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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Caloric restriction disrupts the microbiota and colonization resistance.
Reiner Jumpertz von Schwartzenberg,Jordan E. Bisanz,Svetlana Lyalina,Peter Spanogiannopoulos,Qi Yan Ang,Jingwei Cai,Sophia Dickmann,Marie Friedrich,Su Yang Liu,Stephanie L. Collins,Danielle Ingebrigtsen,Steve Miller,Jessie A. Turnbaugh,Andrew D. Patterson,Katherine S. Pollard,Knut Mai,Joachim Spranger,Peter J. Turnbaugh +17 more
TL;DR: In this article, a randomized human intervention study using a very low-calorie diet (NCT01105143) showed that severe calorie restriction led to a decrease in bacterial abundance and restructuring of the gut microbiome.
Journal ArticleDOI
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
Daniel Straub,Nia Blackwell,Adrian Langarica-Fuentes,Alexander Peltzer,Sven Nahnsen,Sara Kleindienst +5 more
TL;DR: A high-performance computing conformant workflow was constructed to allow FAIR (Findable, Accessible, Interoperable, and Re-usable) 16S rRNA (gene) amplicon sequence analysis starting from raw sequence files, using the most optimal methods identified in this study.
Journal ArticleDOI
More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers?
Ylva Lekberg,Martti Vasar,Lorinda Bullington,Siim-Kaarel Sepp,Pedro M. Antunes,Rebecca A. Bunn,Beau Larkin,Maarja Öpik +7 more
TL;DR: With the exponential increase in sequencing output with high throughput sequencing, AMF sequences are now detected and discussed in studies using general fungal primers that target all soil fungi, and the internal transcribed spacer (ITS) region is the universal barcode for fungi.
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Microplastic pollution alters forest soil microbiome.
Ee Ling Ng,Silk Yu Lin,Ashley M. Dungan,John M. Colwell,Sarah Ede,Esperanza Huerta Lwanga,Ke Meng,Violette Geissen,Linda L. Blackall,Deli Chen +9 more
TL;DR: It is concluded that microplastics aging in the environment may have evolutionary consequences for forest soil microbiome and there is immediate implication for climate change if the observed increase in soil respiration is reproducible in multiple ecosystems.
Journal ArticleDOI
Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life
Naoki Tsukuda,Kana Yahagi,Taeko Hara,Yohei Watanabe,Hoshitaka Matsumoto,Hiroshi Mori,Koichi Higashi,Hirokazu Tsuji,Satoshi Matsumoto,Ken Kurokawa,Takahiro Matsuki +10 more
TL;DR: In this paper, the authors investigated dense longitudinally collected faecal samples from 12 subjects during the first 2 years to identify early life short-chain fatty acids (SCFAs) patterns and their relationships with the microbiota.
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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