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
Citations
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Effect of dietary medium-chain fatty acids on nursery pig growth performance, fecal microbial composition, and mitigation properties against porcine epidemic diarrhea virus following storage
Jordan T. Gebhardt,Katelyn A Thomson,Jason C Woodworth,Steve S Dritz,Michael D. Tokach,Joel M. DeRouchey,Robert D. Goodband,Cassandra K Jones,R. A. Cochrane,Megan C. Niederwerder,Samodha C. Fernando,Waseem Abbas,Thomas E. Burkey +12 more
TL;DR: The use of MCFA in nursery pig diets improves growth performance, provides residual mitigation activity against PEDV, and does not significantly alter fecal microbial composition.
Journal ArticleDOI
Individuality and convergence of the infant gut microbiota during the first year of life
Eric J. de Muinck,Pål Trosvik +1 more
TL;DR: Analysis of fecal specimens from 12 infants during their first year of life highlights the dynamic nature and individuality of the gut colonization process, and the need for high-frequency sampling over an extended period when designing and interpreting infant microbiome studies.
Journal ArticleDOI
Responses of Soil Bacterial Communities to Nitrogen Deposition and Precipitation Increment Are Closely Linked with Aboveground Community Variation
Hui Li,Zhuwen Xu,Shan Yang,Shan Yang,Xiaobin Li,Eva M. Top,Ruzhen Wang,Yuge Zhang,Jiangping Cai,Fei Yao,Xingguo Han,Yong Jiang +11 more
TL;DR: It was observed that N addition caused the significant decrease in bacterial alpha-diversity and dramatic changes in community composition, and the counteractive effects of N addition and increased precipitation imply that the combination with increased precipitation may partially offset this detrimental effect of N deposition.
Journal ArticleDOI
Long-chain fatty acid feeding frequency in anaerobic codigestion impacts syntrophic community structure and biokinetics.
TL;DR: It is suggested that pulse feeding rather than continuous feeding LCFA during anaerobic codigestion selected for higher microbial bioconversion kinetics and functional stability, which were related to changes in the physiological diversity and adaptive capacity of syntrophic and methanogenic communities.
Journal ArticleDOI
Biowaste-source-dependent synthetic pathways of redox functional groups within humic acids favoring pentachlorophenol dechlorination in composting process
TL;DR: Assessment of the synthetic pathways of redox functional groups within HAs from protein-, lignocellulose-, and lignin-rich composts that facilitated the microbially reductive dechlorination of PCP, respectively shows that the aromatic systems are the major electron-accepting moieties of HAs and function as electron shuttles to facilitate the PCP de chlorination.
References
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Journal ArticleDOI
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
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
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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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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