## 3 Antigen Sampling, Tolerance, and Immune Function of Commensal Bacteria  
The culmination of leukocytes and epithelial cells in the gastrointestinal tract synthesizes specific, well-regulated inflammatory responses that eliminate pathogens from the gut, maintain the integrity of the epithelial barrier, and produce an immunological memory [17]. To properly function, these responses must also be capable of recognizing, maintaining, and protecting commensal gut microbiota [4; 13; 17], but there is limited information about the mechanistic relationships between commensal gut microbiota and the immune system [13]. However, there is clear evidence of antigen sampling and commensal microbiota tolerance in the intestinal epithelium and lamina propria. Antigen sampling refers to the mechanistic practice of collecting peptides, glycolipids, and metabolites of gut microbes from the lumen to initiate immune responses or develop tolerance [3]. When studying the physiological source of environmental microbe sampling in the gut of a rat model, [PERSON] and [PERSON] [35] determined that consumption of ferritin-India dye exhibits passage through the follicle-associated epithelium but not in other regions of the epithelium. Additionally, avian species are capable of anti-directional peristaltic muscle contractions of the cloaca to push antigens from the external environment to the bursa of Fabricius located proximal to the vent (also known as bursal drinking) and upwards towards the cecal tonsils [36]. There is evidence that microbe sampling along with the establishment of commensal microbiota in the gastrointestinal tract are beneficial for development of the mucosa-associated immune system [16; 37]. Like the transfer of maternal antibodies to offspring, maternal microbiota can be passed to offspring during and after birth. For avian species, environmental microbes from the eggshell, nesting material,and parental feathers contribute to hatched-offspring gut microbiota [37]. Moreover, by exposing the gastrointestinal tract to environmental microbes during infancy, organisms develop functional lymphatic tissues in the gastrointestinal tract and benefit from the symbiotic relationship of commensal microbiota [38]. A major contributor to early gut microbiota development is segmented filamentous bacteria (SFB): a vertically transmitted, host species-specific, unculturable bacterium whose life cycle is dependent on penetrating the mucus layers of the gut and latching onto gastrointestinal epithelial cells without initiating an inflammatory response in the host [39]. These bacteria have been defined in mammals as well as chicks [40; 41] and can be enriched through probiotic supplementation in feed [42]. In recent years, it was determined that these bacteria play critical roles in protecting young organisms from pathogenic bacteria colonization while their immune systems develop [25; 39]. SFB may also actively contribute to the maturation of mucosal immunity and development of Th17-type subpopulations in the lamina propria [25]. As previously stated, properly regulated Th17 subpopulations are essential for the maintenance of the gut mucosa. In turn, a balanced gastrointestinal microbiome also regulates Th17 populations to prevent autoimmune-type inflammation in the host [30]. Since leukocytes in the gastrointestinal lymphatic tissues are constantly sampling microbes from the intestinal lumen, oral tolerance to commensal microbiota is necessary to maintain homeostasis in the gut. Oral tolerance refers to the body's ability to consume foods and non-pathogenic microbes without experiencing inflammation at the gut epithelial barrier [43]. There are many factors that may contribute to oral tolerance, including the expression of TLR and NOD-like receptors for microbial sensing [44; 45; 46]. For example, TLR4 expression is lower in the lamina propria when compared to other non-mucosal tissues [46].