The More the Merrier? Reduced Fecal Microbiota Diversity in Preterm Infants Treated with Antibiotics
T
he human microbiota (ie, the sum of all microbial life In this issue of The Journal, Greenwood et al6 describe the living in and on the human body) continues to create effects of early empiric antibiotic treatment on the fecal mitremendous excitement in the scientific research comcrobiota of preterm infants. Antibiotics are the most munity. In addition, the human microbiota is considered a commonly prescribed medication in the neonatal intensive major target of future personalized medicine and is receiving care unit. Preterm infants, who are at high risk of infectious increasing attention in the public in discuscomplications often receive empiric antibiSee related article, p sions about antibiotic treatment, probiotic otic therapy, which is defined as treatment supplements, and fecal transplantation. New studies are based on suspected infection without positive culture reemerging that report associations between specific groups sults. The study by Greenwood et al is especially relevant, of bacteria (or other microbial organisms) and human disas failure to establish a healthy microbiota has been linked ease. The growing list of disorders with a suspected microto infections and necrotizing enterocolitis (NEC), the biota component ranges from increased susceptibility to second-most common cause of morbidity in premature viral and bacterial infection, metabolic disorders such as infants. obesity and diabetes, and inflammatory and autoimmune The authors collected diapers from 74 preterm infants diseases (eg, allergies/asthma, inflammatory bowel disease, (#32 weeks’ gestational age), which were divided into groups and multiple sclerosis) to neurodevelopmental problems, of infants who had a brief (1-4 days, 64%), intensive (5such as depression and autism.1 Understanding the true na7 days, 18%), or no course (18%) of empiric antibiotic use within the first week of life. Diapers were collected for 3 ture of the reported relationships between microbiota and consecutive weeks, starting at 4-7 days of life. DNA was isodisease (associative or causative) is imperative, as many of lated from fecal material and used for the amplification and the listed disorders, particularly those with an inflammatory sequencing of bacterial 16S ribosomal RNA genes. Sequences component, have been increasing in highly developed counwere clustered based on similarity into operational taxotries over the past decades. nomic units (species equivalents), which were used to estiThe identification of those potential factors that establish, mate and compare the microbial diversity and taxonomic maintain, or modulate the microbiota is of extreme imporcomposition in the 3 patient groups. The authors show tance and could have tremendous consequences for future that the abundance of several major microbiota members personalized medicine: if we know how to control the microseems to be affected by antibiotic use, although the exact biota, we can manipulate it to our advantage and treat and impact of the antibiotic exposure on the fecal microbiota prevent disease and improve quality of life. Exciting prelimcomposition remains unclear: The genus Enterobacter was inary studies on the modulatory effects of probiotic nutriincreased in preterm infants in week 2 after either brief or tional supplements and fecal transplantation on the intensive antibiotic exposure but not in week 3. Staphylogastrointestinal microbiota of mice and humans raise hopes coccus increased in week 3 in infants with brief antibiotic for new therapeutic tools that might become available in use compared with infants with no antibiotic exposure and the future.1,2 Widespread use of broad-spectrum antibiotics, decreased in week 2 but not week 3 in infants with intensive on the other hand, faces increasing criticism in the light of antibiotic use. The absence of a more uniform microbiota recent microbiota studies. Although indispensable to treat signature in the preterm infants with exposure to antibiotics and prevent bacterial infection, inappropriate use in human could result from interindividual variation, which the auand veterinary medicine has been identified as a major probthors do not discuss in the present publication. However, lem and cause of increased resistance in many pathogenic previous studies have demonstrated that taxonomic microbacteria. Maybe even more importantly, the short- and biota compositions (in contrast to more conserved funclong-term effects of antibiotic exposure on the human microtional microbiota compositions) can vary significantly biota are currently not well understood. Antibiotic use in inbetween healthy individuals and even in the same individual fants has been epidemiologically linked to the development over time.7 Moreover, even bacterial strains from the same of asthma and allergies later in life,3 subtherapeutic exposure 4 to antibiotics increases weight gain in mice, and even a single species can be more or less tolerant or resistant to antibiotics, which could allow the microbiota from different infants with course of antibiotics can permanently alter the human gastrointestinal microbiota.5 The author declares no conflicts of interest.
NEC
Necrotizing enterocolitis
0022-3476/$ - see front matter. Copyright ª 2014 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.jpeds.2014.03.022
1
THE JOURNAL OF PEDIATRICS
similar compositions to show greatly varying responses to antibiotic exposure. What might be more significant than the reported shifts in microbiota compositions in response to antibiotic treatment could be the observations that Greenwood et al made with respect to changes in microbiota diversity in the preterm infant population. The authors assessed microbial diversity by calculating the Simpson index, which reflects both the number of different bacterial species (ie, operational taxonomic units) and how evenly the abundances of these species were distributed across the samples (ie, how much of the microbial communities was made up of rare, low-abundance organisms). While the fecal microbiota of infants without antibiotic exposure increased over the 3-week study period, even brief antibiotic use in the first week of life was associated with reduced microbial diversity in preterm infants after week 2. This reduced diversity phenotype lasted until week 3 in infants with intensive antibiotic exposure, whereas infants with brief exposure returned to their original diversity levels by week 3. In summary, these observations suggest that the gastrointestinal microbiota of (preterm) infants increases in complexity over the first few weeks of life, but this developmental process can be at least temporarily delayed as a consequence of even brief antibiotic exposure or, in case of intensive antibiotic treatment, might even result in long-term consequences for microbiota development. A reduced microbial diversity, often in combination with an increased abundance of Proteobacteria, a group that includes Gram-negative enteric pathogens, has been described as one of the hallmarks of antibiotic-induced dysbiosis in the context of Clostridium difficile infection.8 Infants born via cesarean delivery harbor a less complex fecal microbiota than those delivered vaginally.9 In summary, reductions in microbial diversity rather than the presence or absence of specific microbiota members are beginning to emerge as a universal biomarker indicative for a dysbiotic microbiota with increased susceptibility to disease. From the clinical perspective, the findings by Greenwood et al are interesting and important and highlight the need for future studies to reevaluate antibiotic treatment policies in infant and other patient populations. First, additional work is needed to confirm any causative role of antibiotic administration for the development of later comorbidities in preterm infants. Reduced microbial diversity, as seen in this study for preterm infants with antibiotic exposure, has previously been associated with NEC, and the authors found more of the preterm infants with exposure to antibiotics to develop NEC, sepsis, or death. However, clinical symptoms that prompted empiric antibiotic prescriptions could be indicative of existing preconditions that played a role for later problems regardless of antibiotic exposure. Prospective cohort studies should begin surveillance of the microbiota before the beginning of antibiotic treatment and follow the infants longitudinally to get a more detailed picture of microbiota events preceding antibiotic treatment and disease onset and to differentiate between effects resulting from antibiotic use or other factors. 2
Vol. -, No. -
www.jpeds.com
Second, mechanistic insight is needed into how antibioticinduced microbiota changes may affect the human host: If reductions in microbial diversity increase the susceptibility to comorbidities, which part of the lost taxonomic or functional microbiota repertoire needs to be replenished to avoid disease? Are more easily detectable changes in the abundance of dominant microbiota members even relevant, or should they merely serve as diagnostic markers for functionally more relevant changes affecting other rare organisms that we do not even know about (yet)? Animal (germ-free) model systems seem to be our best option to confirm any hypotheses arising from human studies by translating human findings into animal experiments involving microbiota manipulation. Finally, where do we begin treatment, and what are our therapeutic options? If microbiota optimization is the goal, will it be sufficient to identify 1 generic microbial cocktail for transplantation or is a specific microbiota only good for one patient but bad for another? Do we really need to improve our capabilities for microbiota manipulation, or can we optimize antibiotic drugs to more specifically target pathogens but not the entire microbiota? The narrowspectrum antibiotic drug fidaxomicin, which is used to treat C difficile infection without grossly affecting the whole microbiota, could be an example of where future antibiotic drug developments are leading. Overall, our knowledge of the microbiota and its functional role in human health and disease remains so limited that diagnostic rather than therapeutic applications of the findings by Greenwood et al and others in the field seem to be a more realistic goal in the near future. n W. Florian Fricke, PhD Institute of Biological Chemistry and Nutrition University of Hohenheim Stuttgart, Germany Department of Microbiology and Immunology Institute for Genome Sciences University of Maryland School of Medicine Baltimore, Maryland Reprint requests: W. Florian Fricke, PhD, Institute of Biological Chemistry and Nutrition, University of Hohenheim, Garbenstrasse 30, 70593 Stuttgart, Germany. E-mail: [email protected]
References 1. Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 2013;155:1451-63. 2. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 2013;368:407-15. 3. Storro O, Avershina E, Rudi K. Diversity of intestinal microbiota in infancy and the risk of allergic disease in childhood. Curr Opin Allergy Clin Immunol 2013;13:257-62. 4. Cho I, Yamanishi S, Cox L, Methe BA, Zavadil J, Li K, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 2012; 488:621-6. 5. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated
- 2014 antibiotic perturbation. Proc Natl Acad Sci U S A 2011;108(Suppl 1):4554-61. 6. Greenwood C, Morrow AL, Lagomarcino AJ, Altaye M, Taft DH, Yu Z, et al. Early Empiric Antibiotic Use in Preterm Infants Is Associated with Lower Bacterial Diversity and Higher Relative Abundance of Enterobacter. J Pediatr 2014. 7. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature 2012;489:220-30.
EDITORIAL 8. Song Y, Garg S, Girotra M, Maddox C, von Rosenvinge EC, Dutta A, et al. Microbiota dynamics in patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection. PLoS One 2013;8: e81330. 9. Jakobsson HE, Abrahamsson TR, Jenmalm MC, Harris K, Quince C, Jernberg C, et al. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section. Gut 2014;63:559-66.
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T
he human microbiota (ie, the sum of all microbial life In this issue of The Journal, Greenwood et al6 describe the living in and on the human body) continues to create effects of early empiric antibiotic treatment on the fecal mitremendous excitement in the scientific research comcrobiota of preterm infants. Antibiotics are the most munity. In addition, the human microbiota is considered a commonly prescribed medication in the neonatal intensive major target of future personalized medicine and is receiving care unit. Preterm infants, who are at high risk of infectious increasing attention in the public in discuscomplications often receive empiric antibiSee related article, p sions about antibiotic treatment, probiotic otic therapy, which is defined as treatment supplements, and fecal transplantation. New studies are based on suspected infection without positive culture reemerging that report associations between specific groups sults. The study by Greenwood et al is especially relevant, of bacteria (or other microbial organisms) and human disas failure to establish a healthy microbiota has been linked ease. The growing list of disorders with a suspected microto infections and necrotizing enterocolitis (NEC), the biota component ranges from increased susceptibility to second-most common cause of morbidity in premature viral and bacterial infection, metabolic disorders such as infants. obesity and diabetes, and inflammatory and autoimmune The authors collected diapers from 74 preterm infants diseases (eg, allergies/asthma, inflammatory bowel disease, (#32 weeks’ gestational age), which were divided into groups and multiple sclerosis) to neurodevelopmental problems, of infants who had a brief (1-4 days, 64%), intensive (5such as depression and autism.1 Understanding the true na7 days, 18%), or no course (18%) of empiric antibiotic use within the first week of life. Diapers were collected for 3 ture of the reported relationships between microbiota and consecutive weeks, starting at 4-7 days of life. DNA was isodisease (associative or causative) is imperative, as many of lated from fecal material and used for the amplification and the listed disorders, particularly those with an inflammatory sequencing of bacterial 16S ribosomal RNA genes. Sequences component, have been increasing in highly developed counwere clustered based on similarity into operational taxotries over the past decades. nomic units (species equivalents), which were used to estiThe identification of those potential factors that establish, mate and compare the microbial diversity and taxonomic maintain, or modulate the microbiota is of extreme imporcomposition in the 3 patient groups. The authors show tance and could have tremendous consequences for future that the abundance of several major microbiota members personalized medicine: if we know how to control the microseems to be affected by antibiotic use, although the exact biota, we can manipulate it to our advantage and treat and impact of the antibiotic exposure on the fecal microbiota prevent disease and improve quality of life. Exciting prelimcomposition remains unclear: The genus Enterobacter was inary studies on the modulatory effects of probiotic nutriincreased in preterm infants in week 2 after either brief or tional supplements and fecal transplantation on the intensive antibiotic exposure but not in week 3. Staphylogastrointestinal microbiota of mice and humans raise hopes coccus increased in week 3 in infants with brief antibiotic for new therapeutic tools that might become available in use compared with infants with no antibiotic exposure and the future.1,2 Widespread use of broad-spectrum antibiotics, decreased in week 2 but not week 3 in infants with intensive on the other hand, faces increasing criticism in the light of antibiotic use. The absence of a more uniform microbiota recent microbiota studies. Although indispensable to treat signature in the preterm infants with exposure to antibiotics and prevent bacterial infection, inappropriate use in human could result from interindividual variation, which the auand veterinary medicine has been identified as a major probthors do not discuss in the present publication. However, lem and cause of increased resistance in many pathogenic previous studies have demonstrated that taxonomic microbacteria. Maybe even more importantly, the short- and biota compositions (in contrast to more conserved funclong-term effects of antibiotic exposure on the human microtional microbiota compositions) can vary significantly biota are currently not well understood. Antibiotic use in inbetween healthy individuals and even in the same individual fants has been epidemiologically linked to the development over time.7 Moreover, even bacterial strains from the same of asthma and allergies later in life,3 subtherapeutic exposure 4 to antibiotics increases weight gain in mice, and even a single species can be more or less tolerant or resistant to antibiotics, which could allow the microbiota from different infants with course of antibiotics can permanently alter the human gastrointestinal microbiota.5 The author declares no conflicts of interest.
NEC
Necrotizing enterocolitis
0022-3476/$ - see front matter. Copyright ª 2014 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.jpeds.2014.03.022
1
THE JOURNAL OF PEDIATRICS
similar compositions to show greatly varying responses to antibiotic exposure. What might be more significant than the reported shifts in microbiota compositions in response to antibiotic treatment could be the observations that Greenwood et al made with respect to changes in microbiota diversity in the preterm infant population. The authors assessed microbial diversity by calculating the Simpson index, which reflects both the number of different bacterial species (ie, operational taxonomic units) and how evenly the abundances of these species were distributed across the samples (ie, how much of the microbial communities was made up of rare, low-abundance organisms). While the fecal microbiota of infants without antibiotic exposure increased over the 3-week study period, even brief antibiotic use in the first week of life was associated with reduced microbial diversity in preterm infants after week 2. This reduced diversity phenotype lasted until week 3 in infants with intensive antibiotic exposure, whereas infants with brief exposure returned to their original diversity levels by week 3. In summary, these observations suggest that the gastrointestinal microbiota of (preterm) infants increases in complexity over the first few weeks of life, but this developmental process can be at least temporarily delayed as a consequence of even brief antibiotic exposure or, in case of intensive antibiotic treatment, might even result in long-term consequences for microbiota development. A reduced microbial diversity, often in combination with an increased abundance of Proteobacteria, a group that includes Gram-negative enteric pathogens, has been described as one of the hallmarks of antibiotic-induced dysbiosis in the context of Clostridium difficile infection.8 Infants born via cesarean delivery harbor a less complex fecal microbiota than those delivered vaginally.9 In summary, reductions in microbial diversity rather than the presence or absence of specific microbiota members are beginning to emerge as a universal biomarker indicative for a dysbiotic microbiota with increased susceptibility to disease. From the clinical perspective, the findings by Greenwood et al are interesting and important and highlight the need for future studies to reevaluate antibiotic treatment policies in infant and other patient populations. First, additional work is needed to confirm any causative role of antibiotic administration for the development of later comorbidities in preterm infants. Reduced microbial diversity, as seen in this study for preterm infants with antibiotic exposure, has previously been associated with NEC, and the authors found more of the preterm infants with exposure to antibiotics to develop NEC, sepsis, or death. However, clinical symptoms that prompted empiric antibiotic prescriptions could be indicative of existing preconditions that played a role for later problems regardless of antibiotic exposure. Prospective cohort studies should begin surveillance of the microbiota before the beginning of antibiotic treatment and follow the infants longitudinally to get a more detailed picture of microbiota events preceding antibiotic treatment and disease onset and to differentiate between effects resulting from antibiotic use or other factors. 2
Vol. -, No. -
www.jpeds.com
Second, mechanistic insight is needed into how antibioticinduced microbiota changes may affect the human host: If reductions in microbial diversity increase the susceptibility to comorbidities, which part of the lost taxonomic or functional microbiota repertoire needs to be replenished to avoid disease? Are more easily detectable changes in the abundance of dominant microbiota members even relevant, or should they merely serve as diagnostic markers for functionally more relevant changes affecting other rare organisms that we do not even know about (yet)? Animal (germ-free) model systems seem to be our best option to confirm any hypotheses arising from human studies by translating human findings into animal experiments involving microbiota manipulation. Finally, where do we begin treatment, and what are our therapeutic options? If microbiota optimization is the goal, will it be sufficient to identify 1 generic microbial cocktail for transplantation or is a specific microbiota only good for one patient but bad for another? Do we really need to improve our capabilities for microbiota manipulation, or can we optimize antibiotic drugs to more specifically target pathogens but not the entire microbiota? The narrowspectrum antibiotic drug fidaxomicin, which is used to treat C difficile infection without grossly affecting the whole microbiota, could be an example of where future antibiotic drug developments are leading. Overall, our knowledge of the microbiota and its functional role in human health and disease remains so limited that diagnostic rather than therapeutic applications of the findings by Greenwood et al and others in the field seem to be a more realistic goal in the near future. n W. Florian Fricke, PhD Institute of Biological Chemistry and Nutrition University of Hohenheim Stuttgart, Germany Department of Microbiology and Immunology Institute for Genome Sciences University of Maryland School of Medicine Baltimore, Maryland Reprint requests: W. Florian Fricke, PhD, Institute of Biological Chemistry and Nutrition, University of Hohenheim, Garbenstrasse 30, 70593 Stuttgart, Germany. E-mail: [email protected]
References 1. Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 2013;155:1451-63. 2. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 2013;368:407-15. 3. Storro O, Avershina E, Rudi K. Diversity of intestinal microbiota in infancy and the risk of allergic disease in childhood. Curr Opin Allergy Clin Immunol 2013;13:257-62. 4. Cho I, Yamanishi S, Cox L, Methe BA, Zavadil J, Li K, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 2012; 488:621-6. 5. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated
- 2014 antibiotic perturbation. Proc Natl Acad Sci U S A 2011;108(Suppl 1):4554-61. 6. Greenwood C, Morrow AL, Lagomarcino AJ, Altaye M, Taft DH, Yu Z, et al. Early Empiric Antibiotic Use in Preterm Infants Is Associated with Lower Bacterial Diversity and Higher Relative Abundance of Enterobacter. J Pediatr 2014. 7. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature 2012;489:220-30.
EDITORIAL 8. Song Y, Garg S, Girotra M, Maddox C, von Rosenvinge EC, Dutta A, et al. Microbiota dynamics in patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection. PLoS One 2013;8: e81330. 9. Jakobsson HE, Abrahamsson TR, Jenmalm MC, Harris K, Quince C, Jernberg C, et al. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section. Gut 2014;63:559-66.
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