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Resent studies showed that microbial species with similar genetic potential tend to co-exist in the human gut,suggesting that microbiome assembly is driven by habitat filtering.Population biology theory,however predicts that species need to niche differentiate for extended co-existence.To approach this conundrum we mapped the gene expression alterations of co-existing species across 233 human stool samples.In this way we identified hundreds of microbial species that altered their gene expression when coexisting with specific companion species.