المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/journal_contribution/Timeline_for_mouse_experiment_to_determine_colonize_of_individual_i_E_i_i_coli_i_isolates_/16898937

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.s001

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/journal_contribution/S2_Fig_-/16898940

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.s002

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/journal_contribution/_i_E_i_i_coli_i_isolates_colonize_the_lower_gastrointestinal_tract_of_i_Il10_i_sup_i_-_-_i_sup_mice_with_FMT_competition_/16898943

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.s003

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/journal_contribution/Consistent_i_E_i_i_coli_i_colonizer_CU42ET-1_D5_and_inconsistent_i_E_i_i_coli_i_colonizer_HM670_C2_colonize_the_lower_gastrointestinal_tract_of_i_Il10_i_sup_i_-_-_i_sup_mice_with_FMT_competition_/16898946

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.s004

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/figure/Read_length_distribution_across_samples_using_high-molecular_weight_extraction_and_bead-free_library_prep_/16898949

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.g001

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/figure/Assembled_genomes_illustrating_relative_GC_content_red_and_gene_content_blue_for_each_strain_and_approximate_synteny_between_assemblies_represented_in_gray_where_darker_bars_represent_higher_identity_darkest_gray_is_100_identity_white_is_70/16898952

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.g002

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/figure/Difference_between_16S_a_23S_b_ITS_c_and_entire_rRNA_d_sequences_across_strains_and_copies_/16898955

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.g003

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/figure/Strain_distribution_of_seven_i_E_coli_i_isolates_in_murine_stool_sample_/16898961

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.g005

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/figure/Inflammatory_cytokine_production_by_macrophages_stimulated_with_clinical_i_E_coli_i_strains_/16898958

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.g004

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/figure/Read_length_distribution_for_stool_and_mock_mixture_full-length_rRNA_amplicon_sequencing_/16898964

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.g006

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/figure/Distribution_of_nucleotide_matches_of_the_best_alignment_from_amplified_rRNA_sequencing_/16898967

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.g007

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/dataset/Strains_used_in_study_/16898973

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.t001

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/figure/Strain_representation_based_on_full-length_rRNA_sequencing_from_mock_host_microbial_mixture_/16898970

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.g008

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/dataset/Genome_size_and_number_of_genes_identified_in_assembled_i_E_coli_i_genomes_/16898979

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.t002

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/dataset/Nanopore_sequencing_statistics_for_each_strain_after_demultiplexing_/16898985

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.t004

المؤلفون: Jeremy Wang (383590), Rachel M. Bleich (822389), Sandra Zarmer (3804274), Shiying Zhang (2813257), Belgin Dogan (148469), Kenneth W. Simpson (7388261), Janelle C. Arthur (10911444)

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Immunology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, universal molecular signature, inflammatory bowel diseases, global genomic structure, div >< p, induce inflammatory cytokines, human intestinal tissue, read nanopore sequencing, efficiently tracking strain, excludes host dna, escherichia coli <, difference aiec strains, ibd susceptible mice, model aiec strain, seven strains isolated, read sequencing approach, read sequencing, susceptible host

Relation: https://figshare.com/articles/dataset/Classification_accuracy_using_commonly_amplified_16S_hypervariable_regions_V1-V2_and_V3-V4_the_entire_16S_and_rRNA_operons_and_shotgun_sequencing_of_the_entire_genome_/16898988

الاتاحة: https://doi.org/10.1371/journal.pone.0259141.t005