{"doi":"10.1101/2023.08.07.552389","title":"Infant gut bacteriophage strain persistence during the first three years of life","abstract":"Abstract Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we established a large phage sequence database and used strain-resolved analyses to investigate phage succession in infants throughout the first three years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increased over time and reached adult-like complexity by age three. Approximately 9% of early phage colonizers, mostly maternally transmitted and infecting Bacteroides , persisted for three years and were more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment were more likely to persist than non-recoded phages and generally displayed an increase in in-frame re-assigned stop codons over three years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":410175,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9373,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1011942,"name":"LinXing Chen","orcid":null,"position":1,"is_corresponding":false},{"id":275438,"name":"Adair L. Borges","orcid":"0000-0002-1477-7908","position":2,"is_corresponding":false},{"id":985753,"name":"Jacob West-Roberts","orcid":"0000-0001-8797-5617","position":3,"is_corresponding":false},{"id":496132,"name":"Brian Firek","orcid":"0000-0001-9908-8214","position":4,"is_corresponding":false},{"id":225983,"name":"Michael J. Morowitz","orcid":"0000-0001-8172-637X","position":5,"is_corresponding":false},{"id":206153,"name":"Jillian F. Banfield","orcid":"0000-0001-8203-8771","position":6,"is_corresponding":false},{"id":580478,"name":"Yue Clare Lou","orcid":"0000-0002-0340-2166","position":0,"is_corresponding":true}],"reference_count":105,"raw_metadata":null,"created_at":"2026-07-19T01:21:31.144858Z","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":[]}