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Microbial colonization after birth profoundly affects development of the host. In a recent paper, Gomez de Agüero et al. (2016) reveal a new aspect of ontogeny influenced by the microbiota: the impact of gestational gut bacterial metabolites on early immune maturation of the neonatal intestine., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Unlike mammalian embryogenesis, which takes place in the relatively predictable and stable environment of the uterus, postnatal development can be affected by a multitude of highly variable environmental factors, including diet, exposure to noxious substances, and microorganisms. Microbial colonization of the intestine is thought to play a particularly important role in postnatal development of the gastrointestinal, metabolic, and immune systems. Major changes in environmental exposure occur right after birth, upon weaning, and during pubertal maturation into adulthood. These transitions include dramatic changes in intestinal contents and require appropriate adaptations to meet changes in functional demands. Here, we attempt to both characterize and provide mechanistic insights into postnatal intestinal ontogeny. We investigated changes in global intestinal gene expression through postnatal developmental transitions. We report profound alterations in small and large intestinal transcriptional programs that accompany both weaning and puberty in WT mice. Using myeloid differentiation factor 88 (MyD88)/TIR-domain-containing adapter-inducing interferon-β (TRIF) double knockout littermates, we define the role of toll-like receptors (TLRs) and interleukin (IL)-1 receptor family member signaling in postnatal gene expression programs and select ontogeny-specific phenotypes, such as vascular and smooth muscle development and neonatal epithelial and mast cell homeostasis. Metaanalysis of the effect of the microbiota on intestinal gene expression allowed for mechanistic classification of developmentally regulated genes by TLR/IL-1R (TIR) signaling and/or indigenous microbes. We find that practically every aspect of intestinal physiology is affected by postnatal transitions. Developmental timing, microbial colonization, and TIR signaling seem to play distinct and specific roles in regulation of gene-expression programs throughout postnatal development.

Background: The human intestine is colonized with trillions of microorganisms important to health and disease. There has been an intensive effort to catalog the species and genetic content of this microbial ecosystem. However, little is known of the ecological interactions between these microbes, a prerequisite to understanding the dynamics and stability of this host-associated microbial community. Here we perform a systematic investigation of public goods-based syntrophic interactions among the abundant human gut bacteria, the Bacteroidales., Results: We find evidence for a rich interaction network based on the breakdown and use of polysaccharides. Species that utilize a particular polysaccharide (producers) liberate polysaccharide breakdown products (PBPs) that are consumed by other species unable to grow on the polysaccharide alone (recipients). Cross-species gene addition experiments demonstrate that recipients can grow on a polysaccharide if the producer-derived glycoside hydrolase, responsible for PBP generation, is provided. These producer-derived glycoside hydrolases are public goods transported extracellularly in outer membrane vesicles allowing for the creation of PBP and concomitant recipient growth spatially distant from the producer. Recipients can exploit these ecological interactions and conditionally outgrow producers. Finally, we show that these public goods-based interactions occur among Bacteroidales species coresident within a natural human intestinal community., Conclusions: This study examines public goods-based syntrophic interactions between bacterial members of the human gut microbial ecosystem. This polysaccharide-based network likely represents foundational relationships creating organized ecological units within the intestinal microbiota, knowledge of which can be applied to impact human health., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Our studies have focused on understanding the mechanisms of interactions between the indigenous intestinal flora and the mammalian host in both physiological and nonphysiological conditions. In particular, we have focused on the function of innate microbial pattern recognition by Toll-like receptors in the context of tissue injury and repair, spontaneous colitis, and postnatal development.

After intestinal injury, both the number and type of intestinal epithelial cells must be restored. Intestinal stem cells, located at the base of the intestinal crypt, repopulate the depleted crypt in a process known as compensatory proliferation. In this issue of the JCI, Brown et al. describe a new mechanism by which this process is regulated (see the related article beginning on page 258). Surprisingly, they find that a subset of stromal cells present within the intestinal tissue and expressing the proliferative factor prostaglandin-endoperoxidase synthase 2 (Ptgs2) is repositioned next to the intestinal stem cell compartment where local production of PGE(2) controls injury-induced epithelial cell proliferation.