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oai:figshare.com:article/34000973 2026-09-25T18:20:36Z category_7 category_8 category_13 category_21 category_24 category_272 category_39 category_734 category_64 category_132 category_134 portal_5 item_type_3 month_year_09_2026

Associations between accessory gene features and isolation from middle-ear fluid (MEF) vs. nasopharynx/nasal passages (NP) by naïve Fisher’s exact test with a Benjamini-Hochberg adjusted p-value < 0.05 (FDR), as well as a “best” p-value for phylogenetic gene-trait co-occurrence of < 0.05 (Pairwise Comparisons – Best) from Scoary. All MEF isolates were collected from subjects during acute OM episodes, but NP isolates come from both health and OM disease. The numbers in parentheses indicate the subset of NP isolates collected during OM episodes instead of healthy visits. Further details are in S3 Table, including for two other clinical “traits”: whether isolated from an OM versus healthy visits or (b) whether from an OM-prone versus healthy subject. Only genes/operons that passed both the FDR-adjusted Fisher’s test and “best” comparisons of phylogenetic contrast at p < 0.05 were included. Genes strictly co-inherited across strains were treated as single Jocelyn A. Hammond (25111760) Rachel L. Ehrlich (8293938) Ariel Gonzalez (22389474) Begoña Euba (563215) Kevin M. Raible (25111763) Jill M. Lawrence (25111766) Ari B. Gordon (25111769) Evangeline Williams (11024931) Mary C. Marino (25111772) Jason Limbo (25111775) Steven Lang (7532681) Bhaswati Sen (4599163) Sergey V. Balashov (25111778) Azad Ahmed (121246) Junkal Garmendia (217415) Joris Beld (136102) Garth D. Ehrlich (60143) Michael E. Pichichero (7880588) Ravinder Kaur (1871197) Joshua Chang Mell (7490840) Medicine Microbiology Genetics Biotechnology Evolutionary Biology Environmental Sciences not elsewhere classified Ecology Biological Sciences not elsewhere classified Cancer Infectious Diseases Virology sought new insights predicted functions consistent informed association tests candidate “ anti infected middle ears conferred alkaline sensitivity commonly afflicts children middle ear washes om ” operon div >< p clustered homologous genes bacterial disease burden haemophilus influenzae </ om disease pathogenesis middle ear prone children alkaline tolerance influenzae </ vitro </ spef </ prevalent om om pathogens om disease om arises om ), 12 om significant difference selective advantage polyamine metabolism ph homeostasis persistent colonization otitis media nitrogen metabolism laboratory strain genome sequenced gene absences fold increase distinct lineages clonal lineages associated bacterium across assemblies 9 healthy Associations between accessory gene features and isolation from middle-ear fluid (MEF) vs. nasopharynx/nasal passages (NP) by naïve Fisher’s exact test with a Benjamini-Hochberg adjusted p-value < 0.05 (FDR), as well as a “best” p-value for phylogenetic gene-trait co-occurrence of < 0.05 (Pairwise Comparisons – Best) from Scoary. All MEF isolates were collected from subjects during acute OM episodes, but NP isolates come from both health and OM disease. The numbers in parentheses indicate the subset of NP isolates collected during OM episodes instead of healthy visits. Further details are in S3 Table, including for two other clinical “traits”: whether isolated from an OM versus healthy visits or (b) whether from an OM-prone versus healthy subject. Only genes/operons that passed both the FDR-adjusted Fisher’s test and “best” comparisons of phylogenetic contrast at p < 0.05 were included. Genes strictly co-inherited across strains were treated as single tests and 2026-09-25T17:56:18Z Dataset Dataset 10.1371/journal.ppat.1014649.t001 https://figshare.com/articles/dataset/_p_Associations_between_accessory_gene_features_and_isolation_from_middle-ear_fluid_MEF_i_vs_i_nasopharynx_nasal_passages_NP_by_na_ve_Fisher_s_exact_test_with_a_Benjamini-Hochberg_adjusted_p-value_0_05_FDR_as_well_as_a_best_p-value_for_phyl/34000973 CC BY 4.0