Microbial Physiology of the Digestive Tract and Its Role in Inflammatory Bowel Diseases

36.1.1

Human Component

The human component of the GI tract is composed of tightly attached epithelial cells that line the gut lumen, supporting cells underlying the epithelium, and immune cells resident in the lamina propria. Human, or host, cells are acquired before birth and their physical and functional characteristics are fairly constant throughout life. These characteristics are primarily determined by genetics, which are extremely variable among individuals. The outcome of genetics is influenced by the GI environment, especially the gut microbes in the lumen. Thus, gene and environmental interactions determine host cell gene expression, interactions among host cells, and host cell interactions with microbes.

36.1.2

Microbial Component

In contrast to the human or host component, the microbial component of the GI tract is composed of cells that are more loosely attached to the host epithelium and each other. The microbial community is composed of bacteria, fungi, viruses, archea, and protists. Microbes are primarily acquired after birth and the types of microbes inhabiting the GI tract and their physical and functional characteristics can vary over an individual hosťs lifetime. The trillions of individual microbes in the gut form region- and niche-specific communities that together function as an organ of loosely associated cells. The determinants of microbial community function include microbial genetics, microbe-microbe interactions, host-microbe interactions, and microbial interactions with ingested substances. The colon is the site of the largest and best-characterized microbial population in terms of host-microbe interactions and their role in IBD. Additionally, the majority of microbial studies have focused on bacteria. Therefore, this chapter will primarily focus on bacteria in the colon with the addition of material on other microbes or host sites where it is available.

36.1.3

Organization of Host and Microbial Tissues in the GI Tract

There is a distinct physical separation between host tissues and microbes throughout the GI tract. This barrier serves important functions for both the host and its microbes. First, it limits physical interactions between the host and microbial cells. This prevents direct damage and/or intracellular invasion of intestinal epithelial cells (IEC) by microbes. It also limits microbial access to underlying host tissues. Second, the barrier limits the delivery of microbial components or products to immune sensors in the epithelium to maintain low levels of inflammation and immune tolerance to resident microbes. Third, the barrier protects commensal microbes by minimizing immune targeting and killing of cells that do not express virulence characteristics. Fourth, the barrier allows the host and its microbes to establish relatively stable relationships that prevent incursions of new, potentially pathogenic microbes into the microbial community. Finally, the physical arrangement between the host and microbes allows for stable metabolic interactions between them to provide optimal energy availability for both partners.

Despite the physical separation imposed by the gut antimicrobial barrier, host and microbial cells communicate extensively across the expanse. The barrier is erected and maintained in response to the sensing of microbes in the gut lumen. Likewise, microbes sense and respond to the host components of the barrier. They also make use of them for their own benefit. For example, mucus produced by the host provides attachment sites and carbohydrate sources for microbes. Conversely, the host receives beneficial exports from microbes in the form of metabolites such as short chain fatty acids. Therefore, an intact barrier promotes the health and welfare of both the human and microbial cells in the gut.

The biogeographical organization of the epithelial interface between host and microbes primarily results from acellular physical and chemical defenses produced by the host in response to innate and adaptive immune detection of microbes in the gut lumen. Innate immune mechanisms in IEC and underlying immune cells are activated by structural features of microbes or damage related to microbial attachment or invasion. Toll-like receptors on the cell surface and in endosomes and Nod-like receptors in the cell cytosol are the primary effectors of this detection and their activation leads to inflammation and production of antimicrobial barrier components from the IEC. In the small intestine, IEC produce a thin layer of mucus and copious amounts of antimicrobial peptides near the epithelial surface. Digestive enzymes and bile acids released into the gut lumen also supplement the mucosal defenses to keep the absolute numbers of microbes low relative to the colon. Secretory immunoglobulin A is the primary adaptive immune component of the gut antimicrobial barrier and appears to be primarily produced in the small intestine. It is made by plasma cells of the lamina propria and then translocated into the gut lumen by specialized receptors on IEC. In the colon, the physical space between host and microbe is primarily maintained by cell-associated and secreted mucins. In both the small intestine and colon, epithelial cell turnover also contributes to host defense. While IEC and plasma cells have direct roles in producing the gut antimicrobial barrier, many different cell types feed information regarding the integrity of the barrier to these cells to refine tightly the responses to gut microbes. For example, immune cells in the lamina propria produce cytokines in response to microbial components detected on the host side of the barrier that in turn influence IEC production of barrier components.

Almost all of the data pertaining to the gut antimicrobial barrier has been generated using bacteria as the model microbe. There is some data showing that fungi are also physically separated from the host, although the factors that determine this separation have not been well elucidated. Most of the literature regarding viruses in the GI tract pertains to pathogenic viruses. However, viruses called bacteriophages can infect bacteria and there is a growing appreciation for the role these viruses play in determining survival and behaviors of bacteria in the gut. This suggests that many of the behaviors attributed to individual bacterial species could actually be influenced by or the direct result of bacteriophage infection in those bacteria.

36.2.1

Initial Acquisition of Microbes

The earliest interactions between the GI tract and microbes occur in utero, but the majority of gut microbial colonization occurs after birth. The neonatal GI tract is colonized by vaginal microbes at the time of delivery. These initial microbes are quickly joined by additional microbes derived from the environment to create a more complex community. Over time and with changes in the infant diet from milk to solid foods, the membership undergoes massive upheaval until it resembles the adult microbial community at around 2–5 years of age.

36.2.2

Determinants of Microbial Niche Availability and Occupation

Host and microbial factors interact to determine the nature and availability of macro- and microniches in the GI tract. The host provides a physical space for the microbes to occupy and provides attachment sites and nutrients to the microbes. The mucosal-associated attachment sites consist of the host epithelial tissues themselves, the acellular host proteins and mucins extending from the epithelial surface, and the biofilm formed by microbes that have already colonized the niche. The niche provides macronutrients such as carbohydrates and nitrogen sources along with micronutrients such as oxygen, iron, and salts. The relative concentrations of these nutrients and their availability to incoming microbes is highly dependent on the proximity to the host epithelial surface, host determinants of carbohydrate modification, and the resident microbial community in the niche. This means that the niche encountered by later infiltrating microbes is very different from that encountered by the initial colonizers. It also means that microbes must be able to replicate and recolonize the GI tract, or they will be lost from the community.

The gut lumen is filled with ingested food materials and sloughed host cells that can also be colonized by microbes. The microbes in this niche are thought to be derived from mucosal populations or transiting the GI tract. Material in the gut lumen provides rich sources of biological material for growth and metabolite production by gut microbes and it is likely that the mucosal-associated and luminal populations of microbes influence each other and the host tissues through production of these metabolites. The luminal niche is likely less influenced by host factors and more influenced by diet and other substances ingested by the host.

Both the mucosal-associated and luminal populations of gut microbes are also exposed to host-derived antimicrobial defenses that vary according to the region of the GI tract and determine the nature and availability of microbial niches. As previously discussed, these defenses determine the biogeographical relationship between host and microbial tissues. However, they also determine which microbes colonize the GI tract.

In addition to host factors, microbial factors also influence niche characteristics and the physical availability of space within them. These include structural characteristics of the microbes, metabolic products secreted by microbes, and molecules produced by microbes that influence the behavior or fitness of other microbes. Microbes have both fixed and inducible characteristics, though even relatively fixed characteristics can change to adapt to the environment. The cell surface characteristics of microbes are a product of the type of cell wall that they produce and the physical and chemical properties of that wall. Gram-negative bacteria are covered by a layer of lipopolysaccharide on their surface, Gram-positive bacteria are covered by a thick layer of peptidoglycan, mycobacteria are covered by a thick layer of mycolic acids, and the surface of fungi is coated in mannoproteins. While these surface characteristics are relatively fixed, they can be modified to change interactions with the host or other microbes. For example, modifications to the lipid A component of lipopolysaccharide influence its detection by host TLR4 receptors. Adhesion and motility characteristics are also important determinants of niche occupation. These characteristics are highly influenced by environmental conditions related to the host, other microbes, and diet. Some examples include fimbrae that attach microbes to host tissues or microbial biofilms and flagella that allow them to move into niches or form biofilms. Capsular polysaccharides that modify the microbial cell surface are also inducible and modified depending on environmental conditions. Many of these inducible characteristics are the product of genetic operons that are regulated by invertible genetic elements in the bacterial genome. This allows the entire set of proteins necessary to produce these complex organs to be turned on or off depending on the environmental conditions.

Microbial products can also influence the nature and availability of niches through actions on the host or other microbes. Short chain fatty acids are among the best characterized of the microbial metabolic products. The short chain fatty acids acetate, butyrate, and propionate are produced by bacteria through fiber fermentation. The types and amounts of short chain fatty acids produced by bacteria vary by species and they can be produced by one type of bacteria and utilized by another. Short chain fatty acids also have effects on host tissues that typically promote the health of the IEC. This is an example of a cooperative relationship among microbes and with host tissues, but microbial products can also have direct or indirect effects to exclude other microbes that potentially co-occupy niches. Products with competitive effects include short chain fatty acids produced by commensal bacteria that inhibit the growth of pathogenic bacteria. Likewise, bacteria can produce and deliver antimicrobial agents to competitors in the community through a type VI secretion system. They can also deplete specific substrates necessary for the growth of competitors or secrete waste products that impair the growth of competitors.

The evidence that microbial factors can have a net cooperative effect to encourage colonization by other specific microbes or a net competitive effect that discourages colonization by specific microbes has led to two major concepts related to community organization. The first is the idea that there are keystone microbial species or microbial functions that determine the organizing principles of microbial communities. The second is the idea of pathogenic exclusion. These concepts are the underpinning of the highly embraced theory that healthy microbial communities work to exclude colonization by infiltrating pathogens. Ultimately, community assemblage is the culmination of a huge number of complex interactions among microbes and between microbes and the host. In the end, these interactions establish interconnected, cross-kingdom feedback loops that promote both digestion and defense in the GI tract.