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CHaPter 14  The Microbiota in Immunity and Inflammation                 209



               KeY COnCePtS                                       acquires antibodies of the IgG isotype both in utero and via the
            Definitions                                           breast milk. These antibodies serve to limit enteric infection in
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                                                                  the newborn  and dampen neonatal mucosal T-cell and germinal
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            •  Microbiota: A collective term for all the microscopic organisms that   center (GC) B-cell responses to commensal antigens.  Maternally
              reside on or in the human body.                     acquired anticommensal antibodies can transfer bound microbial
            •  Microbiome: The combined genomes of all the organisms that   molecules to the offspring during gestation and via the breast
              constitute the microbiota.                          milk. This transfer of microbial products contributes to the
            •  Mycobiota: That subset of the microbiota that includes fungi alone.  earliest education of the immune system and limits deleterious
            •  Virome: the collection of all viruses, including viruses integrated into   postnatal  inflammatory  responses.   Breast  milk is  also  a  rich
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              the human genome, found in or on humans.
            •  Dysbiosis: A condition in which there is disequilibrium of the microbial   source of immunosuppressive transforming growth factor-β
              communities that constitute the microbiota at a given body site.  (TGF-β) and interleukin-10 (IL-10) (Chapter 9), which also help
            •  Germ-free: Experimental animals birthed and raised in a sterile environ-  promote tolerogenic responses to the microbiota. 9,10
              ment, devoid of microbes.
            •  Gnotobiotic (“known life”): Describes animals in which the full   MICROBIOTA-DEPENDENT MATURATION OF THE
              complement of colonizing microbes is known.
                                                                  INTESTINAL IMMUNE SYSTEM
                                                                  Microbial colonization prompts a rapid organization of immune
                                                                  structures that are quickly seeded with immune cells. This process
           Prenatal Development of the Immune System              helps avoid overexuberant responses to the microbiota and sets the
           In the fetal liver, some common lymphoid progenitor cells—  stage for continued tolerance of commensals and for defense against
           ancestral to all lymphocytes—develop into a specialized subset   pathogens in the  future. The  intestinal  epithelium limits  direct
           of innate lymphoid cells (ILCs) referred to as lymphoid tissue   encounter between luminal microbes and the immune cells in the
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           inducer (LTi) cells.  As their name implies, LTi cells are essential   underlying lamina propria not only by forming a physical barrier
           for the development of all secondary lymphoid structures   but  also  by  the  production  and/or  transport  of  immune  and
           throughout the body. These structures will eventually become   antimicrobial factors (Fig. 14.4). Thus the epithelium is an essential
           the sites for initiation of immune responses to the commensal   component of the elaborate network of checks and balances that
           microbiota, pathogenic invaders, and self antigens. In the develop-  synergize to help to keep pathogens at bay while limiting or prevent-
           ing fetus, LTi cells promote the development of mesenteric lymph   ing collateral damage induced by pathogens and commensals.
           node (MLN) and of the Peyer patches (PPs) (Chapters 2 and
           20) in the distal ileum (Fig. 14.3). They also recruit B and T   Gut-Associated Lymphoid Tissues
           lymphocytes to these tissues and facilitate their organization   Although MLN and Peyer patches begin to develop before birth,
           into distinct B-cell follicles and T-cell zones, respectively.   complete maturation does not occur until after birth. Germ-free
           Throughout life, the MLN provides a so-called mucosal firewall   or “germ-reduced” mice display reduced size and cellularity and
           that prevents systemic dissemination of gut bacteria.  altered numbers and distribution of immune cells both in the
             Other local mechanisms are also initiated to limit host collateral   gut and gut-associated lymphoid tissues (GALTs). Thus maturation
           damage to the neonatal intestine by early microbial encroachment.   of the mucosal immune system is contingent on the acquisition
           For example, Toll-like receptor 4 (TLR4), the receptor for   of microbiota. A third type of secondary lymphoid tissue—isolated
           lipopolysaccharide (LPS) that is derived from gram-negative   lymphoid follicles (ILFs), which are also induced by LTi cells—is
           bacteria, is highly expressed by intestinal epithelial cells (IECs)   also completely dependent on colonization with the microbiota
           prior to birth, but its  expression and signaling are rapidly   and thus only develops postnatally.
           downregulated following onset of colonization. In addition, a   LTi cells cluster at the base of the crypts in structures referred
           diverse array of lymphocytes collectively referred to as intraepi-  to as cryptopatches. Stimulation of cryptopatches by peptidoglycan
           thelial lymphocytes (IELs) can be found intercalated between   derived from gram-negative bacteria induces recruitment of B
           the IECs. IELs display multiple features of activated cells and   cells, thereby forming ILFs. The importance of ILFs in the direct
           participate in the maintenance of epithelial barrier integrity by   control of bacterial growth is demonstrated by the fact that mice
           limiting bacterial translocation and promoting epithelial repair   devoid of mature ILFs display an overrepresentation of gram-
           following injury. 5                                    negative bacteria. 11
           Passive Acquisition of Antimicrobial Immunity          Innate Lymphoid Cells
           The microbiota of the neonate is acquired from his or her mother,   ILCs represent an early line of defense at mucosal surfaces. ILCs
           who has already established tolerogenic relationship with the   are classified as LTi or “LTi-like” (described above) cells or as
           same microbiota. The mother’s “mucosal memory” also gets   “helper-like” cells. The progenitor of helper-like ILCs is distinct
           transmitted to her offspring. During transvaginal delivery, this   from that of LTi cells or natural killer (NK) cells. “Helper-like”
           mucosal memory is seeded with the mother’s native microbiota.   ILCs are classified into three main subcategories based on their
           Mothers produce antibodies to bacteria-derived antigens. These   expression of particular sets of surface receptors, transcription
           bacteria-responsive antibodies enter the maternal circulation   factors, and secreted proteins. Unlike their adaptive, thymus-
           and ultimately get passed to the offspring in breast milk. Immu-  derived counterparts, ILCs do not express antigen receptors and
           noglobulin A (IgA) is the major antibody isotype generated by   are therefore activated by cytokine signals. This enables ILCs to
           mammary glands (Chapter 15). IgA inhibits bacterial translocation   launch an initial rapid response to microbial challenge and
           across the neonatal intestinal epithelium, thereby limiting col-  facilitate the development of an adaptive lymphocyte-mediated
           lateral damage by an encroaching microbiota and providing   immune response. ILC1s, such as T-helper type 1 (Th1) cells,
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           passive immunity to pathogenic infection.  The offspring also   express the transcription factor Tbet and secrete interferon-γ
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