SEARCH

SEARCH BY CITATION

References

  • 1
    Brook I, Gober AE. The effects of treatment of acute otitis media with a low dose vs a high dose of amoxicillin on the nasopharyngeal flora. Arch Otolaryngol Head Neck Surg 2009; 135: 458461.
  • 2
    Lund B, Edlund C, Rynnel-Dagoo B, Lundgren Y, Sterner J, Nord CE. Ecological effects on the oro- and nasopharyngeal microflora in children after treatment of acute otitis media with cefuroxime axetil or amoxycillin-clavulanate as suspensions. Clin Microbiol Infect 2001; 7: 230237.
  • 3
    Penders J, Thijs C, Vink C et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 2006; 118: 511521.
  • 4
    Blaser M. Antibiotic overuse: stop the killing of beneficial bacteria. Nature 2011; 476: 393394.
  • 5
    Caporaso JG, Kuczynski J, Stombaugh J et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010; 7: 335336.
  • 6
    Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science 2009; 326: 16941697.
  • 7
    Kuczynski J, Costello EK, Nemergut DR et al. Direct sequencing of the human microbiome readily reveals community differences. Genome Biol 2010; 11: 210.
  • 8
    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.
  • 9
    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): 45544561.
  • 10
    Jakobsson HE, Jernberg C, Andersson AF, Sjolund-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.
  • 11
    Lazarevic V, Whiteson K, Hernandez D, François P, Schrenzel J. Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics 2010; 11: 523.
  • 12
    Schloss PD, Westcott SL, Ryabin T et al. Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009; 75: 75377541.
  • 13
    Pruesse E, Quast C, Knittel K et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007; 35: 71887196.
  • 14
    Huse SM, Welch DM, Morrison HG, Sogin ML. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 2010; 12: 18891898.
  • 15
    Haas BJ, Gevers D, Earl AM et al. Chimeric 16s rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011; 21: 494504.
  • 16
    Huang Y, Niu B, Gao Y, Fu L, Li W. CD-HIT suite: a web server for clustering and comparing biological sequences. Bioinformatics 2010; 26: 680682.
  • 17
    Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73: 52615267.
  • 18
    Meyer F, Paarmann D, D'Souza M et al. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008; 9: 386.
  • 19
    Price MN, Dehal PS, Arkin AP. FASTTREE 2–approximately maximum-likelihood trees for large alignments. PLoS ONE. 5: e9490.
  • 20
    Hamady M, Lozupone C, Knight R. Fast unifrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and phylochip data. ISME J 2010; 4: 1727.
  • 21
    Zaura E, Keijser BJ, Huse SM, Crielaard W. Defining the healthy “core microbiome” of oral microbial communities. BMC Microbiol 2009; 9: 259.
  • 22
    Cephas KD, Kim J, Mathai RA et al. Comparative analysis of salivary bacterial microbiome diversity in edentulous infants and their mothers or primary care givers using pyrosequencing. PLoS ONE 2011; 6: e23503.
  • 23
    Crielaard W, Zaura E, Schuller AA, Huse SM, Montijn RC, Keijser BJ. Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med Genomics 2011; 4: 22.
  • 24
    Keijser BJ, Zaura E, Huse SM et al. Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res 2008; 87: 10161020.
  • 25
    Lazarevic V, Whiteson K, François P, Schrenzel J. The salivary microbiome assessed by a high-throughput and culture-independent approach. J Integr Omics 2011; 1: 2535.
  • 26
    Nasidze I, Li J, Schroeder R, Creasey JL, Li M, Stoneking M. High diversity of the saliva microbiome in Batwa pygmies. PLoS ONE 2011; 6: e23352.
  • 27
    Stahringer SS, Clemente JC, Corley RP et al. Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Genome Res 2012; 22: 21462152.
  • 28
    Sutherland R, Croydon EA, Rolinson GN. Amoxycillin: a new semi-synthetic penicillin. Br Med J 1972; 3: 1316.
  • 29
    Lemos LN, Fulthorpe RR, Triplett EW, Roesch LF. Rethinking microbial diversity analysis in the high throughput sequencing era. J Microbiol Methods 2011; 86: 4251.
  • 30
    Ready D, Lancaster H, Qureshi F, Bedi R, Mullany P, Wilson M. Effect of amoxicillin use on oral microbiota in young children. Antimicrob Agents Chemother 2004; 48: 28832887.
  • 31
    Sjolund M, Tano E, Blaser MJ, Andersson DI, Engstrand L. Persistence of resistant Staphylococcus epidermidis after single course of clarithromycin. Emerg Infect Dis 2005; 11: 13891393.
  • 32
    Costelloe C, Metcalfe C, Lovering A, Mant D, Hay AD. Effect of antibiotic prescribing in primary care on antimicrobial resistance in individual patients: systematic review and meta-analysis. BMJ 2010; 340: c2096.
  • 33
    Subcommittee on Management of Acute Otitis Media. Diagnosis and management of acute otitis media. Pediatrics 2004; 113: 14511465.