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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Heavy metals, antibiotics and nutrients affect the bacterial community and resistance genes in chicken manure composting and fertilized soil
Wenwen Deng,Anyun Zhang,Shujuan Chen,Xueping He,Lei Jin,Xiumei Yu,Shengzhi Yang,Bei Li,Liangqian Fan,Ji Lin,Xin Pan,Likou Zou +11 more
TL;DR: Results indicated that the composting process is effective for reducing potential pathogenic bacteria, antibiotics and ARGs, as well as an increase in potentially beneficial taxa and nutrients in soil.
Journal ArticleDOI
Ixodes scapularis does not harbor a stable midgut microbiome
Benjamin D. Ross,Beth M. Hayes,Matthew C. Radey,Xia Lee,Tanya Josek,Jenna Bjork,David F. Neitzel,Susan M. Paskewitz,Seemay Chou,Joseph D. Mougous +9 more
TL;DR: The results suggest that reduced selective pressure from limited microbial populations within ticks may have facilitated the evolutionary loss of genes encoding interbacterial competition pathways from Borrelia.
Journal ArticleDOI
Colitis-induced colorectal cancer and intestinal epithelial estrogen receptor beta impact gut microbiota diversity
Ahmed Ibrahim,Ahmed Ibrahim,Luisa W. Hugerth,Linnea Hases,Linnea Hases,Ashish Saxena,Maike Seifert,Quentin Thomas,Jan-Åke Gustafsson,Lars Engstrand,Cecilia Williams,Cecilia Williams +11 more
TL;DR: It is demonstrated that colitis‐induced CRC reduced the gut microbiota diversity and that loss of ERβ enhanced this process, and the data support that intestinal ERβ contributes to a more favorable microbiome that could attenuate CRC development.
Journal ArticleDOI
Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering.
TL;DR: The data demonstrate that long reads can improve OTU inference; however, the choice of clustering algorithm and associated clustering thresholds has significant impact on performance.
Journal ArticleDOI
Characterisation of the ruminal fermentation and microbiome in lambs supplemented with hydrolysable and condensed tannins.
Saheed A. Salami,Saheed A. Salami,Bernardo Valenti,M. Bella,Michael N. O'Grady,Giuseppe Luciano,Joseph P. Kerry,Eleanor Jones,Alessandro Priolo,Charles J. Newbold,Charles J. Newbold +10 more
TL;DR: Results demonstrated that both HT and CT sources could impact the ruminal microbiome when supplemented at 4% inclusion level and HT-t, CT-m and CT-g extracts displayed specific antimicrobial activity against methanogens and protozoa without compromising ruminal fermentation in a long-term feeding trial.
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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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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Journal ArticleDOI
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
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