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
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Association between the oral microbiome and brain resting state connectivity in smokers.
Dongdong Lin,Dongdong Lin,Kent E. Hutchison,Salvador Portillo,Victor Vegara,Jarrod M. Ellingson,Jingyu Liu,Kenneth Krauter,Amanda Carroll-Portillo,Vince D. Calhoun +9 more
TL;DR: This work is the first attempt to link oral microbiome and brain functional networks, and provides support for future work in characterizing the role of oral microbiome in mediating smoking effects on brain activity.
Journal ArticleDOI
A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes
Naruekamol Pookhao,Michael B. Sohn,Qike Li,Isaac C. Jenkins,Ruofei Du,Hongmei Jiang,Lingling An +6 more
TL;DR: A two-stage statistical procedure for selecting informative features and identifying differentially abundant features between two or more groups of microbial communities and is applied to two real metagenomic datasets related to human health.
Journal ArticleDOI
Linking shifts in bacterial community with changes in dissolved organic matter pool in a tropical lake
Marcelo P. Ávila,Luciana Pena Mello Brandão,Ludmila Silva Brighenti,Denise Tonetta,Mariana P. Reis,Peter A. Staehr,Eero Asmala,André Megali Amado,Francisco A. R. Barbosa,José Fernandes Bezerra-Neto,Andréa M. A. Nascimento +10 more
TL;DR: Results from a 12-day mesocosm study performed in the epilimnion of a tropical lake suggest that taxonomically defined bacterial assemblages play definite roles when influencing DOM fate, either by changing specific fractions of the DOM pool or by regulating light availability and DOC levels.
Journal ArticleDOI
The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection
Harris Onywera,Anna-Lise Williamson,Luca Cozzuto,Sarah Bonnin,Zizipho Z. A. Mbulawa,David Coetzee,Julia Ponomarenko,Tracy L. Meiring +7 more
TL;DR: HIV and HR-HPV infections were strongly associated with greater relative abundances of Staphylococcus and BV-associated bacterial taxa (notably Prevotella, Peptinophilus and Dialister ), respectively, and it is possible that these taxa could increase susceptibility to HIV and HR -HPV acquisition, in addition to creating conditions in which infections persist.
Journal ArticleDOI
High intake of dairy during energy restriction does not affect energy balance or the intestinal microflora compared with low dairy intake in overweight individuals in a randomized controlled trial
Line Q. Bendtsen,Trine Blædel,Jacob Holm,Janne K. Lorenzen,Alicja Budek Mark,Pia Kiilerich,Karsten Kristiansen,Arne Astrup,Lesli H. Larsen +8 more
TL;DR: This study indicates that Papillibacter is involved in body compositional changes and Consumption of a high-dairy diet did not increase fecal fat or accelerate weight and fat-mass loss beyond energy restriction over 24 weeks in overweight and obese adults with a habitual calcium intake of ∼1000 mg/day.
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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