We describe a dramatic remodeling of the gut microbiota over the course of pregnancy. The first trimester gut microbiota are similar to one another and comparable to those of normal healthy controls, but shift substantially in phylogenetic composition and structure over the course of pregnancy. By the third trimester, the between-subject diversity has greatly expanded, even though within-subject diversity is reduced, and an enrichment of Proteobacteria and Actinobacteria is observed a majority of T3 samples. Furthermore, the abundances of health-related bacteria is impacted. For instance, Faecalibacterium
, which is a butyrate-producer with anti-inflammatory effects that is depleted in inflammatory bowel disease (Sokol et al., 2008), is less abundant on average in T3. By the third trimester, each woman’s microbiota has diverged in ways that could not be predicted from the T1 composition, and were not associated with health status or our diet records. Nonetheless, in the majority of women, the shift from T1 to T3 includes an increase in the abundance of Proteobacteria, which has been observed repeatedly for inflammation-associated dysbioses (Mukhopadhya et al., 2012
One of the questions raised by the observation of greater inter individual bacterial diversity and the decrease in bacterial richness in T3 and 1-month postpartum is that an aberrant microbiota might colonize the baby and contribute negatively to the shaping of the immune system from birth, with long-term consequences for health problems, such as allergy development (van Nimwegen et al., 2011
). Nevertheless, we found that regardless of their age, the children’s microbiota were most similar to their mothers’ microbiota at T1, which may indicate that the taxa prevalent in T3 are at a selective disadvantage in the developing infant gut. Furthermore, we did not detect any differences between the microbiotas of GDM+ and GDM− mothers. We did observe an enrichment of Streptococcus
in T3 and in post-partum samples on average, and highest levels for children were in the gut microbiomes of the 1-month olds (although it should be noted that many members of the Streptococcus
are commensal). Such enrichments may serve to educate the developing immune system to important members of the microbiota. As was recently reported for children on 3 continents (Yatsunenko et al., 2012
), similarities between the child and mother microbiota increased with the age of the children, which underscores the importance of shared diet and environment on shaping the microbiota (Koenig et al., 2011
Metabolic syndrome is a range of phenotypes that increase an individual’s risk of developing type 2 diabetes, including hyperglycemia, insulin resistance, excess adiposity and low-grade inflammation (Tilg and Moschen, 2006
; Vijay-Kumar et al., 2010
). Similarly, the latter stages of pregnancy have been described as a diabetogenic state that maintains hyperglycemia in the mother and a continuous supply of nutrients to the fetus. Gains in adiposity also prepare the female body for the energetic demands of lactation. Elevated levels of circulating pro-inflammatory cytokines have been reported for late pregnancy and correlated with levels of insulin resistance, suggesting a possible mechanistic link (Mor and Cardenas, 2010
). The women in our study had reduced insulin sensitivity, circulating blood glucose levels and adiposity over gestation, and in addition, we observed an increase in levels of inflammation markers in stool from T1 to T3. We suggest that a low-grade inflammation develops during pregnancy at the intestinal mucosal epithelium, and this inflammation may drive the microbial dysbiosis into a positive feedback loop with the altered host response (Lupp et al., 2007
Two principal mechanisms have been proposed for how the gut microbiota can contribute to host adiposity: (i) increased energy extraction efficiency from the diet, and (ii) altered host-microbial interactions that promote metabolic inflammation. The results of our microbiota transfer experiments suggest that pregnancy is most similar to the second mechanism, in which a dysbiosis drives changes in metabolism. Our results are very similar to the recently described mouse model for metabolic syndrome in which the microbiota are sufficient and required to transfer aspects of metabolic syndrome to otherwise healthy germ-free wildtype recipient mice, including inflammation, excessive weight gain, hyperglycemia, and reduced insulin sensitivity (Vijay-Kumar et al., 2010
The dysbiosis observed in T3 and reported for the mouse model of metabolic syndrome (Carvalho et al., In Review
; Vijay-Kumar et al., 2010
) are also strikingly similar: Both scenarios are characterized by elevated levels of Proteobacteria, greater between-individual variation, and excess bacterial load (described by Collado et al., 2008
). Proteobacteria are active participants in inflammatory bowel disease (Mukhopadhya et al., 2012
), and indeed colonization with just one member of this group (Escherichia coli
) is sufficient to induce macrophage infiltration into white adipose tissue and impaired glucose and insulin tolerance in GF mice (Caesar et al., 2012
). Not all women showed elevated levels of Proteobacteria in T3, however, indicating that other factors, such as other members of the microbiota, and potentially gene expression profiles, are also likely to be important for promoting inflammation. Although in the present study we pooled randomly selected donor microbiomes, comparison of individual donor effects on mouse phenotype will help identify the specific components of the microbiota driving metabolic inflammation. If the microbiota are not only sufficient but also required for metabolic changes in pregnancy, these components should be widely shared amongst women with normal pregnancies, and might share features with microbiomes of non-pregnant individuals of both sexes with metabolic syndrome.
It is interesting to note that some of the features of the T3 microbiota are similar to those of the obesity-associated microbiome shown to have enhanced energy extraction efficiency. For instance, both the low taxonomic richness and reduced metabolic network modularity that we observed in T3 have previously been reported for obese microbiomes (Greenblum et al., 2012
; Qin et al., 2010
; Turnbaugh et al., 2009a
). In the T3 microbiome, the drivers of these traits are quite different from aspects of the obesity-associated microbiome. In the studies of obesity mentioned above, the microbiome is depleted in Bacteroidetes, such that gene categories related to simple sugar uptake, for instance, are over-represented in obese compared to lean microbiomes. Furthermore, excess energy intake has been shown to favor Firmicutes over Bacteroidetes (Jumpertz et al., 2011
), and in obesity the microbiota have been exposed long term to excess energy intake. In T3 versus T1, the relative abundances of Bacteroidetes and Firmicutes are largely unchanged, and we see no shift in the abundances of specific gene functional categories or metabolic pathways. Additionally, in stark contrast to the obese microbiome, the T3 microbiome is associated with a greater amount of energy lost in stool compared to T1. Thus, although some of the features of the microbiome are shared between the obese and T3 microbiota, the underlying mechanisms by which they impact host adiposity can differ.
In summary, we have shown pregnancy to be associated with a profound alteration of the gut microbiota. The first trimester gut microbiota is similar in many aspects to that of healthy non-pregnant male and female controls, but by the third trimester, the structure and composition of the community resembles a disease-associated dysbiosis that differs among women. The underlying mechanisms resulting in the alteration of the microbiota remain to be clarified, but we speculate that the changes in the immune system at the mucosal surfaces in particular precipitate changes in the microbiota, although hormonal changes may also be important.
Dysbiosis, inflammation, and weight gain are features of metabolic syndrome, which increases the risk of type 2 diabetes in non-pregnant individuals. These same changes are central to normal pregnancy, where they may be highly beneficial, as they promote energy storage in fat tissue and provide for the growth of the fetus. Our work supports the emerging view that the gut microbiota affect host metabolism, however, the context (pregnant or not) defines how the outcome is interpreted (healthy or not). Metabolic changes are necessary to support a healthy pregnancy, which in itself is central to the fitness of a mammalian species. We hypothesize that in mammalian reproductive biology, the host can manipulate the gut microbiota to promote metabolic changes. Thus, the origins of host-microbial interactions that skew host metabolism towards greater insulin resistance, and which underlie much of the present-day obesity epidemic, may lie in reproductive biology.