{"doi":"10.1128/aem.69.2.1251-1262.2003","title":"Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces","abstract":"<jats:title>ABSTRACT</jats:title>\n          <jats:p>\n            New primer-enzyme combinations for terminal restriction fragment length polymorphism (T-RFLP) targeting of the 16S rRNA gene were constructed by using the T-RFLP analysis program (designated TAP T-RFLP) located at the Ribosomal Database Project website, and their performance was examined empirically. By using the fluorescently labeled 516f primer (\n            <jats:italic>Escherichia coli</jats:italic>\n            positions 516 to 532) and 1510r primer (positions 1510 to 1492), the 16S rRNA gene was amplified from human fecal DNA. The resulting amplified product was digested with\n            <jats:italic>Rsa</jats:italic>\n            I plus\n            <jats:italic>Bfa</jats:italic>\n            I or with\n            <jats:italic>Bsl</jats:italic>\n            I. When the T-RFLP was carried out with fecal DNAs from eight individuals, eight predominant operational taxonomic units (OTUs) were detected with\n            <jats:italic>Rsa</jats:italic>\n            I and\n            <jats:italic>Bfa</jats:italic>\n            I digestion and 14 predominant OTUs were detected with\n            <jats:italic>Bsl</jats:italic>\n            I digestion. The distribution of the OTUs was consistent with the results of the computer simulations with TAP T-RFLP. The T-RFLP analyses of the fecal DNAs from individuals gave characteristic profiles, while the variability of the T-RFLP profiles between duplicate DNA preparations from the same samples were minimal. This new T-RFLP method made it easy to predict what kind of intestinal bacterial group corresponded to each OTU on the basis of the terminal restriction fragment length compared with the conventional T-RFLP and, moreover, made it possible to identify the bacterial species that an OTU represents by cloning and sequencing.\n          </jats:p>","journal":"Applied and Environmental Microbiology","year":2003,"id":681572,"datarank":0.8202090211702698,"base_score":5.4680601411351315,"endowment":5.4680601411351315,"self_citation_contribution":0.8202090211702698,"citation_network_contribution":0.0,"self_endowment_contribution":0.8202090211702698,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":236,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1780772,"name":"Takayoshi Hisada","orcid":null,"position":1,"is_corresponding":false},{"id":1780773,"name":"Maremi Sato","orcid":null,"position":2,"is_corresponding":false},{"id":1780774,"name":"Jun Mochizuki","orcid":null,"position":3,"is_corresponding":false},{"id":1780771,"name":"Koji Nagashima","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces","abstract":"<jats:title>ABSTRACT</jats:title>\n          <jats:p>\n            New primer-enzyme combinations for terminal restriction fragment length polymorphism (T-RFLP) targeting of the 16S rRNA gene were constructed by using the T-RFLP analysis program (designated TAP T-RFLP) located at the Ribosomal Database Project website, and their performance was examined empirically. By using the fluorescently labeled 516f primer (\n            <jats:italic>Escherichia coli</jats:italic>\n            positions 516 to 532) and 1510r primer (positions 1510 to 1492), the 16S rRNA gene was amplified from human fecal DNA. The resulting amplified product was digested with\n            <jats:italic>Rsa</jats:italic>\n            I plus\n            <jats:italic>Bfa</jats:italic>\n            I or with\n            <jats:italic>Bsl</jats:italic>\n            I. When the T-RFLP was carried out with fecal DNAs from eight individuals, eight predominant operational taxonomic units (OTUs) were detected with\n            <jats:italic>Rsa</jats:italic>\n            I and\n            <jats:italic>Bfa</jats:italic>\n            I digestion and 14 predominant OTUs were detected with\n            <jats:italic>Bsl</jats:italic>\n            I digestion. The distribution of the OTUs was consistent with the results of the computer simulations with TAP T-RFLP. The T-RFLP analyses of the fecal DNAs from individuals gave characteristic profiles, while the variability of the T-RFLP profiles between duplicate DNA preparations from the same samples were minimal. This new T-RFLP method made it easy to predict what kind of intestinal bacterial group corresponded to each OTU on the basis of the terminal restriction fragment length compared with the conventional T-RFLP and, moreover, made it possible to identify the bacterial species that an OTU represents by cloning and sequencing.\n          </jats:p>","is_dataset_classified":null,"base_score":5.4680601411351315,"endowment":5.4680601411351315,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"12571054","pmcid":"PMC143637","openalex_id":"https://openalex.org/W1970396767","authors":[],"funders":[],"total_grants":0,"fwci":3.0385,"citation_percentile":0.9172357,"influential_citations":0,"citation_trend":[{"year":2012,"count":16},{"year":2013,"count":18},{"year":2014,"count":12},{"year":2015,"count":13},{"year":2016,"count":19},{"year":2017,"count":11},{"year":2018,"count":16},{"year":2019,"count":8},{"year":2020,"count":14},{"year":2021,"count":8},{"year":2022,"count":5},{"year":2023,"count":9},{"year":2024,"count":2},{"year":2025,"count":3}],"oa_status":"green","license":"https://journals.asm.org/non-commercial-tdm-license","oa_locations":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/143637","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/143637","host_type":"repository"},{"url":"https://journals.asm.org/doi/pdf/10.1128/AEM.69.2.1251-1262.2003","host_type":"publisher"},{"url":"https://doi.org/10.1128/aem.69.2.1251-1262.2003","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/12571054","host_type":"repository"},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.318.8416","host_type":""}],"fields_of_study":["Gut microbiota and health","Probiotics and Fermented Foods","Bacterial Genetics and Biotechnology","Bacteria","Cloning, Molecular","Computer Simulation","DNA Primers","DNA, Ribosomal","Deoxyribonuclease HpaII","Deoxyribonucleases, Type II Site-Specific","Feces","Genes, rRNA","Humans","Molecular Sequence Data","Polymerase Chain Reaction","Polymorphism, Restriction Fragment Length","RNA, Ribosomal, 16S","Sequence Analysis, DNA"],"mesh_terms":["Bacteria","Cloning, Molecular","Computer Simulation","DNA, Ribosomal","Feces","Humans","Molecular Sequence Data","Polymorphism, Restriction Fragment Length","RNA, Ribosomal, 16S","Deoxyribonucleases, Type II Site-Specific","Polymerase Chain Reaction","Sequence Analysis, DNA","DNA Primers","Deoxyribonuclease HpaII","Genes, rRNA"],"keywords":["Terminal restriction fragment length polymorphism","Restriction fragment length polymorphism","Biology","Restriction enzyme","Primer (cosmetics)","Genetics","Molecular biology","Ribosomal RNA","Escherichia coli","16S ribosomal RNA","Polymerase chain reaction","Restriction fragment","Gene","Chemistry"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"gen"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-17T18:08:33.572924Z","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":[]}