Table 2 The varying effects of probiotics and prebiotics, and other used drugs on gut microbiota

Proton pump inhibitors (PPIs)

To treat dyspepsia

To eradicate H. pylori in the treatment of peptic ulcer, for Gastro reflux and Barrett’s esophagus

^aRothia, Enterococcus, Streptococcus, Staphylococcus and the potentially pathogenic species Escherichia coli (Jackson et al. 2016)

^bShannon9s diversity

Antidepressants

To balance neurotransmitters

^aEubacterium ramulus, Clostridium

^bE. coli

Laxatives

Treatment and prevention of constipation that affects up to 17% of European adults yearly

^aEnterobacteria and Streptococcus. Also, laxatives decrease Lactobacilli causing intestinal permeability

Oral steroids

Anti inflammatory therapy

^aMethanogenic bacteria associated with obesity and also an escalating BMI

Drinking water of Electrochemically reduced alkaline (pH ≈ 9)

To determine electrochemically reduced alkaline (pH ≈ 9) versus neutral (pH ≈ 7) drinking water (2 L/day) on human gut microbiota and host glucose metabolism

^aClostridiales, family Ruminococcaceae, genus Bacteroides, and species Prevotellacopri

Metformin

Metformin is used to treat Type 2 diabetes

E. coli is predominantly seen

Probiotics Lactobacillus rhamnosus GG (5 × 10⁹ cfu)

To ameliorate the effects of antibiotic use or caesarean birth on infant microbiota

Only breastfed infants showed the

^aBifidobacteria

^bProteobacteria and Clostridia (Korpela et al. 2018)

Auto-FMT during allo-HSCT treatment

To re-establish depleted gut commensal

^aMicrobial diversity and reestablished the intestinal microbiota composition (Taur et al. 2018)

6 g/day prebiotics inulin-type fructans or maltodextrin

To reduce febrile episodes requiring medical attention and to lower the incidence of sinusitis

^aBifidobacterium (with antibiotics)

^bBifidobacterium (non-antibiotic) (Soldi et al. 2019)

Probiotics intervention of Bifidobacterium spp.

To determine the effects of a Bifidobacteria-containing formula on the healthy human intestinal microbiome during the first year of life

^bBacteroides and Blautia spp. (Bazanella et al. 2017)

Synbiotics therapy

To evaluate whether Synbiotic (pre- and probiotics) therapy alters the gut microbiota

^aBifidobacterium

^bRuminococcaceae (Zuo et al. 2018)

Concomitant therapy antibiotic + probiotics regimen

To investigate the effects of a commonly used anti-Helicobacter pylori concomitant therapy on the composition of the gut and throat microbiota

Several alteration based on fecal culture however reverted by day 71 with the exception yeast and Bacteroides spp. (Wang et al. 2017)

Broad-spectrum (oral vancomycin, ciprofloxacin, metronidazole)

To test if microbiome modulation can improve oral rotavirus vaccine (RVV) immunogenicity

^bGut bacterial beta diversity and alters the immune response to RVV (Harris et al. 2018)