Prematurity and Perinatal Antibiotics: A Tale of Two Factors Influencing Development of the Neonatal Gut Microbiota

Abstract

See related article, p 538Despite robust global research efforts, preterm birth remains a relatively intractable and pervasive problem. Indeed, preterm birth continues to impact >10% of live births in the US, and is the leading cause of neonatal morbidity and mortality worldwide.1Lawn J.E. Cousens S. Zupan J. Lancet Neonatal Survival Steering Team4 million neonatal deaths: When? Where? Why?.Lancet. 2005; 365: 891-900Abstract Full Text Full Text PDF PubMed Scopus (2560) Google Scholar Compared with full-term births, preterm deliveries are typified by more frequent use of perinatal antibiotics, that is, antibiotics administered either intra-partum to the mother, or post-partum to the newborn. The decision to treat with perinatal antibiotics is a clinical judgment based on perceived risks and benefits to both mother and baby. However, it is undoubtedly the rare clinician who takes into consideration the potential effects of antibiotics on the infant's future gut microbiota. This might be particularly true when perinatal antibiotics consist of a single dose of intra-partum antibiotics prescribed to the mother, as opposed to a multi-dose post-partum regimen given directly to the newborn. Such a scenario whereby the potential impact of maternal antibiotics on the infant's microbiota receives little consideration is not surprising—at least for now. After all, our current understanding of the effects of antibiotics on microbial communities in the neonatal gut is itself in its infancy and far from complete. To enable such decisions to be evidence-based requires a vastly improved understanding of the establishment of a healthy gut microbiota, including initial community assembly, subsequent succession events, and transient as well as durable responses to various disturbances such as antibiotic exposure.The human body plays host to a rich assembly of diverse microbes—primarily bacteria—residing on mucosal and skin surfaces and in the intestinal lumen. These commensal microbes, which outnumber human cells by at least an order of magnitude, plus their combined genomes, constitute the human microbiome. The microbiome performs a wide array of diverse functions beneficial to its human host, including nutrient acquisition, immune programming, and protection from pathogen invasion, among others.2Turnbaugh P.J. Ley R.E. Hamady M. Fraser-Liggett C.M. Knight R. Gordon J.I. The human microbiome project.Nature. 2007; 449: 804-810Crossref PubMed Scopus (3479) Google Scholar Evidence indicates that the amniotic cavity is sterile during healthy pregnancy3DiGiulio D.B. Diversity of microbes in amniotic fluid.Semin Fetal Neonatal Med. 2012; 17: 2-11Abstract Full Text Full Text PDF PubMed Scopus (246) Google Scholar and that colonization of the newborn gut begins at delivery.4Palmer C. Bik E.M. DiGiulio D.B. Relman D.A. Brown P.O. Development of the human infant intestinal microbiota.PLoS Biol. 2007; 5: e177Crossref PubMed Scopus (2042) Google Scholar, 5Dominguez-Bello M.G. Costello E.K. Contreras M. Magris M. Hidalgo G. Fierer N. et al.Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.Proc Natl Acad Sci U S A. 2010; 107: 11971-11975Crossref PubMed Scopus (2857) Google Scholar Microbial community composition appears to be broadly shaped initially by early environmental factors such as delivery mode (ie, vaginal vs cesarean delivery5Dominguez-Bello M.G. Costello E.K. Contreras M. Magris M. Hidalgo G. Fierer N. et al.Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.Proc Natl Acad Sci U S A. 2010; 107: 11971-11975Crossref PubMed Scopus (2857) Google Scholar) and soon thereafter by incidental exposures to the ambient environment as well as diet.4Palmer C. Bik E.M. DiGiulio D.B. Relman D.A. Brown P.O. Development of the human infant intestinal microbiota.PLoS Biol. 2007; 5: e177Crossref PubMed Scopus (2042) Google Scholar, 6Koenig J.E. Spor A. Scalfone N. Fricker A.D. Stombaugh J. Knight R. et al.Succession of microbial consortia in the developing infant gut microbiome.Proc Natl Acad Sci U S A. 2011; 108: 4578-4585Crossref PubMed Scopus (1644) Google Scholar, 7Costello E.K. Stagaman K. Dethlefsen L. Bohannan B.J. Relman D.A. The application of ecological theory toward an understanding of the human microbiome.Science. 2012; 336: 1255-1262Crossref PubMed Scopus (897) Google ScholarIt is against this backdrop that Arboleya et al in this issue of The Journal report their findings from a longitudinal study of the gut microbiota at 4 sampling time points (2, 10, 30, and 90 days) over the first 3 months of life in 13 term and 27 preterm infants.8Arboleya S. Sánchez B. Milani C. Duranti S. Solís G. Fernández N. et al.Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics.J Pediatr. 2015; 166: 538-544Abstract Full Text Full Text PDF PubMed Scopus (254) Google Scholar The authors found that even at the coarse taxonomic scale of bacterial phyla, distinct differences in community composition between term and preterm infants were evident at the 3 latter time points: preterm infants harbored significantly lower proportions of Bacteroidetes at 10, 30, and 90 days, and higher proportions of Proteobacteria and lower proportions of Actinobacteria at 10 and 30 days. These overall differences in taxonomic composition, which appear to have been driven largely by a handful of bacterial families (especially Bacteroidaceae and Enterobacteriaceae), are broadly consistent with prior reports. Beyond this finding, a particular strength of the report by Arboleya et al is that the distribution in their study of mothers and newborns who received antibiotics enabled an analysis of the potential impact of perinatal antimicrobial use on the developing gut microbiota of preterm infants. Among the 27 preterm deliveries, 14 mothers and 17 neonates received antibiotics, including 9 instances where antibiotics were given to both members of the mother-preterm infant pairs. Using hierarchical clustering analysis, Arboleya et al found that at days 10, 30, and 90, the mother-preterm infant pairs in which any antibiotic was administered perinatally—whether to mother, preterm infant, or both—appeared to demonstrate an effect on gut microbiota composition. The effect following a single dose of intra-partum antibiotics administered solely to the mother appeared to be at least equal to the effect following multiple doses of antibiotics given directly to the neonate after birth. This apparent effect of intra-partum antibiotics was most evident at the 30-day sampling time point and was associated with changes in community composition that in part were qualitatively similar to the differences observed between the preterm and term groups. Indeed, a higher proportion of taxa from the phylum Proteobacteria, driven primarily by an increase in Enterobacteriaceae, were found in preterm infants delivered in the setting of intra-partum antibiotic use. At 90 days, differences in taxonomic composition between the treatment groups were less pronounced but still detectable. Analysis by real-time quantitative polymerase chain reaction targeting specific microbial groups revealed a decreased abundance at 90 days of the genus Bifidobacterium in the group of preterm infants with any antibiotic treatment exposure (ie, either intra-partum to the mother, or post-partum to the infant), compared with the group that received no antibiotic exposure.The findings by Arboleya et al,8Arboleya S. Sánchez B. Milani C. Duranti S. Solís G. Fernández N. et al.Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics.J Pediatr. 2015; 166: 538-544Abstract Full Text Full Text PDF PubMed Scopus (254) Google Scholar although limited and still requiring the type of robust corroboration that comes only from additional investigations, are nonetheless intriguing. In particular, the possibility that indirect exposure to an antibiotic administered as a single dose to the mother during the delivery process might alter the composition of the infant's gut microbiota at 1 to 3 months of age, and possibly beyond, is significant and merits additional investigative efforts. It has been hypothesized for some time that antibiotic administration in the perinatal period (to either the mother or the neonate) might lead to delayed health consequences for the baby as a result of alterations in the developing gut microbiota,9Bedford Russell A.R. Murch S.H. Could peripartum antibiotics have delayed health consequences for the infant?.BJOG. 2006; 113: 758-765Crossref PubMed Scopus (104) Google Scholar but direct evidence has been sparse. The report by Arboleya et al lends support to this hypothesis and argues for additional studies on the establishment and succession of the infant gut microbiota, including in the presence of various disturbances such as antibiotic exposure.The precise process of community assembly of the initial gut microbiota in the neonate remains as yet unclear; however, various general models of microbial community assembly have been proposed. A detailed discussion of these models is beyond the scope of this editorial. The interested reader is referred elsewhere,7Costello E.K. Stagaman K. Dethlefsen L. Bohannan B.J. Relman D.A. The application of ecological theory toward an understanding of the human microbiome.Science. 2012; 336: 1255-1262Crossref PubMed Scopus (897) Google Scholar, 10Hubbell S.P. The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press, Princeton, NJ2001Google Scholar, 11Lindström E.S. Langenheder S. Local and regional factors influencing bacterial community assembly.Environ Microbiol Rep. 2012; 4: 1-9Crossref PubMed Scopus (322) Google Scholar, 12Levy R. Borenstein E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules.Proc Natl Acad Sci U S A. 2013; 110: 12804-12809Crossref PubMed Scopus (237) Google Scholar however, salient features of some overarching models merit brief discussion. One model, termed ‘neutral assembly’, generally proposes that microbial groups gain a foothold in a particular niche primarily as a result of stochastic exposures. This model assumes that functional equivalency exists among trophically similar taxa, thereby effectively neutralizing potential influences exerted by local environmental conditions within a particular niche. A second model proposes that community assembly is a deterministic process that follows ‘assembly rules’. Examples of assembly rules include species assortment (eg, competitive exclusion between microbial species fighting for the same limited resource) and habitat filtering (eg, varying affinities of microbial species for different niches owing to divergent environmental conditions present within those niches).12Levy R. Borenstein E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules.Proc Natl Acad Sci U S A. 2013; 110: 12804-12809Crossref PubMed Scopus (237) Google Scholar These two broad approaches are not mutually exclusive. Indeed, they may contribute in varying degrees to the assembly of a given community, and their relative contributions may vary over time, with the relevant time scale being either developmental or chronological. In fact, the assembly of the gut microbiota has been characterized as having an early ‘unstable’ phase likely resulting from incidental exposures to microbial communities during and soon after delivery,4Palmer C. Bik E.M. DiGiulio D.B. Relman D.A. Brown P.O. Development of the human infant intestinal microbiota.PLoS Biol. 2007; 5: e177Crossref PubMed Scopus (2042) Google Scholar, 6Koenig J.E. Spor A. Scalfone N. Fricker A.D. Stombaugh J. Knight R. et al.Succession of microbial consortia in the developing infant gut microbiome.Proc Natl Acad Sci U S A. 2011; 108: 4578-4585Crossref PubMed Scopus (1644) Google Scholar, 7Costello E.K. Stagaman K. Dethlefsen L. Bohannan B.J. Relman D.A. The application of ecological theory toward an understanding of the human microbiome.Science. 2012; 336: 1255-1262Crossref PubMed Scopus (897) Google Scholar followed by a succession of facultative anaerobes and subsequently strict anaerobes7Costello E.K. Stagaman K. Dethlefsen L. Bohannan B.J. Relman D.A. The application of ecological theory toward an understanding of the human microbiome.Science. 2012; 336: 1255-1262Crossref PubMed Scopus (897) Google Scholar, 13Sommer F. Bäckhed F. The gut microbiota—masters of host development and physiology.Nat Rev Microbiol. 2013; 11: 227-238Crossref PubMed Scopus (1991) Google Scholar that have co-evolved to be adapted to their human host and appear in discrete steps of bacterial succession with abrupt shifts punctuated by life events.6Koenig J.E. Spor A. Scalfone N. Fricker A.D. Stombaugh J. Knight R. et al.Succession of microbial consortia in the developing infant gut microbiome.Proc Natl Acad Sci U S A. 2011; 108: 4578-4585Crossref PubMed Scopus (1644) Google Scholar The early stage of assembly therefore appears to follow, at least in part, a ‘neutral assembly’ model. By contrast, recent studies based on metabolic modeling suggest that an ‘assembly rules’ process and, specifically, habitat filtering, is the dominant structural force in the latter stages of succession.12Levy R. Borenstein E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules.Proc Natl Acad Sci U S A. 2013; 110: 12804-12809Crossref PubMed Scopus (237) Google ScholarA deeper understanding of the assembly process of neonatal gut bacterial communities, including the metabolic interactions of successive communities, is not merely an academic exercise and is potentially of great practical importance. Among the beneficial services that the gut microbiota provides are critical developmental functions that confer potentially long-reaching effects on the host, such as immune system programming and promotion of host tissue differentiation.2Turnbaugh P.J. Ley R.E. Hamady M. Fraser-Liggett C.M. Knight R. Gordon J.I. The human microbiome project.Nature. 2007; 449: 804-810Crossref PubMed Scopus (3479) Google Scholar, 7Costello E.K. Stagaman K. Dethlefsen L. Bohannan B.J. Relman D.A. The application of ecological theory toward an understanding of the human microbiome.Science. 2012; 336: 1255-1262Crossref PubMed Scopus (897) Google Scholar, 13Sommer F. Bäckhed F. The gut microbiota—masters of host development and physiology.Nat Rev Microbiol. 2013; 11: 227-238Crossref PubMed Scopus (1991) Google Scholar Whether specific time windows exist in the lifespan of humans during which particular bacterial consortia must be present in the gut for these functions to be optimally performed is unknown. If such time windows indeed exist, some roles of the host microbiota might be viewed as analogous to developmental programming, whereby events occurring during a critical period of fetal or neonatal life can affect the organism at much later life stages. The classic developmental programming model is based largely on animal studies and proposes that maternal stressors occurring during fetal life cause epigenetic changes that influence physiological function and risk of disease in adult life.14Langley-Evans S.C. Developmental programming of health and disease.Proc Nutr Soc. 2006; 65: 97-105Crossref PubMed Scopus (245) Google Scholar Such a paradigm would suggest that ‘missing’ a window, for example by virtue of a perturbed or otherwise ‘unhealthy’ gut microbiota during a critical time period, might have detrimental effects on the health of the host, possibly at a much later point in life.Studies like the one by Arboleya et al,8Arboleya S. Sánchez B. Milani C. Duranti S. Solís G. Fernández N. et al.Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics.J Pediatr. 2015; 166: 538-544Abstract Full Text Full Text PDF PubMed Scopus (254) Google Scholar which provide longitudinal analyses of the human microbiota during critical life stages and incorporate clinical metadata such as medication exposures and clinical outcomes, are essential for furthering our understanding of the relationship between the microbiome and human health. In addition to conducting such studies at high spatiotemporal resolution and for long sampling durations, investigations that incorporate either natural or controlled community disturbances of interest, such as antibiotic exposure,15Dethlefsen L. Relman D.A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation.Proc Natl Acad Sci U S A. 2011; 108: 4554-4561Crossref PubMed Scopus (1472) Google Scholar are apt to be particularly enlightening. The types of investigative and analytic approaches brought to bear should include multi-‘omics’ methods to interrogate genomic, transcriptomic, proteomic, and metabolomic features and interactions. New insights from these types of investigations hold promise for informing clinical treatment decisions as well as rationally designing potential new interventions for modulating the host microbiota in specific ways to promote better health at various life stages. See related article, p 538Despite robust global research efforts, preterm birth remains a relatively intractable and pervasive problem. Indeed, preterm birth continues to impact >10% of live births in the US, and is the leading cause of neonatal morbidity and mortality worldwide.1Lawn J.E. Cousens S. Zupan J. Lancet Neonatal Survival Steering Team4 million neonatal deaths: When? Where? Why?.Lancet. 2005; 365: 891-900Abstract Full Text Full Text PDF PubMed Scopus (2560) Google Scholar Compared with full-term births, preterm deliveries are typified by more frequent use of perinatal antibiotics, that is, antibiotics administered either intra-partum to the mother, or post-partum to the newborn. The decision to treat with perinatal antibiotics is a clinical judgment based on perceived risks and benefits to both mother and baby. However, it is undoubtedly the rare clinician who takes into consideration the potential effects of antibiotics on the infant's future gut microbiota. This might be particularly true when perinatal antibiotics consist of a single dose of intra-partum antibiotics prescribed to the mother, as opposed to a multi-dose post-partum regimen given directly to the newborn. Such a scenario whereby the potential impact of maternal antibiotics on the infant's microbiota receives little consideration is not surprising—at least for now. After all, our current understanding of the effects of antibiotics on microbial communities in the neonatal gut is itself in its infancy and far from complete. To enable such decisions to be evidence-based requires a vastly improved understanding of the establishment of a healthy gut microbiota, including initial community assembly, subsequent succession events, and transient as well as durable responses to various disturbances such as antibiotic exposure. See related article, p 538 See related article, p 538 The human body plays host to a rich assembly of diverse microbes—primarily bacteria—residing on mucosal and skin surfaces and in the intestinal lumen. These commensal microbes, which outnumber human cells by at least an order of magnitude, plus their combined genomes, constitute the human microbiome. The microbiome performs a wide array of diverse functions beneficial to its human host, including nutrient acquisition, immune programming, and protection from pathogen invasion, among others.2Turnbaugh P.J. Ley R.E. Hamady M. Fraser-Liggett C.M. Knight R. Gordon J.I. The human microbiome project.Nature. 2007; 449: 804-810Crossref PubMed Scopus (3479) Google Scholar Evidence indicates that the amniotic cavity is sterile during healthy pregnancy3DiGiulio D.B. Diversity of microbes in amniotic fluid.Semin Fetal Neonatal Med. 2012; 17: 2-11Abstract Full Text Full Text PDF PubMed Scopus (246) Google Scholar and that colonization of the newborn gut begins at delivery.4Palmer C. Bik E.M. DiGiulio D.B. Relman D.A. Brown P.O. Development of the human infant intestinal microbiota.PLoS Biol. 2007; 5: e177Crossref PubMed Scopus (2042) Google Scholar, 5Dominguez-Bello M.G. Costello E.K. Contreras M. Magris M. Hidalgo G. Fierer N. et al.Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.Proc Natl Acad Sci U S A. 2010; 107: 11971-11975Crossref PubMed Scopus (2857) Google Scholar Microbial community composition appears to be broadly shaped initially by early environmental factors such as delivery mode (ie, vaginal vs cesarean delivery5Dominguez-Bello M.G. Costello E.K. Contreras M. Magris M. Hidalgo G. Fierer N. et al.Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.Proc Natl Acad Sci U S A. 2010; 107: 11971-11975Crossref PubMed Scopus (2857) Google Scholar) and soon thereafter by incidental exposures to the ambient environment as well as diet.4Palmer C. Bik E.M. DiGiulio D.B. Relman D.A. Brown P.O. Development of the human infant intestinal microbiota.PLoS Biol. 2007; 5: e177Crossref PubMed Scopus (2042) Google Scholar, 6Koenig J.E. Spor A. Scalfone N. Fricker A.D. Stombaugh J. Knight R. et al.Succession of microbial consortia in the developing infant gut microbiome.Proc Natl Acad Sci U S A. 2011; 108: 4578-4585Crossref PubMed Scopus (1644) Google Scholar, 7Costello E.K. Stagaman K. Dethlefsen L. Bohannan B.J. Relman D.A. The application of ecological theory toward an understanding of the human microbiome.Science. 2012; 336: 1255-1262Crossref PubMed Scopus (897) Google Scholar It is against this backdrop that Arboleya et al in this issue of The Journal report their findings from a longitudinal study of the gut microbiota at 4 sampling time points (2, 10, 30, and 90 days) over the first 3 months of life in 13 term and 27 preterm infants.8Arboleya S. Sánchez B. Milani C. Duranti S. Solís G. Fernández N. et al.Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics.J Pediatr. 2015; 166: 538-544Abstract Full Text Full Text PDF PubMed Scopus (254) Google Scholar The authors found that even at the coarse taxonomic scale of bacterial phyla, distinct differences in community composition between term and preterm infants were evident at the 3 latter time points: preterm infants harbored significantly lower proportions of Bacteroidetes at 10, 30, and 90 days, and higher proportions of Proteobacteria and lower proportions of Actinobacteria at 10 and 30 days. These overall differences in taxonomic composition, which appear to have been driven largely by a handful of bacterial families (especially Bacteroidaceae and Enterobacteriaceae), are broadly consistent with prior reports. Beyond this finding, a particular strength of the report by Arboleya et al is that the distribution in their study of mothers and newborns who received antibiotics enabled an analysis of the potential impact of perinatal antimicrobial use on the developing gut microbiota of preterm infants. Among the 27 preterm deliveries, 14 mothers and 17 neonates received antibiotics, including 9 instances where antibiotics were given to both members of the mother-preterm infant pairs. Using hierarchical clustering analysis, Arboleya et al found that at days 10, 30, and 90, the mother-preterm infant pairs in which any antibiotic was administered perinatally—whether to mother, preterm infant, or both—appeared to demonstrate an effect on gut microbiota composition. The effect following a single dose of intra-partum antibiotics administered solely to the mother appeared to be at least equal to the effect following multiple doses of antibiotics given directly to the neonate after birth. This apparent effect of intra-partum antibiotics was most evident at the 30-day sampling time point and was associated with changes in community composition that in part were qualitatively similar to the differences observed between the preterm and term groups. Indeed, a higher proportion of taxa from the phylum Proteobacteria, driven primarily by an increase in Enterobacteriaceae, were found in preterm infants delivered in the setting of intra-partum antibiotic use. At 90 days, differences in taxonomic composition between the treatment groups were less pronounced but still detectable. Analysis by real-time quantitative polymerase chain reaction targeting specific microbial groups revealed a decreased abundance at 90 days of the genus Bifidobacterium in the group of preterm infants with any antibiotic treatment exposure (ie, either intra-partum to the mother, or post-partum to the infant), compared with the group that received no antibiotic exposure. The findings by Arboleya et al,8Arboleya S. Sánchez B. Milani C. Duranti S. Solís G. Fernández N. et al.Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics.J Pediatr. 2015; 166: 538-544Abstract Full Text Full Text PDF PubMed Scopus (254) Google Scholar although limited and still requiring the type of robust corroboration that comes only from additional investigations, are nonetheless intriguing. In particular, the possibility that indirect exposure to an antibiotic administered as a single dose to the mother during the delivery process might alter the composition of the infant's gut microbiota at 1 to 3 months of age, and possibly beyond, is significant and merits additional investigative efforts. It has been hypothesized for some time that antibiotic administration in the perinatal period (to either the mother or the neonate) might lead to delayed health consequences for the baby as a result of alterations in the developing gut microbiota,9Bedford Russell A.R. Murch S.H. Could peripartum antibiotics have delayed health consequences for the infant?.BJOG. 2006; 113: 758-765Crossref PubMed Scopus (104) Google Scholar but direct evidence has been sparse. The report by Arboleya et al lends support to this hypothesis and argues for additional studies on the establishment and succession of the infant gut microbiota, including in the presence of various disturbances such as antibiotic exposure. The precise process of community assembly of the initial gut microbiota in the neonate remains as yet unclear; however, various general models of microbial community assembly have been proposed. A detailed discussion of these models is beyond the scope of this editorial. The interested reader is referred elsewhere,7Costello E.K. Stagaman K. Dethlefsen L. Bohannan B.J. Relman D.A. The application of ecological theory toward an understanding of the human microbiome.Science. 2012; 336: 1255-1262Crossref PubMed Scopus (897) Google Scholar, 10Hubbell S.P. The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press, Princeton, NJ2001Google Scholar, 11Lindström E.S. Langenheder S. Local and regional factors influencing bacterial community assembly.Environ Microbiol Rep. 2012; 4: 1-9Crossref PubMed Scopus (322) Google Scholar, 12Levy R. Borenstein E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules.Proc Natl Acad Sci U S A. 2013; 110: 12804-12809Crossref PubMed Scopus (237) Google Scholar however, salient features of some overarching models merit brief discussion. One model, termed ‘neutral assembly’, generally proposes that microbial groups gain a foothold in a particular niche primarily as a result of stochastic exposures. This model assumes that functional equivalency exists among trophically similar taxa, thereby effectively neutralizing potential influences exerted by local environmental conditions within a particular niche. A second model proposes that community assembly is a deterministic process that follows ‘assembly rules’. Examples of assembly rules include species assortment (eg, competitive exclusion between microbial species fighting for the same limited resource) and habitat filtering (eg, varying affinities of microbial species for different niches owing to divergent environmental conditions present within those niches).12Levy R. Borenstein E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules.Proc Natl Acad Sci U S A. 2013; 110: 12804-12809Crossref PubMed Scopus (237) Google Scholar These two broad approaches are not mutually exclusive. Indeed, they may contribute in varying degrees to the assembly of a given community, and their relative contributions may vary over time, with the relevant time scale being either developmental or chronological. In fact, the assembly of the gut microbiota has been characterized as having an early ‘unstable’ phase likely resulting from incidental exposures to microbial communities during and soon after delivery,4Palmer C. Bik E.M. DiGiulio D.B. Relman D.A. Brown P.O. Development of the human infant intestinal microbiota.PLoS Biol. 2007; 5: e177Crossref PubMed Scopus (2042) Google Scholar, 6Koenig J.E. Spor A. Scalfone N. Fricker A.D. Stombaugh J. Knight R. et al.Succession of microbial consortia in the developing infant gut microbiome.Proc Natl Acad Sci U S A. 2011; 108: 4578-4585Crossref PubMed Scopus (1644) Google Scholar, 7Costello E.K. Stagaman K. Dethlefsen L. Bohannan B.J. Relman D.A. The application of ecological theory toward an understanding of the human microbiome.Science. 2012; 336: 1255-1262Crossref PubMed Scopus (897) Google Scholar followed by a succession of facultative anaerobes and subsequently strict anaerobes7Costello E.K. Stagaman K. Dethlefsen L. Bohannan B.J. Relman D.A. The application of ecological theory toward an understanding of the human microbiome.Science. 2012; 336: 1255-1262Crossref PubMed Scopus (897) Google Scholar, 13Sommer F. Bäckhed F. The gut microbiota—masters of host development and physiology.Nat Rev Microbiol. 2013; 11: 227-238Crossref PubMed Scopus (1991) Google Scholar that have co-evolved to be adapted to their human host and appear in discrete steps of bacterial succession with abrupt shifts punctuated by life events.6Koenig J.E. Spor A. Scalfone N. Fricker A.D. Stombaugh J. Knight R. et al.Succession of microbial consortia in the developing infant gut microbiome.Proc Natl Acad Sci U S A. 2011; 108: 4578-4585Crossref PubMed Scopus (1644) Google Scholar The early stage of assembly therefore appears to follow, at least in part, a ‘neutral assembly’ model. By contrast, recent studies based on metabolic modeling suggest that an ‘assembly rules’ process and, specifically, habitat filtering, is the dominant structural force in the latter stages of succession.12Levy R. Borenstein E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules.Proc Natl Acad Sci U S A. 2013; 110: 12804-12809Crossref PubMed Scopus (237) Google Scholar A deeper understanding of the assembly process of neonatal gut bacterial communities, including the metabolic interactions of successive communities, is not merely an academic exercise and is potentially of great practical importance. Among the beneficial services that the gut microbiota provides are critical developmental functions that confer potentially long-reaching effects on the host, such as immune system programming and promotion of host tissue differentiation.2Turnbaugh P.J. Ley R.E. Hamady M. Fraser-Liggett C.M. Knight R. Gordon J.I. The human microbiome project.Nature. 2007; 449: 804-810Crossref PubMed Scopus (3479) Google Scholar, 7Costello E.K. Stagaman K. Dethlefsen L. Bohannan B.J. Relman D.A. The application of ecological theory toward an understanding of the human microbiome.Science. 2012; 336: 1255-1262Crossref PubMed Scopus (897) Google Scholar, 13Sommer F. Bäckhed F. The gut microbiota—masters of host development and physiology.Nat Rev Microbiol. 2013; 11: 227-238Crossref PubMed Scopus (1991) Google Scholar Whether specific time windows exist in the lifespan of humans during which particular bacterial consortia must be present in the gut for these functions to be optimally performed is unknown. If such time windows indeed exist, some roles of the host microbiota might be viewed as analogous to developmental programming, whereby events occurring during a critical period of fetal or neonatal life can affect the organism at much later life stages. The classic developmental programming model is based largely on animal studies and proposes that maternal stressors occurring during fetal life cause epigenetic changes that influence physiological function and risk of disease in adult life.14Langley-Evans S.C. Developmental programming of health and disease.Proc Nutr Soc. 2006; 65: 97-105Crossref PubMed Scopus (245) Google Scholar Such a paradigm would suggest that ‘missing’ a window, for example by virtue of a perturbed or otherwise ‘unhealthy’ gut microbiota during a critical time period, might have detrimental effects on the health of the host, possibly at a much later point in life. Studies like the one by Arboleya et al,8Arboleya S. Sánchez B. Milani C. Duranti S. Solís G. Fernández N. et al.Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics.J Pediatr. 2015; 166: 538-544Abstract Full Text Full Text PDF PubMed Scopus (254) Google Scholar which provide longitudinal analyses of the human microbiota during critical life stages and incorporate clinical metadata such as medication exposures and clinical outcomes, are essential for furthering our understanding of the relationship between the microbiome and human health. In addition to conducting such studies at high spatiotemporal resolution and for long sampling durations, investigations that incorporate either natural or controlled community disturbances of interest, such as antibiotic exposure,15Dethlefsen L. Relman D.A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation.Proc Natl Acad Sci U S A. 2011; 108: 4554-4561Crossref PubMed Scopus (1472) Google Scholar are apt to be particularly enlightening. The types of investigative and analytic approaches brought to bear should include multi-‘omics’ methods to interrogate genomic, transcriptomic, proteomic, and metabolomic features and interactions. New insights from these types of investigations hold promise for informing clinical treatment decisions as well as rationally designing potential new interventions for modulating the host microbiota in specific ways to promote better health at various life stages. Intestinal Microbiota Development in Preterm Neonates and Effect of Perinatal AntibioticsThe Journal of PediatricsVol. 166Issue 3PreviewTo assess the establishment of the intestinal microbiota in very low birthweight preterm infants and to evaluate the impact of perinatal factors, such as delivery mode and perinatal antibiotics. Full-Text PDF