Evolution of the Gut Microbiome in Infancy within an Ecological Context

Abstract

Purpose of the Review:

Humans and their commensal microbiota coexist in a complex ecosystem molded by evolutionary and ecological factors. Ecological opportunity is the prospective, lineage specific characteristic of an environment that contains both niche availability leading to persistence and niche discordance that drives selection within that lineage. The newborn gut ecosystem represents vast ecological opportunity. Herein, factors affecting perinatal infant microbiome composition are discussed.

Recent findings:

Establishing a healthy microbiota in early life is required for immunological programming and prevention of both short- and long-term health outcomes. The holobiont theory infers that host genetics contributes to microbiome composition. However, in most human studies environmental factors are predominantly responsible for microbiome composition and function. Key perinatal elements are route of delivery, diet and the environment in which that infant resides. Vaginal delivery seeds an initial microbiome and breastfeeding refines the community by providing additional microbes, human milk oligosaccharides and immunological proteins.

Summary:

Early life represents an opportunity to implement clinical practices that promote the optimal seeding and feeding of the gut microbial ecosystem. These include reducing non-emergent cesarean deliveries, avoiding the use of antibiotics, and promoting exclusive breastfeeding.

INTRODUCTION

Over the past decade, cataloguing the composition of the human microbiome across the life span has emerged as one of the most compelling areas of human clinical medicine [1, 2]. Application of high throughput sequencing methods enabled taxonomical phenotyping based on variable regions of the 16S ribosomal rRNA (rRNA) due to the pioneering work of Carl Woese and George Fox [3]. More recently, whole-genome shotgun sequencing and other ‘omic approaches (metatranscriptomics, metabolomics, proteomics) have been applied to better understand the diversity of microbes present in the gut and their metabolic potential [4]. It is well accepted that the human gut microbiome is an abundant and complex collection of bacteria, archaea, phages, and single-cell eukaryotes (protozoa and fungi) [2, 4].

This rapidly expanding body of research has changed the clinical paradigm of host-microbe interactions primarily being focused on pathogens and preventing infections to an appreciation of the fundamental role of the microbiome in shaping human development and health [2, 5, 6]. While the field has rapidly advanced in its understanding of “who is there”, the genetic and environmental factors that determine which species colonize and persist over time within an individual is less well described and is currently an active area of scientific investigation [2]. The findings from this research will have clinical, scientific and, ultimately, regulatory implications [2, 7, 8] as novel food [8–10], probiotic or microbial transplant [7] intervention strategies are developed to influence the gut microbiome and host health through personalized medicine [2, 11].

EVOLUTIONAL AND ECOLOGICAL FACTORS

Research conducted using germ-free and gnotobiotic animals have demonstrated the essential role of the microbiome in proper immune [12, 13], metabolic [12] and neural/cognitive [14] development, and growth [15, 16]. The microbiota are not only critical for optimal development of the host under normal physiological growth, but also important to ensure proper host development during nutrient scarcity or disease conditions [16]. Exposure to microbes, and their specific microbe-associated molecular patterns (MAMPS) within the first 6 months of life is essential for establishing infant gut and immune maturation [reviewed in 13] and disrupted establishment of this ‘microbial organ’ has implications for life-long health [2, 17–19].

Evolutionary [20] and ecological [13, 20, 21] theories have been applied to provide frameworks in which to study how microbiomes assemble and interact with the host. The human body and its resident microbiota can be viewed as a “holobiont” and their collective genomes as a “hologenome”, which exist within a complex ecosystem that is under selection pressure to minimize conflict between the host and symbionts [22]. Foster and colleagues proposed that symbionts typically evolve to compete within the host system, whereas hosts evolve to keep the ecosystem “on a leash” [23]. Bacterial co-evolution with the host could occur over longer periods of time [24]. However, given the rapid generation times and estimated mutation rates of bacteria, it was proposed that bacteria and bacteriophages could evolve within the host over periods of weeks and months [20], which was recently confirmed [25, 26]. Within hosts, genetic differences that accumulate over 6-month timescales are most commonly due to resident strains acquiring a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency, rather than replacement with distantly related strains [26]. Gorud and colleagues concluded that “gut bacteria can evolve on human-relevant timescales, and that connections exist between these short-term evolutionary dynamics and longer-term evolution across hosts” [26]. Host–bacterial co-evolution is illustrated by the relationship between human milk oligosaccharides (HMO) and the Bifidobacterium longum subsp. infantis ATCC15697, which contains a novel 43 kbp gene cluster encoding extracellular solute binding proteins, permeases and catabolic genes predicted to be active on lower molecular weight HMO [27]. This gene cluster is not present in other strains of bifidobacteria, including Bifidobacterium longum subsp. logum, and bifidobacterial species commonly found in adults [17, 27].

The holobiont theory [22] suggest that host genetics, particularly host immune mechanisms [28], plays a role in determining microbiome composition However, a study of the genotype and microbiota of 1046 individuals with several distinct ancestral origins, but who shared a relatively common environment, founds that gut microbiota composition was not associated with ancestry [29]. Thus, many studies have taken an ecological approach to uncovering the environmental factors that affect microbiome composition. Ecological concepts such as richness/alpha-diversity, beta-diversity, dispersion, resilience, resistance, selection and succession are routinely included in human microbiome papers [13, 17].

Early microbial colonization proceeds in succession through a process of “seeding and feeding” [17, 30]. Immediately following birth, the first colonizers are facultative and aerotolerant genera, which reduce oxygen levels in the intestine, thereby facilitating the subsequent proliferation of a complex community dominated by obligate anaerobic bacteria, such as Bifidobacterium [17, 30]. This process is influenced by both host and environmental factors, including route of delivery (vaginal vs. cesarean section), where the child is delivered (home vs. hospital), whether antibiotics are administered and how the infant is fed. The impact of these factors on infant microbiome development are well documented in other primary literature and review articles; therefore, due to space limitations, readers are referred to those manuscripts [13, 17, 31, 32].

Vertical transmission from the mother is important in seeding the infant microbiota. Bäckhed and colleagues studied the gut microbiota of 98 Swedish infants born either vaginally or by cesarean section (15% of infants) at 3 days and again at4 and 12 month postpartum [30]. The fecal microbiome of vaginally delivered newborns shared 72% of the taxonomically annotated MetaOTUs with their mother’s stool, compared to only 41% species match between cesarean-delivered infants and their mothers [30]. In addition, mother to infant transmission of Bifidobacterium was lower in cesarean-delivered infants. Additionally seeding of the infant microbiome is purported to occur through the human milk microbiome [33].

Among the most well-studied environmental factors are where people live and what they eat (Figure 1a). Fecal microbiota composition varies among populations living in different geographical locations, however, it is nearly impossible to disentangle geography from dietary patterns and cultural practices [1, 34, 35]. As populations become more urbanized, they have less intimate contact with soil, plant and animal microbiomes [21]. In addition, they are exposed to medical practices and highly processed “Western” diets that reduce microbial diversity and change microbial composition [36, 37]. A higher abundance of Prevotella commonly discriminates populations living in less industrialized settings from those in more urbanized environments [36, 37]. Yatsunenko and colleagues studied healthy populations living in the Amazonas of Venezuela, rural Malawi and in metropolitan cities in the U.S. [1]. Distinct differences in both taxa and functional genes between individuals living the U.S. compared to Venezuela and Malawi were observed across the lifespan. Overall, using UniFrac distances, an algorithm that measures similarity among microbial communities, the authors observed that: inter-individual variation was greater among children than among adults [1]. In addition, the differences in microbial composition between children and adults decreased with increasing age in all three populations, with child microbial composition evolving toward the adult by 3 years of age [1]. Despite these overall similarities among the populations, Malawian and Amerindian children and adults were more similar to one another than to U.S. children and adults [1].

Reinforcing the importance of environment, a recent study investigated what happens when seven individuals (5 adults, 2 children) moved from urban settings to a rain forest village for 16 days [38]. In this study, the initial alpha diversity the skin microbiota and the children’s fecal and oral microbiota was lower in the urban dwellers. During the rainforest period, all visitors experienced microbiota changes. For all body sites, the microbiota of the visiting children was more similar to microbiota conformations in villagers of the same age than those of the visiting adults. The results suggest higher stability in the adult microbiota, with the less resilient children’s microbiota responding more to environmental changes [38].

INFANCY – A CRITICIAL WINDOW OF OPPORTUNITY TO AFFECT DEVELOPMENT AND HEALTH

Ecological opportunity within the gut ecosystem varies over time and the newborn infant gut represents a unique ecological opportunity [20]. In addition to the seeding of microbes through vaginal delivery [30] and breastfeeding [33], diet is of vital importance to feed beneficial microbes [31, 32]. Compared to adults, during infancy, the diet proceeds temporally towards greater complexity, with punctuated changes during the introduction of solid foods and complete weaning (Figure 1b). Thus, it is expected that the infant microbiome would proceed through defined periods of development. However, sufficient data sets to model this succession were previously unavailable. Stewart and colleagues analyzed longitudinal stool samples from 903 children between 3 and 46 months-of-age that were collected as part of The Environmental Determinants of Diabetes in the Young (TEDDY) study [39]. The full data set included both 16S rRNA (n=12,005) and metagenomic (n=10,867) sequences. Their findings illustrate three distinct phases of microbiome progression: a developmental phase (months 3–14), a transitional phase (months 15–30), and a stable phase (months 31–46). [39]. Breastfeeding, either exclusive or partial, was the most significant factor associated with higher levels of Bifidobacterium species and weaning was associated with an increase in Firmicutes. Consistent with the findings of Bäckhed [30], mode of delivery was associated with the microbiome during the developmental phase, driven by higher levels of Bacteroides species in vaginally-delivered infants. Consistent with other studies, they also identified environmental factors including geographical location and household exposures (such as siblings and furry pets) as important covariates affecting microbiome composition [39].

CONCLUSIONS:

Clinical and epidemiologic evidence have established strong associations between the gut microbiome in early life and long-term health outcomes [13, 17, 32]. While in many cases, the mechanisms of action are waiting to be uncovered in humans, there is sufficient evidence to recommend adherence to recommended clinical practices of avoiding preterm delivery, reducing the rates of cesarean-delivery unless medically necessary, and promoting and supporting breastfeeding (Figure 2). In addition, antibiotics should be avoided unless medically necessary as a recent study showed that even a single course of amoxicillin or macrolide changed the relative abundance of bifidobacteria, enterobacteria and clostridia, and that the dysbiosis lasted for several months [40].

Due to the differences in the microbiome by mode of delivery, vaginal seeding an on-going area of investigation [41]. Vaginal seeding refers to the practice of inoculating a cotton gauze or a cotton swab with vaginal fluids to transfer the vaginal flora to the mouth, nose, or skin of a newborn infant. In 2017, the American College of Obstetricians and Gynecologists “did not recommend or encourage vaginal seeding outside of the context of an institutional review board-approved research protocol, and it is recommended that vaginal seeding otherwise not be performed until adequate data regarding the safety and benefit of the process become available” [42].

In response to differences in the fecal microbiome composition of breast- and formula-fed infants, the practice of adding prebiotics to infant formulae has become common throughout the world [31, 32]. The effect of prebiotics on the composition of infant microbiota has been recently reviewed by our group [31, 32]; most studies show that prebiotics increase the abundance of Bifidobacterium and, sometimes, Lactobacillus compared to fecal microbiota of infants fed control formula [31, 32]. Several studies reported a decrease in opportunistic pathogens, such as Escherichia coli, enterococci, and clostridia [31, 32]. Two HMOs, 2ˊ-fucosyllactose (2ˊ-FL) and lacto-N-neoteraose (LNnT), have also been added to infant formula. Both are well-tolerated and support age-appropriate growth of infants [31, 32]. Although prebiotics are safe, they are not recommended for routine use in infant formula [43].

Similarly, while some encouraging data exist on the efficacy of probiotics on disease prevention [reviewed in 31, 32], no broad consensus exists to recommend the use of probiotics in these conditions [43, 44]. Although probiotics are safe for use in healthy infants, concerns have been raised related to the administration of probiotics early in life when gut microbiota is not fully established and long-term consequences of such administration should be carefully evaluated.

KEY POINTS:

• The gut microbiota and its human host exist as a holobiont in a complex and changing ecosystem.

• Environmental factors, particularly diet, are the key determinants of microbiome structure and function. The high concentrations of oligosaccharides in human milk and the presence of specific HMO-metabolizing genes in the infant-associated B. infantis represent co-evolution host and symbiont.

• Reducing cesarean delivery, promoting breastfeeding and avoiding antibiotics are key modifiable clinical practices to support the establishment of a healthy microbiome.

• Prebiotics and probiotics are safe for healthy infants, but not recommended for routine use by pediatric clinical societies.

• At this time, the American College of Obstetricians and Gynecologists does not recommendvaginal seeding.is by