Data extraction was performed by the two reviewers independently, and included the following information: Author (year), country, design of the study, range of age of patients, sampling site, type of sample, the platform of sequencing; method of sequencing (16S rRNA or metagenomics or metranscriptomics), method of data analysis and bioinformatics; and abundance of species considered as low-abundant/minority microrganisms. All extracted data was checked by a third reviewer.

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