{"doi":"10.1101/2020.12.14.422699","title":"<i>Microbe-seq</i> : high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome","abstract":"Abstract We present Microbe-seq , a high-throughput single-microbe method that yields strain-resolved genomes from complex microbial communities. We encapsulate individual microbes into droplets with microfluidics and liberate their DNA, which we amplify, tag with droplet-specific barcodes, and sequence. We use Microbe-seq to explore the human gut microbiome; we collect stool samples from a single individual, sequence over 20,000 microbes, and reconstruct nearly-complete genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe genomic signatures of microbial interactions: we reconstruct the horizontal gene transfer (HGT) network within the individual and observe far greater exchange within the same bacterial phylum than between different phyla. We probe bacteria-virus interactions; unexpectedly, we identify a significant in vivo association between crAssphage, an abundant bacteriophage, and a single strain of Bacteroides vulgatus. Microbe-seq contributes high-throughput culture-free capabilities to investigate genomic blueprints of complex microbial communities with single-microbe resolution.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":121838,"datarank":0.29188652235829704,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.0,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9468,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":550235,"name":"Shijie Zhao","orcid":"0000-0002-6609-0710","position":1,"is_corresponding":false},{"id":562032,"name":"Yehang Yin","orcid":"0000-0001-5126-6544","position":2,"is_corresponding":false},{"id":562569,"name":"Huidan Zhang","orcid":null,"position":3,"is_corresponding":false},{"id":562033,"name":"David M. Needham","orcid":"0000-0001-7257-2516","position":4,"is_corresponding":false},{"id":562034,"name":"Ethan D. Evans","orcid":"0000-0002-9383-2185","position":5,"is_corresponding":false},{"id":109701,"name":"Chengzhen L. Dai","orcid":"0000-0002-3073-211X","position":6,"is_corresponding":false},{"id":562035,"name":"Peter J. Lu","orcid":"0000-0003-1489-5725","position":7,"is_corresponding":false},{"id":29035,"name":"Eric J. Alm","orcid":"0000-0001-8294-9364","position":8,"is_corresponding":false},{"id":20636,"name":"David A. Weitz","orcid":"0000-0001-6678-5208","position":9,"is_corresponding":false},{"id":501522,"name":"Wenshan Zheng","orcid":"0000-0001-9319-7348","position":0,"is_corresponding":true}],"reference_count":65,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T23:14:46.979435Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}