Developmental microbial ecology of the neonatal gastrointestinal tract

Developmental microbial ecology of the neonatal gastrointestinal tract1,2 Roderick I Mackie, Abdelghani Sghir, and H Rex Gaskins ABSTRACT The gastrointestinal tract of a normal fetus is sterile. During the birth process and rapidly thereafter, microbes from the mother and surrounding environment colonize the gastrointestinal tract of the infant until a dense, complex microbiota develops. The succession of microbes colonizing the intestinal tract is most marked in early development, during which the feeding mode shifts from breast-feeding to formula feeding to weaning to the introduction of solid food. Dynamic balances exist between the gastrointestinal microbiota, host physiology, and diet that directly influence the initial acquisition, developmental succession, and eventual stability of the gut ecosystem. In this review, the development of the intestinal microbiota is discussed in terms of initial acquisition and subsequent succession of bacteria in human infants. Intrinsic and extrinsic factors influencing succession and their health significance are discussed. The advantages of modern molecular ecology techniques that provide sensitive and specific, cultureindependent evaluation of the gastrointestinal ecosystem are introduced and discussed briefly. Further advances in our understanding of developmental microbial ecology in the neonatal gastrointestinal tract are dependent on the application of these modern molecular techniques. Am J Clin Nutr 1999;69(suppl):1035S–45S. KEY WORDS Intestinal microbiota, acquisition, succession, breast-feeding, formula feeding, lactobacilli, bifidobacteria, obligate anaerobes INTRODUCTION The microbial community inhabiting the gastrointestinal tract is characterized by its high population density, wide diversity, and complexity of interactions. All major groups of microbes are present in the gut. Bacteria are predominant but a variety of protozoans are commonly found (1–3). Anaerobic fungi are widely distributed in the gastrointestinal tract of herbivores (4) as are yeasts (5) and bacteriophages (6). It has been estimated that the human colon contains > 1011 bacterial cells/g contents belonging to as many as 400 different species (7–9). Note that these numbers were derived from fecal samples and may not accurately represent the intestinal microbiota, especially in terms of species abundance and their relative importance. The prominent role played by anaerobic bacteria in this dynamic ecosystem is evident from the finding that > 99% of the bacteria isolated from human fecal specimens will not grow in the presence of atmospheric oxygen (9). Importantly, bacterial cells outnumber animal (host) cells by a factor of 10 and have a profound influence on immunologic, nutritional, physiologic, and protective processes in the host animal (10, 11). In fact, the gastrointestinal microbiota can be considered a metabolically adaptable and rapidly renewable organ of the body. The gastrointestinal tract is a specialized tube divided into various well-defined anatomical regions extending from the lips to the anus. For the purposes of this and most papers on gut microbiology, discussion is restricted to the stomach, small intestine, and large intestine as well as fecal material, because it is more readily obtained. Indigenous bacteria are not distributed randomly throughout the gastrointestinal tract but instead are found at population levels and in species distributions that are characteristic of specific regions of the tract. The stomach and proximal small intestine contain relatively low numbers of microbes (103–105 bacteria/g or mL content) because of low pH and rapid flow in this region. Acid-tolerant lactobacilli and streptococci predominate in the upper small intestine. The distal small intestine (ileum) maintains a more diverse microbiota and higher bacterial numbers (108/g or mL content) than the upper bowel and is considered a transition zone preceding the large intestine. The large intestine (colon) is the primary site of microbial colonization because of slow turnover and is characterized by large numbers of bacteria (1010–1011/g or mL content), low redox potential, and relatively high short-chain fatty acid concentrations. In addition to an increasing gradient of indigenous microbes from the stomach to the colon, there are also characteristic spatial distributions of organisms within each gut compartment. At least 4 microhabitats have been described: the intestinal lumen, the unstirred mucus layer or gel that covers the epithelium of the entire tract, the deep mucus layer found in intestinal crypts, and the surface of mucosal epithelial cells (8, 10). The distinction between indigenous (autochthonous) and nonindigenous (allochthonous) microbes in studies of the acquisi- 1 From the Department of Animal Sciences and the Division of Nutritional Sciences, the University of Illinois at Urbana-Champaign. 2 Address reprint requests to RI Mackie, University of Illinois at UrbanaChampaign, 1207 West Gregory Drive, Urbana, IL 61801. E-mail: . Am J Clin Nutr 1999;69(suppl):1035S–45S. Printed in USA. © 1999 American Society for Clinical Nutrition 1035S 1036S MACKIE ET AL FIGURE 1. Flow chart of possible molecular approaches to the phylogenetic identification and detection of microbial groups or species in the complex microbial ecosystem of the gastrointestinal tract. Molecular microbial ecology techniques are generally based on the informational content encoded in nucleic acid (DNA and RNA) molecules as described in the text. Refer to the reviews by Amann et al (16), Olsen and Woese (20), Raskin et al (17), and Stahl and Amann (21) for more detailed information. rRNA, ribosomal RNA; DGGE, denaturing gradient gel electrophoresis; RAPD, rapid analysis of random amplified polymorphic DNA. tion and development of gastrointestinal microbiota is critical to an ecological understanding of colonization, succession, and mechanisms of interaction between intestinal microbes and their host. This distinction is difficult especially in infants, in whom bacteria are acquired transiently during and immediately after the birth process as well as from the surrounding environment during this important developmental phase. In general, the terms autochthonous and indigenous are considered as synonyms and imply that these microbes are ubiquitous in the gastrointestinal ecosystem and occupy all habitats and niches available (12, 13). On the other hand, allochthonous species found in a habitat would not be established but merely in passage being derived from food or water, from another habitat in the gastrointestinal ecosystem, or from elsewhere on the host (12, 13). Clearly, some pathogens are autochthonous to the gut ecosystem and can live in harmony with their hosts, becoming pathogenic only when the ecosystem is disturbed in some way. Also, a particular microbial species may be autochthonous to one habitat in the intestinal tract but allochthonous to anothe (...truncated)