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The terminal ileum and the large bowel (cecum and colon) are hospitable places for bacterial proliferation, and a complex and numerous bacterial community resides in this site. This community is often referred to as the normal gut microbiota (microflora). Many of the numerically important members of the gut microbiota have not yet been cultivated under laboratory conditions and are known and detected on the basis of their 16S rRNA gene sequences. Comparisons of the characteristics of germfree and conventional animals have clearly demonstrated that the gut microbiota has considerable influences on host biochemistry, physiology, immunology, and low-level resistance to gut infections. Cytoskeletal rearrangements within the enterocyte form a socket by which the filament becomes permanently attached to the mucosal surface. The influence of the gut microbiota of neonates on the immune system is of especial interest because of the observed increase in the incidence of allergies in children in affluent countries over recent decades. The adherence of Lactobacillus cells to, and proliferation on, epithelial surfaces in rodents, pigs, and poultry has tempted some researchers to consider that the same phenomenon occurs in the human gut. This overlooks the differences in the anatomy and histology of the human gut relative to that of other monogastric animals. In other words, the immune systems of different humans or other animals recognize different epitopes. This is apparent from experimental-animal studies because the composition of the gut microbiota of HLA-B27 rats and interleukin-10-deficient mice is different, yet colitis results in both types of animals.

This chapter suggests ways in which knowledge of the microbial ecology of the human bowel can be obtained using modern technologies. Probiotics aimed at altering the composition of oral and vaginal ecosystems have been developed or are under development, most products target bowel health. There is little doubt that lacto-bacilli transit the digestive tract following consumption of probiotic products, but in order to evaluate the probiotics phenomenon, one must consider the microbial ecology of the human gut. Some members of the medical profession, as well as the laity, have greeted with enthusiasm the use of current probiotic products as prophylaxis for atopic diseases (allergies), inflammatory bowel diseases (Crohn’s disease [CD] and ulcerative colitis [UC]), and pouchitis. Regulatory mechanisms generated within the ecosystem (autogenic factors) and by external forces (allogenic factors) permit the episodic persistence of some bacterial populations but the elimination of others in a classical biological succession. The best evidence for the efficacy of probiotics in inflammatory conditions of the bowel comes from studies of the maintenance of remission of pouchitis. Metabolomics is the nontargeted, holistic, quantitative analysis of changes in the complete set of metabolites in the cell (the metabolome) in response to environmental or cellular changes. The study of the metabonome might contribute to a full systems biology approach to understanding and maintaining bowel health. The primary aim of the research will be to understand how all of the heterogeneous parts are integrated, with a supplementary aim of identifying biomarkers of health or disease.

This chapter focuses on the indigenous microbiota of the human large bowel, arguably the best-known ecosystem of the body. The study of microbial communities falls within the domain of microbial ecology—the study of the interrelationships that occur between populations within a community and between the community and the environment in which it is located. Microbial ecology is about how ecosystems work and therefore details the functions of populations, individually and collectively, in nature. The indigenous microbiota is a potent source of opportunistic infections that arise when the mechanisms that normally confine the microbes to a particular site are disrupted. Anaerobic infections following bowel surgery, urinary tract infections, chronic respiratory tract infections, dental/gingival diseases, and annoying skin conditions come into this category. Medical knowledge focuses on the pathogenesis of diseases and the derivation of intervention strategies. To understand health, one must learn about the mechanisms that operate in the healthy body by which stable ecosystems are sustained and maintained. Then, health might be guarded by reason, perhaps by interventions that would produce predictable outcomes on the basis of knowledge of molecular networks. Fortunately, the technological approaches to achieve these goals are at the fingertips of microbiologists: metagenomics to access and assess community genetics, and metabolomics to analyze functional attributes of the indigenous microbiota in concert with that of the host.

Three molecular analytical approaches based on small ribosomal subunit RNA (16S rRNA) sequences have proven to be able to provide reliable knowledge about the richness (diversity of species) and evenness (population sizes) of the fecal microflora of humans. These approaches are phylogenetic analysis by PCR, cloning, sequencing; total fluorescent in situ hybridization (FISH) analysis using oligonucleotide probes that target specific 16S rRNA sequences; and oligonucleotide/total bacterial RNA hybridizations on membranes. Relatively well-described examples of the biological succession that occurs in the infant gut are provided by investigations of the acquisition of the intestinal microflora by mice and humans. Enterococci are inherently more resistant to antimicrobial drugs than other clinically important gram-positive bacteria, but the reason for this is not clear. Enterococci inhabit the gastrointestinal tract or environments contaminated by human waste and as such may be exposed to antibiotics that pass through the gastrointestinal tract. It is unlikely that enterococcal species experience selection with respect to antibacterial drugs during human infections. On the basis of these observations, it can be assumed that the intrinsic resistance of enterococci to many antimicrobials might have resulted from their need to survive and persist in highly competitive, and potentially detrimental, ecosystems such as the intestinal tract. The impact of imipenem on the composition of the intestinal microflora is, however, worthy of attention because enterococci have been isolated more frequently from pediatric cases of septicemia after the introduction of antibacterial drug.