title: Middle ear microbiome differences in indigenous Filipinos with chronic otitis media due to a duplication in the A2ML1 gene.
abstract: BACKGROUND
  Previously rare A2ML1 variants were identified to confer otitis media susceptibility in an indigenous Filipino community and in otitis-prone US children. The goal of this study is to describe differences in the middle ear microbiome between carriers and non-carriers of an A2ML1 duplication variant that increases risk for chronic otitis media among indigenous Filipinos with poor health care access.
  
  
  METHODS
  Ear swabs were obtained from 16 indigenous Filipino individuals with chronic otitis media, of whom 11 carry the A2ML1 duplication variant. Ear swabs were submitted for 16S rRNA gene sequencing.
  
  
  RESULTS
  Genotype-based differences in microbial richness, structure, and composition were identified, but were not statistically significant. Taxonomic analysis revealed that the relative abundance of the phyla Fusobacteria and Bacteroidetes, and genus Fusobacterium were nominally increased in carriers compared to non-carriers, but were non-significant after correction for multiple testing. We also detected rare bacteria including Oligella that was reported only once in the middle ear.
  
  
  CONCLUSIONS
  These findings suggest that A2ML1-related otitis media susceptibility may be mediated by changes in the middle ear microbiome. Knowledge of middle ear microbial profiles according to genetic background can be potentially useful for therapeutic and prophylactic interventions for otitis media and can guide public health interventions towards decreasing otitis media prevalence within the indigenous Filipino community.
authors: Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. regie.santos-cortez@ucdenver.edu.|Current affiliation: Department of Otolaryngology, University of Colorado School of Medicine, Aurora, CO, 80045, USA. regie.santos-cortez@ucdenver.edu.
authors: Regie Lyn P
authors: RL
authors: Santos-Cortez
authors: Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research (CMMR), Baylor College of Medicine, Houston, TX, 77030, USA.
authors: Diane S
authors: DS
authors: Hutchinson
authors: Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research (CMMR), Baylor College of Medicine, Houston, TX, 77030, USA.
authors: Nadim J
authors: NJ
authors: Ajami
authors: Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.|Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines.
authors: Ma Rina T
authors: MR
authors: Reyes-Quintos
authors: Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.
authors: Ma Leah C
authors: ML
authors: Tantoco
authors: Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines.
authors: Patrick John
authors: PJ
authors: Labra
authors: Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.
authors: Sheryl Mae
authors: SM
authors: Lagrana
authors: Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.
authors: Melquiadesa
authors: M
authors: Pedro
authors: Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.|Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines.
authors: Erasmo Gonzalo D V
authors: EG
authors: Llanes
authors: Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.|Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines.
authors: Teresa Luisa
authors: TL
authors: Gloria-Cruz
authors: Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.|Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines.
authors: Abner L
authors: AL
authors: Chan
authors: Institute of Human Genetics, UPM-NIH, Manila, 1000, Philippines.|Philippine Genome Center, University of the Philippines, Diliman, Quezon City, 1101, Philippines.
authors: Eva Maria
authors: EM
authors: Cutiongco-de la Paz
authors: Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.|Current address: Illumina, Inc, San Diego, CA, 92122, USA.
authors: John W
authors: JW
authors: Belmont
authors: Division of Pediatric Infectious Disease and Immunology, Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, 77555, USA.
authors: Tasnee
authors: T
authors: Chonmaitree
authors: Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.|Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines.
authors: Generoso T
authors: GT
authors: Abes
authors: Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research (CMMR), Baylor College of Medicine, Houston, TX, 77030, USA.
authors: Joseph F
authors: JF
authors: Petrosino
authors: Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
authors: Suzanne M
authors: SM
authors: Leal
authors: Philippine National Ear Institute, University of the Philippines Manila - National Institutes of Health (UPM-NIH), Manila, 1000, Philippines.|Department of Otorhinolaryngology, University of the Philippines College of Medicine - Philippine General Hospital, Manila, 1000, Philippines.
authors: Charlotte M
authors: CM
authors: Chiong
mesh_terms: D000293:Adolescent; D002648:Child; D002675:Child, Preschool; D004269:DNA, Bacterial / Q000235:genetics*; D004432:Ear, Middle / Q000382:microbiology*; D005260:Female; D020131:Genes, Duplicate / Q000235:genetics*; D006801:Humans; D008297:Male; D064307:Microbiota; D010033:Otitis Media / Q000235:genetics* / Q000382:microbiology; D010679:Philippines; D044382:Population Groups; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA; D055815:Young Adult; D000511:alpha-Macroglobulins / Q000235:genetics* / Q000378:metabolism
chemical_list: C510358:A2ML1 protein, human; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D000511:alpha-Macroglobulins
keywords: A2ML1; Indigenous population; Microbiome; Middle ear; Oligella; Otitis media; Philippines