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
Citations
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Oral Antibiotic Treatment of Mice Exacerbates the Disease Severity of Multiple Flavivirus Infections.
Larissa B. Thackray,Scott A. Handley,Matthew J. Gorman,Subhajit Poddar,Prachi Bagadia,Carlos G. Briseño,Derek J. Theisen,Qing Tan,Barry L. Hykes,Hueylie Lin,Tiffany M. Lucas,Chandni Desai,Jeffrey I. Gordon,Kenneth M. Murphy,Herbert W. Virgin,Michael S. Diamond +15 more
TL;DR: The results identify oral Abx therapy as a potential environmental determinant of systemic viral disease, and they raise the possibility that perturbation of the gut microbiota may have deleterious consequences for subsequent flavivirus infections.
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Fecal Microbiota Transplantation Reduces Symptoms in Some Patients With Irritable Bowel Syndrome With Predominant Abdominal Bloating: Short- and Long-term Results From a Placebo-Controlled Randomized Trial.
Tom Holvoet,Tom Holvoet,Marie Joossens,Jorge F. Vázquez-Castellanos,Evelien Christiaens,Lander Heyerick,Jerina Boelens,Bruno Verhasselt,Hans Van Vlierberghe,Martine De Vos,Jeroen Raes,Danny De Looze,Danny De Looze +12 more
TL;DR: In a randomized trial of patients with treatment-refractory IBS with predominant bloating, FMT relieved symptoms compared with placebo (autologous transplant), although effects decreased over 1 year.
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Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice
Se-Hoon Lee,Se-Hoon Lee,Sung Yup Cho,Youngmin Yoon,Changho Park,Jinyoung Sohn,Jin Ju Jeong,Bu-Nam Jeon,Mongjoo Jang,Choa An,Suro Lee,Yun Yeon Kim,Gihyeon Kim,Sujeong Kim,Yunjae Kim,Gwang Bin Lee,Eun Ju Lee,Sang Gyun Kim,Hong Sook Kim,Yeongmin Kim,Hyun Young Kim,Hyun Yang,Sarang Kim,Seong-Gon Kim,Hayung Chung,Myeong Hee Moon,Myung Hee Nam,Jee Young Kwon,Sungho Won,Joon Suk Park,George M. Weinstock,Charles Lee,Charles Lee,Kyoung Wan Yoon,Hansoo Park +34 more
TL;DR: In this article, the authors integrated metagenomics, genomics and transcriptomics of bacteria, and analyses of mouse intestinal transcriptome and serum metabolome data to reveal an additional mechanism by which bacteria determine the efficacy of cancer therapeutics.
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Methods in Lung Microbiome Research
Sharon M. Carney,Jose C. Clemente,Michael J. Cox,Robert P. Dickson,Yvonne J. Huang,Georgios D Kitsios,Kirsten M. Kloepfer,Janice M. Leung,Tricia D. LeVan,Philip L. Molyneaux,Philip L. Molyneaux,Bethany B. Moore,David N O'Dwyer,Leopoldo N. Segal,Stavros Garantziotis +14 more
TL;DR: This review identifies and addresses several key elements of microbiome research: conceptual modeling and hypothesis framing, study design, experimental methodology and pitfalls, data analysis and reporting considerations, and explores possible future directions and research opportunities.
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Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates
Hannah Fehlner-Peach,Cara Magnabosco,Varsha Raghavan,Jose U. Scher,Adrian Tett,Laura M. Cox,Claire Gottsegen,Aaron Watters,John D. Wiltshire-Gordon,Nicola Segata,Richard Bonneau,Dan R. Littman +11 more
TL;DR: It is demonstrated that genomically distinct isolates, which can be categorized into different P. copri complex clades, utilize defined sets of polysaccharides, which were predicted in part from genomic and metagenomic data.
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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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