Waste not, want not: why rarefying microbiome data is inadmissible.
Paul J. McMurdie,Susan Holmes +1 more
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TLDR
It is advocated that investigators avoid rarefying altogether and supported statistical theory is provided that simultaneously accounts for library size differences and biological variability using an appropriate mixture model.Abstract:
Current practice in the normalization of microbiome count data is inefficient in the statistical sense. For apparently historical reasons, the common approach is either to use simple proportions (which does not address heteroscedasticity) or to use rarefying of counts, even though both of these approaches are inappropriate for detection of differentially abundant species. Well-established statistical theory is available that simultaneously accounts for library size differences and biological variability using an appropriate mixture model. Moreover, specific implementations for DNA sequencing read count data (based on a Negative Binomial model for instance) are already available in RNA-Seq focused R packages such as edgeR and DESeq. Here we summarize the supporting statistical theory and use simulations and empirical data to demonstrate substantial improvements provided by a relevant mixture model framework over simple proportions or rarefying. We show how both proportions and rarefied counts result in a high rate of false positives in tests for species that are differentially abundant across sample classes. Regarding microbiome sample-wise clustering, we also show that the rarefying procedure often discards samples that can be accurately clustered by alternative methods. We further compare different Negative Binomial methods with a recently-described zero-inflated Gaussian mixture, implemented in a package called metagenomeSeq. We find that metagenomeSeq performs well when there is an adequate number of biological replicates, but it nevertheless tends toward a higher false positive rate. Based on these results and well-established statistical theory, we advocate that investigators avoid rarefying altogether. We have provided microbiome-specific extensions to these tools in the R package, phyloseq.read more
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Arbuscular mycorrhizal fungal community differentiation along a post-coal mining reclamation chronosequence in South Africa: A potential indicator of ecosystem recovery
Obinna T. Ezeokoli,Obinna T. Ezeokoli,Sannie K. Mashigo,Sannie K. Mashigo,Mark Maboeta,Cornelius Carlos Bezuidenhout,Damase P. Khasa,Rasheed Adeleke +7 more
TL;DR: The study suggests that AMF community differentiation reflect ecosystem development over chronological space-time and may be included as part of a minimum dataset for monitoring ecosystem restoration following post-mining reclamation.
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Differential Analysis of the Nasal Microbiome of Pig Carriers or Non-Carriers of Staphylococcus aureus.
Carmen Espinosa-Gongora,Niels Larsen,Kristian Schønning,Merete Fredholm,Luca Guardabassi,Luca Guardabassi +5 more
TL;DR: The results show that the nasal microbiome of pigs that are not colonized with S. aureus harbours several species/taxa that are significantly less abundant in pig carriers, suggesting that the nose microbiota may play a role in the individual predisposition to S.aureus nasal carriage in pigs.
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Shrinkage improves estimation of microbial associations under different normalization methods
TL;DR: It is shown that shrinkage estimation, a standard technique in high-dimensional statistics, can universally improve the quality of association estimates for microbiome data and that variance-stabilizing and log-ratio approaches provide for the most consistent estimation of taxonomic and structural coherence.
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Metabarcoding of bacteria associated with the acute oak decline syndrome in England.
Melanie Sapp,Erin Lewis,Stephen Moss,Ben Barrett,Susan Kirk,John G. Elphinstone,Sandra Denman +6 more
TL;DR: Key players in healthy and symptomatic tissue were identified and included members of the Gammaproteobacteria related to Pseudomonas sp.
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Steering root microbiomes of a commercial horticultural crop with plant-soil feedbacks
Hai-Kun Ma,Ana Pineda,S. Emilia Hannula,Anna M. Kielak,Syahida Nindya Setyarini,T. Martijn Bezemer +5 more
TL;DR: Results show that inoculating glasshouse soils with desired soil microbiomes can steer the root microbiome in this crop, but this study also highlights that steering live glasshouse soil with a disease-related microbiome into a healthy state remains challenging.
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J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
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