Not only does your diet fuel your body, but it also fuels and shapes your microbiome, which in turn can alter your mood, change your response to pathogens, and maybe, just maybe, alter your energy metabolism.
80 post-menopausal women who were overweight participated in a sixteen-week study of the effects of caloric restriction on their weight and microbiome. This current report summarizes the impact on their gut bacteria. The treatment group underwent eight weeks of an 800-calorie liquid diet, four weeks of a more conventional calorically restricted diet, and four weeks of weight maintenance. The controls were just asked to maintain their weight.
From a weight point of view, that degree of caloric restriction was impactful; the mean loss was nearly 28 pounds in the three months, about 14% of body weight. By analyzing the DNA present in the participants' feces, the researchers were able to determine that the greatly diminished calories
- reduced the overall size of the microbiome
- shifted the relative numbers of various members of the gut’s community
The end result was that the microbiome "community" moved from bacteria that specialized in metabolizing a diet of plant “sugars” (polysaccharides) and towards bacteria that fed on “host glycan.”
Host glycan is a more scientific way to describe the mucous secreted by the cells lining our GI tract, providing protection, lubrication, and maintaining the integrity and functioning of the mucosa. In the absence of necessary calories, the microbiome shifts to a more scavenger, foraging population – foraging food that plays a vital role in our physiology.
“…the VLCD [very low-calorie diet] induced marked changes in both the structure and metabolic activity of the human gut microbiome and promoted the expansion of bacteria that can feed on host glycans.”
These changes were reversible, as the participants returned to a more conventional but still calorie-restricted diet. But here is an interesting finding. When “germ-free” mice were fed the microbiome of those participants with the most significant weight loss, those mice lost roughly 13% of their body weight two days after “fecal transplantation” despite being fed a normal amount of calories and nutrients.  It seems the microbiome “contributes” to our weight loss by making our energy extraction less efficient – in a world with a calorie shortage, it is every microbe for itself. They try to meet their needs before those of their host – that would be you and me.
“Mice colonized with post-diet microbiota replicated human phenotypes, including decreased weight and adiposity, driven in part by an inability to restrict the growth of C. difficile.”
This last statement is intriguing and raises, for me, interesting speculation. Could the C. difficile infections that plague hospitalized patients be, in part, a response to their underlying malnutrition? Patients with chronic diseases are often malnourished with respect to protein, which directly impacts the functioning of their immune system. Lying in a hospital bed doesn’t require many calories, but being sick and mobilizing your defenses does. We rarely provide enough calories and nutrients to our hospitalized patients; perhaps better caloric replacement would reduce the incidence of this complication.
For now, we will have to content ourselves in knowing that our diet affects our life and the lives we contain. And that those contained lives, our microbiome, continue to morph to meet their needs in the nutritional environment we create. We literally are what we do and don't eat - in ways we are just beginning to understand.
 Germ-free mice are often, but not always, created by in vitro fertilization and then implanted into germ-free mothers. Transferring the gut microbe to another creature is termed fecal transplantation. It involves bypassing our taste receptors and installing a slurry of saline and feces directly into our gut. Appetizing
Source: Caloric restriction disrupts the microbiota and colonization resistance Nature DOI:10.1038/s41586-021-03663-4