How long should I wait to collect my sample after finishing antibiotics?

Ideally wait at least one month after finishing antibiotics or antimicrobials before collecting a sample. After a short course of broad-spectrum antibiotics — five to 10 days — most gut microbial species return to baseline within one to two months.
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Some changes can persist for a year or more, and there's limited data on prolonged antibiotic use, where recovery is likely to take longer. One study showed recovery only after nine months following three months of amoxicillin.
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So the one-month minimum is what we advise based on current research, with the understanding that full recovery may take longer in some cases.