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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Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions
Stien Beirinckx,Tom Viaene,Annelies Haegeman,Jane Debode,Fien Amery,Steven Vandenabeele,Hilde Nelissen,Dirk Inzé,Raul Y. Tito,Jeroen Raes,Caroline De Tender,Sofie Goormachtig +11 more
TL;DR: It is indicated that chilling temperatures affect the bacterial community composition within the maize root endosphere, and two promising strains that promoted maize growth under chilling conditions were identified that belonged to the root endophytic bacterial families, from which the relative abundance remained unchanged by variations in the growth temperature.
Journal ArticleDOI
Culture-independent analysis of an endophytic core microbiome in two species of wheat: Triticum aestivum L. (cv. 'Hondia') and the first report of microbiota in Triticum spelta L. (cv. 'Rokosz').
Agnieszka Kuźniar,Kinga Włodarczyk,Jarosław Grządziel,Weronika Goraj,Anna Gałązka,Agnieszka Wolińska +5 more
TL;DR: It was demonstrated that wheat, which is an important crop plant, was associated with beneficial endophytic bacteria inside the endosperms, germs, roots, leaves, and coleoptiles, and for the first time, biodiversity was recognized in the cole optiles of the investigated wheat species.
Journal ArticleDOI
Co-digestion of blackwater with kitchen organic waste: effects of mixing ratios and insights into microbial community.
TL;DR: In this article, the effects of mixing ratios on anaerobic co-digestion of blackwater and kitchen organic waste were investigated and the results suggest that blackwater energy recovery can be improved by codigesting blackwater with kitchen waste.
Journal ArticleDOI
eDNA metabarcoding as a biomonitoring tool for marine protected areas.
TL;DR: In this article, the authors compared fish communities inside and outside the Scorpion State Marine Reserve off Santa Cruz Island, CA using eDNA metabarcoding and underwater visual census surveys and found that eDNA captured 76% (19/25) of fish species and 95% of fish genera observed during pairwise underwater visual survey.
Journal ArticleDOI
Incorporating microbial community data with machine learning techniques to predict feed substrates in microbial fuel cells.
Wen-Fang Cai,Wen-Fang Cai,Keaton Larson Lesnik,Matthew J. Wade,Matthew J. Wade,Elizabeth S. Heidrich,Yun-Hai Wang,Hong Liu +7 more
TL;DR: The results suggest that incorporating microbial community data with machine learning algorithms can be used for the prediction of feed substrate and for the potential improvement of MFC-based biosensor signal specificity, providing a new use of machine learning techniques that has substantial practical applications in biotechnological fields.
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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