Proton pump inhibitors are often prescribed for prevention and treatment of gastroesophageal reflux and peptic ulcer disease16, 17 and rank eighth among the top therapeutic prescription classes in the United States.18 The relative efficacy and safety of PPIs have contributed to their significant overutilisation.19, 20 However, meta‐analyses have shown that PPI use was associated with increased incidence of Clostridium difficile infection,21, 22 higher rates of C. difficile recurrence in hospitalised patients,23 increased risk of other enteric infections24, 25 and community‐acquired Streptococcus pneumoniae.26 A recent study including 400 cirrhotic patients reported that PPI prescription was an independent predictor of infection.27

Jackson et al analysed PPI data and faecal samples from a cohort of 1827 individuals from the United Kingdom (90% were female with an average age of 62 years). They found a significantly lower α diversity in the gut microbiota of PPI users compared to non‐users. However, the observed negative association between PPI use and α diversity did not withstand correction for family and twin structure, body mass index, age, frailty and gastrointestinal indication (Shannon P = .67; OTU count P = .67; Phylogenetic Diversity P = .64; Chao1 P = .86). 28 Another study by Imhann et al evaluated three Dutch cohorts: (1) 1174 individuals participating in the Netherlands’ general population study “LifeLines‐DEEP”; 29 (2) 300 patients with IBD from the department of Gastroenterology and Hepatology University Medical Center Groningen, the Netherlands; (3) 189 patients with irritable bowel syndrome and 152 matched controls from Maastricht University Medical Center, the Netherlands. No significant change in α diversity was found in any of the three cohorts when considered separately. However, in a combined analysis of all three data sets, they identified a significant decrease in α diversity of PPI users compared to non‐users with Shannon ( P = .01) and species richness ( P = .02) metrics. 30 Moreover, Zhernakova et al in another cohort of 1135 Dutch participants, found that PPI medication was strongly associated with composition distance (adonis R 2 = .004, adjusted P = .0006), a measure of β diversity that here shows PPI use to be associated with specific changes in the architecture of the intestinal microbiome. 29 The same significant change in the overall gut microbiota architecture after PPI use was previously reported by Bajaj et al in controls and in patients with cirrhosis ( P < .0001). 31 A study by Seto et al also found a decrease in α diversity after both 1 week and 1 month of PPI treatment (observed OTUs, P = .004), in line with the trend found in treatment‐naïve patients infected with C. difficile . 32 In a trial with 12 healthy volunteers, Freedberg et al found that a 4‐week regimen of PPI medication (omeprazole 40 mg twice) was not associated with within‐individual changes in diversity. 33 O'Donoghue et al found that PPI use was significantly associated with increased microbial diversity, but only in patients receiving more than two antibiotics ( P < .01) and suggested that PPI use may counter antibiotics‐associated dysbiosis. 34

3.1.2 Taxonomic changes in the gut microbiota of PPI users

Jackson et al identified 22 OTUs with significantly lower abundance in PPI users, and 32 OTUs positively associated with PPI use (adjusted P‐value association with PPI use <.05), as detailed in Table 1. The strongest association was with a Bifidobacterium OTU, followed by a Streptococcus OTU (adjusted P‐value association with PPI use <10−4). At the level of species, seven were found to be negatively associated with PPI use, mainly assigned to Erysipelotrichales or Clostridiales, and 24 were found positively associated with PPI use. At the level of genera, nine were found to be negatively associated with PPI use, which were largely Firmicutes, with members of the family Erysipelotrichaceae being the most significantly decreased, and 24 positively associated with PPI use. At the level of families, five were found negatively associated with PPI use, and 10 were significantly positively associated with PPI use.28 Using the Human Microbiome Project data to determine body site preferences of bacteria, they also found that microbial families more abundant in PPI users were more often found in the mouth/throat, skin/nose or vaginal sites than in the gut.35

Table 1. Association with PPI use from Jackson et al OTU Species level Genus level Family level Positively associated with PPI use 32 OTUs, 20 from the order Bacteroidales and seven assigned to the Streptococcus genus

genus strongest association: Bifidobacterium (adjusted P < 10−4, R2 = .45), and Streptococcus (adjusted P <10−4, R2 = .44) 24 species

strongest association: Rothia mucilaginosa (adjusted P <10−6, R2 = .51) and Streptococcus anginosus (adjusted P <10−6, R2 = .48) 24 genera

strongest association: Rothia (adjusted P value <10−5, R2 = .45) and Streptococcus (adjusted P <10−6, R2 = .47) 10 families

strongest association: Streptococcaceae (adjusted P value <10−6, R2 = .46) and Micrococcaceae (adjusted P <10−5, R2 = .46) Negatively associated with PPI use 22 OTUs: all assigned to phylum Firmicutes Seven species, all assigned to Erysipelotrichales or Clostridiales (except for one Cyanobacteria) Nine genera, mainly Firmicutes Five families

strongest association: Lachnospiraceae (adjusted P = .004, R2 = −.35) and Ruminococcaceae (adjusted P < .0007, R2 = −.26

In a trial with 12 healthy volunteers, Freedberg et al found that a 4‐week regimen of PPI medication (omeprazole 40 mg twice) induced a significant within‐individual increase in Enterococcaceae (log2‐Fold change, P = .03), Micrococcaceae (log2‐Fold change, P = .01), and Streptococcaceae (log2‐Fold change, P < .01) and a significant decrease in Clostridiaceae (P = .03), corresponding to changes associated with predisposition to C. difficile infection.33 This significant increase in the relative abundance of Streptococcaceae after PPI use was previously reported by Bajaj et al, when compared with baseline in both patients with cirrhosis (baseline 0.0% vs 8.9%, adjusted P = .008) and controls (baseline 0.2% vs 5.7%, adjusted P = .007).31

In the analysis of three cohorts encompassing a total of 1815 participants, Imhann et al identified significant changes in 20% of the bacterial taxa in PPI users, with significant increase in the genera Enterococcus, Streptococcus, Staphylococcus and the potentially pathogenic species Escherichia coli. The order Actinomycetales, families Streptococcoceae, Micrococcoceae, genus Rothia and species Lactobacillus salivarius were increased in participants using PPI in each cohort. None of the individual cohorts contained any significantly decreased taxa (adjusted P <.05). In Cohort 1, 41 OTU were significantly increased, including the family Enterococcoceae, the genera Streptococcus, Veillonella and Enterococcus. In Cohort 2, PPI use was associated with an increase in 12 OTU, including the family Lactobacillaceae, the genera Streptococcus and Lactobacillus. In Cohort 3, 18 OTU were significantly increased, including the order Lactobacillales. Another important finding was the over‐representation of multiple oral bacteria in the faecal microbiome of PPI‐users, the most significantly increased being genera Rothia, Scardovia and Actinomyces (adjusted P <.05).30

In a prospective cohort study of 98 hospitalised patients, Vincent et al found that PPI medication was positively associated with Potyvirus (P = .006), Morganella (P = .011) and Pyramidobacter (P = .04); and negatively associated with Adlercreutzia (P = .003), Mitsuokella (P = .004), unclassified Clostridiaceae (P = .004), Campylobacter (P = .006), Pseudoflavonifractor (P = .007), Coprobacter (P = .01), Eubacterium (P = .02), Odoribacter (P = .02), Streptococcus (P = .02), Ruminococcus (P = .03), unclassified Clostridiales Family XI (P = .03) and Coprobacillus (P = .04).36