FEEDING TIME & METABOLIC DISEASE

Like almost all living organisms, the gut microbiota regulate many of their changes in cellular activity and behavior over 24-hour cycles known as the circadian clock or rhythm. The microbiome has been shown to rhythmically fluctuate in both community composition and gene expression in a circadian dependent manor with respect to host feeding schedules. Disruption of the microbiome circadian rhythm is associated with metabolic disease in mice.
— Trinder, M. et al (2015)

Human testing is limited in the area of microbiome research, however, it's fairly well established that consistent 'after dark, or night-time feeding' will lead to metabolic issues and weight gain. 

Despite the changes in cycling bacterial communities and gene expression being relatively small, impairment of these microbiome circadian fluctuations by arrhythmic feeding has been found to exacerbate the progression of metabolic diseases such as diabetes & obesity.
— Trinder, M. et al (2015)

WHAT you eat is not the only thing that matters. WHEN you eat also turns out to be of utmost importance. In addition to the timing of feeding having an influence on the overall composition & diversity of the gut bacteria, it may also be involved in controlling - through its effect on hormone levels - gastrointestinal inflammation. 

Perturbances in microbiome rhythmicity could exacerbate weight gain via a decreased bacterial utilization of consumed nutrients, upregulation of host nutrient uptake machinery, decreased host energy utilization, and/or increased appetite. Alternatively, it is interesting to speculate about how short timescale microbiome cycling may prevent excessive immune recruitment and inflammation to the gastrointestinal tract.
— Trinder, M. et al. (2015)

As approximately 75% of the human immune system is located within the alimentary canal, inflammation in the gut also ties closely into host immune function. Artificial light, irregular sleep patters, arrhythmic feeding, shift work, & jet lag have all exacerbated complications with human immune function in the modern world.

Many studies have shown that microbes are crucial for immune system development and maturation. Furthermore, the immune system has been shown to respond in a circadian manner in response to stimulation by the gastrointestinal microbes.1,2. Many studies have shown that microbes are crucial for immune system development and maturation. Furthermore, the immune system has been shown to respond in a circadian manner in response to stimulation by the gastrointestinal microbes.1,2.
— Trinder, M. et at. (2015)
Therefore, it is possible that host-microbe circadian rhythm-mediated disturbances to the immune system could influence immunopathologies such as Crohn’s disease, inflammatory bowel disease, systemic autoimmune diseases, and cancer risk.
— Trinder, M. et al. (2015)

Whether or not microbial diversity supported by rhythmic feeding on 'high quality REAL food' is directly related to a 'sufficiently strong' immune system, remains to be seen, but, my completely amateur sense is that scientists in this field will soon discover, that indeed it is.

This is based on my own experience with a high fiber, '6-9 cups of veggies per day' paleo diet, daily prebiotic consumption, as well as my regimented sleeping & eating patterns. 

Future research in the field should be exciting. Several websites, such as caloriesproper.com, come highly recommended for consistent updates in the area of clearly explaining the importance of circadian rhythms, and the gut microbiota.