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Table 1 Summary of human studies evaluating long-term changes to the microbiota following exposure to antibiotics

From: Gut microbiota-host interactions and juvenile idiopathic arthritis

Study Antibiotic Patient population Comparison Group Habitat Method of assessment Duration of follow-up Results
De la Cochetiere (2005)
Amoxicillin x 5 days 6 adults None Feces TTGE of 16S rDNA amplicons Two months After two months, profiles were >90 % similar to baseline in 5/6 subjects.
Dethlefsen 2011 [28] Two courses of ciprofloxacin x 5 days 3 adults None Feces Sequencing of 16S rDNA 10 months Altered community composition in 3/3, although there was more variability between subjects vs before and after abx.
Dethlefsen 2008 [73] One course of ciprofloxacin x 5 days 3 adults None Feces Sequencing of 16S rDNA 30 days Samples returned to baseline at the community level after 30 days, although individual taxa failed to recover.
Fouhy 2012a [74] One course of ampicillin and gentamycin 9 full-term neonates under age 2 days 9 full-term neonates Feces Sequencing of 16S rDNA 8 weeks Decreased evenness and richness; alterations in multiple genera. Of note, 9/9 controls but only 4/9 patients were delivered vaginally
Jakobsson 2010 [75] One course of metronidazole and clarithromycin x 7 days 3 adults 3 adults Throat and feces Sequencing of 16S rDNA and T-RFLP 4 years General recovery of loss of diversity in both habitats. However, long-lasting effects at the taxonomic level were seen, particularly in the throat.
Jernberg 2007 [27] One course of clindamycin x 7 days 4 adults 4 adults Feces T-RFLP and rep-PCR on Bacteroides 2 years Decreased number of bacteroides clonal types in exposed subjects
Lode 2001b [76] Linezolid x 7 days 12 adults None Feces Culture and identification 35 days No lasting effect
Lode 2001b [76] Amoxicillin / clav x 7 days 12 adults None Feces Culture and identification 35 days No lasting effect
Mangin 2012 [77] Amoxicillin / clav x 5 days 18 adult men None Feces qPCR for Bifidobacterium and PCR-TTGE 64 days No difference in total bifidobacteria; however, similarity to baseline dropped to 50 % rapidly and never reached 60 %.
Savino 2011 [78] Ceftriaxone x 5 days 26 full-term breast-fed infants None Feces Culture 20 days No changes noted in counts of enterobacteriaceae, enterococci, lactobacilli, or total bacteria
Vervoort 2015c [79] Nitrofurantoin x 3 – 15 days Five or eight subjects Four or five subjects Feces Sequencing of 16S rDNA 28 days Only transient differences in the frequency of the phyla.
  1. aThe duration of treatment was not specified. bThis Lode study was a crossover design with a 35 days washout, in which half received amoxicillin / clavulonic acid first and the other half received linezolid first. cThe methods said five pts and four controls, but the table said 8 and 5, respectively. No information on the age or sex of the subjects. Abbreviations: qPCR quantitative PCR, rDNA ribosomal DNA, rep-PCR repetitive sequence-based PCR, RFLP restriction fragment length polymorphisms, T-RFLP terminal restriction fragment length polymorphism, TTGE temporal temperature gradient gel electrophoresis