The microbiome pays attention to light and does control Time -- 'Human Gut Bacteria Are Sensitive to Melatonin and Express Endogenous Circadian Rhythmicity'

"...Altogether, these data demonstrate a circadian clock in a non-cyanobacterial prokaryote and suggest the human circadian system may regulate its microbiome through the entrainment of bacterial clocks."
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0146643

Circadian rhythms are fundamental properties of most eukaryotes, but evidence of biological clocks that drive these rhythms in prokaryotes has been restricted to Cyanobacteria. In vertebrates, the gastrointestinal system expresses circadian patterns of gene expression, motility and secretion in vivo...