Journal ArticleDOI
UPARSE: highly accurate OTU sequences from microbial amplicon reads
TLDR
The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% correct bases commonly reported by other methods.Abstract:
Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.read more
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IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies
Ilias Lagkouvardos,Divya Joseph,Martin Kapfhammer,Sabahattin Giritli,Matthias Horn,Dirk Haller,Thomas Clavel +6 more
TL;DR: IMNGS (Integrated Microbial Next Generation Sequencing), an innovative platform that uniformly and systematically screens for and processes all prokaryotic 16S rRNA gene amplicon datasets available in SRA and uses them to build sample-specific sequence databases and OTU-based profiles.
Journal ArticleDOI
Bacterial community profiling of plastic litter in the Belgian part of the North Sea
TL;DR: Light is shed on the possible role of plastic as transport vehicle for bacteria through the aquatic environment and the differential abundance of known primary and secondary colonizers across the various plastics may indicate different stages of bacterial colonization.
Journal ArticleDOI
Biodegradation of Polyethylene and Plastic Mixtures in Mealworms (Larvae of Tenebrio molitor) and Effects on the Gut Microbiome.
Anja Malawi Brandon,Shu-Hong Gao,Renmao Tian,Daliang Ning,Daliang Ning,Shan-Shan Yang,Jizhong Zhou,Jizhong Zhou,Jizhong Zhou,Wei-Min Wu,Craig S. Criddle +10 more
TL;DR: It is found that PE biodegrades at comparable rates to PS and mixtures, and the results suggest that adaptability of the mealworm gut microbiome enables degradation of chemically dissimilar plastics.
Journal ArticleDOI
Response of soil microbial communities and microbial interactions to long-term heavy metal contamination
Xiaoqi Li,Delong Meng,Juan Li,Huaqun Yin,Hongwei Liu,Xueduan Liu,Cheng Cheng,Yunhua Xiao,Zhenghua Liu,Mingli Yan +9 more
TL;DR: The present study indicated that the microbial community composition, as well as network interactions was shift to strengthen adaptability of microorganisms to heavy metal contamination, and archaea were resistant to heavyMetal contamination and may contribute to the adaption to heavy metals.
Journal ArticleDOI
A New Approach to Modify Plant Microbiomes and Traits by Introducing Beneficial Bacteria at Flowering into Progeny Seeds.
Birgit Mitter,Nikolaus Pfaffenbichler,Richard Bailey Flavell,Stéphane Compant,Livio Antonielli,Alexandra Petric,Teresa Berninger,Muhammad Naveed,Raheleh Sheibani-Tezerji,Geoffrey von Maltzahn,Angela Sessitsch +10 more
TL;DR: It is discovered that by introducing the endophyte Paraburkholderia phytofirmans PsJN to the flowers of parent plants the authors could drive its inclusion in progeny seed microbiomes, thereby inducing vertical inheritance to the offspring generation.
References
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QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
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Journal ArticleDOI
UCHIME improves sensitivity and speed of chimera detection
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
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QIIME allows analysis of high-throughput community sequencing data.
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