Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets
نویسندگان
چکیده
منابع مشابه
Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets
Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic...
متن کاملPhylogenetic factorization of compositional data
1 Marker gene sequencing of microbial communities has generated big datasets 2 of microbial relative abundances varying across environmental conditions, sam3 ple sites and treatments. These data often come with putative phylogenies, 4 providing unique opportunities to investigate how shared evolutionary history 5 a ects microbial abundance patterns. Here, we present a method to identify the 6 p...
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Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers, metagenomes or metatranscriptomes are commonplace and being used to study human disease states, ecological differences between sites, and the built environment. There is increasing awareness that microbiome datasets generated by HTS are compositional because they have an arbitrary total imposed by the instrument....
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Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts. The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization. However, such correlations are of long-standing interest in fields including ecology. We propose a novel Bayesian framework (BAnOCC: Bayes...
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Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to ...
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ژورنال
عنوان ژورنال: PeerJ
سال: 2017
ISSN: 2167-8359
DOI: 10.7717/peerj.2969