摘要：SummaryUnderstanding microbial communities' roles in human health and disease requires methods that accurately characterize the microbial composition and their activity and effects within human biological samples. We present sMETASeq (small RNAMetagenomics bySequencing), a novel method that uses sequencing of small RNAs to jointly measure host small RNA expression and create metagenomic profiles and detect small bacterial RNAs. We evaluated the performance of sMETASeq on a mock bacterial community and demonstrated its use on different human samples, including colon cancer, oral leukoplakia, cervix cancer, and a panel of human biofluids. In all datasets, the detected microbes reflected the biology of the different sample types.Graphical AbstractDisplay OmittedHighlights•Our method “sMETASeq” generates metagenomic profiles from small RNA sequencing data•sMETASeq jointly profiles host and microbe small RNAs in human samples•sMETASeq measures and detects changes in abundance of microbes at species level•sMETASeq is available as open source scriptsGenomics; Microbiology; Bioinformatics
