Analysis
    • Shao, X., Ding, X., Wang, B., Li, L., An, X., Yao, Q., Song, R., Zhang, J.A., Antibiotic Exposure in Early Life Increases Risk of Childhood Obesity: A Systematic Review and Meta-Analysis. Front. Endocrinol. (Lausanne), 8, 2017, 170.
    • (2017) Front. Endocrinol. (Lausanne) , vol.8 , pp. 170
    • Shao, X.1    Ding, X.2    Wang, B.3    Li, L.4    An, X.5    Yao, Q.6    Song, R.7    Zhang, J.A.8
  • 49
    • 84871956840 scopus 로고    scopus 로고
    • Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
    • Sharon, I., Morowitz, M.J., Thomas, B.C., Costello, E.K., Relman, D.A., Banfield, J.F., Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 23 (2013), 111–120.
    • (2013) Genome Res. , vol.23 , pp. 111-120
    • Sharon, I.1    Morowitz, M.J.2    Thomas, B.C.3    Costello, E.K.4    Relman, D.A.5    Banfield, J.F.6
  • 51
    • 47749156020 scopus 로고    scopus 로고
    • A unified approach to false discovery rate estimation
    • Strimmer, K., A unified approach to false discovery rate estimation. BMC Bioinformatics, 9, 2008, 303.
    • (2008) BMC Bioinformatics , vol.9 , pp. 303
    • Strimmer, K.1
  • 57
    • 84859728797 scopus 로고    scopus 로고
    • Association of repeated exposure to antibiotics with the development of pediatric Crohn's disease–a nationwide, register-based finnish case-control study
    • Virta, L., Auvinen, A., Helenius, H., Huovinen, P., Kolho, K.L., Association of repeated exposure to antibiotics with the development of pediatric Crohn's disease–a nationwide, register-based finnish case-control study. Am. J. Epidemiol. 175 (2012), 775–784.
    • (2012) Am. J. Epidemiol. , vol.175 , pp. 775-784
    • Virta, L.1    Auvinen, A.2    Helenius, H.3    Huovinen, P.4    Kolho, K.L.5
  • 61
    • 85052760428 scopus 로고    scopus 로고
    • Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features
    • this issue
    • Zmora, N., Zilberman-Schapira, G., Suez, J., Mor, U., Dori-Bachash, M., Bashiardes, S., Kotler, E., Zur, M., Regev-Lehavi, D., Brik, R.B.-Z., et al. Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell 174 (2018), 1388–1405 this issue.
    • (2018) Cell , vol.174 , pp. 1388-1405
    • Zmora, N.1    Zilberman-Schapira, G.2    Suez, J.3    Mor, U.4    Dori-Bachash, M.5    Bashiardes, S.6    Kotler, E.7    Zur, M.8    Regev-Lehavi, D.9    Brik, R.B.-Z.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.