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The Unknown Effect of Antibiotic-Induced Dysbiosis on the Gut Microbiota
Chapter 20
The Unknown Effect of AntibioticInduced Dysbiosis on the Gut Microbiota Aleksandr Birg, Nathaniel L. Ritz and Henry C. Lina Medicine Service, New Mexico VA Health Care System and the Division of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, NM, United States
INTRODUCTION In recent years, evaluation of changes in the gut microbial community after antibiotic exposure has gained traction as an important health topic. While antibiotic use has proven to be extremely beneficial in combatting infectious disease, the classic vignette has been that microbes are costly and deleterious to life and should be eliminated at every opportunity. This stance has been reversed in recent years, with our growing knowledge of microbial communities and their role in promoting host health and homeostasis. Therefore, the paradoxical widespread and frequent overuse of antibiotics, in hospitals, agriculture, and the food industry, can be counterproductive to the health of the microbiota and subsequently to the health of the host. Increasing focus has been given, to evaluate how the intestinal microbiome is impacted by antibiotic use, both acutely and long term. Following the use of antibiotics, the beneficial properties of the gut microbiota can be lost and can promote the evolution of antibiotic-resistant pathogens. The intestinal microbiota is a densely populated microbial ecosystem, comprised of trillions of microbes belonging to hundreds of species [1]. The composition of the gut microbiota is altered by numerous environmental factors, including the general health of the host, diet, lifestyle, and antibiotic use. Gastrointestinal microbial colonization increases both from proximal to distal gut (stomach 101 microbial cells/g contents, small intestine 103 7 cells/g, and colon 1012 cells/g), and within the intestinal lumen, from lateral (regions adherent and adjacent to host tissues) to medial [2]. In healthy individuals, there is great microbial richness and diversity, both within individuals (alpha diversity) and between individuals (beta diversity). Despite this high diversity at the species level, the microbiota consists of only a few bacterial phyla, with greater than 90% belonging to Bacteroidetes, Firmicutes, Actinobacteria, and Proteobacteria [3,4]. Verrucomicrobia, Fusobacteria, and Cyanobacteria combine for most of the remaining bacteria, in low numbers. Bacteroidetes are gram-negative bacteria that ferment polysaccharides and otherwise indigestible carbohydrates and produce short-chain fatty acids (SCFAs) that have many beneficial effects in the gut. Firmicutes are primarily composed of gram-positive bacteria that range from mutualistic symbionts (e.g., Lactobacillus spp., Clostridium clusters IV-XIVa) to pathobionts (e.g., Clostridium difficile, Clostridium perfringens). Actinobacteria are gram-positive bacteria that are usually beneficial (e.g., Bifidobacterium spp.) and commonly used as probiotics. Proteobacteria are a diverse group of gram-negative bacteria that tend to increase in number during dysbioses (e.g., Enterobacteriaceae family) [5]. While bacteria make up the vast majority of microbial biomass in the gut and are the most commonly studied, it is important to note that there are also eukaryotes (mostly yeasts), viruses (mostly bacteriophage), and archaea (mostly methanogens) present with distinct roles within the microbial community. Following perturbation, the proportion and representation of these groups can be thrown into a state of imbalance, or dysbiosis, that can cause a loss of functionality and lead to disease.
a. Senior author.
Microbiome and Metabolome in Diagnosis, Therapy, and other Strategic Applications. https://doi.org/10.1016/B978-0-12-815249-2.00020-8 Copyright © 2019 Elsevier Inc. All rights reserved.
195
196 BLOCK | III Established and Experimental Interventions
BACTERIAL BIOFILMS There has been a growing appreciation for the complexity of the interrelationships, among the large consortia of microbes of the gut. A prominent example of this is seen when microbes form biofilms by adhering to surfaces, aggregate, and become embedded in extracellular matrices. These systems provide defense against antimicrobials and allow direct access for microbial nutrient transfer. Biofilms have been shown to be beneficial for the host, by aiding the digestion of luminal contents and creating a barrier to prevent the colonization of pathogens [6]. In fact, colonization resistance is one of the most significant defensive mechanisms a healthy, intact microbiota provides. However, biofilms can also behave pathologically, with estimates that 65% of infections were associated with biofilm production [7].
ANTIBIOTIC ADMINISTRATION Antibiotics can alter the microbiota, by selecting for antibiotic-resistant species. Resistance genes spread through vertical (i.e., resistant mutation passed down from parent to offspring) or horizontal (i.e., transformation or conjugation) transmission. Following antibiotic use, resistant organisms and mobile elements can remain within the population, for an extended period of time. Studies have reported that resistant species can persist 3e4 years, after patients were originally treated with antibiotics [4,5]. The antibiotic spectrum, dose and duration, pharmacokinetic and pharmacodynamic properties, and route of administration, all contribute to how the microbiota is affected [8]. Different classes of antibiotics will not only affect different microbes but also have different host absorption and clearance properties, which impact the distribution and excretion of the compounds in relation to the microbiota, where the site of greatest impact is within the distal gut.
ANTIBIOTIC SPECTRUM Oral administration of broad-spectrum and poor absorption antibiotics have a greater impact on the gut microbiota, compared to narrow-spectrum and high absorption antibiotics [9]. The spectrum of activity for an antibiotic can play an important role in pathobiont (any organism with the potential to become pathological) overgrowth and/or acute pathogen infection. This scenario is exemplified following a narrow-spectrum antibiotic treatment, which primarily targets anaerobes, resulting in a vastly increased risk of overgrowth by facultative anaerobes Enterococcus and Streptococcus; this event is not seen following the use of broad-spectrum antibiotics [10].
BACTERIAL DIVERSITY Multiple studies testing the effects on antibiotics have shown that while total microbial numbers may return to normal after a 1e2 week period, the overall diversity significantly decreases, and certain bacterial taxa may be permanently lost. Additionally, colonization resistance to common nosocomial pathogens was lost, until microbiota diversity was restored [11e14]. The burgeoning replacement bacterial populations within the microbiota varied across studies and depended on the initial colonization of microbes still present after cessation of the antibiotic treatment.
PROTEOBACTERIA OVERGROWTH Worrisomely, bacteria of the phylum Proteobacteria frequently expanded following antibiotic treatments. One explanation for the Proteobacteria bloom in dysbioses is that both intestinal inflammation and antibiotic treatment increase epithelial oxygenation in the colon, creating a more aerobic atmosphere, favoring the facultative over obligate anaerobes [15]. These include major pathogens, some of them multiresistant to antibiotics, such as Salmonella, Escherichia coli, Yersinia, Pseudomonas, Klebsiella, Shigella, Proteus, Enterobacter, and Serratia.
ANTIBIOTIC-INDEPENDENT LOSS OF DIVERSITY The loss of microbiome diversity has been reported in a multitude of diseases, impacting the gastrointestinal system, and parallels changes seen with antibiotics. Inflammatory bowel disease has been studied extensively, showing a loss of diversity in both ulcerative colitis and Crohn’s disease patients [16]. Variable results in regard to alpha diversity, in inflammatory bowel disease, have been reported in the literature, with some studies showing significant change in phyla, particularly Proteobacteria and Bacteroidetes, while other studies show no notable change [16].
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Irritable bowel syndrome also shows a loss of diversity in the diarrhea subtype, via sequencing of the stool [17]. Reduced diversity of the microbiome was also noted in Clostridium difficileeinfected patients, with symptoms of acute diarrhea [18]. Interestingly, this trend in loss of microbial diversity has been reported in diseases outside the gut lumen. Patients evaluated with chronic liver disease were also shown to have a loss of gut bacterial diversity [19].
BACTERIAL CROSS TALK The changes seen in bacterial diversity during a disease process emphasize the communication and interplay between the host and gut microbiota. With similar bacterial community changes seen during antibiotic use, any administration of antibacterial therapy needs to be carefully evaluated, for potential impact on the host [20]. It is also important to emphasize that antibiotics have been used extensively to treat a multitude of gastrointestinal infections and diseases, through the years.
ANTIBIOTIC THERAPY OF INTESTINAL DYSBIOSIS More recently, antibiotics have been applied to treat dysbiosis [21]. The rationale here is to treat overgrowth of bacteria in the microbiome, as one would treat overgrowth of bacteria in the setting of an infection. While there is some comparability between these two types of overgrowth, the desired outcomes are drastically different.
ANTIBIOTICS IN URINARY INFECTION Urinary tract infections are a common disease process that is often treated with antibiotics for abnormal changes in urinary microbiome that can cause symptoms to the host [22]. With recent studies evaluating urine via genetic sequencing, it has been determined that the bladder lumen is associated with a specific microbiome (as opposed to being a sterile environment). Changes to that microbiome can lead to an overgrowth of a certain species that can cause symptoms of a urinary infection [22].
THE URINARY MICROBIOME The bacterial density of a healthy urine microbiome is magnitudes lower than that of the gut, usually ranging from 102 to 105 colony-forming units per milliliter, compared to 1012 colony-forming units per milliliter in intestines [22]. Urine cultures from urinary tract infections usually grow only one species, most commonly E. coli that is responsible for symptoms. These can typically be treated with narrow-coverage antibiotics [22]. Symptom improvement is seen after treatment with antibiotics, which curb the growth of the uropathogen.
URINARY VERSUS GASTROINTESTINAL DYSBIOSIS The gut microbiota is a more complex system, with a significantly higher number of species present, compared to the urinary tract system; therefore changes that occur will impact host physiology differently [22]. When dealing with the gastrointestinal system, symptomatic dysbiosis does not occur due to alterations in a single species or a specific collection of species [21]. Treatment with narrow-range antibiotics will not yield the same results of symptom resolution, in patients with intestinal dysbiosis, as it would in patients with urinary tract infections. Broad-spectrum antibiotics have been shown to be successful, in diminishing gastrointestinal symptoms in the setting of dysbiosis [23]. Many recent efforts have gone into the reasoning, behind the beneficial effects of the broadspectrum antimicrobials. Outside of the usual bactericidal and bacteriostatic activity of antibiotics, additional properties must be involved in the exact effects on the altered microbiome, in order to facilitate restoration of the normal function [21].
NON-ANTIBIOTIC MANAGEMENT OF DYSBIOSIS There has been a revitalization of efforts, delving into alternative therapies to improve symptoms of dysbiosis. As antibiotics have been shown to cause loss of gut bacterial diversity that can lead to further deleterious changes, advantageous properties of probiotics and prebiotics have been acknowledged as useful therapies.
198 BLOCK | III Established and Experimental Interventions
PROBIOTICS Probiotics are live organisms that provide benefits to the host after consumption [24]. Probiotics have been used to treat liver injury and hepatic inflammation, in the event of intestinal bacterial overgrowth, by maintaining permeability of tight junctions and preventing pathogen translocation [25]. In addition, JAMA meta-analysis has shown that probiotics can reduce antibiotic-associated diarrhea by up to 40%, while a review by Cochrane has shown that probiotic use in Clostridium difficile colitis will reduce diarrhea by up to 64% [26]. Single-strain probiotics have been shown to increase bacterial gut diversity as well [19].
PREBIOTICS Prebiotics are nondigestible food ingredients that propagate beneficial microbial activity of the microbiome [24]. Prebiotics are usually oligosaccharides that provide nutrients selectively to intestinal symbionts [27]. Prebiotics, in themselves, have to work through probiotic strains, to provide benefits to the host and alter probiotic bacteria to control pathogens [25]. However, it is important to note that as of this time, probiotics are not regularly recommended for symptom control, except for known cases of antibiotic-induced diarrhea [28].
FECAL TRANSPLANTS Fecal microbiota transplants (FMT) are another method developed to help control altered microbial changes [29]. The exact mechanism as to how FMT works is not well understood and needs further research [30]; however, FMT have shown to be very effective, for treating altered microbiota in the setting of C. difficile colitis [29]. Despite probiotics, prebiotics, and FMT showing great potential benefit to treat antibiotic alteration in the microbiome, there are still significant unknowns involved, which do not translate to regular use in medicine [25]. It has been reported that single-strain probiotics have very limited success in treating intestinal dysbiosis [31]. The lack of knowledge into long-term effects keeps these alternative therapies from being considered viable treatment options, for severe conditions that occur with antibiotic use (i.e., C. difficile colitis) [32].
ECOSYSTEM EVALUATION Future research into changes seen in the gut microbiota will focus less on individual species that can be observed through culture and will need to emphasize the role of larger community variations. Culturing the gut microbiota is no longer considered a viable option, to truly understand those changes, as only 80% are culturable, and many genera are too difficult to grow under standard conditions [33,34]. Important and useful concepts, such as alpha and beta diversity, cannot be evaluated with the use of culturing and lead to lack of complete understanding of the changes that take place [35].
MULTIOMICS INVESTIGATION When considering the complex and evolving changes, occurring in an intestinal environment after antibiotic exposure, interactions between the host and microbiota require more involved strategies [25]. Several “omic” technologies have emerged to the forefront, to study how the microbial community and microbial metabolites are affected, including changes by antibiotic disruption [25].
DIAGNOSTIC OPTIONS As more of these techniques are being incorporated into everyday practice, the cost becomes more favorable. This allows for easier access and future integration into personalized medicine [25]. The current “gold standard” for studying microbial communities is 16S rRNA next-generation sequencing (also known as high-throughput sequencing) that allows for genetic definition of pathogens, rather than relying on their morphology [34]. In addition to genetic sequencing to analyze gut microbiome, several other techniques have emerged to study functional changes such as metagenomics and metatranscriptomics [34]. Another mechanism to study disruption in microbiome is evaluating metabolites in a technique called metabolomics, which is used to detect microbial products in urine, blood, saliva, and feces [25]. As we learn more about metagenomics and metabolomics and understand the role of microbes in human health and disease, future therapies can be based around the microbiome as well [27].
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ONGOING STUDIES Evaluating human data regarding alterations of the microbiome by antibiotics is difficult, lacking in human trials [25]. The major question in the coming years will be to determine the exact changes in the gut microbiota that will cause a disruption in function, and what specific parameters will be responsible for diseases and symptoms.
ACKNOWLEDGMENTS This study is supported by the Winkler Bacterial Overgrowth Research Fund.
DISCLAIMER Dr. Lin has patent rights in related area.
REFERENCES [1] Rajilic-Stojanovic M, de Vos WM. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 2014;38:996e1047. [2] Sekirov I, Russell SL, Antunes LCM, Finlay BB. Gut microbiota in health and disease. Physiol Rev 2010;90:859e904. [3] Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D. Role of the normal gut microbiota. World J Gastroenterol 2015;21:8787e803. [4] Kim S, Covington A, Pamer EG. The intestinal microbiota: antibiotics, colonization resistance, and enteric pathogens. Immunol Rev 2017;279:90e105. [5] Looft T, Johnson TA, Allen HK, et al. In-feed antibiotic effects on the swine intestinal microbiome. Proc Natl Acad Sci U S A 2012;109:1691e6. [6] Bollinger RR, Barbas AS, Bush EL, Lin SS, Parker W, Parker W. Biofilms in the normal human large bowel: fact rather than fiction. Gut 2007;56:1481e2. [7] Potera C. Forging a link between biofilms and disease. Science 1999;283(1837):1839. [8] Jernberg C, Lofmark S, Edlund C, Jansson JK. Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 2010;156:3216e23. [9] Levison ME, Levison JH. Pharmacokinetics and pharmacodynamics of antibacterial agents. Infect Dis Clin North Am 2009;23:791e815. [10] Taur Y, Xavier JB, Lipuma L, et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis 2012;55:905e14. [11] Lewis BB, Buffie CG, Carter RA, et al. Loss of microbiota-mediated colonization resistance to Clostridium difficile infection with oral vancomycin compared with metronidazole. J Infect Dis 2015;212:1656e65. [12] Isaac S, Scher JU, Djukovic A, et al. Short- and long-term effects of oral vancomycin on the human intestinal microbiota. J Antimicrob Chemother 2017;72:128e36. [13] Buffie CG, Jarchum I, Equinda M, et al. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-Induced colitis. Infect Immun 2012;80:62e73. [14] Ubeda C, Taur Y, Jenq RR, et al. Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J Clin Invest 2010;120:4332e41. [15] Litvak Y, Byndloss MX, Tsolis RM, Bäumler AJ. Dysbiotic Proteobacteria expansion: a microbial signature of epithelial dysfunction. Curr Opin Microbiol 2017;39:1e6. [16] Hansen R, Russell RK, Reiff C, et al. Microbiota of de-novo pediatric IBD: increased Faecalibacterium prausnitzii and reduced bacterial diversity in Crohn’s but not in ulcerative colitis. Am J Gastroenterol 2012;107:1913e22. [17] Rajilic-Stojanovic M, Jonkers DM, Salonen A, et al. Intestinal microbiota and diet in IBS: causes, consequences, or epiphenomena? Am J Gastroenterol 2015;110:278e87. [18] Chang JY, Antonopoulos DA, Kalra A, et al. Decreased diversity of the fecal microbiome in recurrent Clostridium difficileeassociated diarrhea. J Infect Dis 2008;197:435e8. [19] Chen Y, Yang F, Lu H, et al. Characterization of fecal microbial communities in patients with liver cirrhosis. Hepatology 2011;54:562e72. [20] Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 2008;6:e280. [21] Walker AW, Lawley TD. Therapeutic modulation of intestinal dysbiosis. Pharmacol Res 2013;69:75e86. [22] Brubaker L, Wolfe AJ. The female urinary microbiota, urinary health and common urinary disorders. Ann Transl Med 2017;5. https://doi.org/ 10.21037/atm.2016.11.62. [23] Vemuri RC, Gundamaraju R, Shinde T, Eri R. Therapeutic interventions for gut dysbiosis and related disorders in the elderly: antibiotics, probiotics or faecal microbiota transplantation? Benef Microbes 2017;8:179e92. [24] Mayer EA, Savidge T, Shulman RJ. Brainegut microbiome interactions and functional bowel disorders. Gastroenterology 2014;146:1500e12.
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[25] Khalsa J, Duffy LC, Riscuta G, Starke-Reed P, Hubbard VS. Omics for understanding the gut-liver-microbiome axis and precision medicine. Clin Pharmacol Drug Dev 2017;6:176e85. [26] Bo L, Li J, Tao T, et al. Probiotics for preventing ventilator-associated pneumonia. In: Deng X, editor. Cochrane database of systematic reviews. Chichester, UK: John Wiley & Sons, Ltd.; 2014. CD009066. [27] Candela M, Maccaferri S, Turroni S, Carnevali P, Brigidi P. Functional intestinal microbiome, new frontiers in prebiotic design. Int J Food Microbiol 2010;140:93e101. [28] Acree M, Davis AM. Acute diarrheal infections in adults. JAMA 2017;318. https://doi.org/10.1053/j.gastro.2016.12.039. [29] Wischmeyer PE, Mcdonald D, Knight R. Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness. Curr Opin Crit Care 2016;22(4):347e53. https://doi.org/10.1097/MCC.0000000000000321. [30] Shetty SA, Hugenholtz F, Lahti L, Smidt H, De Vos WM. Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies. FEMS Microbiol Rev 2017;45:182e99. [31] Difficile C. Role of the intestinal microbiota in resistance to colonization by Clostridium difficile. Gastroenterology 2014;146:1547e53. [32] Cox LM, Blaser MJ. Antibiotics in early life and obesity. Nat Rev Endocrinol 2014;11:182e90. [33] De La Cochetière MF, Durand T, Lepage P, Bourreille A, Galmiche JP, Doré J. Resilience of the dominant human fecal microbiota upon shortcourse antibiotic challenge. J Clin Microbiol 2005;43:5588e92. [34] Keeney KM, Yurist-Doutsch S, Arrieta M-C, Finlay BB. Effects of antibiotics on human microbiota and subsequent disease. Annu Rev Microbiol 2014;68. https://doi.org/10.1146/annurev-micro-091313-103456. [35] Bokulich NA, Chung J, Battaglia T, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med 2016;8. http://stm.sciencemag.org.libproxy.unm.edu/content/scitransmed/8/343/343ra82.full.pdf.
The Unknown Effect of AntibioticInduced Dysbiosis on the Gut Microbiota Aleksandr Birg, Nathaniel L. Ritz and Henry C. Lina Medicine Service, New Mexico VA Health Care System and the Division of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, NM, United States
INTRODUCTION In recent years, evaluation of changes in the gut microbial community after antibiotic exposure has gained traction as an important health topic. While antibiotic use has proven to be extremely beneficial in combatting infectious disease, the classic vignette has been that microbes are costly and deleterious to life and should be eliminated at every opportunity. This stance has been reversed in recent years, with our growing knowledge of microbial communities and their role in promoting host health and homeostasis. Therefore, the paradoxical widespread and frequent overuse of antibiotics, in hospitals, agriculture, and the food industry, can be counterproductive to the health of the microbiota and subsequently to the health of the host. Increasing focus has been given, to evaluate how the intestinal microbiome is impacted by antibiotic use, both acutely and long term. Following the use of antibiotics, the beneficial properties of the gut microbiota can be lost and can promote the evolution of antibiotic-resistant pathogens. The intestinal microbiota is a densely populated microbial ecosystem, comprised of trillions of microbes belonging to hundreds of species [1]. The composition of the gut microbiota is altered by numerous environmental factors, including the general health of the host, diet, lifestyle, and antibiotic use. Gastrointestinal microbial colonization increases both from proximal to distal gut (stomach 101 microbial cells/g contents, small intestine 103 7 cells/g, and colon 1012 cells/g), and within the intestinal lumen, from lateral (regions adherent and adjacent to host tissues) to medial [2]. In healthy individuals, there is great microbial richness and diversity, both within individuals (alpha diversity) and between individuals (beta diversity). Despite this high diversity at the species level, the microbiota consists of only a few bacterial phyla, with greater than 90% belonging to Bacteroidetes, Firmicutes, Actinobacteria, and Proteobacteria [3,4]. Verrucomicrobia, Fusobacteria, and Cyanobacteria combine for most of the remaining bacteria, in low numbers. Bacteroidetes are gram-negative bacteria that ferment polysaccharides and otherwise indigestible carbohydrates and produce short-chain fatty acids (SCFAs) that have many beneficial effects in the gut. Firmicutes are primarily composed of gram-positive bacteria that range from mutualistic symbionts (e.g., Lactobacillus spp., Clostridium clusters IV-XIVa) to pathobionts (e.g., Clostridium difficile, Clostridium perfringens). Actinobacteria are gram-positive bacteria that are usually beneficial (e.g., Bifidobacterium spp.) and commonly used as probiotics. Proteobacteria are a diverse group of gram-negative bacteria that tend to increase in number during dysbioses (e.g., Enterobacteriaceae family) [5]. While bacteria make up the vast majority of microbial biomass in the gut and are the most commonly studied, it is important to note that there are also eukaryotes (mostly yeasts), viruses (mostly bacteriophage), and archaea (mostly methanogens) present with distinct roles within the microbial community. Following perturbation, the proportion and representation of these groups can be thrown into a state of imbalance, or dysbiosis, that can cause a loss of functionality and lead to disease.
a. Senior author.
Microbiome and Metabolome in Diagnosis, Therapy, and other Strategic Applications. https://doi.org/10.1016/B978-0-12-815249-2.00020-8 Copyright © 2019 Elsevier Inc. All rights reserved.
195
196 BLOCK | III Established and Experimental Interventions
BACTERIAL BIOFILMS There has been a growing appreciation for the complexity of the interrelationships, among the large consortia of microbes of the gut. A prominent example of this is seen when microbes form biofilms by adhering to surfaces, aggregate, and become embedded in extracellular matrices. These systems provide defense against antimicrobials and allow direct access for microbial nutrient transfer. Biofilms have been shown to be beneficial for the host, by aiding the digestion of luminal contents and creating a barrier to prevent the colonization of pathogens [6]. In fact, colonization resistance is one of the most significant defensive mechanisms a healthy, intact microbiota provides. However, biofilms can also behave pathologically, with estimates that 65% of infections were associated with biofilm production [7].
ANTIBIOTIC ADMINISTRATION Antibiotics can alter the microbiota, by selecting for antibiotic-resistant species. Resistance genes spread through vertical (i.e., resistant mutation passed down from parent to offspring) or horizontal (i.e., transformation or conjugation) transmission. Following antibiotic use, resistant organisms and mobile elements can remain within the population, for an extended period of time. Studies have reported that resistant species can persist 3e4 years, after patients were originally treated with antibiotics [4,5]. The antibiotic spectrum, dose and duration, pharmacokinetic and pharmacodynamic properties, and route of administration, all contribute to how the microbiota is affected [8]. Different classes of antibiotics will not only affect different microbes but also have different host absorption and clearance properties, which impact the distribution and excretion of the compounds in relation to the microbiota, where the site of greatest impact is within the distal gut.
ANTIBIOTIC SPECTRUM Oral administration of broad-spectrum and poor absorption antibiotics have a greater impact on the gut microbiota, compared to narrow-spectrum and high absorption antibiotics [9]. The spectrum of activity for an antibiotic can play an important role in pathobiont (any organism with the potential to become pathological) overgrowth and/or acute pathogen infection. This scenario is exemplified following a narrow-spectrum antibiotic treatment, which primarily targets anaerobes, resulting in a vastly increased risk of overgrowth by facultative anaerobes Enterococcus and Streptococcus; this event is not seen following the use of broad-spectrum antibiotics [10].
BACTERIAL DIVERSITY Multiple studies testing the effects on antibiotics have shown that while total microbial numbers may return to normal after a 1e2 week period, the overall diversity significantly decreases, and certain bacterial taxa may be permanently lost. Additionally, colonization resistance to common nosocomial pathogens was lost, until microbiota diversity was restored [11e14]. The burgeoning replacement bacterial populations within the microbiota varied across studies and depended on the initial colonization of microbes still present after cessation of the antibiotic treatment.
PROTEOBACTERIA OVERGROWTH Worrisomely, bacteria of the phylum Proteobacteria frequently expanded following antibiotic treatments. One explanation for the Proteobacteria bloom in dysbioses is that both intestinal inflammation and antibiotic treatment increase epithelial oxygenation in the colon, creating a more aerobic atmosphere, favoring the facultative over obligate anaerobes [15]. These include major pathogens, some of them multiresistant to antibiotics, such as Salmonella, Escherichia coli, Yersinia, Pseudomonas, Klebsiella, Shigella, Proteus, Enterobacter, and Serratia.
ANTIBIOTIC-INDEPENDENT LOSS OF DIVERSITY The loss of microbiome diversity has been reported in a multitude of diseases, impacting the gastrointestinal system, and parallels changes seen with antibiotics. Inflammatory bowel disease has been studied extensively, showing a loss of diversity in both ulcerative colitis and Crohn’s disease patients [16]. Variable results in regard to alpha diversity, in inflammatory bowel disease, have been reported in the literature, with some studies showing significant change in phyla, particularly Proteobacteria and Bacteroidetes, while other studies show no notable change [16].
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Irritable bowel syndrome also shows a loss of diversity in the diarrhea subtype, via sequencing of the stool [17]. Reduced diversity of the microbiome was also noted in Clostridium difficileeinfected patients, with symptoms of acute diarrhea [18]. Interestingly, this trend in loss of microbial diversity has been reported in diseases outside the gut lumen. Patients evaluated with chronic liver disease were also shown to have a loss of gut bacterial diversity [19].
BACTERIAL CROSS TALK The changes seen in bacterial diversity during a disease process emphasize the communication and interplay between the host and gut microbiota. With similar bacterial community changes seen during antibiotic use, any administration of antibacterial therapy needs to be carefully evaluated, for potential impact on the host [20]. It is also important to emphasize that antibiotics have been used extensively to treat a multitude of gastrointestinal infections and diseases, through the years.
ANTIBIOTIC THERAPY OF INTESTINAL DYSBIOSIS More recently, antibiotics have been applied to treat dysbiosis [21]. The rationale here is to treat overgrowth of bacteria in the microbiome, as one would treat overgrowth of bacteria in the setting of an infection. While there is some comparability between these two types of overgrowth, the desired outcomes are drastically different.
ANTIBIOTICS IN URINARY INFECTION Urinary tract infections are a common disease process that is often treated with antibiotics for abnormal changes in urinary microbiome that can cause symptoms to the host [22]. With recent studies evaluating urine via genetic sequencing, it has been determined that the bladder lumen is associated with a specific microbiome (as opposed to being a sterile environment). Changes to that microbiome can lead to an overgrowth of a certain species that can cause symptoms of a urinary infection [22].
THE URINARY MICROBIOME The bacterial density of a healthy urine microbiome is magnitudes lower than that of the gut, usually ranging from 102 to 105 colony-forming units per milliliter, compared to 1012 colony-forming units per milliliter in intestines [22]. Urine cultures from urinary tract infections usually grow only one species, most commonly E. coli that is responsible for symptoms. These can typically be treated with narrow-coverage antibiotics [22]. Symptom improvement is seen after treatment with antibiotics, which curb the growth of the uropathogen.
URINARY VERSUS GASTROINTESTINAL DYSBIOSIS The gut microbiota is a more complex system, with a significantly higher number of species present, compared to the urinary tract system; therefore changes that occur will impact host physiology differently [22]. When dealing with the gastrointestinal system, symptomatic dysbiosis does not occur due to alterations in a single species or a specific collection of species [21]. Treatment with narrow-range antibiotics will not yield the same results of symptom resolution, in patients with intestinal dysbiosis, as it would in patients with urinary tract infections. Broad-spectrum antibiotics have been shown to be successful, in diminishing gastrointestinal symptoms in the setting of dysbiosis [23]. Many recent efforts have gone into the reasoning, behind the beneficial effects of the broadspectrum antimicrobials. Outside of the usual bactericidal and bacteriostatic activity of antibiotics, additional properties must be involved in the exact effects on the altered microbiome, in order to facilitate restoration of the normal function [21].
NON-ANTIBIOTIC MANAGEMENT OF DYSBIOSIS There has been a revitalization of efforts, delving into alternative therapies to improve symptoms of dysbiosis. As antibiotics have been shown to cause loss of gut bacterial diversity that can lead to further deleterious changes, advantageous properties of probiotics and prebiotics have been acknowledged as useful therapies.
198 BLOCK | III Established and Experimental Interventions
PROBIOTICS Probiotics are live organisms that provide benefits to the host after consumption [24]. Probiotics have been used to treat liver injury and hepatic inflammation, in the event of intestinal bacterial overgrowth, by maintaining permeability of tight junctions and preventing pathogen translocation [25]. In addition, JAMA meta-analysis has shown that probiotics can reduce antibiotic-associated diarrhea by up to 40%, while a review by Cochrane has shown that probiotic use in Clostridium difficile colitis will reduce diarrhea by up to 64% [26]. Single-strain probiotics have been shown to increase bacterial gut diversity as well [19].
PREBIOTICS Prebiotics are nondigestible food ingredients that propagate beneficial microbial activity of the microbiome [24]. Prebiotics are usually oligosaccharides that provide nutrients selectively to intestinal symbionts [27]. Prebiotics, in themselves, have to work through probiotic strains, to provide benefits to the host and alter probiotic bacteria to control pathogens [25]. However, it is important to note that as of this time, probiotics are not regularly recommended for symptom control, except for known cases of antibiotic-induced diarrhea [28].
FECAL TRANSPLANTS Fecal microbiota transplants (FMT) are another method developed to help control altered microbial changes [29]. The exact mechanism as to how FMT works is not well understood and needs further research [30]; however, FMT have shown to be very effective, for treating altered microbiota in the setting of C. difficile colitis [29]. Despite probiotics, prebiotics, and FMT showing great potential benefit to treat antibiotic alteration in the microbiome, there are still significant unknowns involved, which do not translate to regular use in medicine [25]. It has been reported that single-strain probiotics have very limited success in treating intestinal dysbiosis [31]. The lack of knowledge into long-term effects keeps these alternative therapies from being considered viable treatment options, for severe conditions that occur with antibiotic use (i.e., C. difficile colitis) [32].
ECOSYSTEM EVALUATION Future research into changes seen in the gut microbiota will focus less on individual species that can be observed through culture and will need to emphasize the role of larger community variations. Culturing the gut microbiota is no longer considered a viable option, to truly understand those changes, as only 80% are culturable, and many genera are too difficult to grow under standard conditions [33,34]. Important and useful concepts, such as alpha and beta diversity, cannot be evaluated with the use of culturing and lead to lack of complete understanding of the changes that take place [35].
MULTIOMICS INVESTIGATION When considering the complex and evolving changes, occurring in an intestinal environment after antibiotic exposure, interactions between the host and microbiota require more involved strategies [25]. Several “omic” technologies have emerged to the forefront, to study how the microbial community and microbial metabolites are affected, including changes by antibiotic disruption [25].
DIAGNOSTIC OPTIONS As more of these techniques are being incorporated into everyday practice, the cost becomes more favorable. This allows for easier access and future integration into personalized medicine [25]. The current “gold standard” for studying microbial communities is 16S rRNA next-generation sequencing (also known as high-throughput sequencing) that allows for genetic definition of pathogens, rather than relying on their morphology [34]. In addition to genetic sequencing to analyze gut microbiome, several other techniques have emerged to study functional changes such as metagenomics and metatranscriptomics [34]. Another mechanism to study disruption in microbiome is evaluating metabolites in a technique called metabolomics, which is used to detect microbial products in urine, blood, saliva, and feces [25]. As we learn more about metagenomics and metabolomics and understand the role of microbes in human health and disease, future therapies can be based around the microbiome as well [27].
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ONGOING STUDIES Evaluating human data regarding alterations of the microbiome by antibiotics is difficult, lacking in human trials [25]. The major question in the coming years will be to determine the exact changes in the gut microbiota that will cause a disruption in function, and what specific parameters will be responsible for diseases and symptoms.
ACKNOWLEDGMENTS This study is supported by the Winkler Bacterial Overgrowth Research Fund.
DISCLAIMER Dr. Lin has patent rights in related area.
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