a response in Josh Mitteldorf's blog

 
Regards Telomeres:
while I'm not sure if the measurements are reflective of increases throughout, say stem cells, it has been claimed that a vegetarian diet combined with even modest low intensity exercise can increase the length of telomeres in humans by a noticeable amount.

Regards Thymus:
I've heard that some doses of melatonin are able to reverse thymic involution in nonhuman animals.

Regards natural substances, we have to remember that some can interact with regulatory proteins and alter gene expression.

For example I believe that CR is at least in  part  probably an artefact of metabolic regulatory networks and not a primarily evolved survival mechanism, it works up to around 65% restriction in some animals but requires optimal nutrition unlikely in any natural environment at that level of restriction.   If you can mess directly with the signaling pathways there's no telling what the limits are, as you wouldn't be bound by minimum survival necessary caloric intake limits, and multiple substances are emerging that appear to affect the signalling directly such as nicotinamide riboside, and the various partial cr-mimetics(resveratrol, fisetin, pterostilbene,etc).  There's also probable dietary means of also activating these signaling pathways such as low methionine diets, which can be combined with the substances and probably yield additive effect.

update:
The telomere study wasn't large but iirc, it took measures after five years, which should give time for changes to accumulate,  between comparison groups and had noticeable differences

"The group that made the lifestyle changes experienced a “significant” increase in telomere length of approximately 10 percent. Further, the more people changed their behavior by adhering to the recommended lifestyle program, the more dramatic their improvements in telomere length, the scientists learned.

By contrast, the men in the control group who were not asked to alter their lifestyle had measurably shorter telomeres – nearly 3 percent shorter – when the five-year study ended. Telomere length usually decreases over time."-http://www.ucsf.edu/news/2013/09/108886/lifestyle-changes-may-lengthen-telomeres-measure-cell-aging

"I believe CR is an evolved mechanism for population regulation. Think of it as aging extra fast when there is a temporary plentitude of food, so overpopulation is a risk. The idea that CR life extension only works with optimal nutrition has become part of the biological lore, but it has never really been tested. At the very least, there are big exceptions, as when insufficient protein and methionine help to ENHANCE life extension from CR."

While I don't remember the source I've also heard it must be gradually undertaken or else no lifespan benefits are seen if it is  introduced all of a sudden in adult organisms, in nature it seems sudden famine is more likely.  Also it seems to work up to about 65% in some animals, even if we were to assume no supplementation is necessary in more mild calorie restriction, it is unlikely there wouldn't be serious malnutrition at such extreme levels, yet it keeps on working past what would seem like natural environment nutrient limits.  
Regards methionine, iirc, it's believed to be one of the key signals of nutrient availability which is used by the mechanisms of cr, but it cannot be reduced beyond a certain point without severe side effects.

As for testing malnutrition CR I would imagine you consider CR not effective in humans or else some of the poorest on earth would be breaking records, which they're not and would serve as a test if it is effective in humans.