The community of bacteria living in the digestive tract affects digestion, immune function and possibly much more. That is established. The products sold on the basis of it mostly are not.
What is known
That the microbiome differs between healthy people and those with certain conditions – inflammatory bowel disease, some metabolic conditions. That antibiotics disrupt it and recovery takes time. That diet shapes it substantially.
That transplanting gut bacteria from a healthy donor treats one specific infection extremely effectively, which is the clearest demonstration that the microbiome can be a therapeutic target.
What is not
That any commercial probiotic reliably changes the microbiome in a lasting way. Most contain a few strains that pass through without establishing themselves.
That microbiome testing tells an individual anything actionable. The tests report what bacteria are present; what to do about it is not known for most results.
The causal direction in most associations. A different microbiome in people with a condition does not mean the microbiome caused it.
What actually affects it
Dietary fibre, which feeds beneficial bacteria and is under-consumed in most rich countries. Dietary diversity. Avoiding unnecessary antibiotics.
These are boring recommendations and they are the ones with evidence.
How to read a claim
Ask whether the specific product was tested in humans for the specific outcome claimed. Most probiotic marketing cites general microbiome research and applies it to a product that was never tested.
Where the science is going
Towards engineered organisms designed to establish themselves and produce specific compounds. That is a genuine therapeutic direction and it is early.