My gut samples show Lactococcus, Streptococcus thermophilus and Leuconostoc as significant — is this real biology or diet?

Possibly diet. These are typical passengers from cheese, yoghurt and fermented vegetables and are often detected in stool without colonising.

To check, run your taxa list in TSEA against the Food matrix library (mixed-level or species-level tab) in addition to the host-intrinsic library. The food sets are core microbiomes of specific foods (e.g. milk kefir core, cheddar core, sauerkraut core) derived from cFMD and FoodMicrobionet. If your list enriches for food cores and not for disease signatures, the more likely explanation is food intake — or food handling contamination — rather than host biology. Each set carries an EFSA FoodEx2 code so you can see which food category it belongs to.

For strain-level data, there is also a food strain library of sequenced isolates from foods; note that it is heavy with food-safety surveillance genomes (Salmonella, Listeria, Campylobacter, E. coli), so a hit there may also point to a food-borne pathogen.