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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Functional overlap of the Arabidopsis leaf and root microbiota
Yang Bai,Daniel B. Müller,Girish Srinivas,Ruben Garrido-Oter,Ruben Garrido-Oter,Eva Potthoff,Matthias Rott,Nina Dombrowski,Philipp C. Münch,Stijn Spaepen,Mitja N. P. Remus-Emsermann,Bruno Hüttel,Alice C. McHardy,Julia A. Vorholt,Paul Schulze-Lefert +14 more
TL;DR: It is shown that the isolates form assemblies resembling natural microbiota on their cognate host organs, but are also capable of ectopic leaf or root colonization, which raises the possibility of reciprocal relocation between root and leaf microbiota members.
Journal ArticleDOI
Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data.
TL;DR: This protocol details MicrobiomeAnalyst, a user-friendly, web-based platform for comprehensive statistical, functional, and meta-analysis of microbiome data, a one-stop shop that enables microbiome researchers to thoroughly explore their preprocessed microbiome data via intuitive web interfaces.
Journal ArticleDOI
Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring
Shelly A. Buffington,Gonzalo Viana Di Prisco,Thomas A. Auchtung,Nadim J. Ajami,Joseph F. Petrosino,Mauro Costa-Mattioli +5 more
TL;DR: It is reported that maternal high-fat diet induces a shift in microbial ecology that negatively impacts offspring social behavior, and a single commensal strain is identified that corrects oxytocin levels, LTP, and social deficits in MHFD offspring.
Journal ArticleDOI
Correlation between the human fecal microbiota and depression
Ali Naseribafrouei,K. Hestad,K. Hestad,Ekaterina Avershina,Monika Sekelja,A. Linløkken,Robert C. Wilson,Knut Rudi,Knut Rudi +8 more
TL;DR: The aim of this work was to identify potential correlations between human fecal microbiota (as a proxy for gut microbiota) and depression.
Journal ArticleDOI
Chemically induced mouse models of acute and chronic intestinal inflammation
Stefan Wirtz,Vanessa Popp,Markus Kindermann,Katharina Gerlach,Benno Weigmann,Stefan Fichtner-Feigl,Markus F. Neurath +6 more
TL;DR: This protocol update describes an adaptation of the existing protocol that modifies the technique that has been used to generate improved mouse models that better reflect the nature of IBDs in humans.
References
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QIIME allows analysis of high-throughput community sequencing data.
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Search and clustering orders of magnitude faster than BLAST
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UCHIME improves sensitivity and speed of chimera detection
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