Supplementary Table 3

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Supplementary Table 3: Differential abundance of species across CSTs.

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Formula = abundance +(1|PATIENTID)
model = LMCLR


Supplementary Table 4

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Supplementary Table 4: Differential abundance of Antibiotic Resistance Genes (ARGs) across CSTs.

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Formula = abundance +(1|PATIENTID)
model = CPLM


Supplementary Table 5

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Supplementary Table 5: Differential abundance of Mobile Genetic Elements (MGEs) across CSTs.

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Formula = abundance +(1|PATIENTID)
model = CPLM