Microbial symbiosis and immunity

General principles

Microbial symbiosis relies on interspecies communication.

In the gastrointestinal tract

The gastrointestinal tract consists of the mouth, pharynx, esophagus, stomach, small intestine, and large intestine, and is a 9-meter-long continuous tube; the largest body surface area exposed to the external environment. The intestine offers nutrients and protection to microbes, enabling them to thrive. Therefore, the intestine is home to a microbial community of 100 trillion beneficial and pathogenic bacteria, archaea, viruses, and eukaryotes. For reference, humans are home to 10¹³ to 10¹⁴ bacteria in total.

The immune system’s primary home is in the gut; so gastrointestinal microbiota has a direct effect on the body’s immune responses. The immune system is a host defense system consisting of anatomical barriers and physiological and cellular responses, which protect the host against harmful parasites while limiting inflammation by tolerating harmless symbionts. The immune system must strike a balance between protecting the host without inducing excessive inflammation in the gastrointestinal tract. However, without a regular microbiota, the body is more susceptible to infectious and non-infectious diseases.

Regulation of immune responses

Survival of commensal bacteria in the GI tract despite the abundance of local immune cells is remarkable. Surprisingly, homeostasis in the intestine requires stimulation of toll-like receptors by commensal microbes. When mice are raised in germ-free conditions, they lack circulating antibodies, and cannot produce mucus, antimicrobial proteins, or mucosal T-cells. Additionally, mice raised in germ-free conditions lack tolerance and often suffer from hypersensitivity reactions. These data suggest that commensal microbes aid in intestinal homeostasis and immune system development.

To prevent constant activation of immune cells and resulting inflammation, hosts and bacteria have evolved to maintain intestinal homeostasis and immune system development. For example, the human symbiont Bacteroides fragilis produces polysaccharide A (PSA), which binds to toll-like receptor 2 (TLR-2) on CD4⁺ T cells. While TLR2 signaling can activate clearance of peptides, PSA induces an anti-inflammatory response when it binds to TLR2 on CD4⁺ T cells. Through TLR2 binding, PSA suppresses pro-inflammatory Th17 responses, promoting tolerance and establishing commensal gut colonization.

Commensal bacteria may also regulate immune responses that cause allergies. For example, commensal bacteria stimulate TLR4, which may inhibit allergic responses to food.

Development of isolated lymphoid tissues

Microbes trigger development of isolated lymphoid follicles in the small intestine, which are sites of mucosal immune response. Isolated lymphoid follicles (ILFs) collect antigens through M cells, develop germinal centers, and contain many B cells. Commensals trigger development of isolated lymphoid follicles. Gram-negative commensal bacteria trigger the development of inducible lymphoid follicles by releasing peptidogylcans containing diaminopimelic acid during cell division. The peptidoglycans bind to the NOD1 receptor on intestinal epithelial cells. As a result, the intestinal epithelial cells express chemokine ligand 20 (CCL20) and Beta defensin 3. CCL20 and Beta defensin 3 activate cells which mediate the development of isolated lymphoid tissues, including lymphoid tissue inducer cells and lymphoid tissue organizer cells.

Additionally, there are other mechanisms by which commensals promote maturation of isolated lymphoid follicles. For example, commensal bacteria products bind to TLR2 and TLR4, which results in NF-κB mediated transcription of TNF, which is required for the maturation of mature isolated lymphoid follicles.

Protection against pathogens

Microbes can prevent growth of harmful pathogens by altering pH, consuming nutrients required for pathogen survival, and secreting toxins and antibodies that inhibit growth of pathogens.

Immunoglobulin A

IgA prevents entry and colonization of pathogenic bacteria in the gut. It can be found as a monomer, dimer, or tetramer, which means that it can bind multiple antigens simultaneously. In a process called immune exclusion, IgA coats pathogenic bacterial and viral surfaces. This prevents their attachment to mucosal cells, which is required for colonization. IgA can also neutralize MAMPs. IgA can also promote the development of TH17 and FOXP3+ regulatory T cells. Given its critical function in the GI tract, the number of IgA-secreting plasma cells in the jejunum is greater than the total plasma cell population of the bone marrow, lymph, and spleen combined.

Microbiota-derived signals recruit IgA-secreting plasma cells to mucosal sites. For example, bacteria on the apical surfaces of epithelial cells are phagocytosed by dendritic cells located beneath peyer's patches and in the lamina propria, ultimately leading to differentiation of B cells into plasma cells that secrete IgA specific for intestinal bacteria. The role of microbiota-derived signals in recruiting IgA-secreting plasma cells was confirmed in experiments with antibiotic-treated specific pathogen free and MyD88 KO mice, which have limited commensals and a decreased ability to respond to commensals. The number of intestinal CD11b⁺ IgA⁺ plasma cells was reduced in these mice, suggesting the role of commensals in recruiting IgA-secreting plasma cells. Therefore, commensals can protect the host from harmful pathogens by stimulating IgA production.

Antimicrobial peptides

Microbiota are capable of producing antimicrobial peptides, protecting humans from excessive intestinal inflammation and microbial-associated diseases. Various commensals (primarily Gram-positive bacteria), secrete bacteriocins, peptides which bind to receptors on closely related target cells, forming ion-permeable channels and large pores. The resulting efflux of metabolites and cell contents and dissipation of ion gradients causes bacterial cell death. However, bacteriocins can also induce death by translocating into the periplasmic space and cleaving DNA non-specifically (colicin E2), inactivating the ribosome (colicin E3), inhibiting synthesis of peptidoglycan, a major component of the bacterial cell wall (colicin M).

Bacteriocins have immense potential to treat human disease. For example, diarrhea can be caused by a variety of factors, but is often caused by bacteria such as C. difficile. Microbispora ATCC PTA-5024 secretes the bacteriocin microbisporicin, which kills clostridia by targeting prostaglandin synthesis. Additionally, bacteriocins are particularly promising because they kill bacteria differently than antibiotics do. As a result, many antibiotic-resistant bacteria succumb to death at the hands of bacteriocins. For example, in vitro growth of methicillin-resistant S. aureus was inhibited by the bacteriocin nisin A, produced by Lactococcus lactis. Nisin A inhibits methicillin-resistant S. aureus by binding to the precursor to bacterial cell wall synthesis, lipid II. This hinders the ability to synthesize the cell wall, resulting in increased membrane permeability, disruption of electrochemical gradients, and possible death.

Fortification fucose

The intestinal epithelium is reinforced with carbohydrates like fucose expressed on the apical surface of epithelial cells. B. thetaiotaomicron, a bacterial species in the ileum and colon, stimulates the gene encoding fucose, Fut2, in intestinal epithelial cells. In this mutualistic interaction, the intestinal epithelial barrier is fortified and humans are protected against invasion of destructive microbes, and the microbe benefits because fucose is nutritious and regulates the expression of bacterial genes.

On the epidermis

Natural cutaneous microbiota on human skin is vital for the epidermis to fulfill its role as a line of defense against infection. Important microflora that live on the skin, such as Staphylococcus epidermidis produce antimicrobial peptides (AMPs). These AMPs signal immune responses and maintain an inflammatory homeostasis by modulating the release of cytokines. S. epidermis secretes a small molecule which leads to increased expression of Human β-defensins, an AMP. Staphylococcus epidermidis and other important microflora work similarly to support homeostasis and general health in areas all over the human body such as the oral cavity, vagina, gastrointestinal tract, and oropharynx.

Role in disease

An equilibrium of symbionts and pathobionts is critical to fight off outside pathogens and avoid inflammatory bowel disease. Dysbiosis, or imbalances in the bacterial composition of the intestine, has been implicated in inflammatory bowel disease, obesity, and allergic diseases in humans and other animals.

Cancer

Gut microbes may play a role in cancer development through a variety of mechanisms. Sulfate-reducing bacteria produce hydrogen sulfide, which results in genomic DNA damage. Higher rates of colon cancer are associated with higher amounts of sulfate-reducing bacteria in the gut. Additionally, anaerobic bacteria in the colon transform primary bile acids into secondary bile acid which has been implicated in colorectal carcinogenesis. Gram-negative bacteria produce lipopolysaccharide (LPS), which binds to TLR-4 and through TGF-β signaling, leads to the expression of growth factors and inflammatory mediators that promote neoplasia.

Inflammatory bowel disease (IBD)

Activation of mucosal immunity and the intestinal microbiota may contribute to inflammatory bowel disease. A variety of bacteria cause inflammation. For example, E. coli replicate in macrophages and secrete the pro-inflammatory cytokine tumor necrosis factor. However, some bacteria may prevent colitis. The human symbiont Bacteroides fragilis produces polysaccharide A (PSA), which may prevent colitis. PSA induces production of IL-10, an immunosuppressive cytokine that suppresses inflammation. Treatment of bone-marrow-derived dendritic cells and naïve CD4⁺ T cells with purified PSA resulted in increased IL-10 production.

To mimic colitis and activate inflammatory T cells in an experimental condition, wild-type mice were treated with trinitrobenzen sulphonic acid (TNBS). Thereafter, these mice were given PSA orally. Pro-inflammatory cytokine expression (IL-17a and TNFα) in CD4⁺ cells was measured with ELISA. The researchers found that compared to the CD4⁺ cells in the control mice, CD4⁺ cells in PSA-treated mice produced reduced levels of the pro-inflammatory cytokines IL-17a and TNFα. Furthermore, after intestinal colonization with B. fragilis, IL-23 expression by splenocytes was markedly reduced. These data suggest that PSA secreted by Bacteroides fragilis suppresses the inflammatory process during colitis by leading to increased production of IL-10 and decreased production of IL-17, TNFα, and IL-23.

Obesity

Studies with germ-free mice have suggested that the absence of gut microbes protects against obesity. While the exact mechanism by which microbes play a role in obesity has yet to be elucidated, it has been hypothesized that the intestinal microbiota is involved in converting food to usable energy and fat storage.