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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Journal ArticleDOI
Impacts of Flood Damage on Airborne Bacteria and Fungi in Homes after the 2013 Colorado Front Range Flood
Joanne B. Emerson,Patricia B Keady,Tess E. Brewer,Nicholas Clements,Emily E Morgan,Jonathan Awerbuch,Shelly L. Miller,Noah Fierer +7 more
TL;DR: It is suggested that bacterial and fungal communities continue to be affected by flooding, even after relative humidity has returned to baseline levels and remediation has removed any visible evidence of flood damage.
Journal ArticleDOI
Marine microplastic-associated bacterial community succession in response to geography, exposure time, and plastic type in China's coastal seawaters.
Xiyuan Xu,Shuai Wang,Fenglei Gao,Jingxi Li,Li Zheng,Chengjun Sun,Changfei He,Zongxing Wang,Lingyun Qu +8 more
TL;DR: High-throughput sequencing was applied to investigate the successional stages of microbial communities attached to polypropylene and polyvinyl chloride microplastics exposed for one year in the coastal seawater of China to elucidate the long-term changes in the community composition of microorganisms that colonize microplastic and expand the understanding of plastisphere microbial communities present in the marine environment.
Journal ArticleDOI
Strong responses of Drosophila melanogaster microbiota to developmental temperature
Neda Nasiri Moghadam,Pia Mai Thorshauge,Torsten Nygaard Kristensen,Nadieh de Jonge,Simon Bahrndorff,Henrik Kjeldal,Jeppe Lund Nielsen +6 more
TL;DR: It was found that the temperature during development affected thermal tolerance and the microbial composition of male D. melanogaster, and flies that developed at high temperature were the most heat tolerant and had the highest abundance of Acetobacter.
Journal ArticleDOI
Lactic Acid Bacteria in Durum Wheat Flour Are Endophytic Components of the Plant during Its Entire Life Cycle.
Fabio Minervini,Giuseppe Celano,Anna Lattanzi,Luigi Tedone,Giuseppe De Mastro,Marco Gobbetti,Maria De Angelis +6 more
TL;DR: Assessment of the dynamics of lactic acid bacteria and other Firmicutes associated with durum wheat organs and processed products showed that Lactobacillus, Streptococcus, Enteritiscus, and Lactococcus were the main epiphytic and endophytic genera among lactic Acid bacteria.
Journal ArticleDOI
Probiotic Mixture of Lactobacillus plantarum Strains Improves Lipid Metabolism and Gut Microbiota Structure in High Fat Diet-Fed Mice.
TL;DR: Results indicated that the mixed lactobacilli supplementation could manipulate the gut microbiota and its metabolites (acetic acid and butyric acid), resulting in reduced liver lipid accumulation and improved lipid metabolism of adipose tissue, which inhibited obesity.
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
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
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Journal ArticleDOI
UCHIME improves sensitivity and speed of chimera detection
TL;DR: UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus.
Journal ArticleDOI
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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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