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Table 1 The varying effects of antibiotics usage against alteration caused to gut microbiota

From: The varying effects of antibiotics on gut microbiota

Antibiotics Clinical/RCT use Alteration in the gut
Amoxicillin and clarithromycin Used for short term treatment of certain bacterial species, duodenal ulcers aFirmicutes and bBacteriodetes (Oh et al. 2016)
Clindamycin Commonly used in broad based antibiotics for treatment of skin and vaginal infections aLactobacilli, Clostridia, Bacteroides, Bifidobacteria, C. dificile
bEnterococci and Enterobacteria (Klebsiella, Enterobacter and Citrobacter) (Clemente et al. 2012)
Clarythromycin To treat wide range of infections including skin, respiratory and stomach ulcers caused by H. pylori aFirmicutes, Proteobacteria, Enterococci, bile-salt hydrolase (Korpela et al. 2016)
bActinobacteriaBifidobacteria, Actinobacteria, resistance gene erm (B) (Jakobsson et al. 2010)
Cefprozil To treat wide range of bacterial infections aLacnoclostridiumbolteaeand
bBacteriodes enterotype
Cefepime To treat bacterial infections such as, urinary tract infections (UTI), pneumonia and skin infections bE. coli and Bifidobacteria
Ceftazidime To treat severe or life-threatening bacterial infections bEnterobacteriaceae and Lactobacilli
Imipenem To treat severe infection of heart, lungs, blood, bones, joints, female reproductive organs etc. bEnterobacteriaceae, Clostridia, Bacteriodes and Enterococci
Meropenem To treat infections of the abdomen such as appendicitis and peritonitis, bacterial meningitis infections aEnterococci, Enterobacteriaceae, Clostridia and Bacteriodes
Chlortetracycline and sulfamethazine Use for cattle feeding aProteobacteria, profoundly E. coli (Reijnders et al. 2016)
Piperacillin/tazabactam To treat bacterial pneumonia and skin, also gynecological and abdominal disorders bEnterobacteriaceae, Bifidobacteria, Eubacteria and Lactobacilli
Ciprofloxacin To treat various types of bacterial infections, skin, joint, bone UTIs, sinus and respiratory aEnterococciand bEnterobacteriacea (Stewardson et al. 2015)
Levoflaxacin To treat bacterial infection of lungs, ears, airways, bones, sinuses and joints bE. coli
Azithromycin + metronidazole
To treat respiratory infections and asthma-like episodes in children Short-term—bBifidobacterium (Wei et al. 2018)
Faecal calprotectin declined significantly (Levine et al. 2019)
Amoxicillin–clavulanate (AC) To treat infections like, Sinusitis, pneumonia, ear infections, UTIs etc. aEscherichia, Parabacteroides, Enterobacter and bRoseburia (Kabbani et al. 2017)
Vancomycin, (obese and pre-diabetes men) To treat infections caused by C. dificile and methicillin resistance Staphylococcus areaus (MRSA)
CDI treatment
bFirmicutes (Reijnders et al. 2016)
bFirmicutes (Cannon et al. 2017)
(Ciprofloxacin, vancomycin and metronidazole) for 7 To test whether disruption of the gut microbiota affects systemic innate immune responses during endotoxemia in healthy subjects bGut diversity however, no impact on agents of sepsis (Streptococcus pneumonia, Klebsiella pneumonia, E. coli) (Lankelma et al. 2017)
Surotomycin To determine the impacts of ascending doses of surotomycin on major organism groups in the gut microbiota
CDI treatment
bClostridia, Lactobacillus-Bifidobacterium, Enterococcus-streptococcus and Enterobacteria and B. fragilis persisted (Citron et al. 2016)
aBacteroidetes and Prevotella (Cannon et al. 2017)
Preterm birth + antibiotic To determine whether the differences in gut microbiota between late preterm and full-term infants results from prematurity or external exposures Prevalence differences in Bifidobacteria in full-term and bdiversity late preterm neonates (Bajaj et al. 2018)
Rifaximin (open-label treatment for 2 weeks)
Rifaximin [common variable immunodeficiency (CVID) patients]
To explore potential effects of rifaximin on the gastrointestinal microbial community in patients with IBS-D bPeptostreptococcaceae, Verrucomicrobiaceae, Enterobacteriaceae at a 10% false discovery rate threshold (Oh et al. 2016)
The gut bacteria in the CVID dysbiosis index were not changed (Jørgensen et al. 2019)
Lactulose and rifaximin) + FMT (Lacnospiraceae and Ruminococcaceae) The role of faecal microbial transplant (FMT) in restoring gut microbial function is unclear in cirrhosis bMicrobial diversity and autochthonous taxa relative abundance (Harris et al. 2018)
Fluoroquinolone antibiotic moxifloxacin + DAV132 To deliver a powerful adsorbent, activated charcoal, in the late ileum of human volunteers Preserved gut microbial diversity (de Gunzburg et al. 2018)
  1. aDenotes increased in abundance, expansion etc.
  2. bDenotes decreased in abundance, reduced etc.