During the active phase, when animals are awake and feeding, high densities of diverse gut microbes are tolerated because they generate crucial metabolites, which are absorbed into the bloodstream via a porous gut lining (Fig. 2a). Because metabolites are crossing the gut-blood barrier during feeding, the permeable gut lining is vulnerable to opportunistic bacterial attack. To lower infection risk, most non-commensal bacteria are kept away from the mucosal layer by allowing only specific mucosal commensals to adhere to the gut lining 10,13. In mice, this function appears to be largely performed by commensal SFBs. SFBs, as well as mucosal commensals Bacteroidetes fragilis and Akkermansia muciniphila, are suggested to perform this role in humans 46. The physical interaction between mucosal commensals and host epithelial cells, in particular at the start of the active phase 11,13, triggers the mass release of components of innate immunity, including AMPs 13, that protect the host against a broad range of pathogens during feeding 13, and also feed back to control gut microbial rhythms 11. Mucosal commensals also trigger the release of major histocompatibility complex (class II)-mediated cytokines 10, which, whilst part of the adaptive arm of the vertebrate immune system, act to modulate the innate immune response 55. Innate immune protection does not last the entire active phase, but begins to decline in the second half of the active phase 10,13. The reason for this is unclear, although it may be due to the feeding bouts that typically occur at the start of the active phase in mice 56.
Maintaining a high level of immune control across a 24-hour period is energetically expensive, and excessive inflammation causes immunopathology 57. Many aspects of innate immunity are therefore downregulated during the rest phase when the gut lining becomes less permeable and the host is less likely to encounter pathogens (Fig. 3b). This leads to higher host susceptibility to pathogens during the rest phase 58, with pathogens such as Salmonella colonising at higher abundances compared to the active phase 16. The downregulation of innate immunity in the gut is preceded by the detachment of mucosal commensals from the mucosal layer via mechanisms which remain unclear to date, thereby triggering a reduction in the number of cytokines and AMPs secreted into the gut. In the absence of nutrients from food, the gut bacterial population declines, and remaining bacteria migrate to the gut epithelium to feed on the mucosal layer, replacing the protective layer of commensals 11,13 (Fig. 3b). Perhaps to protect the integrity of the epithelial layer from feeding bacteria, the intestinal mucosal layer thickens during the rest phase 11.
Despite higher infection susceptibility during the rest phase, animals are not altogether undefended. A key gut antibody, secretory (s)IgA, is upregulated during sleep 59 (Fig 3b). SIgA is secreted by mucosal membranes and is present across all mammals and bird species 60,61. It acts as bridge between innate and adaptive immunity, being able to distinguish between gut commensals and non-commensals 62. During the rest phase, upregulated sIgA neutralises non-commensals and their toxins, which are tolerated during the active phase. Thus, IgA ensures that any potential pathogens introduced and proliferating during the active phase are neutralized. Another function of sIgA is to bind to beneficial mucosal commensals and control their adhesion to the mucosal layer 62,63, and it is therefore a key agent in triggering the circadian cycles of the gut microbiota at the start to the active phase 59. A peak in sIgA just prior to the start of the active phase is likely involved in bringing mucosal commensals back to the epithelial layer to begin the circadian cycle anew, although the exact mechanisms are still unknown. Interestingly, sIgA secretion is controlled by food intake rather than the master clock, with food intake repressing sIgA levels 59 in order to increase tolerance to gut bacteria during the active phase.