American Journal of Gastroenterology Lecture

Intestinal Microbiota and the Role of Fecal Microbiota Transplant (FMT) in Treatment of C. difficile Infection

Lawrence J Brandt MD; MACG


Am J Gastroenterol. 2013;108(2):177-185. 

In This Article

The Intestinal Microbiota

We are witness to a paradigm shift in the way the microbial flora that dwell within our inner recesses are viewed. No longer is it simply that the host is "good" and the bacteria that live therein "bad", but the vital roles our intestinal flora, now called microbiota, have in maintaining health are being increasingly appreciated. Results of the Human Microbiome Project launched by the National Institutes of Health in 2007 along with related ventures such as the MetaHit (Metagenomics of the Human Intestinal tract) consortium, which involves 13 research centers from 8 countries, are now beginning to be published and will revolutionize knowledge of our microbes and our bodies.[2] For example, although we knew the human body is inhabited by a vast number of microorganisms including bacteria, archea (single-celled prokaryotic microorganisms separately classified from bacteria), viruses, fungi, and even parasites, all of which normally live in peaceful coexistence with us, their hosts, we soon learned that only 5–20% of the intestinal microbiota can be cultured and that culture can reliably distinguish among bacterial phylogenetic groups, but not down to species- or strain-level.[2,3] New approaches to study our microbiota were developed using culture-independent techniques including bacterial 16S ribosomal RNA gene sequencing and DNA fingerprinting methods, such as terminal restriction fragment length polymorphisms. A new vocabulary was even developed to help detail the "meta" family techniques used to evaluate the microbiomic functional capacity including metagenomics (study of genes collected and sequenced from the environment), metabolomics (study of metabolites that are end-products of cellular processes), metaproteomics (study of all proteins in an environment), and metatranscriptomics (study of all RNA molecules produced in a population of cells). Microbial communities differed remarkably at each of the 15 (male) to 18 (female) Human Microbiome Project-sampled body sites (nasal passages, oropharynx, skin, stool, and vagina) and the diversity of each habitat's signature microbes varied widely among healthy individuals, with further variation not just dependent upon ethnicity and host genetics, but also on one's diet and environment.[2] Stool, representing the distal bowel, showed relatively high intra- and inter-subject diversity. The majority of our microbiota is anaerobic, and although more than 50 bacterial phyla have been described, only four constitute the majority of mammalian intestinal microbiota (Bacteroidetes, Firmicutes, Actinobacteria, and Proteobacteria) and only two predominate in our intestinal tract: the Bacteroidetes and the Firmicutes; most of the Firmicutes phyla are members of the Clostridia class.[4] It is estimated that about 4,000 bacterial species reside in our gastrointestinal tract, and that the human microbiota contains as many as 1014 bacterial cells, a number that is 10 times greater than the number of human cells in our body.[5] Per gram of contents, there is a marked and progressive distal increase in the number of bacteria: 101 in the stomach, 103 in the duodenum, 104 in the jejunum, 107 in the ileum, and 1012 in the colon. This longitudinal heterogeneity of the microbiota population has a predominance of Firmicutes and Proteobacteria (notably Helicobacter pylori in the stomach), Firmicutes and Actinobacteria in the small intestine and a prevalence of Bacteroidetes and the Lachnospirae family of Firmicutes in the colon; of note, bacteria account for 60% of the dry weight of feces. The microbiota within the intestinal lumen differs significantly from that dwelling in close proximity to or within the intestinal epithelium.[6] Therefore, fecal micro-organisms cannot be used as a surrogate for all communities of the bowel microflora. Moreover, luminal microbial communities and surface adherent/associated populations are distinct and fulfill different roles, only some of which I will mention briefly.

Our intestine becomes colonized with micro-organisms during or shortly after birth and the intestinal microbiota of infants delivered by cesarean section differs from that of vaginally-delivered infants.[7,8] The gastrointestinal tract of the newborn is still sterile after caesarian section and its microbiota is initiated with feeding; in breast-fed infants Bifidobacteria predominate with minor representation from lactobacilli and streptococci, whereas in formula-fed infants, similar amounts of Bacteroides and Bifidobacteria are found with minor representation from Staphylococci, Escherichia coli, and Clostridia.[8] The first colonization of the intestine is a profound immunological exposure and early maternal inoculation, as occurs with vaginal delivery, likely has an important role in subsequent immune reactions and our susceptibility or resistance to certain diseases. Indeed, this initial exposure heralds the continuing intimate roles our microbiota will have with our diet and environment, and initiates the vital interactions of the microbiota with our metabolic activities, as well as with the immunological apparatus that constitutes our major defense system against foreign antigens. (Figures 1 and 2). We know that reduced microbial stimulation during infancy results in slowed postnatal maturation of the immune system and delayed development of an optimal balance between TH1 and TH2-like immunity.[9] During the first year of life, the total number of IgA-, IgG- and IgM-secreting cells is lower in infants born by vaginal delivery than in those born by cesarean section, possibly reflecting excessive antigen exposure across the vulnerable intestine.[7]

Figure 1.

Inter-relationships of nutrients, immune responses and the microbiome. Ingested nutrients (1) influence our microbiota (2) which, in turn, changes the nutritional value of the consumed food. (3) Absorbed dietary components interact with a variety of immune cells (e.g., omega 3-fatty acids). (4) Microbial signals in the form of Microbe Associated Molecular Patterns (MAMPs) also modify local mucosal immune responses through innate signaling pathways, e.g., the inflammasome or Toll-like receptors (TLRs. (5) Additionally, microbe-modified dietary components (e.g., acetate produced from fermentation of polysaccharides) provide signals by which the immune system can monitor the metabolic activities of the microbiota. (6) An example of micronutrients directly modifying intestinal microbial ecology is vitamin A, which can modify the representation of segmented filamentous bacterium (SFB) in the mouse gut microbiota; SFB induce differentiation of Th17 cells. From Kau et al. 54

Figure 2.

Some examples of the effects of intestinal microbiota and host physiology. The intestinal microbiota can affect many aspects of normal host development and function. Members of the microbiota, with their various components or products of metabolism are shown in red. Microbial effects on the host are shown in green. Affected host phenotypes are shown in blue. AMP, antimicrobial peptides; DC, dendritic cells; Gm, Gram negative; HPA, hypothalamus-pituitary adrenal; Iap, intestinal alkaline phosphatase; PG, peptidoglycan; PSA, polysaccharide. From Sekirov et al.3

The numbers and types of our intestinal microbiota increase over the first year of life to assume a relatively stable adult pattern at the phylum level, but continue to evolve at the species level with subsequent dietary and environmental exposures, including antimicrobial therapies.[3] In one study, diet inventories of 98 individuals were correlated with participants' fecal enterotypes to show that the Bacteroides enterotype was highly associated with animal protein, a variety of amino acids, and saturated fats (western diet), whereas the Prevotella enterotype was associated with low values for these groups but high values for carbohydrates and simple sugars (agrarian diet). Moreover, microbiome composition changed within 24 h of dietary alteration.[10]

Intestinal microbiota has important roles in the post-natal structural and functional maturation of the gut. Germ-free animals have, for example, enlarged ceca; increased enterochromaffin cell area; a reduced intestinal surface area with narrower villi resulting from reduced cell regeneration and prolonged cell cycle time, and a smaller villous capillary network; hypotonic and hyporesponsive mesenteric vasculature; impaired lymphoid organs; impaired peristalsis; and abnormal cholesterol and bile acid metabolism.[3] It has been shown, for example, that Bacteroides thetaiotaomicron can induce angiogenesis;[11] influence enteric nerve function, and, therefore, possibly peristalsis;[12] and also modulate intestinal glycocalyx structure.[13] Various microbiota, including B.thetaiotaomicron and Lactobacilli, are also involved in maintaining intestinal barrier integrity through maintenance of cell-to-cell junctions and promotion of epithelial repair after injury.[1]

The areas in which microbiota have a major influence are legion, growing, and far beyond the scope of this general overview. One such area is mucosal immunity with influence on immunocytes, gut-associated lymphoid tissue, Peyer's patches, IgA-producing plasma cells, immunoglobulin secretion, and pattern recognition receptors including toll-like and NOD-like receptors. As a specific example, the deficiency of CD4+ T-cells in germ-free mice can be completely reversed by mono-contamination with Bacteroides fragilis or administration of its polysaccharide capsular antigen.[14] The gastrointestinal tract needs to coexist with the dense carpet of bacteria that overlies its mucosa without inducing excessive immune reaction, and the intestinal microbiota mediates such antigenic tolerance. As examples, intestinal dendritic cells are conditioned to a tolerogenic phenotype by intestinal epithelial cells that are stimulated by Lactobacillus spp and certain E. coli strains;[15]B. thetaiotaomicron prevents activation of the proinflammatory transcription factor NF k β;[16] and Aeromonas or Pseudomonas promote intestinal alkaline phosphatase, which dephosphorylates and inactivates the lipopolysaccharide found in the outer membrane of Gram-negative bacteria thus protecting against septic shock.[17] Our commensal bacteria, their structural components and their metabolic products can induce expression and activation of antimicrobial proteins to protect against pathogens and to prevent overgrowth of the commensals themselves.[3] For example, B. thetaiotaomicron colonization of germ-free mice induces Paneth cells to express matrilysin, a matrix metalloproteinase that activates defensins. Even the mere presence of microbiota in the gastrointestinal tract, especially Gram-positive anaerobes, serves as a deterrent to pathogen colonization; as an example, Lactobacilli and Bifidobacteria prevent Listeria infection of cultured epithelial cells.[18]

As mentioned above, our intestinal microbiota is related to the type of food we eat, but it also is very much involved with appetite regulation, energy utilization, digestion and absorption of ingested nutrients, and drug metabolism. Bacterial metabolism of dietary fiber to short chain fatty acids, and conversion of indigestible polysaccharides to absorbable monosaccharides are well known examples of such interaction. B. thetaiotaomicron, as another example, has been shown to upregulate expression of pancreatic co-lipase and an intestinal Na ++ /glucose co-transporter.[12] Awareness of the interplay between these complex metabolic functions and the intestinal microbiome sets the stage to study whether manipulation of the microbiome can be used to understand and treat conditions of obesity and underweight.[19] Inter-individual and inter-population differences in intestinal microbiomes with their attendant varied metabolic profiles may explain the different toxicities of commonly used therapeutics in varied geographic/cultural populations and set the stage for the development of personalized medicine-based on one's intestinal microbiome profile.[20]