Previous work had shown that gut microbial communities can be remarkably resilient after brief ABX perturbations: while ABX can have dramatic effect in short-term, communities often regain much of their baseline composition in weeks following treatment.
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But because these pioneering studies were based on 16S data, we know very little about how this ecological robustness is implemented at the strain level. Do species recover bc external strains recolonize the host after treatment? Or do resident strains evolve in response to ABX?
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To address these Q's,
@MortezaRoodgar generated an amazing metagenomic timecourse for a single host microbiome using@10xGenomics linked reads. This allowed us to track evolutionary dynamics w/in 36 different species during a period of health, disease, ABX treatment, and recoveryPrikaži ovu nit -
We observed widespread shifts in genetic composition w/in species during & after ABX. But genetic responses were rarely consistent with simple extinction & recolonization picture. Nor were they consistent with simple model of ABX resistance evol'n via classic selective sweeps.
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Instead, we more commonly observed incomplete genome-wide sweeps involving multiple linked SNPs, many of which were already present in the pre-ABX pop'n. In months following ABX, many sweeping haplotypes eventually returned to their original freqs (at the single bp level!)
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This suggests that ecological resilience may extend all the way down to the genetic level. Also suggests that quasi-stable coexistence *within species* in this community may be more common than we typically assume (echoing previous finding by
@Shijie_Zhao@conTaminatedsci & co)Prikaži ovu nit -
Understanding the generality of these results (across other hosts, other ABX, & other perturbations) -- and their implications for short-term evolution in the microbiome -- are a big focus of our current work. Questions and comments welcome!
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