Table 2

Summary of studies included in the review

Study ID	Country	Design	Population	Setting	Infection	Antibiotic of interest (and dosage)	Sample and analysis	Primary outcome	Results
Amoxicillin
De La Cochetière et al (2005)37	France	Cohort	N=6 adults	Volunteers	Healthy	Amoxicillin (500 mg three times a day for 5 days)	Faecal samples; 16S rRNA PCR and TTGE gel analysis and sequence analysis	To assess the ability of the human faecal microbiota to return to its original dominant species profile after a 5-day course of amoxicillin	Similarity indices of the TTGE profiles on D1 ranged from 93% to 99%; on D3 62%–82% and D4 46%–94%. On D30 and D60, these had raised back to 65%–95% and 66%–98%, respectively. Bands excised from the gel related to Clostridium nexile and Ruminococcus torques (and β-Proteobacteria). No normalisation of bacterial abundance D55 after antibiotic treatment.
Monreal et al (2005)38	Brazil	Prospective	N=42 adults; 20 controls	Emergency department; blood donor centres	Bacterial respiratory infections (sinusitis, pneumonia)	Amoxicillin	Faecal samples analysed by culture and CFU on blood agar	Investigated the influence of respiratory tract infections and of amoxicillin therapy on the normal intestinal microbiota of patients	Concentrations of Bacteroides, Bifidobacterium spp Lactobacillus spp were significantly decreased in the antibiotic group. After 30 days, abundance of Bifidobacterium and Lactobacillus had normalised.
Pallav et al (2014)39	USA	RCT	N=24; 8 with amoxicillin, 8 controls, 8 other	Clinical and translational science centre	Healthy	Amoxicillin 250 mg three times a day for 7 days	16S rRNA gene sequencing region ns Roche 454 GS FLX Titanium GreenGenes/RDP/NCBI Database	Effect of amoxicillin vs controls	The genera that are most abundant are Faecalibacterium, Bacteroides, Rosburia, Clostridium and Ruminococcus. No change in bacterial abundance in the control group. The most notable change was an increase in Escherichia/Shigella during antibiotic treatment. Also increase in Bacteroides but decrease in Faecalibacterium spp. Antibiotic-associated changes persisted to the end of the study, 42 days after antibiotic therapy ended.
Abeles et al (2016)40	USA	Cohort of unrelated cohabiting individuals randomly assigned	N=56 adults	University campus	Self-reported health status	Amoxicillin 500 mg twice daily for 3 and 7 days	16S rRNA amplified from DNA using QIAGEN stool Mini Kit; sequencing	Effects of commonly prescribed antibiotics on microbiota	Microbiota grew more dissimilar over time but not significant. Most abundant taxa in gut were Bacteroidaceae, Lachnospiraceae and Ruminococcaceae. Lachnospiraceae, Veillonellaceae, Bacteroidales and Porphyromonadaceae were significantly decreased. Fusobacteriaceae increased. Bifidobacteriales and Erysipelotrichaecae initially decreased. There were sustained reductions in microbiome diversity in response to amoxicillin over 6 months.
Mangin et al (2010)41	Chile	Study trial	N=42 infants; 31 with treatment	Health centre	Acute bronchitis	Amoxicillin 50 mg/kg/day in three daily doses for 7 days	Faecal; real-time PCR for Bifidobacterium, TTGE and sequence analysis	To investigate the quantitative and qualitative changes occurring in the faecal bifidobacterial populations in 18-month children after a 1-week amoxicillin treatment	Total bacteria and numbers of Bifidobacteria were not significantly altered by amoxicillin treatment. However, treatment changed species diversity, a complete disappearance of B. adolescentis, increase in B. bifidum. No effect on B. longum, B. pseudocatenulatum/B. catenulatum.
Christensson et al (1991)42	Sweden	Randomised double-blind parallel multicentre trial	N=84 adults; 44 with treatment (38/44 completed)	Outpatients	Lower respiratory tract infection	Amoxicillin 250 mg twice daily for 7 days	Faecal; cultured aerobically and anaerobically in broth to ID pathogenic microorganism and on selective plates for analysis of microflora changes	To compare cefaclor and amoxicillin as treatment for lower respiratory tract infections and in their ability to influence colonisation resistance	No change in abundance of Enterococcus spp, Staphylococcus spp or Streptococcus spp, while enterobacteria significantly increased. Pseudomonas sp and Candida albicans were isolated from some samples. Anaerobic cocci numbers were reduced in some patients and increased in others. Lactobacilli, bifidobacteria, bacteroides and eubacteria increased. A couple of patients were colonised with C. difficile.
Brismar et al (1993)43	Sweden	Single blind randomised trial	N=20 adults; 10 with treatment	Not specified	Healthy volunteers	Amoxicillin 500 mg every 8 hours for 7 days	Faecal; selective media, MICs, beta lactamase activity	To study the oral and intestinal microflora before, during and after administration of cefpodoxime proxetil and amoxicillin	Numbers of aerobic intestinal microflora were slightly affected by amoxicillin administration. A minor decrease in numbers of streptococci and staphylococci, an over growth of Klebsiella and Enterobacter in a couple of samples. No overgrowth of enterococci or yeasts occurred. Eubacteria was reduced by amoxicillin. Increase in amoxicillin-resistant Enterobactericaeae (E. coli, Klebsiella sp and Enterobacter sp) No change in abundance of Bacteroides spp, Bifidobacterium spp, Enterococcus spp, Lactobacillus spp or yeast. No new colonisation with C. difficile. Normalisation of bacterial abundance 14 days after antibiotic treatment.
Edlund et al (1994)44	Sweden	Cohort	N=44 adults, 10 with treatment	Not specified	Not specified	Amoxicillin 500 mg t.i.d for 7 days	Faecal; serial dilutions and selective plating aerobic and anaerobic	The investigation was focused on drug concentrations in faeces, beta lactamase production by the intestinal microflora, alterations in the microflora and susceptibility patterns	Administration of amoxicillin affected the aerobic intestinal microflora to a minor extent. There was an overgrowth of Klebsiella spp and Enterobacter spp in some samples. No change in abundance of anaerobic bacteria, Bacteroides spp, Bifidobacterium spp, Enterococcus spp, E. coli, Clostridium spp, Lactobacillus spp or yeast. No colonisation with C. difficile. Intestinal microflora returned to normal 2 weeks after treatment stopped.
Ladirat et al (2014)45	The Netherlands	Double-blinded randomised parallel intervention study	N=12 adults (two not analysed due to non-compliance)	Not specified	Healthy volunteers	Amoxicillin 375 mg three times daily for 5 days	Faecal; Intestinal (I)-Chip microarray, total bacteria and Bifidobacterium spp using qPCR	Determined the effects of prebiotic intake on the microbiota of healthy adult subjects during and after treatment with amoxicillin	Total bacteria and Bifidobacterium were similar in both groups before treatment. Numbers of Bifidobacterium decreased over time due to amoxicillin treatment in both groups, but more so in the antibiotic only group (no prebiotic). After antibiotic treatment, numbers in the antibiotic only group were still lower than with prebiotics. Abundance of Bifidobacterium spp, B. longum and B. thermophilum was significantly higher in the prebiotic group. The composition of the microbiota in most subjects returned to normal after 3 weeks. Due to amoxicillin treatment, a decrease in the abundance of Bifidobacterium spp, an overgrowth of Enterobacteriaceae.
Floor et al (1994)46	The Netherlands	Randomised double-blind study	N=80 adults	Recruited from 9 general practices	Chronic bronchitis with purulent sputum	Amoxicillin, 500 mg three times a day for 7 days	Faecal; cultured aerobically and anaerobically on selective media, testing for C. difficile, enterococci, staphylococci, yeasts and biochemical identification	Effect of both amoxicillin and loracarbef on oropharyngeal and intestinal microflora	No change in abundance of anaerobic bacteria or E. faecalis. Total numbers of aerobic Gram-negative bacteria significantly higher on days 8–10 than at baseline. Enterococci cultured in one patient in amoxicillin group. Yeast numbers increased significantly but returned to baseline on days 21–28. Presence of other aerobic bacteria occurred in a slightly higher percentage of patients in the amoxicillin group. 13/15 new acquired bacteria in the amoxicillin group were Klebsiella. No new colonisation with C. difficile. Normalisation of bacterial and fungal abundance 21 days after treatment.
Amoxicillin and clavulanic acid
Korpela et al (2016)31	Finland	Part of a cohort from larger probiotic trial	N=236 children; 142 donated faecal samples	Day-care centres	Antibiotic use for respiratory (88%) other mainly urinary (5%)	Penicillins (amoxicillin with or without clavulanic acid and penicillin V), macrolides (azithromycin and clarithromycin) and sulphonamide–trimethoprim	Faecal by 16S rRNA and sequence analysis; operational taxonomic unit (OTU); culture-based antibiotic sensitivity testing	Use of phylogenetics, metagenomics and antibiotic use on microbiota composition and metabolism	Macrolide use reduced abundance of Actinobacteria and increased Bacteroidetes and Proteobacteria. Penicillin groups did not have distinctly different phyla. Firmicutes was reduced. The effect of macrolide use was long lasting and was associated with increased risk of asthma and antibiotic-associated weight gain.
Mangin et al (2012)47	France	Trial	N=18 treated, no controls	Study centre	Healthy volunteers	875/125 mg oral dose of amoxicillin/clavulanic acid twice a day for 5 days	Faecal samples, real-time PCR TTGE	Amoxicillin-clavulanic acid treatment on total bacteria and on Bifidobacterium species balance in human colonic microbiota	Total bacterial concentrations as well as bifidobacteria concentrations were significantly reduced after antibiotic treatment. The mean similarity percentages of TTGE bacteria and TTGE bifidobacteria profiles were significantly reduced. Occurrence of B. adolescentis, B. bifidum and B. pseudocatenulatum/B. catenulatum species significantly decreased. Occurrence of B. longum remained stable. Moreover, the number of distinct Bifidobacterium species per sample significantly decreased. Bacterial abundance was not normalised 2 months after antibiotics stopped.
Forssten et al (2014)48	Finland	Randomised double-blind placebo controlled parallel study	N=80 adults; 40:40 probiotic:placebo	Volunteers	Healthy	Augmentin (875 mg amoxicillin and 125 mg clavulanate) for 7 days	Faecal samples; qPCR for specific microbial groups	To investigate the effect of a specific combination of probiotic strains on the incidence of antibiotic-induced microbiota disturbances	Generally, Lactobacillus and Bifidobacterium were increased/restored in the probiotic group and reduced in the placebo group. Antibiotics reduced levels of Clostridium in both groups, but increased Enterobacteriaceae.
Young et al (2004)49	USA	Case report	N=1 adult male	Not detailed	Acute sinusitis	Amoxicillin-clavulanic acid (875 and 125 mg, respectively, twice daily for 10 days)	Faecal sample 16S rRNA PCR and sequencing and analysis	Molecular phylogenetic survey of the faecal microbiota from a patient who developed antibiotic-associated diarrhoea during the administration of a broad-spectrum antibiotic	D0,sequences clustered within four bacterial groups: Bacteroides spp, Clostridium sp IV, Clostridium sp XIVa and Bifidobacterium. At D4, Bacteroides still a major component, but B. distasonis group not B. fragilis cluster. No Clostridium sp XIVa or Bifidobacterium spp. 34% were now Enterobacteriaceae. D24, partial reversal, B. fragilis predominated and cluster XIVa returned, no Enterobacteriaceae, no Bifidobacterium spp normalisation of abundance 14 days after treatment.
Engelbrekston et al (2009)50	USA	Probiotic-antibiotic study arm	N=40 adults	Not specified	Healthy volunteers	Agumentin (amoxicillin and clavulanic acid), 875 mg twice daily for 7 days	Faecal; TRF analysis, PCR and enzyme digest, bacterial culturing on selective media for enumeration of different species	Analysis of faecal terminal restriction fragment length polymorphism data for treatment effects of probiotic treatment concurrent with antibiotic therapy	There was large subject-to-subject variability. Subjects fell into two categories: those with stable baseline microbiota and those where it varied significantly. Antibiotics had a significant effect on faecal microbiota across all subjects. Culture data also had large variation in counts. Increasing trends were visible in Bacteroides and enterics at day 21. There was no trend seen for Clostridium, Bifidobacterium and Lactobacillus. The placebo group had a significant change from baseline at day 21 in numbers of bacteria.
Lode et al (2001)51	Germany	Volunteers	N=12 adults	Not specified	Healthy	Amoxicillin/clavulanic acid 1000 mg (750:125 mg, respectively) daily	Faecal; culture on selective agar, colonies counted, isolated and identified to genus level	Investigate the ecological effects of linezolid, compared with those of amoxicillin/clavulanic acid, on the intestinal human microflora	Amoxicillin/Clavulanic acid was associated with significant increase in numbers of enterococci and E. coli. Other aerobic bacteria were largely unaffected. Anaerobic Bifidobacterium spp, Clostridium spp, Lactobacillus spp decreased significantly. No change in abundance of Bacteroides spp, Gram-positive bacilli or Klebsiella spp. C. difficile were isolated from 3 of the volunteers. Some resistant enterobacteria such as E. coli, Klebsiella sp and Enterobacter sp were isolated. The microflora was normalised 35 days after the end of administration.
Kabbani et al (2017)52	USA	Single-centre, open-label, randomised controlled	N=49, 12 antiobiotic treated, 12 controls	Clinical and translational science centre	Healthy volunteers	Amoxicillin/clavulanate 875/125 mg twice daily for 7 days	16S rRNA gene sequencing	To compare and contrast the effects of a probiotic and antibiotic, the main endpoint was change from baseline in the composition of the gut microbiota	Lower diversity (OTUs, Chao index) d10 and d21. Increased abundance of Parabacteroides spp persisted 14 days after antibiotic treatment was stopped. Control subjects had a stable microbiota throughout the study period. Significant microbiota changes in antibiotic treatment group included reduced prevalence of the genus Roseburia and increases in Escherichia, Parabacteroides and Enterobacter. Microbiota alterations reverted toward baseline, but were not yet completely restored 2 weeks after treatment stopped.
Nitrofurantoin
Stewardson et al (2015)53	Switzerland	Prospective cohort	N=40 adults; 10 nitrofuratonin	Ambulatory care	Lower UTI	Nitrofuratonin (100 mg twice daily for 5 days)	Faecal by 16S rRNA and sequence analysis; OTU	Compare the effects of ciprofloxacin and nitrofurantoin on the gut microbiota composition of non-hospitalised patients with UTIs compared with patients without antibiotic exposure and household contacts of patients receiving ciprofloxacin	Ciprofloxacin caused changes in a number of genus of gut bacteria. Substantial recovery after 4 weeks. Nitrofuratonin treatment correlated with a non-significant increase in Clostridium spp and decrease in Faecalibacterium spp. No change in abundance of Alistipes spp, Bacteroides spp, Bifidobacterium spp, Blautia spp, Dialister spp, Eubacterium spp. Oscillospira spp, Roseburia spp or Ruminococcus spp.
Vervoort et al (2015)54	Belgium and Poland	Prospective cohort	N=13; 5 controls	Ambulatory patients visiting GPs	Uncomplicated UTI	Nitrofurantoin (100 mg three times daily for 3–15 days)	Faecal; 16S rDNA PCR, sequencing and analysis	The impact of nitrofurantoin treatment on the gastrointestinal flora of patients with uncomplicated UTIs	Nitrofurantoin treatment did not significantly impact on the faecal microbiota other than a temporary increase in the Actinobacteria phylum (Bifidobacterium spp). No change in abundance of Bacteroidetes, Firmicutes, Proteobacteria, Tenericutes or Verrucomicrobia. Normalisation in abundance of Actinobacteria d31-43 after treatment.
Mavromanolakis et al (1997)55	Greece	Randomised	N=21 women; 7 with treatment	Not specified	UTI (at least three episodes caused by Enterobacteriaceae in the preceding 12 months)	Nitrofurantoin (100 mg daily for 30 days)	Faecal samples (and urine) cultured and plated on selective agar, API test kits for identification	Impact of doses of norfloxacin, trimethoprim-sulfamethoxazole and nitrofurantoin on aerobic bowel flora	Before antibiotic treatment, all stools contained Enterobacteriaceae and Enterococcus spp. Nitrofurantoin did not alter abundance of Enterobacteriaceae or Enterococcus spp in the colonic flora during treatment. No increased resistance to nitrofurantoin in Gram-negative aerobic bacteria. No patient receiving the drug was found to be colonised by yeasts.
Doxycycline
Heimdahl & Nord (1983)56	Sweden	Trial	N=10	Not specified	Healthy volunteers	Doxycycline 100 mg daily for 7 days	Faecal culture on selective media	Effect of doxycycline on the normal human flora and on colonisation of the oral cavity and colon	No change in abundance of Bacteroides spp, Bifidobacterium spp, Clostridium spp, Eubacterium spp, Lactobacillus spp or Veillonella spp. Fusobacteria were eliminated. A 2–3 log decrease in enterococci, streptococci and enterobacteria. Emergence of new strains Klebsiella pneumoniae, Proteus mirabilis and Enterobacter cloacae in some subjects. All colonising microorganisms were resistant to doxycycline. Normalisation of aerobic bacterial abundance 9 days after antibiotic treatment.
Walker et al (2005)57	USA	RCT	N=69 adult; 55 analysed	Clinic	Periodontitis	20 mg doxycycline	Faecal samples plated on a number of selective agar and incubated for CFU counts	To determine if a 9-month regimen of suboptimal doxycycline had an effect on either the intestinal or the vaginal microflora	The only statistically significant differences between the two treatment groups occurred in the doxycycline-resistant counts at the baseline sample. No between-treatment differences were detected at 3-month or 9-month period either in the predominant bacterial taxa or in antibiotic susceptibilities
Matto et al (2008)58	Finland	Not specified	N=19; 10 controls	Not specified	Not specified	Doxycycline 150 mg daily for 10 days with probiotic	Faecal 16S rRNA PCR for Bifidobacterium sp and DGGE and culturing and sequencing	To evaluate the influence of doxycycline therapy on the composition and antibiotic susceptibility of intestinal bifidobacteria	Bifidobacterium diversity was markedly higher in the control group than antibiotic group; each subject had 2–3 genotypes in the control group; 0–3 in the antibiotic group. The isolated bifidobacteria represented B. adolescentis⁄ B. ruminantium, B. longum, B. catenulatum⁄ B. pseudocatenulatum, B. bifidum and B. dentium. Tetracycline-resistant Bifidobacterium isolates were more commonly detected in the antibiotic group than in the control group, thus increasing the pool of resistant commensal bacteria in the intestine.
Rashid et al (2013)59	Sweden	Double-blind, randomised, placebo-controlled, parallel group study	N=34, 17 treated, 17 controls	Clinical trial unit	Healthy volunteers	Doxycycline 40 mg capsules orally once daily	Culture on selective media aerobic and anaerobic	Primary objective of this study was to assess the impact of antimicrobial treatment on the oropharyngeal and intestinal microflora during and after administration of 40 mg doxycycline capsule given once daily to healthy volunteers	Doxycycline was detectable in stool up to 16 weeks. No changes in abundance (>2 log CFU/g) of Bacteroides spp, Bifidobacterium spp, Clostridium spp, Candida spp, Lactobacillus spp or Enterobacteriaceae anaerobic intestinal microflora. No new colonisation with C. difficile. At week 20, the anaerobic microflora was normal. In aerobic intestinal microflora, there were changes (2 log CFU/g) in the numbers of enterococci and E. coli during the 16-week treatment. Other microorganisms such as other enterobacteria, Candida spp and other microorganisms were not affected. The aerobic microflora was normal at week 20. Increase in doxycycline resistance in Bifidobacterium spp, anaerobic cocci and Gram-positive rods.
Clarithromycin
Brismar et al (1991)60	Sweden	Cohort study	N=10 adults	Not specified	Healthy volunteers	Clarithromycin 250 mg twice daily for 7 days	Culture on selective and non-selective agar	To compare the effect of clarithromycin and erythromycin on the normal flora	Clarithromycin decreased the numbers of Bacteroides spp, Bifidobacterium spp, Lactobacillus spp and Streptococcus spp. Anaerobic cocci increased and C. albicans was isolated from two patients. No changes in the abundance of Bacillus spp, Clostridium spp, Corynebacterium spp, Enterococcus spp, Eubacterium spp, Micrococcus spp, Staphylococcus spp or Veillonella spp. Normalisation in abundance of Enterobacteriaceae, Lactobacillus spp and Streptococcus spp but not of Bacteroides spp and Bifidobacterium spp 14 days after antibiotic treatment.
Edlund et al (2000)61	Sweden	Healthy volunteers	N=12 male adult	Not specified	Healthy	Clarithromycin 500 mg twice daily for 7 days	Faecal; inhibition assay, culture on selective and non-selective agar	To investigate the ecological effects of moxifloxacin with those of clarithromycin on the intestinal human microflora	Clarithromycin significantly reduced E. coli in numbers during treatment but returned to pretreatment levels at day 35. Six subjects were colonised by resistant aerobic Gram-negative rods, Citrobacter, Klebsiella, Proteus and Pseudomonas. No overgrowth of yeasts. Total number of anaerobic bacteria decreased during treatment. Bifidobacteria were eliminated or strongly reduced. Bacteroides declined. Lactobacilli and clostridia were markedly declined but not significantly. Only minor alterations in numbers of peptostreptococci, veillonellacocci. No overgrowth of C. difficile. Bacterial abundance was normalised 28 days after antibiotic treatment.
Edlund et al (2000)62	Sweden	Randomised double-blind controlled study	N=20 adults	Not specified	Healthy	Clarithromycin 500 mg for 10 days	Faecal; culture on selective agar aerobic and anaerobic, Gram stain and biochemical tests, gas liquid chromatography	Assess the impact of antibiotic on intestinal microflora	Moderate disturbances in aerobic intestinal microflora, number of E. coli significantly reduced at day 10. Overgrowth of Klebsiella, Citrobacter and Enterobacter spp occurred in six subjects receiving clarithromycin. No significant overgrowth of Candida spp. There was a marked reduction in Bifidobacterium spp, Clostridia spp, Lactobacillus spp, Micrococcus spp and Staphylococcus spp. No change in the total numbers of anaerobic bacteria, Enterococcus spp, Peptostreptococcus spp, Bacteroides spp, Candida spp, Streptococcus spp or Veillonella spp. The lower numbers of Bifidobacterium spp and Lactobacillus spp persisted even after 14 days of no antibiotics.
Matute et al (2002)63	The Netherlands	Double blind-randomised trial	N=18, 6 treatment, 6 controls	Medical centre	Healthy volunteers	Clarithromycin 500 mg twice a day orally for 7 days	Faecal culture on selective agar aerobic and anaerobic	To compare the effect of 3-day, twice daily clarithromycin and with placebo on the faecal microflora	No change in abundance of Candida spp or Enterococcus spp. No new colonisation with C. difficile or non-fermenters. No increase in clarithromycin-resistant bacteria. The number of organisms of the family Enterobacteriaceae decreased slightly after antibiotic, but levels normalised by day 21 after therapy. The total number of anaerobic bacteria was not affected in the study group.
Phenoxymethylpenicillin
Heimdahl & Nord (1979)64	Sweden	Trial	N=20, 10 with phenoxymethylpenicillin	Research Institute	Healthy volunteers	Phenoxymethylpenicillin 800 mg as a loading dose, 800 mg twice daily for 7 days	Faecal culture on selective media under aerobic and anaerobic conditions. Bacterial identification by API strips	Effect of phenoxymethylpenicillin (and clindamycin) on the aerobic and anaerobic microflora in the human mouth, throat and colon	No change in abundance of Acidaminococcus spp, Bacteroides spp, Bifidobacterium spp, Clostridium spp, Enterobactericaeae, Enterococcus spp, Eubacterium spp, Fusobacterium spp, Lactobacillus spp, Megashaera spp, Streptococcus spp or Veillonella spp
Adamsson et al (1997)65	Sweden	Healthy volunteers	N=20 adults; 10 with treatment	Not specified	Healthy	Phenoxymethylpenicillin 1000 mg twice a day for 10 days	Faecal antimicrobial assay and culture	To investigate the ecological effects of phenoxymethylpenicillin, on the oropharyngeal and intestinal human microflora	No change in abundance of Bacillus spp, Bacteroides spp, Enterococcus spp or Streptococcus spp. There were minor alterations in numbers of E. coli. Three subjects became colonised with Klebsiella and one with high numbers of non-fermentative gram-negative rod. Numbers of Clostridium increased. No change in total numbers of aerobic or anaerobic bacteria. Normalisation of bacterial abundance day 14 after antibiotic treatment.
Erythromycin
Heimdahl & Nord (1982)66	Sweden	Trial	N=10	Research institute	Healthy volunteers	Erythromycin stearate was given orally in doses of 500 mg twice daily for 7 days	Faecal specimens were taken up to 16 days for cultivation of aerobic and anaerobic bacteria	The impact of erythromycin administration on the normal human flora and on colonisation of the oral cavity, throat and colon	Suppression of both aerobic and anaerobic faecal flora occurred. All subjects were colonised by erythromycin-resistant enterobacteria, clostridia or yeasts in the colon. In aerobes, the number of enterobacteria, enterococci and streptococci were reduced. In anaerobes, no change in abundance of Bifidobacterium spp, Eubacterium spp or Lactobacillus spp. However, Bacteroides, fusobacteria and Veillonella were eliminated in some subjects.
Brismar et al (1991)60	Sweden	Cohort study	N=10 adults	Not specified	Healthy	Erythromycin 1000 mg twice daily for 7 days	Faecal culture on selective media	Compare the effect of clarithromycin and erythromycin on intestinal microflora	Changes in the intestinal aerobic and anaerobic microflora. Streptococci eliminated, enterobacteria strongly suppressed. Minor reduction in enterococci and corynebacterial. Staphylococci and C. albicans increased. Normalisation in abundance of Bifidobacterium spp and Lactobacillus spp 14 days after treatment. Anaerobic, lactobacilli, bifidobacteri, clostridia and bacteroides reduced. No normalisation in abundance of Bacteroides spp and Clostridium spp 14 days after antibiotic treatment.

CFU, colony-forming unit ; GPs, general practitioners; RCT, randomised controlled trial; TTGE, temporal temperature gradient gel electrophoresis; UTI, urinary tract infection.