REVIEW published: 24 November 2020 doi: 10.3389/fcimb.2020.572912 Antibiotics as Major Disruptors of Gut Microbiota Jaime Ramirez 1,2, Francisco Guarner 3*, Luis Bustos Fernandez 4, Aldo Maruy 5, Vera Lucia Sdepanian 6 and Henry Cohen 7 1 Gastroenterology and Nutrition Department, Instituto Nacional de Pediatria, Mexico City, Mexico, 2 Facultad Nacional de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico, 3 Digestive System Research Unit, Vall d’Hebron Institute of Research (VHIR), Barcelona, Spain, 4 Instituto de Gastroenterologia, Centro Medico Bustos Fernandez (CMBF), Buenos Aires, Argentina, 5 Catedra de Pediatria, Hospital Cayetano Heredia, Universidad Peruana Cayetano Heredia, Lima, Peru, 6 Division of Pediatric Gastroenterology, Pediatric Department, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil, 7 Gastroenterology, National School of Medicine, Montevideo, Uruguay Advances in culture-independent research techniques have led to an increased understanding of the gut microbiota and the role it plays in health and disease. The intestine is populated by a complex microbial community that is organized around a network of metabolic interdependencies. It is now understood that the gut microbiota is Edited by: vital for normal development and functioning of the human body, especially for the priming Gianluca Ianiro, and maturation of the adaptive immune system. Antibiotic use can have several negative Catholic University of the Sacred Heart, Italy effects on the gut microbiota, including reduced species diversity, altered metabolic Reviewed by: activity, and the selection of antibiotic-resistant organisms, which in turn can lead to Benjamin Mullish, antibiotic-associated diarrhea and recurrent Clostridioides difficile infections. There is also Imperial College London, evidence that early childhood exposure to antibiotics can lead to several gastrointestinal, United Kingdom Jonathan Segal, immunologic, and neurocognitive conditions. The increase in the use of antibiotics in Imperial College London, recent years suggests that these problems are likely to become more acute or more United Kingdom prevalent in the future. Continued research into the structure and function of the gut *Correspondence: Francisco Guarner microbiota is required to address this challenge. fguarner@telefonica.net Keywords: antibiotic overuse, antibiotic resistance, gut microbiota, microbial diversity, antibiotic-associated diarrhea (AAD), enterotypes Specialty section: This article was submitted to Microbiome in Health and Disease, a section of the journal INTRODUCTION Frontiers in Cellular and Infection Microbiology Scientific advances made in recent decades have led to an increased recognition of the role of the Received: 17 June 2020 human gut microbiota in health and disease (Ananthakrishnan et al., 2019). Prior to that, little Accepted: 28 October 2020 research had been conducted into the non-pathogenic microorganisms that inhabit the Published: 24 November 2020 gastrointestinal tract (Guarner, 2012). Because most of these microorganisms cannot be cultured, Citation: they remained largely unexplored before the advent of molecular techniques. Ample experimental Ramirez J, Guarner F, and clinical evidence now shows that gut microorganisms are required for the optimal functioning Bustos Fernandez L, Maruy A, of the human body (Guarner, 2015). Sdepanian VL and Cohen H In 1885, Louis Pasteur hypothesized that animals raised in sterile conditions would not be able to (2020) Antibiotics as Major Disruptors of Gut Microbiota. survive (Pasteur, 1885). Bernard S. Wostmann and his team proved Pasteur’s hypothesis wrong Front. Cell. Infect. Microbiol. 10:572912. when they developed methods for breeding animals in germ-free conditions (Wostmann, 1981). doi: 10.3389/fcimb.2020.572912 However, they discovered that germ-free animals required large quantities of nutrient-rich food, yet Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 1 November 2020 | Volume 10 | Article 572912 Ramirez et al. Antibiotics and the Gut Microbiota continued to have stunted growth and development compared Composition with normal animals. Germ-free animals had smaller hearts, The genome of a single symbiotic microbial species is likely to be lungs, and livers, lower cardiac output, thinner intestinal walls, insufficient for survival (Guarner, 2015). As a result, multispecies reduced gastrointestinal motility, lower serum gamma globulin communities organized around a complex network of metabolic levels, and atrophied lymph nodes (Wostmann, 1981). Most of interdependencies, such as those found in the human gut, these deficiencies can be restored by introducing intestinal represent the natural environment for most symbiotic microbiota from animals raised under normal conditions. microbes (Guarner, 2015). Therefore, while microbial colonization may not be essential The development of culture-independent research methods for life, it is critical for health (Guarner and Malagelada, 2003; that combine genetic sequencing with bioinformatics has led to O’Hara and Shanahan, 2006). rapid advances in the study of the human gut microbiota The knowledge gained from germ-free animal models is (Guarner, 2015). One of the most common methods used for currently being translated to human physiology and medicine taxonomic identification and assessment of species diversity of through research into commensal microorganisms (Gilbert et al., prokaryotes (Bacteria and Archaea) is sequencing of the gene 2018). Ecological niches located along the gastrointestinal tract, that encodes the small subunit of ribosomal RNA (16S rRNA) from mouth to anus, contain the largest microbial communities (Guarner, 2015). Of the 55 phyla that comprise the domain found in the human body, comprising approximately 3.9×1013 Bacteria, only seven to nine are found in the human gut, with the bacterial cells, which can be investigated in fecal samples using a majority (90%) belonging to the Bacteroidetes and Firmicutes combination of genomic and culture-based approaches (Browne phyla (Eckburg et al., 2005). Other phyla consistently identified et al., 2016; Sender et al., 2016). Magnetic resonance imaging in the human gut include Proteobacteria, Actinobacteria, indicates that the large intestine is inhabited by several hundred Fusobacteria, and Verrucomicrobia, while very few Archaea grams of microbes, which is not surprising because it has the optimal species have been detected (Eckburg et al., 2005). conditions for microbial proliferation (i.e., constant temperature, Another culture-independent research method is whole anaerobiosis, and slow motility) (Bendezú Garcı́a et al., 2016). genome sequencing, which yields an inventory of all the genes The development of antibiotics is widely regarded as one of the present in a sample. Whole genome sequencing also allows the greatest medical advances of the 20th century (Bud, 2007; Royal analysis of the functional and metabolic networks, as well as the College of Physicians of Edinburgh, 2010). Worldwide antibiotic detection of genes that belong to non-bacterial members of use increased by 65% between 2000 and 2015 (Klein et al., 2018). the microbial community, such as viruses, yeasts, and protists. Although most courses of antibiotic treatment have no apparent In total, approximately 10 million non-redundant microbial adverse effects, antibiotics can cause significant changes in gut genes have been identified in human fecal samples (Li et al., microbiota that have both short- and long-term health 2014). On average, 600,000 non-redundant microbial genes are consequences (Dethlefsen and Relman, 2011). An association present in the gastrointestinal tract of a human, of which 300,000 between early antibiotic exposure and childhood asthma, allergies, genes are shared by people living in Europe, North America, and and airway illnesses has long been suspected (Foliaki et al., 2009). China (Li et al., 2014). Observational studies also implicate antibiotic use in the There are differences between the microbial communities pathogenesis of other increasingly prevalent conditions, including inhabiting the lumen and mucosa within the same individual gastrointestinal infections, weight gain and obesity, inflammatory (Eckburg et al., 2005; Donaldson et al., 2016). Furthermore, bowel disease (IBD), and colorectal cancer (Lange et al., 2016). bacterial species found in the lumen vary from the cecum to the Another serious consequence of antibiotic use is the development of rectum. In the cecum, slow transit time and lack of simple sugars bacterial antibiotic resistance (Giedraitiene et al., 2011). promote the proliferation of fermentative polysaccharide- The aim of this article is to review the literature on the gut degrading anaerobes, notably Prevotella, Roseburia, microbiota and its importance in human health, as well as to Faecalibacterium, Lachnospira, and Eubacterium. In distal describe the risks associated with the use of antibiotics and to sections of the colon, mucolytic and proteolytic species are outline some of the approaches that can minimize these risks. common (e.g., Bacteroides, Ruminococcus, Akkermansia, Bifidobacterium, Methanobrevibacter, Desulfovibrio, Proteus, and Escherichia). Mucosa-associated bacteria from the terminal HUMAN GUT MICROBIOTA ileum to the rectum tend to be more stable at the phylum and genus level, but patches of heterogeneity within the same Microbiota is defined as the assemblage of microorganisms intestinal area have been described (Donaldson et al., 2016). present in a particular environment, while the term Most strains that comprise the gut microbiota are resident for “microbiome” refers to the entire habitat, including the decades, although their relative abundance varies over time in a microorganisms (bacteria, archaea, lower and higher given individual (Donaldson et al., 2016). However, longitudinal eurkaryotes, and viruses), their genomes and the studies show that factors such as diet, drug intake, lifestyle environmental conditions that obtain in that habitat (Marchesi (smoking, travelling, physical activity), co-morbidities, or and Ravel, 2015). Bacteria, archaea, eukaryotes (fungi and colonic transit time have an impact on the microbial protists), and viruses that inhabit the gastrointestinal tract of composition of fecal samples obtained from a unique host humans are collectively referred to as the human gut microbiota. (Gilbert et al., 2018; Allaband et al., 2019; Zmora et al., 2019). Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 2 November 2020 | Volume 10 | Article 572912 Ramirez et al. Antibiotics and the Gut Microbiota Although intra-individual changes in gut microbiota the discrete nature of these states suggests that the structure of composition can be significant, for example, due to an episode the human gut microbiota is primarily determined by of acute infectious diarrhea or after antibiotic treatment, over interactions between various bacterial genera (Guarner, 2015). time it tends to return to its pre-disturbance state, a quality The clinical implications of enterotypes have been the subject known as resilience (Gilbert et al., 2018; Allaband et al., 2019). of several studies (Costea et al., 2018). The Bacteroides The diversity of gut microbiota also changes with age, increasing enterotype has been associated with decreased microbial from infancy to adulthood and decreasing in the elderly. Gut genetic diversity, insulin resistance, and the risk of obesity and microbial changes in elderly individuals correlate with measures non-alcoholic steatohepatitis (Le Chatelier et al., 2013; Costea of frailty, nutritional status, and markers of inflammation, et al., 2018). Perhaps unsurprisingly, long-term dietary patterns suggesting that diet-driven microbiota alterations play a role in may be one of the factors that determine the enterotype (Wu the varying rates of age-associated health decline (Kuipers, 2019). et al., 2011). Diets rich in animal protein and fat are associated The gut microbiota of each individual person contains many with the Bacteroides enterotype, while diets characterized by the unique strains not found in other individuals, and inter- predominance of plant carbohydrates are associated with the individual differences in microbiota composition are much Prevotella enterotype (Wu et al., 2011). larger than intra-individual variations (Allaband et al., 2019). Sex, ethnicity and geographic location affect the taxonomic Functions composition of the microbiome (Gaulke and Sharpton, 2018). The functions of the human gut microbiota fall into three For example, the fecal microbiota of adults from the categories, namely metabolic, defensive, and trophic functions metropolitan areas of Europe and North America is less (Guarner and Malagelada, 2003) (Figure 1). diverse compared with adults from rural populations in Africa The metabolic function involves the fermentation of non- and South America (Clemente et al., 2015; Sonnenburg and digestible dietary substrates and recovery of energy and Sonnenburg, 2019). nutrients. In humans, digestion of vegetables, fruits, nuts, and wholegrain cereals is mostly performed by gut microbes since Enterotypes our enzymatic resources for the digestion of carbohydrates are Despite intra- and inter-individual differences, an analysis of the limited to amylases and disaccharidases. In addition, microbial composition of fecal samples from American, fermentation of complex carbohydrates in the colon produces European, and Japanese individuals showed similarities in the short-chain fatty acids that are absorbed by the host (Litvak et al., structure of gut microbiota at the genus level (Arumugam et al., 2018). Butyrate produced by Faecalibacterium prausnitzii and 2011). Multidimensional scaling and principal coordinates others inhibits interleukin-17, generates regulatory T cells and analysis revealed the existence of three clusters, or enterotypes, has anti-inflammatory effects in experimental models (Litvak each of which was characterized by the predominance of one et al., 2018). Colonic microorganisms also break down genus: Bacteroides (enterotype 1), Prevotella (enterotype 2), or xenobiotics and other foreign compounds, contribute to amino Ruminococcus (enterotype 3). Clustering was not driven by age, acid and vitamin synthesis, and provide a variety of nutrients in sex, nationality, or body mass index (Arumugam et al., 2011). individuals on monotonous diets (Zmora et al., 2019). The results of this study indicate that there are a limited number The gut microbiota performs a defensive function by of well-balanced, host-microbiota symbiotic states. In addition, competing for attachment sites and nutrients with indigenous FIGURE 1 | Functions of human gut microbiota. Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 3 November 2020 | Volume 10 | Article 572912 Ramirez et al. Antibiotics and the Gut Microbiota fungi or bacteria with pathogenic potential, such as Candida and guidelines (Mullish et al., 2018). Less successful results have been Clostridioides difficile, thereby preventing invasion or observed with attempts to treat IBD. There are four randomized overgrowth of these organisms (McFarland, 2008). Resident trials that evaluated fecal transplant as induction therapy for microorganisms also inhibit the growth of their competitors by achieving remission in active ulcerative colitis, and these producing bacteriocins (McFarland, 2008). collectively show statistical improvement compared with The trophic function of gut microbiota includes promotion of control. At 8 weeks, 37% of participants in the stool transplant epithelial cell proliferation and differentiation, stimulation of group were in remission compared with 18% of participants in intestinal motor activity and neuro-endocrine pathways of gut the control group (Imdad et al., 2018). Additional studies are origin, and regulation of the immune system and the central needed to further define transplant material rich in microbial nervous system (Mayer et al., 2015). populations identified as missing in the patient, and avoiding Induction and regulation of the adaptive immune system is transplants rich in aggressive, over-represented microbes. one of the major aspects of the trophic function of the gut A loss of species diversity seems to be a common feature of a microbiota. The large surface area of the gastrointestinal tract is disturbed gut microbiota. Low microbial richness is associated constantly exposed to a variety of antigens. As a result, intestinal with an overabundance of pro- versus anti-inflammatory immunity is the largest and most complex part of the overall microbial species, and this may lead to intestinal inflammation immune system, with at least 80% of all antibodies produced in and disrupted function of the mucosal barrier. In a study that adults originating in the intestinal mucosa (Brandtzaeg, 2010). used the number of microbial genes in fecal samples as a proxy The intestinal immune system must be able to discriminate for diversity, individuals with low gene counts were more likely between pathogens and antigens derived from food or from to have insulin or leptin resistance, adiposity, or dyslipidemia, commensal non-pathogenic microbes, because an inflammatory and a more marked inflammatory phenotype, compared with reaction to a foreign antigen can also harm the host (Tanoue those with high gene counts (Le Chatelier et al., 2013). This et al., 2016). The gut microbiota affects the development of the association might indicate that low microbial richness increases adaptive immune system by stimulating the growth of lymphoid an individual’s risk of developing metabolic syndrome (i.e., structures, T- and B-cell differentiation and the establishment of obesity, arterial hypertension, type 2 diabetes, dyslipidemia, immune tolerance (Zhao and Elson, 2018). and non-alcoholic steatohepatitis). In terms of the functional capacity of the gut microbiota, a Perturbation of the Gut Microbiota low microbial gene count appears to be associated with a reduced The term dysbiosis refers to a persistent perturbation of the gut production of short-chain fatty acids (particularly butyrate) for microbiota, and has been defined as an alteration in both the the host (Le Chatelier et al., 2013). Failure to produce butyrate composition and function of the microbiota caused by host- increases the flow of oxygen towards the mucosa and perturbs related and environmental factors that overwhelms the resistance the micro-ecosystem in a way that favors the survival of oxygen- and resilience capabilities of the microbial ecosystem (Levy et al., resistant bacteria and precludes recovery of strict anaerobes 2017). Alterations in gut microbiota may be implicated in the (Litvak et al., 2018). In this way, dysbiosis has been described pathogenesis of several non-communicable diseases and in the as disruption of the symbiotic balance between microbiota and transition of these conditions to chronicity. Numerous studies host. Such changes critically affect the resilience capacity of the have shown links between changes in the composition of the gut ecosystem and increase the likelihood that the imbalance will microbiota and diseases, including recurrent diarrhea associated become chronic. with C. difficile, some bowel disorders (including IBD), colorectal cancer, non-alcoholic steatohepatitis, type 2 diabetes, obesity, and advanced chronic liver disease (Duvallet et al., 2017; Wirbel et al., 2019). However, for some of these examples, the studies are EFFECTS OF ANTIBIOTICS ON inconsistent, possibly because the methodology has not been GUT MICROBIOTA standardized. Furthermore, rather than necessarily indicating a causative role in the pathogenesis of a disease, these associated Antibiotic treatment reduces the overall diversity of gut microbiota changes could be a consequence of the disease microbiota species, including loss of some important taxa, itself. Thus, follow-up cohort studies are needed, particularly which causes metabolic shifts, increases gut susceptibility to studies of interventions that may restore the composition of colonization, and stimulates the development of bacterial gut microbiota. antibiotic resistance (Lange et al., 2016). Nevertheless, studies in rodents have shown that it is possible to use fecal transplants to transfer certain disease phenotypes, Reduced Diversity including insulin resistance, obesity, anxiety, and intestinal Antibiotic use is associated with reduced microbiota diversity. In inflammation. This suggests that some gut microbiota changes children, restoration of microbial diversity following antibiotic may have a causative role in those diseases. In humans, fecal treatment has been reported to take approximately 1 month microbiota transplantation has a well-established role in the (Yassour et al., 2016). In adults, administration of a combination treatment of recurrent diarrhea caused by C. difficile infection of meropenem, gentamicin, and vancomycin resulted in an (CDI) (Cammarota et al., 2017). Fecal transplant has become increase in the prevalence of Enterobacteriaceae and other standard therapy for this condition as recommended by national pathobionts, and a decrease in Bifidobacterium and butyrate- Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 4 November 2020 | Volume 10 | Article 572912 Ramirez et al. Antibiotics and the Gut Microbiota FIGURE 2 | Four-day antibiotic treatment induced large shifts in bacterial abundances. Graphs show relative abundance of representative species according to their pattern of change after four-day antibiotic treatment over a 180-day follow-up period. Adapted from Palleja et al. (2018). producing species (Palleja et al., 2018) (Figure 2). While the have been associated with an increased susceptibility to CDI, baseline composition of the gut microbiota was mostly restored potentially by serving as a growth substrate. Vancomycin/ within 1.5 months, several common species remained imipenem also reduced the relative abundance of undetectable for the rest of the observation period (180 days) Lachnospiraceae and Ruminococcaceae bacteria that normally (Palleja et al., 2018). convert arabinitol to pentose sugars. Immediately after the Antibiotics can also disrupt the balance that normally exists cessation of vancomycin/imipenem, a small but significant between the various species of gut microbiota. For instance, by reduction in the level of arginine was observed that correlated causing a decrease in species diversity, antibiotics can lead to the with increased prevalence of Escherichia and Shigella species and overgrowth of pathobionts, such as toxigenic C. difficile (Ianiro reduced prevalence of Ruminococcaceae and Bacteroides. An et al., 2020). increase in arginine observed 9 days after the end of It should be noted that reduced diversity does not necessarily vancomycin/imipenem was correlated with increased mean a reduced number of bacteria overall. As the antibiotic- prevalence of organisms from the Enterobacter genus and susceptible bacteria are eliminated, antibiotic-resistant bacteria reduced prevalence of Alistipes. Arginine serves as a precursor multiply and take their place. In fact, the total microbial load may for a number of immunomodulatory compounds (Choo increase after antibiotic treatment, even though species diversity et al., 2017). is reduced. In a study of patients treated with broad-spectrum Antibiotic exposure produces changes in the gut metabolome antibiotics, treatment with b-lactams over the course of 7 days that may or may not correlate with changes in the microbiome. increased the microbial load in fecal samples two-fold (Panda In patients with metabolic syndrome, oral administration of et al., 2014). In this study, broad-spectrum antibiotic use also vancomycin decreased fecal secondary bile acids, with a increased the ratio of Bacteroidetes to Firmicutes (Panda simultaneous postprandial increase in primary bile acids in et al., 2014). plasma. Concomitantly, vancomycin affected host physiology by decreasing peripheral insulin sensitivity (Vrieze et al., 2014). Altered Metabolome Antibiotic-induced changes in bile acid metabolism may affect The complete set of small molecules (<1500 Da) found in a host physiology and susceptibility to infection. biological system is referred to as the metabolome of that system (Lamichhane et al., 2018). The effects of antibiotics on the gut Antibiotic Resistance metabolome are less well studied than their effects on gut Antibiotic resistance is defined as the capacity of a species of microbial diversity. One factor that makes research into this bacteria to survive antibiotic concentrations that inhibit or kill connection more complex is metabolomic redundancy. Despite other bacteria of the same species (Sabtu et al., 2015). It first these challenges, some of the effects of antibiotics on the gut evolved in antibiotic-producing bacteria as a way to defend metabolome in mice have been described (Cho et al., 2012; Choo against their own products and compete with other microbes et al., 2017). In a study in young mice, low-dose antibiotics led to (Rolain, 2013). Worldwide, antibiotic resistance has emerged as a increased adiposity and elevated hormones associated with the significant public health concern. Between 2000 and 2015, global metabolism of carbohydrates, lipids and cholesterol (Cho et al., antibiotic consumption increased by 65% (Klein et al., 2018), 2012). In another study, vancomycin-imipenem administration with amoxicillin and amoxicillin/clavulanic acid being the most resulted in increased levels of arabinitol and sugars (e.g. sucrose) commonly used antibiotics (World Health Organization, 2018). in feces (Choo et al., 2017). Elevated levels of these compounds Between 2000 and 2015, the greatest increases in antibiotic use Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 5 November 2020 | Volume 10 | Article 572912 Ramirez et al. Antibiotics and the Gut Microbiota were observed in developing countries and the gap between CLINICAL CONSEQUENCES OF developing and developed countries decreased. Antibiotic ANTIBIOTIC USE resistance is responsible for an estimated 35,000 deaths in the US and 25,000 deaths in Europe each year (European Medicines Short- and Medium-Term Consequences Agency and European Centre for Disease Prevention and Antibiotic-Associated Diarrhea Control, 2009; Centers for Disease Control and Prevention, Antibiotic-associated diarrhea (AAD) is defined as diarrhea that 2019). According to one estimate, by 2050 the number of occurs in association with the administration of antibiotics and deaths per year caused by antibiotic resistance will be 317,000 that cannot be explained otherwise (Bartlett, 2002). Diarrhea can in North America, 390,000 in Europe, 392,000 in Latin America, occur during antibiotic treatment and up to 8 weeks after 4,150,000 in Africa, and 4,730,000 in Asia (Sugden et al., 2016). treatment cessation (McFarland, 2008). The World Health Organization estimates that the number of Under normal conditions, homeostasis of the intestinal antibiotic resistance-related deaths could reach 10 million by epithelium is maintained by a number of mechanisms, 2050 (World Health Organization, 2019). In China, resistance including a thick mucus layer and tight junctions to maintain has increased dramatically due to large-scale antibiotic use in the integrity of the intestinal epithelium (Willing et al., 2011). livestock (Van Boeckel et al., 2015). Inappropriate use of The number of gut bacteria is controlled by antimicrobial antibiotics, facilitated by their availability over the counter and peptides (C-type lectins, defensins, and cathelicidins), which on the internet, is the primary driver of antibiotic resistance are secreted into the mucus layer along with secretory (Sabtu et al., 2015). The increased prevalence of antibiotic- immunoglobulin A (IgA) in response to microorganism- resistant bacteria results in infections that are difficult and associated microbial patterns. Antibiotic exposure eliminates expensive to treat. As older antibiotics lose effectiveness due to subsets of the normal gut microbes, thereby reducing exposure resistance, newer antibiotics must be used. However, these drugs to microorganism-associated microbial patterns and decreasing are more expensive and may not be available to many of those secretion of antimicrobial peptides (Willing et al., 2011). In who need them, particularly in countries with a high burden of addition, some antibiotics cause thinning of the mucus layer infectious diseases (Klein et al., 2018). and disruption of tight junctions, rendering the intestinal Bacteria have developed a range of processes to elude the epithelium more susceptible to damage. Changes in microbial effects of antibiotics, including protection against the uptake of proteases could also affect mucosal barrier function. Collectively, antibiotics through their cell membranes, developing enzymatic these processes facilitate successful invasion by enteric pathogens processes that modify or degrade the antibiotic, altering the (Willing et al., 2011). molecules that antibiotics target, and actively removing The prevalence of AAD among patients who receive antibiotics from the cell via specialized efflux proteins antibiotics is approximately 5–35% (McFarland, 2008). In a (Giedraitiene et al., 2011). Bacterial enzymes that are able to study of adult ambulatory patients receiving antibiotics for 5– neutralize antibiotics include b-lactamases, aminoglycoside- 10 days, the incidence of AAD was 17.5% (Beaugerie et al., 2003). modifying enzymes, and chloramphenicol acetyltransferases The clinical course of AAD differed depending on whether C. (Giedraitiene et al., 2011). Bacteria are also able to mutate the difficile was involved, with most episodes of non-C. difficile AAD molecular targets of antibiotics, interfering with the highly being mild in severity and self-limiting, lasting only a few days specific interaction between the antibiotic and its target (Beaugerie et al., 2003). molecule through small structural modifications. For example, Meta-analyses have indicated that specific strains of probiotics mutations in penicillin-binding proteins reduce the efficacy of b- may be useful for the prevention of AAD. Compared with placebo lactams, mutations in 23S rRNA confer resistance to macrolides, or no treatment, the risk of AAD among adults and children treated lincosamides and streptogramin B, and mutations in DNA with antibiotics was significantly reduced with probiotic therapy topoisomerase II and IV lead to resistance to quinolones and comprised of Lactobacillus rhamnosus GG (relative risk, 0.49; 95% fluoroquinolones (Giedraitiene et al., 2011). Bacteria can CI, 0.29–0.83) (Szajewska and Kolodziej, 2015a) or Saccharomyces eliminate antimicrobial agents by pumping them out via efflux boulardii (risk ratio, 0.47; 95% CI, 0.38–0.57) (Szajewska and proteins located in the bacterial cell membrane. Although these Kolodziej, 2015b). proteins can be antibiotic-specific, most are multidrug The 2016 European Society for Paediatric Gastroenterology, transporters. Another mechanism of resistance is reduced Hepatology and Nutrition guidelines on probiotics and prebiotics outer membrane permeability, which results in a decreased recommend L. rhamnosus GG and S. boulardii for prevention of uptake of antibiotics (Giedraitiene et al., 2011). AAD in children, in both cases as a strong recommendation with In humans, the gut microbiota contains a pool of antibiotic moderate quality of evidence (Szajewska et al., 2016). resistance genes. Antibiotic treatment rapidly increases the pool of resistance genes present in the gut, which slowly declines after C. difficile-Associated Diarrhea treatment is discontinued (Rolain, 2013). Antibiotic-resistant gut C. difficile is a Gram-positive, spore-forming, anaerobic bacillus bacteria can be transferred to a newborn from his/her mother at birth with spores that are highly resistant to desiccation, chemicals, and thereafter may persist for weeks. In a Swedish study, tetracycline and extreme temperatures, and can remain viable for years resistance was detected in 12% of commensal E. coli strains from (Edwards et al., 2016). C. difficile produces toxins A and B that infants who had not received tetracycline (Karami et al., 2006). can damage the gut mucosa (Kuehne et al., 2010). Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 6 November 2020 | Volume 10 | Article 572912 Ramirez et al. Antibiotics and the Gut Microbiota In 2011, 453,000 cases of CDI and 29,000 CDI-associated composition in line with Hp-negative controls (Li et al., 2017). deaths were recorded in the US (Leffler and Lamont, 2015). A On the other hand, Hp eradication has been reported to significant proportion of CDIs are nosocomial, with the cause changes in microbiota composition that can negatively incidence of CDI being approximately 20 cases per 100,000 affect the host (Yap et al., 2016). Hp eradication was associated person-years in the community and approximately 15 per 1000 with a decrease in the relative abundance of Bacteroidetes hospital discharges (Leffler and Lamont, 2015). The most and an increase in Firmicutes. Increasing the prevalence of significant risk factor for CDI is antibiotic use, with the most bacteria that produce short-chain fatty acids can lead to an commonly associated drugs being ampicillin, amoxicillin, increased risk of metabolic disorders (Yap et al., 2016). cephalosporins, clindamycin, and fluoroquinolones. Both the Failure of Hp eradication therapy has been linked to poor duration of antibiotic therapy and the number of drugs used compliance due to antibiotic-associated adverse events are positively correlated with higher CDI risk. Other risk factors (Losurdo et al., 2018). include old age, compromised immunity, and hospitalization, An Hp eradication strategy that combined probiotics (S. particularly in an intensive care unit (Leffler and Lamont, 2015). boulardii) with triple therapy was more effective and had a Diagnosis of CDI in patients with diarrhea is based on the better adverse event profile than placebo or no intervention presence of bacteria in the stools. CDI is considered severe if plus triple therapy (Szajewska et al., 2010; Szajewska et al., 2015). serum albumin levels are <3 g/dl and either the white blood cell The addition of Lactobacillus- and Bifidobacterium-containing count is ≥15,000 per mm3 or abdominal tenderness is present probiotics to Hp eradication therapy was also associated with an (Surawicz et al., 2013). A two-step algorithm for detecting C. improved effectiveness and safety profile relative to eradication difficile in stool samples has been proposed that allows rapid therapy without probiotics (Wang et al., 2013; Losurdo et al., diagnosis within 4 h. Step 1 consists of detecting C. difficile- 2018). In a meta-analysis of studies in patients receiving specific glutamate dehydrogenase antigen and step 2 is detection antibiotic therapy for Hp eradication, L. acidophilus, L. casei of toxin A or B. Approximately 87.3% of suspected cases can be DN-114001, L. gasseri, and Bifidobacterium infantis 2036 excluded at the first step. If no toxin is detected at the second supplementation was associated with significantly higher step, culture should be performed (Fenner et al., 2008). eradication rates compared with controls (no probiotic Recommended treatments for CDI include metronidazole supplementation) (Dang et al., 2014). 500 mg orally three times daily for 10 days in mild and moderate cases, and vancomycin 125 mg four times daily for Long-Term Consequences 10 days in severe cases. Antibiotics that led to CDI should be Antibiotics are widely used in infants and children, systemic discontinued if possible (Surawicz et al., 2013; Neut et al., 2017). antibiotics being the most commonly prescribed drugs for Several meta-analyses have evaluated the use of probiotics for children in the US (Chai et al., 2012). Antibiotic use in prevention of CDI in children or adults receiving antibiotics. Two childhood has been associated with several negative outcomes meta-analyses showed that the incidence of CDI is lower in adult later in life, including the development of obesity, asthma, patients who receive probiotics in addition to antibiotic treatment allergy, and IBD (Cho et al., 2012; Bokulich et al., 2016; than in those who received placebo (Johnson et al., 2012; Korpela et al., 2016; Turta and Rautava, 2016). Goldenberg et al., 2013), while another meta-analysis produced Exposure to antibiotics during infancy has been associated similar findings in children (Goldenberg et al., 2015). Despite these with delayed gut microbiota development. In a study of infants findings, the evidence that probiotics prevent CDI was considered aged ≤2 years, the delay in microbiota development after insufficient to support their routine use (Surawicz et al., 2013). antibiotic use was particularly pronounced between the ages of 6 and 12 months (Bokulich et al., 2016). Enterobacteriaceae, Helicobacter pylori Infection Lachnospiraceae, and Erysipelotrichaceae species were among the Helicobacter pylori (Hp) is a Gram-negative, spiral-shaped, micro- operational taxonomic units that were depleted by antibiotics aerophilic bacterium that colonizes the gastric mucosa of humans (Bokulich et al., 2016). Furthermore, frequent use of macrolide (Perez-Perez and Blaser, 1996; Suerbaum and Michetti, 2002). Hp antibiotics in the first 2 years of life was significantly associated infection produces an inflammatory response in the gastric mucosa. either with current asthma and obesity or with the subsequent In most cases, this is a low-level and asymptomatic reaction. development of these conditions (Korpela et al., 2016). However, in some individuals, the infection can lead to gastric Early exposure to antibiotics and resulting dysbiosis are and duodenal ulcers, intestinal metaplasia, and gastric cancer thought to contribute to IBD pathogenesis. A population-based (Suerbaum and Michetti, 2002). cohort study showed that infants who received anti-anaerobic Currently, in areas of high clarithromycin resistance (>15%), antibiotics in the first year of life were more likely to be bismuth quadruple or non-bismuth quadruple concomitant (e.g., diagnosed with IBD than those not treated with antibiotics proton-pump inhibitor, amoxicillin, clarithromycin, and (Kronman et al., 2012). Similarly, a nationwide Danish cohort metronidazole) therapies are recommended (Malfertheiner study of children reported that the probability of developing IBD et al., 2017). However, in areas of both high clarithromycin was highest in the first 3 months after antibiotic use and in and metronidazole resistance, bismuth quadruple therapy is children who had received at least seven courses of antibiotics recommended as first-line therapy (Malfertheiner et al., 2017). (Hviid et al., 2011). A nationwide Finnish case-control study also Hp eradication can have both positive and negative effects. showed a stronger association between Crohn’s disease and On the one hand, eradication of Hp restores the microbiota antibiotic use in boys than in girls; the antibiotic class with the Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 7 November 2020 | Volume 10 | Article 572912 Ramirez et al. Antibiotics and the Gut Microbiota strongest association with Crohn’s disease was cephalosporins AUTHOR CONTRIBUTIONS (Virta et al., 2012). Human genetics and diet are known to play an important All authors (JR, LB, VS, FG, AM, and HC) wrote, edited, and role in determining body weight; however, it is now widely reviewed the drafts of the manuscript, and agree to be accepted that the increased prevalence of obesity over the past accountable for the content of the work. All authors 30 years may also be attributable to alterations in gut contributed to the article and approved the submitted version. microbiota composition (Biedermann and Rogler, 2015). In particular, early-life antibiotic exposure has been associated with the development of adiposity in humans (Trasande FUNDING et al., 2013). The development of this review article was funded by Biocodex France. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this CONCLUSIONS article or the decision to submit it for publication. Recent research has shown the gut microbiota to be an intricate network of metabolically interdependent microorganisms. A symbiotic gut microbiota performs several vital functions by ACKNOWLEDGMENTS aiding digestion, stimulating and regulating the immune system and preventing the growth of pathogens. The increasingly We would like to thank Georgii Filatov of Springer Healthcare widespread use of antibiotics is a major cause for concern as Communications, who provided editorial assistance in the antibiotics disrupt the gut microbiota. In order to address this preparation of this manuscript, and Sarah Greig, PhD, of challenge, further research is necessary to improve our Springer Healthcare Communications, who styled the understanding of the gut microbiota and strategies to reverse manuscript for submission. This medical writing assistance was these disruptions, including the use of probiotics. funded by Biocodex. transplantation in clinical practice. Gut. 66, 569–580. doi: 10.1136/gutjnl- REFERENCES 2016-313017 Allaband, C., McDonald, D., Vazquez-Baeza, Y., Minich, J. J., Tripathi, A., Centers for Disease Control and Prevention (2019). About antibiotic resistance. Brenner, D. A., et al. (2019). Microbiome 101: studying, analyzing, and Available at: https://www.cdc.gov/drugresistance/about.html (Accessed 16 interpreting gut microbiome data for clinicians. Clin. Gastroenterol. Hepatol. February, 2020). 17, 218–230. doi: 10.1016/j.cgh.2018.09.017 Chai, G., Governale, L., McMahon, A. W., Trinidad, J. P., Staffa, J., and Murphy, D. Ananthakrishnan, A. N., Singal, A. G., and Chang, L. (2019). The gut microbiome (2012). Trends of outpatient prescription drug utilization in US children, 2002- and digestive health - a new frontier. Clin. Gastroenterol. Hepatol. 17, 215–217. 2010. Pediatrics. 130, 23–31. doi: 10.1542/peds.2011-2879 doi: 10.1016/j.cgh.2018.10.040 Cho, I., Yamanishi, S., Cox, L., Methe, B. A., Zavadil, J., Li, K., et al. (2012). Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Antibiotics in early life alter the murine colonic microbiome and adiposity. et al. (2011). Enterotypes of the human gut microbiome. Nature. 473, 174–180. Nature. 488, 621–626. doi: 10.1038/nature11400 doi: 10.1038/nature09944 Choo, J. M., Kanno, T., Zain, N. M., Leong, L. E., Abell, G. C., Keeble, J. E., et al. Bartlett, J. G. (2002). Clinical practice. Antibiotic-associated diarrhea. N. Engl. J. (2017). Divergent relationships between fecal microbiota and metabolome Med. 346, 334–339. doi: 10.1056/NEJMcp011603 following distinct antibiotic-induced disruptions. mSphere 2, e00005–17. Beaugerie, L., Flahault, A., Barbut, F., Atlan, P., Lalande, V., Cousin, P., et al. doi: 10.1128/mSphere.00005-17 (2003). Antibiotic-associated diarrhoea and Clostridium difficile in the Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., et al. community. Aliment Pharmacol. Ther. 17, 905–912. doi: 10.1046/j.1365- (2015). The microbiome of uncontacted Amerindians. Sci. Adv. 1, e1500183. 2036.2003.01531.x doi: 10.1126/sciadv.1500183 Bendezú Garcı́a, R., Barba, E., Burri, E., Cisternas, D., Accarino, A., Quiroga, S., Costea, P. I., Hildebrand, F., Arumugam, M., Backhed, F., Blaser, M. J., et al. (2016). Colonic content in health and its relation to functional gut Bushman, F. D., et al. (2018). Enterotypes in the landscape of gut microbial symptoms. Neurogastroenterol. Motil. 28, 849–854. doi: 10.1111/nmo.12782 community composition. Nat. Microbiol. 3, 8–16. doi: 10.1038/s41564- Biedermann, L., and Rogler, G. (2015). The intestinal microbiota: its role in health 017-0072-8 and disease. Eur. J. Pediatr. 174, 151–167. doi: 10.1007/s00431-014-2476-2 Dang, Y., Reinhardt, J. D., Zhou, X., and Zhang, G. (2014). The effect of probiotics Bokulich, N. A., Chung, J., Battaglia, T., Henderson, N., Jay, M., Li, H., et al. supplementation on Helicobacter pylori eradication rates and side effects (2016). Antibiotics, birth mode, and diet shape microbiome maturation during during eradication therapy: a meta-analysis. PloS One 9, e111030. early life. Sci. Transl. Med. 8, 343ra82. doi: 10.1126/scitranslmed.aad7121 doi: 10.1371/journal.pone.0111030 Brandtzaeg, P. (2010). Function of mucosa-associated lymphoid tissue in antibody Dethlefsen, L., and Relman, D. A. (2011). Incomplete recovery and individualized formation. Immunol. Invest. 39, 303–355. doi: 10.3109/08820131003680369 responses of the human distal gut microbiota to repeated antibiotic Browne, H. P., Forster, S. C., Anonye, B. O., Kumar, N., Neville, B. A., Stares, M. perturbation. Proc. Natl. Acad. Sci. U. S. A. 108 Suppl 1, 4554–4561. D., et al. (2016). Culturing of ‘unculturable’ human microbiota reveals novel doi: 10.1073/pnas.1000087107 taxa and extensive sporulation. Nature. 533, 543–546. doi: 10.1038/ Donaldson, G. P., Lee, S. M., and Mazmanian, S. K. (2016). Gut biogeography of nature17645 the bacterial microbiota. Nat. Rev. Microbiol. 14, 20–32. doi: 10.1038/ Bud, R. (2007). Antibiotics: the epitome of a wonder drug. BMJ. 334 Suppl 1, s6. nrmicro3552 doi: 10.1136/bmj.39021.640255.94 Duvallet, C., Gibbons, S. M., Gurry, T., Irizarry, R. A., and Alm, E. J. (2017). Meta- Cammarota, G., Ianiro, G., Tilg, H., Rajilic-Stojanovic, M., Kump, P., Satokari, R., analysis of gut microbiome studies identifies disease-specific and shared et al. (2017). European consensus conference on faecal microbiota responses. Nat. Commun. 8, 1784. doi: 10.1038/s41467-017-01973-8 Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 8 November 2020 | Volume 10 | Article 572912 Ramirez et al. Antibiotics and the Gut Microbiota Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Kronman, M. P., Zaoutis, T. E., Haynes, K., Feng, R., and Coffin, S. E. (2012). et al. (2005). Diversity of the human intestinal microbial flora. Science. 308, Antibiotic exposure and IBD development among children: a population-based 1635–1638. doi: 10.1126/science.1110591 cohort study. Pediatrics. 130, e794–e803. doi: 10.1542/peds.2011-3886 Edwards, A. N., Karim, S. T., Pascual, R. A., Jowhar, L. M., Anderson, S. E., and Kuehne, S. A., Cartman, S. T., Heap, J. T., Kelly, M. L., Cockayne, A., Minton, N. McBride, S. M. (2016). Chemical and stress resistances of Clostridium difficile P., et al. (2010). and toxin B in Clostridium difficile infection. Nature. 467, 711– spores and vegetative cells. Front. Microbiol. 7, 1698. doi: 10.3389/fmicb. 713. doi: 10.1038/nature09397 2016.01698 Kuipers, E. J. (2019). Encyclopedia of gastroenterology (Amsterdam, The European Medicines Agency and European Centre for Disease Prevention and Netherlands: Elsevier Science). Control (2009). The bacterial challenge: time to react. A call to narrow the gap Lamichhane, S., Sen, P., Dickens, A. M., Oresic, M., and Bertram, H. C. (2018). Gut between multidrug-resistant bacteria in the EU and development of new metabolome meets microbiome: A methodological perspective to understand antibacterial agents. Available at: http://www.ema.europa.eu/documents/ the relationship between host and microbe. Methods. 149, 3–12. doi: 10.1016/ report/bacterial-challenge-time-react_en.pdf (Accessed 19 February, 2019). j.ymeth.2018.04.029 Fenner, L., Widmer, A. F., Goy, G., Rudin, S., and Frei, R. (2008). Rapid and Lange, K., Buerger, M., Stallmach, A., and Bruns, T. (2016). Effects of antibiotics reliable diagnostic algorithm for detection of Clostridium difficile. J. Clin. on gut microbiota. Dig. Dis. 34, 260–268. doi: 10.1159/000443360 Microbiol. 46, 328–330. doi: 10.1128/JCM.01503-07 Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., et al. Foliaki, S., Pearce, N., Bjorksten, B., Mallol, J., Montefort, S., von Mutius, E., et al. (2013). Richness of human gut microbiome correlates with metabolic markers. (2009). Antibiotic use in infancy and symptoms of asthma, rhinoconjunctivitis, Nature. 500, 541–546. doi: 10.1038/nature12506 and eczema in children 6 and 7 years old: International Study of Asthma and Leffler, D. A., and Lamont, J. T. (2015). Clostridium difficile infection. N. Engl. J. Allergies in Childhood Phase III. J. Allergy Clin. Immunol. 124, 982–989. Med. 372, 1539–1548. doi: 10.1056/NEJMra1403772 doi: 10.1016/j.jaci.2009.08.017 Levy, M., Kolodziejczyk, A. A., Thaiss, C. A., and Elinav, E. (2017). Dysbiosis and Gaulke, C. A., and Sharpton, T. J. (2018). The influence of ethnicity and geography the immune system. Nat. Rev. Immunol. 17, 219–232. doi: 10.1038/nri.2017.7 on human gut microbiome composition. Nat. Med. 24, 1495–1496. Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., et al. (2014). An integrated doi: 10.1038/s41591-018-0210-8 catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, Giedraitiene, A., Vitkauskiene, A., Naginiene, R., and Pavilonis, A. (2011). 834–841. doi: 10.1038/nbt.2942 Antibiotic resistance mechanisms of clinically important bacteria. Medicina Li, T. H., Qin, Y., Sham, P. C., Lau, K. S., Chu, K. M., and Leung, W. K. (2017). (Kaunas). 47, 137–146. doi: 10.3390/medicina47030019 Alterations in gastric microbiota after H. pylori eradication and in different Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V., and Knight, histological stages of gastric carcinogenesis. Sci. Rep. 7, 44935. doi: 10.1038/ R. (2018). Current understanding of the human microbiome. Nat. Med. 24, srep44935 392–400. doi: 10.1038/nm.4517 Litvak, Y., Byndloss, M. X., and Baumler, A. J. (2018). Colonocyte metabolism Goldenberg, J. Z., Ma, S. S., Saxton, J. D., Martzen, M. R., Vandvik, P. O., shapes the gut microbiota. Science, 362, eaat9076. doi: 10.1126/science.aat9076 Thorlund, K., et al. (2013). Probiotics for the prevention of Clostridium Losurdo, G., Cubisino, R., Barone, M., Principi, M., Leandro, G., Ierardi, E., et al. difficile-associated diarrhea in adults and children. Cochrane Database Syst. (2018). Probiotic monotherapy and Helicobacter pylori eradication: a Rev. 5, CD006095. doi: 10.1002/14651858.CD006095.pub3 systematic review with pooled-data analysis. World J. Gastroenterol. 24, 139– Goldenberg, J. Z., Lytvyn, L., Steurich, J., Parkin, P., Mahant, S., and Johnston, B. C. 149. doi: 10.3748/wjg.v24.i1.139 (2015). Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Malfertheiner, P., Megraud, F., O’Morain, C. A., Gisbert, J. P., Kuipers, E. J., Axon, Cochrane Database Syst. Rev. 12, CD004827. doi: 10.1002/14651858. A. T., et al. (2017). Management of Helicobacter pylori infection-the CD004827.pub4 Maastricht V/Florence Consensus Report. Gut 66, 6–30. doi: 10.1136/gutjnl- Guarner, F., and Malagelada, J. R. (2003). Gut flora in health and disease. Lancet. 2016-312288 361, 512–519. doi: 10.1016/S0140-6736(03)12489-0 Marchesi, J. R., and Ravel, J. (2015). The vocabulary of microbiome research: a Guarner, F. (2012). The enteric microbiota (San Rafael, CA: Morgan & Claypool proposal. Microbiome. 3, 31. doi: 10.1186/s40168-015-0094-5 Publishers). Mayer, E. A., Tillisch, K., and Gupta, A. (2015). Gut/brain axis and the microbiota. Guarner, F. (2015). The gut microbiome: what do we know? Clin. Liver Dis. J. Clin. Invest. 125, 926–938. doi: 10.1172/JCI76304 (Hoboken). 5, 86–90. doi: 10.1002/cld.454 McFarland, L. V. (2008). Antibiotic-associated diarrhea: epidemiology, trends and Hviid, A., Svanstrom, H., and Frisch, M. (2011). Antibiotic use and inflammatory treatment. Future Microbiol. 3, 563–578. doi: 10.2217/17460913.3.5.563 bowel diseases in childhood. Gut. 60, 49–54. doi: 10.1136/gut.2010.219683 Mullish, B. H., Quraishi, M. N., Segal, J. P., McCune, V. L., Baxter, M., Marsden, G. L., Ianiro, G., Mullish, B. H., Kelly, C. R., Kassam, Z., Kuijper, E. J., Ng, S. C., et al. et al. (2018). The use of faecal microbiota transplant as treatment for (2020). Reorganisation of faecal microbiota transplant services during the recurrent or refractory Clostridium difficile infection and other potential COVID-19 pandemic. Gut. 69, 1555–1563. doi: 10.1136/gutjnl-2020-321829 indications: joint British Society of Gastroenterology (BSG) and Healthcare Imdad, A., Nicholson, M. R., Tanner-Smith, E. E., Zackular, J. P., Gomez-Duarte, Infection Society (HIS) guidelines. Gut 67, 1920–1941. doi: 10.1136/gutjnl- O. G., Beaulieu, D. B., et al. (2018). Fecal transplantation for treatment of 2018-316818 inflammatory bowel disease. Cochrane Database Syst. Rev. 11, CD012774. Neut, C., Mahieux, S., and Dubreuil, L. J. (2017). Antibiotic susceptibility of doi: 10.1002/14651858.CD012774.pub2 probiotic strains: Is it reasonable to combine probiotics with antibiotics? Med. Johnson, S., Maziade, P. J., McFarland, L. V., Trick, W., Donskey, C., Currie, B., Mal. Infect. 47, 477–483. doi: 10.1016/j.medmal.2017.07.001 et al. (2012). Is primary prevention of Clostridium difficile infection possible O’Hara, A. M., and Shanahan, F. (2006). The gut flora as a forgotten organ. EMBO with specific probiotics? Int. J. Infect. Dis. 16, e786–e792. doi: 10.1016/ Rep. 7, 688–693. doi: 10.1038/sj.embor.7400731 j.ijid.2012.06.005 Palleja, A., Mikkelsen, K. H., Forslund, S. K., Kashani, A., Allin, K. H., Nielsen, Karami, N., Nowrouzian, F., Adlerberth, I., and Wold, A. E. (2006). Tetracycline T., et al. (2018). Recovery of gut microbiota of healthy adults following resistance in Escherichia coli and persistence in the infantile colonic antibiotic exposure. Nat. Microbiol. 3, 1255–1265. doi: 10.1038/s41564-018- microbiota. Antimicrob. Agents Chemother. 50, 156–161. doi: 10.1128/ 0257-9 AAC.50.1.156-161.2006 Panda, S., El khader, I., Casellas, F., Lopez Vivancos, J., Garcia Cors, M., Santiago, A., Klein, E. Y., Van Boeckel, T. P., Martinez, E. M., Pant, S., Gandra, S., Levin, S. A., et al. (2014). Short-term effect of antibiotics on human gut microbiota. PloS One et al. (2018). Global increase and geographic convergence in antibiotic 9, e95476. doi: 10.1371/journal.pone.0095476 consumption between 2000 and 2015. Proc. Natl. Acad. Sci. U. S. A. 115, Pasteur, L. (1885). Observations relatives à la note pré cé dente de M. Duclaux. C. R. E3463–E3E70. doi: 10.1073/pnas.1717295115 Acad. Sci. 100, 68–69. Korpela, K., Salonen, A., Virta, L. J., Kekkonen, R. A., Forslund, K., Bork, P., et al. Perez-Perez, G., and Blaser, M. (1996). “Chapter 23: Campylobacter and (2016). Intestinal microbiome is related to lifetime antibiotic use in Finnish Helicobacter,” in Medical Microbiology. Ed. S. Baron (Galveston, TX: pre-school children. Nat. Commun. 7, 10410. doi: 10.1038/ncomms10410 University of Texas Medical Branch at Galveston). Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 9 November 2020 | Volume 10 | Article 572912 Ramirez et al. Antibiotics and the Gut Microbiota Rolain, J. M. (2013). Food and human gut as reservoirs of transferable antibiotic Vrieze, A., Out, C., Fuentes, S., Jonker, L., Reuling, I., Kootte, R. S., et al. resistance encoding genes. Front. Microbiol. 4, 173. doi: 10.3389/fmicb. (2014). Impact of oral vancomycin on gut microbiota, bile acid 2013.00173 metabolism, and insulin sensitivity. J. Hepatol. 60, 824–831. doi: 10.1016/ Royal College of Physicians of Edinburgh (2010). Top 20 most important medical j.jhep.2013.11.034 developments of the last 50 years. Available at: http://www.rcpe.ac.uk/sites/ Wang, Z. H., Gao, Q. Y., and Fang, J. Y. (2013). Meta-analysis of the efficacy and default/files/documents/pressreleases/rcpe-top20-list.pdf (Accessed 18 safety of Lactobacillus-containing and Bifidobacterium-containing probiotic February, 2019). compound preparation in Helicobacter pylori eradication therapy. J. Clin. Sabtu, N., Enoch, D. A., and Brown, N. M. (2015). Antibiotic resistance: what, Gastroenterol. 47, 25–32. doi: 10.1097/MCG.0b013e318266f6cf why, where, when and how? Br. Med. Bull. 116, 105–113. doi: 10.1093/bmb/ Willing, B. P., Russell, S. L., and Finlay, B. B. (2011). Shifting the balance: antibiotic ldv041 effects on host-microbiota mutualism. Nat. Rev. Microbiol. 9, 233–243. Sender, R., Fuchs, S., and Milo, R. (2016). Revised estimates for the number of doi: 10.1038/nrmicro2536 human and bacteria cells in the body. PloS Biol. 14, e1002533. doi: 10.1371/ Wirbel, J., Pyl, P. T., Kartal, E., Zych, K., Kashani, A., Milanese, A., et al. (2019). journal.pbio.1002533 Meta-analysis of fecal metagenomes reveals global microbial signatures that are Sonnenburg, J. L., and Sonnenburg, E. D. (2019). Vulnerability of the industrialized specific for colorectal cancer. Nat. Med. 25, 679–689. doi: 10.1038/s41591-019- microbiota. Science 366, eaaw9255. doi: 10.1126/science.aaw9255 0406-6 Suerbaum, S., and Michetti, P. (2002). Helicobacter pylori infection. N. Engl. J. World Health Organization (2018). WHO report on surveillance of antibiotic Med. 347, 1175–1186. doi: 10.1056/NEJMra020542 consumption: 2016-2018 early implementation. Available at: http://apps.who. Sugden, R., Kelly, R., and Davies, S. (2016). Combatting antimicrobial resistance int/iris/bitstream/handle/10665/277359/9789241514880-eng.pdf?ua=1 globally. Nat. Microbiol. 1, 16187. doi: 10.1038/nmicrobiol.2016.187 (Accessed 18 February, 2019). Surawicz, C. M., Brandt, L. J., Binion, D. G., Ananthakrishnan, A. N., Curry, S. R., World Health Organization (2019). No time to wait: securing the future from drug- Gilligan, P. H., et al. (2013). Guidelines for diagnosis, treatment, and resistant infections. Available at: https://www.who.int/antimicrobial-resistance/ prevention of Clostridium difficile infections. Am. J. Gastroenterol. 108, 478– interagency-coordination-group/IACG_final_report_EN.pdf?ua=1 (Accessed 98; quiz 99. doi: 10.1038/ajg.2013.4 16 February, 2020). Szajewska, H., and Kolodziej, M. (2015a). Systematic review with meta-analysis: Wostmann, B. S. (1981). The germfree animal in nutritional studies. Annu. Rev. Lactobacillus rhamnosus GG in the prevention of antibiotic-associated Nutr. 1, 257–279. doi: 10.1146/annurev.nu.01.070181.001353 diarrhoea in children and adults. Aliment Pharmacol. Ther. 42, 1149–1157. Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y. Y., Keilbaugh, S. A., et al. doi: 10.1111/apt.13404 (2011). Linking long-term dietary patterns with gut microbial enterotypes. Szajewska, H., and Kolodziej, M. (2015b). Systematic review with meta-analysis: Science 334, 105–108. doi: 10.1126/science.1208344 Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea. Yap, T. W., Gan, H. M., Lee, Y. P., Leow, A. H., Azmi, A. N., Francois, F., et al. Aliment Pharmacol. Ther. 42, 793–801. doi: 10.1111/apt.13344 (2016). Helicobacter pylori eradication causes perturbation of the human gut Szajewska, H., Horvath, A., and Piwowarczyk, A. (2010). Meta-analysis: the effects microbiome in young adults. PloS One 11, e0151893. doi: 10.1371/ of Saccharomyces boulardii supplementation on Helicobacter pylori eradication journal.pone.0151893 rates and side effects during treatment. Aliment Pharmacol. Ther. 32, 1069– Yassour, M., Vatanen, T., Siljander, H., Hamalainen, A. M., Harkonen, T., 1079. doi: 10.1111/j.1365-2036.2010.04457.x Ryhanen, S. J., et al. (2016). Natural history of the infant gut microbiome Szajewska, H., Horvath, A., and Kolodziej, M. (2015). Systematic review with and impact of antibiotic treatment on bacterial strain diversity and stability. meta-analysis: Saccharomyces boulardii supplementation and eradication of Sci. Transl. Med. 8, 343ra81. doi: 10.1126/scitranslmed.aad0917 Helicobacter pylori infection. Aliment Pharmacol. Ther. 41, 1237–1245. Zhao, Q., and Elson, C. O. (2018). Adaptive immune education by gut microbiota doi: 10.1111/apt.13214 antigens. Immunology. 154, 28–37. doi: 10.1111/imm.12896 Szajewska, H., Canani, R. B., Guarino, A., Hojsak, I., Indrio, F., Kolacek, S., et al. Zmora, N., Suez, J., and Elinav, E. (2019). You are what you eat: diet, health and (2016). Probiotics for the prevention of antibiotic-associated diarrhea in the gut microbiota. Nat. Rev. Gastroenterol. Hepatol. 16, 35–56. doi: 10.1038/ children. J. Pediatr. Gastroenterol. Nutr. 62, 495–506. doi: 10.1097/ s41575-018-0061-2 MPG.0000000000001081 Tanoue, T., Atarashi, K., and Honda, K. (2016). Development and maintenance of Conflict of Interest: FG is a member of the advisory boards at Biocodex and intestinal regulatory T cells. Nat. Rev. Immunol. 16, 295–309. doi: 10.1038/ Instituto Danone; and has received research grants from AB Biotics, Takeda and nri.2016.36 Abbvie. AM is a speaker and member of the advisory board at Biocodex France. Trasande, L., Blustein, J., Liu, M., Corwin, E., Cox, L. M., and Blaser, M. J. (2013). HC is an advisor for Biocodex and Megapharma. Infant antibiotic exposures and early-life body mass. Int. J. Obes. (Lond). 37, 16–23. doi: 10.1038/ijo.2012.132 The remaining authors declare that the research was conducted in the absence of Turta, O., and Rautava, S. (2016). Antibiotics, obesity and the link to microbes - any commercial or financial relationships that could be construed as a potential what are we doing to our children? BMC Med. 14, 57. doi: 10.1186/s12916-016- conflict of interest. 0605-7 Van Boeckel, T. P., Brower, C., Gilbert, M., Grenfell, B. T., Levin, S. A., Robinson, Copyright © 2020 Ramirez, Guarner, Bustos Fernandez, Maruy, Sdepanian and T. P., et al. (2015). Global trends in antimicrobial use in food animals. Proc. Cohen. This is an open-access article distributed under the terms of the Creative Natl. Acad. Sci. U. S. A. 112, 5649–5654. doi: 10.1073/pnas.1503141112 Commons Attribution License (CC BY). The use, distribution or reproduction in other Virta, L., Auvinen, A., Helenius, H., Huovinen, P., and Kolho, K. L. (2012). forums is permitted, provided the original author(s) and the copyright owner(s) are Association of repeated exposure to antibiotics with the development of credited and that the original publication in this journal is cited, in accordance with pediatric Crohn’s disease–a nationwide, register-based finnish case-control accepted academic practice. No use, distribution or reproduction is permitted which study. Am. J. Epidemiol. 175, 775–784. doi: 10.1093/aje/kwr400 does not comply with these terms. Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 10 November 2020 | Volume 10 | Article 572912