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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Microbiota triggers STING-type I IFN-dependent monocyte reprogramming of the tumor microenvironment
Khiem C. Lam,Romina E. Araya,April Huang,Quanyi Chen,Martina Di Modica,Richard R. Rodrigues,Amélie Lopès,Sarah B. Johnson,Benjamin A. Schwarz,Eric Bohrnsen,Alexandria P. Cogdill,Catharine M. Bosio,Jennifer A. Wargo,Maxwell P. Lee,Romina S. Goldszmid +14 more
TL;DR: In this paper, a mechanistic link between the microbiota and the tumor microenvironment (TME) was uncovered, which can be harnessed to improve cancer therapies and showed that the predicted intratumoral IFN-I and immune compositional differences between responder and non-responder individuals can be transferred by fecal microbiota transplantation.
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Rhizosphere bacteriome structure and functions
TL;DR: In this article , the authors used 557 pairs of published 16S rDNA amplicon sequences from the bulk soils and rhizosphere in different ecosystems around the world to generalize bacterial characteristics with respect to community diversity, composition, and functions.
Journal ArticleDOI
Gut Microbiome Diversity Is Associated with Sleep Physiology in Humans
Robert Smith,Cole G. Easson,Cole G. Easson,Sarah M. Lyle,Ritishka Kapoor,Chase P. Donnelly,Eileen J. Davidson,Esha Parikh,Jose V. Lopez,Jaime L. Tartar +9 more
TL;DR: Actigraphy is used to quantify sleep measures coupled with gut microbiome sampling to determine how the gut microbiome correlates with various measures of sleep physiology, and positive correlations between total microbiome diversity and interleukin-6, a cytokine previously noted for its effects on sleep are found.
Journal ArticleDOI
Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease
Feargal J. Ryan,Anna M. Ahern,Rachel S. Fitzgerald,Emilio J Laserna-Mendieta,E. M. Power,Adam G. Clooney,Adam G. Clooney,K. W. O’Donoghue,Paul J. McMurdie,Shoko Iwai,Alexander Crits-Christoph,Donal Sheehan,Carthage Moran,Burkhardt Flemer,Aldert Zomer,Aine Fanning,John O'Callaghan,Janette Walton,Andriy Temko,W. Stack,L. Jackson,Susan A. Joyce,Silvia Melgar,Todd Z. DeSantis,Jordana T. Bell,Fergus Shanahan,Marcus J. Claesson +26 more
TL;DR: Investigation of mucosa-associated microbiota using endoscopically-targeted biopsies from inflamed and non-inflamed colon in patients with Crohn’s disease and ulcerative colitis finds associations with inflammation and host epigenomic alterations.
Journal ArticleDOI
Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces
Aleksandra Checinska Sielaff,Aleksandra Checinska Sielaff,Camilla Urbaniak,Ganesh Babu Malli Mohan,Victor G. Stepanov,Quyen Tran,Jason M. Wood,Jeremiah J. Minich,Daniel McDonald,Teresa Mayer,Rob Knight,Fathi Karouia,Fathi Karouia,George E. Fox,Kasthuri Venkateswaran +14 more
TL;DR: This study provides the first comprehensive catalog of both total and intact/viable bacteria and fungi found on surfaces in closed space systems and can be used to help develop safety measures that meet NASA requirements for deep space human habitation.
References
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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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