General lifestyle changes are the main mode of action that people have on their microbiome. From altering hygiene habits affecting the skin microbiome to usage of mouthwash affecting the oral microbiome, the microbiome in general is highly dynamic and variable. One more such body site microbial community that can be changed by lifestyle changes is the gut microbiome.
The most obvious change that can impact the gut microbial community is that of diet. This can affect change via two different mechanisms: prebiotics and probiotics.
Prebiotics refers to food that humans eat that microbes use as substrates to sustain growth and reproduction. Prebiotics usually encompasses most fibers, especially soluble fibers, because these components are not digestible by the human body so microbes have free reign to digest these fibers. The presence of these fibers in the diet preferentially selects for microbes that can digest the same fibers. That doesn’t mean that prebiotic fibers are the only thing that microbes will consume. There have been recorded differences in gut microbial communities in people with and without high fiber intakes (vegans and high proportion meat eaters), which suggests that diet outside of specifically named prebiotics also has an effect on the microbial community of the gut
Probiotics are a different story altogether. These are foods that contain bacteria in them already, and these bacteria are the same ones that like to colonize the gut. When people eat these probiotic foods, they introduce these microbes to the general gut microbial community. With sustained, repeated exposure to probiotic foods, the probiotic bacteria will colonize and begin to grow in the gut, effectively changing the microbial community.
With the two prior changes, there is not necessarily a precedent as to whether or not the change will result in a healthier microbial community, because everything is variable between human microbiomes, and what may be invaluably healthful to one person may be entirely harmful to another.
One possible change that could be universally healthy is a decrease in stress. The gut and the brain are linked by the Vagus nerve, and what one does has an impact on the other: the gut microbiome can be affected by the brain and vice versa. This overall reduction in stress can come from meditation, mental health therapies, or exercise. Each of these lifestyle changes have been associated with change in the microbiome, which suggests that stress has an impact on the gut microbiome. It has been further theorized that the microbiome has an impact on stress, so there is the potential for a positive feedback loop that can work for or against stress. General stress may lead to negative changes in the microbiome which may in turn have a negative effect on stress which can further negatively impact the microbiome, and so on. Therefor, reduction in stress could overall positively affect the microbiome.