title: Zero-inflated negative binomial mixed model: an application to two microbial organisms important in oesophagitis.
abstract: Altered microbial communities are thought to play an important role in eosinophilic oesophagitis, an allergic inflammatory condition of the oesophagus. Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. However, these data consist of non-negative, highly skewed sequence counts with a large proportion of zeros. In addition, hierarchical study designs are often performed with repeated measurements or multiple samples collected from the same subject, thus requiring approaches to account for within-subject variation, yet only a small number of microbiota studies have applied hierarchical regression models. In this paper, we describe and illustrate the use of a hierarchical regression-based approach to evaluate multiple factors for a small number of organisms individually. More specifically, the zero-inflated negative binomial mixed model with random effects in both the count and zero-inflated parts is applied to evaluate associations with disease state while adjusting for potential confounders for two organisms of interest from a study of human microbiota sequence data in oesophagitis.
authors.affiliation: Department of Biostatistics and Informatics,Colorado School of Public Health,University of Colorado Denver,Aurora,CO,USA.
authors.forename: R
authors.initials: R
authors.lastname: Fang
authors.affiliation: Department of Biostatistics and Informatics,Colorado School of Public Health,University of Colorado Denver,Aurora,CO,USA.
authors.forename: B D
authors.initials: BD
authors.lastname: Wagner
authors.affiliation: Department of Pediatrics,Division of Pulmonology,University of Colorado Denver,School of Medicine,Aurora,CO,USA.
authors.forename: J K
authors.initials: JK
authors.lastname: Harris
authors.affiliation: Department of Pediatrics, Section of Gastroenterology, Hepatology and Nutrition,Digestive Health Institute,Gastrointestinal Eosinophilic Diseases Program,Mucosal Inflammation Program,Children's Hospital Colorado, University of Colorado Denver,School of Medicine,Aurora,CO,USA.
authors.forename: S A
authors.initials: SA
authors.lastname: Fillon
mesh_terms: D004941:Esophagitis / Q000453:epidemiology* / Q000382:microbiology; D005673:Fusobacterium / Q000502:physiology*; D005674:Fusobacterium Infections / Q000453:epidemiology* / Q000382:microbiology; D006190:Haemophilus / Q000502:physiology*; D006192:Haemophilus Infections / Q000453:epidemiology* / Q000382:microbiology; D006801:Humans; D015233:Models, Statistical
keywords: Analysis of data; Haemophilus; medical microbiology; statistics