Table 1.

Guiding queries used to examine gut microbiome–circadian interactions.

Query	Conditions	Examples of Evidences
How does circadian rhythm affect gut microbiota?	Light/dark cycles	Effect of diurnal variation and altered light/dark cycles on gut microbiome
	Sleep status	Gut microbiome in sleep deprivation/sleep fragmentation
	Diet	High fat diet, night eating
How does gut microbiota affect circadian rhythm?	Antibiotic-induced gut microbial alterations	Do antibiotics affect sleep or circadian-controlled metabolic states?
	Microbial dysbiosis due to intestinal disease	Chronic gut disorders with altered microbiota showing co-morbidities in sleep
	Microbial metabolites	Short chain fatty acids, Secondary bile acids
		Vitamins
		Biogenic amines
		Hydrogen sulfide