DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan,Paul J. McMurdie,Michael J. Rosen,Andrew W. Han,Amy Jo A. Johnson,Susan Holmes +5 more
TLDR
The open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors is presented, revealing a diversity of previously undetected Lactobacillus crispatus variants.Abstract:
We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.read more
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Gut dysbiosis in Huntington's disease: associations among gut microbiota, cognitive performance and clinical outcomes
Cory I. Wasser,Emily-Clare Mercieca,Geraldine Kong,Anthony J. Hannan,Anthony J. Hannan,Sonja J. McKeown,Yifat Glikmann-Johnston,Julie C. Stout +7 more
TL;DR: The findings suggest an altered gut microbiome in Huntington’s disease gene expansion carriers, which highlight the importance of gut biomarkers and raise interesting questions regarding the role of the gut in Huntington's disease, and whether it may be a potential target for future therapeutic intervention.
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Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes.
Xuefeng Peng,St. Elmo Wilken,Thomas S. Lankiewicz,Thomas S. Lankiewicz,Sean P. Gilmore,Jennifer L. Brown,John K. Henske,Candice L. Swift,Asaf Salamov,Kerrie Barry,Igor V. Grigoriev,Michael K. Theodorou,David L. Valentine,Michelle A. O’Malley,Michelle A. O’Malley +14 more
TL;DR: The authors carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities.
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TreeCluster: Clustering biological sequences using phylogenetic trees.
TL;DR: It is argued that tree-based clustering is under-utilized, and a family of optimization problems that return the minimum number of clusters such that all clusters adhere to constraints on their heterogeneity are defined.
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Characterising and predicting cyanobacterial blooms in an 8-year amplicon sequencing time course.
Nicolas Tromas,Nathalie Fortin,Larbi Bedrani,Yves Terrat,Pedro Cardoso,David F. Bird,Charles W. Greer,B. Jesse Shapiro +7 more
TL;DR: It is found that bloom events significantly alter the bacterial community without reducing overall diversity, suggesting that a distinct microbial community—including non-cyanobacteria—prospers during the bloom.
Journal ArticleDOI
Gut Microbiome Directs Hepatocytes to Recruit MDSCs and Promote Cholangiocarcinoma.
Qianfei Zhang,Chi Ma,Yi Duan,Yi Duan,Bernd Heinrich,Umberto Rosato,Laurence P. Diggs,Lichun Ma,Soumen Roy,Qiong Fu,Zachary J. Brown,Simon Wabitsch,Vishal Thovarai,Jianyang Fu,Dechun Feng,Benjamin Ruf,Linda L. Cui,Varun Subramanyam,Karen M. Frank,Sophie Wang,David E. Kleiner,Thomas Ritz,Thomas Ritz,Christian Rupp,Bin Gao,Thomas Longerich,Alexander Kroemer,Xin Wei Wang,Mathuros Ruchirawat,Mathuros Ruchirawat,Firouzeh Korangy,Bernd Schnabl,Bernd Schnabl,Giorgio Trinchieri,Tim F. Greten +34 more
TL;DR: It is demonstrated that the gut microbiome controls hepatocytes to form an immunosuppressive environment by increasing PMN-MDSC to promote liver cancer.
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TL;DR: The Human Microbiome Project Consortium reported the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome as discussed by the authors.
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