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

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

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)