Differential abundance analysis for microbial marker-gene surveys
TLDR
It is shown that metagenomeSeq outperforms the tools currently used in this field and relies on a novel normalization technique and a statistical model that accounts for undersampling in large-scale marker-gene studies.Abstract:
We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for undersampling-a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field.read more
Citations
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Alterations of the Treatment-Naive Gut Microbiome in Newly Diagnosed Hepatitis C Virus Infection.
Salma Sultan,Mohammed El-Mowafy,Abdelaziz Elgaml,Mohamed El-Mesery,Ahmed El Shabrawi,Mohamed Elegezy,Riadh Hammami,Walid Mottawea +7 more
TL;DR: The findings reveal the alteration of gut microbiota in treatment naive HCV patients and suggest that gut microbiota may hold diagnostic promise in HCV infection.
Journal ArticleDOI
The bacterial communities of the small intestine and stool in children with short bowel syndrome.
TL;DR: While diminished diversity and alterations in microbiota composition are likely consequences of SBS, future efforts aimed at increasing microbial diversity and interventions targeting specific microbiota characteristics might constitute a testable approach to ameliorate some clinical SBS clinical consequences.
Journal ArticleDOI
Exploring bacterial pathogen community dynamics in freshwater beach sediments: A tale of two lakes
Danielle VanMensel,Subba Rao Chaganti,Subba Rao Chaganti,Ian G. Droppo,Christopher G. Weisener +4 more
TL;DR: This study used high-throughput sequencing to investigate sediment microbial communities at four freshwater public beaches in southern Ontario, Canada and analyzed community structure, function, and gene expression with relation to geographical characteristics, indicating beach sediments at the sediment-water interface could serve as potential sources of bacterial contamination under low-energy environments.
Journal ArticleDOI
Methane Seeps and Independent Methane Plumes in the South China Sea Offshore Taiwan
Susan Mau,Tzu-Hsuan Tu,Marius Becker,Christian dos Santos Ferreira,Jhen-Nien Chen,Li-Hung Lin,Pei-Ling Wang,Saulwood Lin,Gerhard Bohrmann +8 more
Abstract: In the northern South China Sea (SCS) we explored methane dynamics in the water column during SONNE-cruise SO266 in October/November 2018. Two depth zones contained elevated methane concentrations: the upper 400 m ( 10°C and > 20°C, respectively. Both 16S rRNA gene and pmoA amplicon analyses revealed distinct microbial and methanotrophic communities in water with temperature of 27°C, ~10°C, and 3°C. Second, we found elevated methane concentrations in 200-400 m in the FWCR-region whereas increased methane concentrations occurred in the uppermost 100 m above SSFR. The deeper plume above FWCR might be due to an intrusion of the Kuroshio water mass into SCS keeping the methane from being aerobically oxidized in the warm surface water and vented to the atmosphere. Finally, all peak methane concentrations occurred in water depth, with rather low backscatter, i.e. in water depth with less suspended matter. At the seafloor, ocean currents and long-term seepage appeared to control methane dynamics. We derived methane fluxes of 0.08-0.12 mmol m-2 d-1 from a 4.5 km2 area at FWCR and of 3.0-79.9 mmol m-2 d-1 from a 0.01 km2 area at SSFR. Repetitive sampling of the area at SSFR indicated that changing directions of ocean currents possibly affected methane concentrations and thus flux. In contrast to these seepage sites with distinct methane plumes, retrieval of drilling equipment produced no methane plume. Even gas emission triggered by seafloor drilling did not supply measureable methane concentrations after 3 hours, but caused an increase in methanotrophic activity as determined by rate measurements and molecular-biological analyses. Apparently, only long-term seepage can generate methane anomalies in the ocean.
Posted ContentDOI
Ecological assembly processes of the bacterial and fungal microbiota of wild and domesticated wheat species
M. Amine Hassani,M. Amine Hassani,Ezgi Özkurt,Ezgi Özkurt,Sören Franzenburg,Eva H. Stukenbrock,Eva H. Stukenbrock +6 more
TL;DR: This study shows that the bacterial and fungal microbiota of wild and domesticated wheat species follow distinct community assembly patterns, and proposes that domestication has relaxed selective processes in the assembly of the wheat microbiota.
References
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Journal ArticleDOI
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
Journal ArticleDOI
QIIME allows analysis of high-throughput community sequencing data.
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
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
TL;DR: The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
Journal ArticleDOI
Differential expression analysis for sequence count data.
Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
Journal ArticleDOI
Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +7 more
TL;DR: A new method for metagenomic biomarker discovery is described and validates by way of class comparison, tests of biological consistency and effect size estimation to address the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.
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