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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Enteral High Fat-Polyunsaturated Fatty Acid Blend Alters the Pathogen Composition of the Intestinal Microbiome in Premature Infants with an Enterostomy
TL;DR: Enteral HF‐PUFA supplementation was associated with decreased abundance of pathogenic bacteria, greater bacterial diversity, and shifts in the potential metabolic functions of intestinal microbiota.
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Biliary Microbiota, Gallstone Disease and Infection with Opisthorchis felineus.
Irina V. Saltykova,Irina V. Saltykova,Irina V. Saltykova,Vjacheslav A. Petrov,Maria D. Logacheva,Polina G. Ivanova,Nikolay V. Merzlikin,A. E. Sazonov,Ludmila M. Ogorodova,Paul J. Brindley +9 more
TL;DR: Overall, infection with the liver fluke O. felineus modified the biliary microbiome, increasing abundance of bacterial and archaeal phylotypes.
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Composition of the teat canal and intramammary microbiota of dairy cows subjected to antimicrobial dry cow therapy and internal teat sealant
TL;DR: Qualitative analysis revealed a high degree of commonality between pre-DCT and postpartum microbiota of both niches of the udder, suggesting that the DCT approach of the present study had limited success in eliminating a considerable proportion of bacteria during the dry period.
Posted ContentDOI
Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications
Koen Van den Berge,Fanny Perraudeau,Charlotte Soneson,Michael I. Love,Davide Risso,Jean-Philippe Vert,Mark D. Robinson,Sandrine Dudoit,Lieven Clement +8 more
TL;DR: A weighting strategy is introduced, based on a zero-inflated negative binomial (ZINB) model, that identifies excess zero counts and generates gene and cell-specific weights to unlock bulk RNA-seq DE pipelines for zero- inflated data, boosting performance for scRNA-seq.
Journal ArticleDOI
Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants.
Joseph N. Paulson,Brent L. Williams,Christine Hehnly,Nischay Mishra,Shamim A. Sinnar,Lijun Zhang,Paddy Ssentongo,Edith Mbabazi-Kabachelor,Dona Saumya S. Wijetunge,Benjamin von Bredow,Ronnie Mulondo,Julius Kiwanuka,Francis Bajunirwe,Joel Bazira,Lisa M. Bebell,Kathy Burgoine,Mara Couto-Rodriguez,Jessica E. Ericson,Timothy B. Erickson,Matthew J. Ferrari,Melissa Gladstone,Cheng Guo,Murali Haran,Mady Hornig,Albert M. Isaacs,Brian Nsubuga Kaaya,Sheila M. Kangere,Abhaya V. Kulkarni,Elias Kumbakumba,Xiaoxiao Li,David D. Limbrick,Joshua Magombe,Sarah U. Morton,John Mugamba,James Ng,Peter Olupot-Olupot,Justin Onen,Mallory R. Peterson,Farrah Roy,Kathryn Sheldon,R. Reid Townsend,Andrew Weeks,Andrew Whalen,John Quackenbush,Peter Ssenyonga,Michael Y. Galperin,Mathieu Almeida,Hannah M Atkins,Benjamin C. Warf,W. Ian Lipkin,James R. Broach,Steven J. Schiff +51 more
TL;DR: Findings show that an unbiased pan-microbial approach enabled characterization of Paenibacillus in CSF samples from PIH cases, and point toward a pathway of more optimal treatment and prevention for PIH and other proximate neonatal infections.
References
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QIIME allows analysis of high-throughput community sequencing data.
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Metagenomic biomarker discovery and explanation
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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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