Multiple copies of 16S rRNA gene affect the restriction patterns and DGGE profile revealed by analysis of genome database

Kang, Yijun; Cheng, Jin; Mei, Lijuan; Hu, Ji; Piao, Zhe; Yin, Suisui

doi:10.1134/s0026261710050103

Cited by 21 publications

(16 citation statements)

References 29 publications

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“…In general, fingerprinting techniques rely onthe amplification of 16S rRNA gene fragments by PCR, but 16S rRNA gene copy number per genome vary from 1 up to 15 or more copies depending on the bacterial species. The numbers of rRNA gene copies are related to the life strategy of bacteria; taxa with low copy numbers and inhabit low nutrient environment (oligotrophic) (Větrovský and Baldrian, 2013;Kang et al, 2010).…”

Section: Fingerprinting Techniquesmentioning

confidence: 99%

Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review

Lagos

Maruyama

Nannipieri

et al. 2015

J. Soil Sci. Plant Nutr.

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The rhizosphere (soil zone influenced by roots) is a complex environment that harbors diverse bacterial populations, which have an important role in biogeochemical cycling of organic matter and mineral nutrients. Nevertheless, our knowledge of the ecology and role of these bacteria in the rhizosphere is very limited, particularly regarding how indigenous bacteria are able to communicate, colonize root environments, and compete along the rhizosphere microsites. In recent decades, the development and improvement of molecular techniques have provided more accurate knowledge of bacteria in their natural environment, refining microbial ecology and generating new questions about the roles and functions of bacteria in the rhizosphere. Recently, advances insoil post-genomic techniques (metagenomics, metaproteomics and metatranscriptomics) are being applied to improve our understanding of the microbial communities at a higher resolution. Moreover, advantages and limitations of classical and post-genomic techniques must be considered when studying bacteria in the rhizosphere. This review provides an overview of the current knowledgeon the study of bacterial community in the rhizosphere by using modern molecular techniques, describing the bias of classical molecular techniques, next generation sequencing platforms and post-genomics techniques.

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Section: Fingerprinting Techniquesmentioning

confidence: 99%

Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review

Lagos

Maruyama

Nannipieri

et al. 2015

J. Soil Sci. Plant Nutr.

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show abstract

“…Although PCR-DGGE analysis indicated the presence of different phylotypes of Weissella (Fig. 2B,C, Table 3), it could not confirm the same because the pattern may also be due to the presence of multiple heterogeneous copies of rRNA genes indicating intraspecies sequence divergence (Kim et al 2009;Kang et al 2010). Similar to the previous findings (Lopez et al 2003), prominent bands corresponding to chloroplast and mitochondrial genome of bamboo were detected in all the stages of soidon fermentation and in the raw bamboo shoot during PCR-DGGE analysis.…”

Section: Discussionmentioning

confidence: 96%

Three‐phase succession of autochthonous lactic acid bacteria to reach a stable ecosystem within 7 days of natural bamboo shoot fermentation as revealed by different molecular approaches

2015

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Microbial community structure and population dynamics during spontaneous bamboo shoot fermentation for production of 'soidon' (indigenous fermented food) in North-east India were studied using cultivation-dependent and cultivation-independent molecular approaches. Cultivation-dependent analyses (PCR-amplified ribosomal DNA restriction analysis and rRNA gene sequencing) and cultivation-independent analyses (PCR-DGGE, qPCR and Illumina amplicon sequencing) were conducted on the time series samples collected from three independent indigenous soidon fermentation batches. The current findings revealed three-phase succession of autochthonous lactic acid bacteria to attain a stable ecosystem within 7 days natural fermentation of bamboo shoots. Weissella spp. (Weissella cibaria, uncultured Weissella ghanensis) and Lactococcus lactis subsp. cremoris predominated the early phase (1-2 days) which was joined by Leuconostoc citreum during the mid-phase (3 days), while Lactobacillus brevis and Lactobacillus plantarum emerged and became dominant in the late phase (5-7 days) with concurrent disappearance of W. cibaria and L. lactis subsp. cremoris. Lactococcus lactis subsp. lactis and uncultured Lactobacillus acetotolerans were predominantly present throughout the fermentation with no visible dynamics. The above identified dominant bacterial species along with their dynamics can be effectively utilized for designing a starter culture for industrialization of soidon production. Our results showed that a more realistic view on the microbial ecology of soidon fermentation could be obtained by cultivation-dependent studies complemented with cultivation-independent molecular approaches. Moreover, the critical issues to be considered for reducing methodological biases while studying the microbial ecology of traditional food fermentation were also highlighted with this soidon fermentation model.

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“…Note that the effect estimates for bacterial 16S rRNA quantification and cytokine mRNA expression cannot be compared directly. Despite being the current gold standard for organism identification, sequence-based detection of 16S rRNA cannot differentiate between viable and unviable organisms nor can it account for organisms with multiple copies of the 16S rRNA gene [42]. Nevertheless, compared with the clinical standard for diagnosis of BV, the Nugent Gram strain-based method, which is in fact an arithmetically derived index of mixed bacterial morphotypes, our use of 16S rRNA quantification in this study is appropriate given our novel statistical approach.…”

Section: Discussionmentioning

confidence: 99%

Bacterial and Cytokine Mixtures Predict the Length of Gestation and are Associated with miRNA Expression in the Cervix

et al. 2016

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Aim: Bacterial vaginosis may lead to preterm birth through epigenetic programming of the inflammatory response, specifically via miRNA expression. Methods: We quantified bacterial 16S rRNA, cytokine mRNA and 800 miRNA from cervical swabs obtained from 80 women at 16-19 weeks' gestation. We generated bacterial and cytokine indices using weighted quantile sum regression and examined associations with miRNA and gestational age at delivery. Results & discussion: Each decile of the bacterial and cytokine indices was associated with shorter gestations (p < 0.005). The bacterial index was associated with miR-494, 371a, 4286, 185, 320e, 888 and 23a (p < 0.05). miR-494 remained significant after false discovery rate correction (q < 0.1). The cytokine index was associated with 27 miRNAs (p < 0.05; q < 0.01). Conclusion: Future investigation into the role of bacterial vaginosis-and inflammation-associated miRNA and preterm birth is warranted.

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Multiple copies of 16S rRNA gene affect the restriction patterns and DGGE profile revealed by analysis of genome database

Cited by 21 publications

References 29 publications

Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review

Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review

Three‐phase succession of autochthonous lactic acid bacteria to reach a stable ecosystem within 7 days of natural bamboo shoot fermentation as revealed by different molecular approaches

Bacterial and Cytokine Mixtures Predict the Length of Gestation and are Associated with miRNA Expression in the Cervix

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Multiple copies of 16S rRNA gene affect the restriction patterns and DGGE profile revealed by analysis of genome database

Cited by 21 publications

References 29 publications

Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini&#8210;review

Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini&#8210;review

Three‐phase succession of autochthonous lactic acid bacteria to reach a stable ecosystem within 7 days of natural bamboo shoot fermentation as revealed by different molecular approaches

Bacterial and Cytokine Mixtures Predict the Length of Gestation and are Associated with miRNA Expression in the Cervix

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Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review

Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review