scholarly journals Chemoselective Coupling Preserves the Substrate Integrity of Surface-Immobilized Oligonucleotides for Emulsion PCR-Based Gene Library Construction

2016 ◽  
Vol 19 (1) ◽  
pp. 9-14 ◽  
Author(s):  
Marie L. Malone ◽  
Valerie J. Cavett ◽  
Brian M. Paegel
2003 ◽  
Vol 19 (5) ◽  
pp. 1460-1467 ◽  
Author(s):  
A. Ikeuchi ◽  
Y. Kawarasaki ◽  
T. Shinbata ◽  
T. Yamane

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Dieter M. Tourlousse ◽  
Koji Narita ◽  
Takamasa Miura ◽  
Mitsuo Sakamoto ◽  
Akiko Ohashi ◽  
...  

Abstract Background Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples. Results In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories. Conclusions The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products.


2017 ◽  
Vol 62 (2) ◽  
Author(s):  
DongLing Niu ◽  
RuiLing Wang ◽  
YaE Zhao ◽  
Rui Yang ◽  
Li Hu ◽  
...  

AbstractThe research of


2012 ◽  
Vol 152 (4) ◽  
pp. 451-455 ◽  
Author(s):  
A. M. Dygai ◽  
V. E. Goldberg ◽  
A. V. Artamonov ◽  
A. A. Bekarev ◽  
E. I. Vereschagin ◽  
...  

2010 ◽  
Vol 77 (3) ◽  
pp. 1076-1085 ◽  
Author(s):  
Magdalena Mulet ◽  
Zoyla David ◽  
Balbina Nogales ◽  
Rafael Bosch ◽  
Jorge Lalucat ◽  
...  

ABSTRACTThe Galicia seashore, in northwestern Spain, was one of the shorelines affected by thePrestigeoil spill in November 2002. The diversity of autochthonousPseudomonaspopulations present at two beaches (Carnota municipality) was analyzed using culture-independent and culture-dependent methods. The first analysis involved the screening of anrpoDgene library. The second involved the isolation of 94Pseudomonasstrains that were able to grow on selective media by direct plating or after serial enrichments on several carbon sources: biphenyl, gentisate, hexadecane, methylnaphthalene, naphthalene, phenanthrene, salicylate, xylene, and succinate. Eight denitrifyingPseudomonasstrains were also isolated by their ability to grow anaerobically with nitrate. The calculated coverage index forPseudomonasspecies was 89% when clones and isolates were considered together, and there were 29 phylospecies detected. The most abundant were members of the speciesP. stutzeri,P.putida,P. anguilliseptica, andP. oleovorans. Thirty-one isolates could not be identified at the species level and were considered representatives of 16 putative novelPseudomonasspecies. One isolate was considered representative of a novelP. stutzerigenomovar. Concordant results were obtained when the diversities of the cloned DNA library and the cultured strains were compared. The clone library obtained by therpoDPCR method was a useful tool for evaluatingPseudomonascommunities and also for microdiversity studies ofPseudomonaspopulations.


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