Journal
EPIDEMIOLOGY AND INFECTION
Volume 144, Issue 11, Pages 2447-2455Publisher
CAMBRIDGE UNIV PRESS
DOI: 10.1017/S0950268816000662
Keywords
Analysis of data; Haemophilus; medical microbiology; statistics
Funding
- National Center for Advancing Translational Sciences, National Institutes of Health, Colorado CTSI grant [KL2 TR001080]
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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.
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