Adverse effects of reduced food variety on microbiome

We often see, in Sci-fi, food being produced from, say, algae or yeast. What could be the effect of such a limited diet on the gut microbiome? Would there be any believable side-effect that would have an influence on the brain?

I'm thinking of a first colony on Mars where people start behaving strangely, but I'm not sure how believable it would be to have them really affected, except to make them more, or less, autistic.

EDIT: I'm looking more into lack of certain bacteria than pathological elements.

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Adverse effects of reduced food variety on microbiome

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