ML is a Marie Sk?odowska\Curie fellow and receives funding from Horizon 2020 (H2020\MSCAIF\2014; grant 661594).. of homeostasis in the gut and beyond. Introduction Our gut is home to a large and complex community of microorganisms termed the intestinal microbiota. The dynamic environment within the intestine presents a challenge to both the host and the intestinal microbiota to maintain a mutualistic relationship throughout life (Tannock, 2007). In this review, we focus on the factors which influence bacterial composition throughout the gastrointestinal tract, and on the cross\talk between the microbiota and the host at the gastrointestinal (GI) barrier, which results in the development of a precise GI organisation and functionality. We discuss this in the context of what is currently known about gut microbiota conversation with host defences, and research tools and models that can be used to study these interactions. Following pioneering experiments in clinical and animal models over a century ago (Cushing and Livingood, 1900) researchers have generated a variety of tools, including animal models devoid of microorganisms (germ\free/axenic models) providing insight into the host processes regulated by the presence and/or composition of the gut microbiota in health and disease (Reyniers, 1959; Smith (Fanning (Marshall, 2002) and opportunistic pathogens. Those bacteria which initially colonise neonatal AZD5438 guts establish a mutualistic relationship with the gastrointestinal tract that can last a lifetime (Human Microbiome Project C, 2012). The birthing process has been reported to influence the type of bacteria that first colonise the infant gut; as infants acquire bacteria either by vertical transmission from the mother through the vaginal canal, and/or their environment (including the mother’s skin) after caesarean section. Vaginal delivery results in the gut colonisation by pioneer bacteria including and and to those observed in vaginally delivered babies (Dominguez\Bello and reduced levels of (Harmsen and (Pretzer and enriched communities in discrete inter\fold regions of the colonic mucosa and and in the lumen (Nava and to persist in the outer mucus layer (Li work employing a AZD5438 range of germ\free animal models, including mice, rats, pigs, drosophila, zebrafish, chickens and others (a number of which are summarised in Table ?Table1).1). Below, we discuss interactions between gut microbes, the intestinal epithelial layer and immune and nervous systems. Table 1 Summary of germ\free phenotypes in animal models. organoid models, detailed below, demonstrate that microbial signalling can alter epithelial turnover via activation of pattern recognition receptors (PRR) expressed on crypt stem cells, to alter cell proliferation and survival decisions (Neal (EHEC), and (Shin and invasive can target these defences by secreting proteases and neuro\immune stimulatory ligands to impair brush border formation AZD5438 (Lhocine for example exploits host cholesterol to obtain resistance to the antimicrobial peptide LL\37 in the gerbil intestine (McGee Typhimurium contamination prevented the translocation bacteria to the draining mesenteric lymph nodes, indicating that target M cells as sites of entry, via intracellular trafficking mechanisms, by specifically killing the M cells to create an entry portal, or more generally by inducing a local inflammatory immune response to create a leaky epithelium (Jones techniques to study microbial\gut interactions The specific niches which exist throughout the gastrointestinal tract are largely dictated by diet/nutrients and host\derived factors. Disentangling how different species colonise and change these niches can be difficult in previously colonised animal models, in which colonisation resistance prevents the establishment of new bacterial strains, unless the resident gut microbiota is usually first depleted with antibiotics (Stecher techniques have been established including continuous culture systems, the generation of intestinal tissue cell lines and organoids from intestinal explants, and mock community analysis to study host\microbe interactions. Many of these systems, such as continuous culture systems, can replicate flow dynamics and the microbial and physicochemical characteristics of the luminal content in the proximal and distal colon of a variety of human and animal models (Macfarlane culture techniques (Sato system to study the effect of the microbiota SYNS1 on stem and other crypt AZD5438 cells. Colonoids and small intestinal enteroids can be generated from primary tissues, biopsies and adult and induced pluripotent stem cells (iPSCs) from humans, mice and other species to form self\organising 3D cultures made up of multiple differentiated epithelial cell types which recapitulate many functions of the original organ (Spence models (Pritts in gastric organoids (Wroblewski technologies for studying microbial conversation with epithelium and other cells of the intestine. HIOs: human intestinal organoids, hPSCs: human pluripotent stem cells A further limitation of organoids is usually that they fail.
