ArticleExtremophiles : life under extreme conditions2016
Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning.
Article in Extremophiles : life under extreme conditions, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Physicochemical characteristics and microbial community analysis of a wetland system treating acid mine drainage.Scientific reports · 2025Article
- Description and genomic characterization of Cohnella caldifontis sp. nov., isolated from hot springs in Yunnan province, south-west China.Antonie van Leeuwenhoek · 2024Article
- Long-amplicon MinION-based sequencing study in a salt-contaminated twelfth century granite-built chapel.Applied microbiology and biotechnology · 2022Article
- Bacterial diversity in aqueous/sludge phases within diesel fuel storage tanks.World journal of microbiology & biotechnology · 2020Article
- Bioinoculants play a significant role in shaping the rhizospheric microbial community: a field study with Cajanus cajan.World journal of microbiology & biotechnology · 2020Article
- Studying safe storage time of orange peel (Citrus reticulata) using high-throughput sequencing and conventional pure culture.Food science & nutrition · 2018Article
- Targeting Bacteria and Methanogens To Understand the Role of Residual Slurry as an Inoculant in Stored Liquid Dairy Manure.Applied and environmental microbiology · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
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