| Title |
Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning
|
|---|---|
| Published in |
Extremophiles, June 2016
|
| DOI | 10.1007/s00792-016-0855-5 |
| Pubmed ID | |
| Authors |
Lucia Kraková, Katarína Šoltys, Jaroslav Budiš, Tomáš Grivalský, František Ďuriš, Domenico Pangallo, Tomáš Szemes |
| Abstract |
Different protocols based on Illumina high-throughput DNA sequencing and denaturing gradient gel electrophoresis (DGGE)-cloning were developed and applied for investigating hot spring related samples. The study was focused on three target genes: archaeal and bacterial 16S rRNA and mcrA of methanogenic microflora. Shorter read lengths of the currently most popular technology of sequencing by Illumina do not allow analysis of the complete 16S rRNA region, or of longer gene fragments, as was the case of Sanger sequencing. Here, we demonstrate that there is no need for special indexed or tailed primer sets dedicated to short variable regions of 16S rRNA since the presented approach allows the analysis of complete bacterial 16S rRNA amplicons (V1-V9) and longer archaeal 16S rRNA and mcrA sequences. Sample augmented with transposon is represented by a set of approximately 300 bp long fragments that can be easily sequenced by Illumina MiSeq. Furthermore, a low proportion of chimeric sequences was observed. DGGE-cloning based strategies were performed combining semi-nested PCR, DGGE and clone library construction. Comparing both investigation methods, a certain degree of complementarity was observed confirming that the DGGE-cloning approach is not obsolete. Novel protocols were created for several types of laboratories, utilizing the traditional DGGE technique or using the most modern Illumina sequencing. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 57 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| France | 1 | 2% |
| Unknown | 56 | 98% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 17 | 30% |
| Student > Master | 10 | 18% |
| Student > Bachelor | 7 | 12% |
| Student > Doctoral Student | 4 | 7% |
| Researcher | 4 | 7% |
| Other | 4 | 7% |
| Unknown | 11 | 19% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 19 | 33% |
| Environmental Science | 9 | 16% |
| Biochemistry, Genetics and Molecular Biology | 7 | 12% |
| Immunology and Microbiology | 3 | 5% |
| Engineering | 2 | 4% |
| Other | 2 | 4% |
| Unknown | 15 | 26% |
Attention Score in Context
This research output has an Altmetric Attention Score of 8. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 26 June 2016.
All research outputs
#4,088,065
of 22,879,161 outputs
Outputs from Extremophiles
#113
of 799 outputs
Outputs of similar age
#72,549
of 352,801 outputs
Outputs of similar age from Extremophiles
#8
of 23 outputs
Altmetric has tracked 22,879,161 research outputs across all sources so far. Compared to these this one has done well and is in the 82nd percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 799 research outputs from this source. They receive a mean Attention Score of 4.2. This one has done well, scoring higher than 85% of its peers.
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We're also able to compare this research output to 23 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 65% of its contemporaries.