{"doi":"10.1128/msystems.00537-21","title":"Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance","abstract":"To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications. Using this method, we detected several novel phage genera along with those previously established. Our approach of using the whole-genome sequences of hundreds of bacterial isolates from the same site enabled us to make host assignments with high confidence, several at strain levels. Certain phage genes suggest that they provide an environment-specific selective advantage to their bacterial hosts. Our study lays the foundation for future research on directed phage isolations using specific bacterial host strains to further characterize groundwater phages, their life cycles, and their effects on groundwater microbiome and biogeochemistry.","journal":"mSystems","year":2021,"id":187380,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":18,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9337,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":106775,"name":"Simon Roux","orcid":"0000-0002-5831-5895","position":1,"is_corresponding":false},{"id":582800,"name":"Hanqiao Zhang","orcid":"0000-0001-7394-8781","position":2,"is_corresponding":false},{"id":583081,"name":"Anatori Prieto","orcid":null,"position":3,"is_corresponding":false},{"id":571520,"name":"Drishti Soneja","orcid":"0000-0002-0137-0906","position":4,"is_corresponding":false},{"id":52532,"name":"John‐Marc Chandonia","orcid":"0000-0002-5153-9079","position":5,"is_corresponding":false},{"id":322837,"name":"Sarah J. Spencer","orcid":"0000-0002-2744-8994","position":6,"is_corresponding":false},{"id":322836,"name":"Xiaoqin Wu","orcid":"0000-0002-9718-4381","position":7,"is_corresponding":false},{"id":583082,"name":"Sara Altenburg","orcid":null,"position":8,"is_corresponding":false},{"id":582801,"name":"Matthew W. Fields","orcid":"0000-0001-9053-1849","position":9,"is_corresponding":false},{"id":336360,"name":"Adam M. Deutschbauer","orcid":"0000-0003-2728-7622","position":10,"is_corresponding":false},{"id":2171,"name":"Adam P. Arkin","orcid":"0000-0002-4999-2931","position":11,"is_corresponding":false},{"id":29035,"name":"Eric J. Alm","orcid":"0000-0001-8294-9364","position":12,"is_corresponding":false},{"id":322842,"name":"Romy Chakraborty","orcid":"0000-0001-9326-554X","position":13,"is_corresponding":false},{"id":560171,"name":"Aindrila Mukhopadhyay","orcid":"0000-0002-6513-7425","position":14,"is_corresponding":false},{"id":582799,"name":"Ankita Kothari","orcid":"0000-0002-6241-5821","position":0,"is_corresponding":true}],"reference_count":62,"raw_metadata":null,"created_at":"2026-07-18T23:48:55.420619Z","pmid":"34184913","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":[]}