After the antibiotics had cleared the way, the standard probiotics could easily colonize the gut of everyone in the second group, but to the team's surprise, this probiotic colonization prevented the host's normal microbiome and gut gene expression profile from returning to their normal state for months afterward. In contrast, the aFMT resulted in the third group's native gut microbiome and gene program returning to normal within days.
The second Elinav study, “Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT” involved a mouse model and human patients. One cohort of mice and a parallel human group was given the same probiotic strain used in the first study to see if they had more success repopulating their gut microbiota after a round of antibiotics. Another “watch-and-wait” cohort didn’t take probiotics to assist gut microbiome recovery after antibiotic-related depletion. A third cohort was given an “autologous fecal microbiome transplant” (aFMT) which consisted of a patient’s own gut microbiota that had been collected before he or she started a cycle of antibiotics.

The concept of probiotics is credited to Élie Metchnikoff, a Russian scientist born in the mid-1800s, whose work provided profound insights into immunology and microbes. He developed a theory about aging that over the years had been forgotten in mainstream medicine but is now embraced by many scientists: namely, that health is influenced by toxic bacteria in the gastrointestinal (GI) tract. He is said to have noticed that people who lived to be over 100 years old in the Balkan States and Russia drank sour milk, which we now call yogurt or kefir, every day. In fact, Bulgarian yogurt cultures even today are regarded as highly therapeutic.

However, these quality of life improvements are varied, and some improvements are quite mild. Sample group, types of allergies, symptoms, and results are across a broad spectrum. For example, numerous studies have shown that allergic rhinitis responses to the household dust mite decrease significantly in adults and children when probiotics were used. However, people allergic to birch pollen saw neither a decrease in general allergic responses to birch pollen or to apple food.
In the new study, the researchers analyzed information from 15 healthy volunteers who took either a probiotic product containing 11 strains of bacteria, or a placebo, for four weeks. The participants also underwent colonoscopies and upper endoscopies before they took the probiotics or the placebo, and again after the four-week treatment period. (An upper endoscopy looks at the upper part of the digestive tract.) During these procedures, the researchers took samples from inside participants' guts.
A popular dish in Japan consisting of fermented soybeans, natto contains the extremely powerful probiotic bacillus subtilis, which has been proven to bolster your immune system, support cardiovascular health and enhance digestion of vitamin K2. Natto can also contain vitamin B12, which is usually lacking in vegan diets. It’s also one of the highest plant-based proteins.