{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T06:57:36Z","timestamp":1782543456521,"version":"3.54.5"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T00:00:00Z","timestamp":1747958400000},"content-version":"vor","delay-in-days":22,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"CIC-MIC"},{"name":"Yunnan Tobacco Company","award":["2024530000241001"],"award-info":[{"award-number":["2024530000241001"]}]},{"name":"PhD Scientific Research and Innovation Foundation of the Education Department of Hainan Province Joint Project of Sanya Yazhou Bay Science and Technology City, Biological Breeding-Major","award":["2023ZD04076"],"award-info":[{"award-number":["2023ZD04076"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The advanced single-microbe RNA sequencing (smRNA-seq) technique addresses the pressing need to understand the complexity and diversity of microbial communities, as well as the distinct microbial states defined by different gene expression profiles. Current analyses of smRNA-seq data heavily rely on the integrity of reference genomes within the queried microbiota. However, establishing a comprehensive collection of microbial reference genomes or gene sets remains a significant challenge for most real-world microbial ecosystems. Here, we developed an unbiased embedding algorithm utilizing K-mer signatures, named mKmer, which bypasses gene or genome alignment to enable species identification for individual microbes and downstream functional enrichment analysis. By substituting gene features in the canonical cell-by-gene matrix with highly conserved K-mers, we demonstrate that mKmer outperforms gene-based methods in clustering and motif inference tasks using benchmark datasets from crop soil and human gut microbiomes. Our method provides a reference genome-free analytical framework for advancing smRNA-seq studies.<\/jats:p>","DOI":"10.1093\/bib\/bbaf227","type":"journal-article","created":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T12:25:06Z","timestamp":1748003106000},"source":"Crossref","is-referenced-by-count":2,"title":["mKmer: an unbiased <i>K<\/i>-mer embedding of microbiomic single-microbe RNA sequencing data"],"prefix":"10.1093","volume":"26","author":[{"given":"Fangyu","family":"Mo","sequence":"first","affiliation":[{"name":"Hainan Institute, Zhejiang University , Zhenzhou Road, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, Hainan Province ,","place":["China"]},{"name":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinghong","family":"Qian","sequence":"additional","affiliation":[{"name":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaolin","family":"Lu","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and James D. Watson Institute of Genome Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dihuai","family":"Zheng","sequence":"additional","affiliation":[{"name":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjie","family":"Cai","sequence":"additional","affiliation":[{"name":"Liangzhu Laboratory (Zhejiang Provincial Laboratory for Systems Medicine and Precision Diagnosis), Zhejiang University , 1369 Wenyi West Road, Yuhang District, Hangzhou 311121, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Yao","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and James D. Watson Institute of Genome Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongyu","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujie","family":"Huang","sequence":"additional","affiliation":[{"name":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanling","family":"Wu","sequence":"additional","affiliation":[{"name":"Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifei","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine , 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yinqi","family":"Bai","sequence":"additional","affiliation":[{"name":"BGI-Sanya, Zhenzhou Road, Yazhou Bay Science and Technology City , Yazhou District, Sanya 572025, Hainan Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongcheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Liangzhu Laboratory, Zhejiang University , 1369 Wenyi West Road, Yuhang District, Hangzhou 311113, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiqin","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang Province ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longjiang","family":"Fan","sequence":"additional","affiliation":[{"name":"Hainan Institute, Zhejiang University , Zhenzhou Road, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, Hainan Province ,","place":["China"]},{"name":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","place":["China"]},{"name":"Institute of Bioinformatics and James D. 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