A PHP Error was encountered

Severity: Warning

Message: Creating default object from empty value

Filename: models/publicacao_item.php

Line Number: 20

PyroTRF-ID: a novel bioinformatics methodology for the affiliation of... » Isaúde
  Pesquisar Publicações Científicas  
  Especialidade: carregando especialidades...  Carregando...
Nome da revista:   Volume:   Número:
BMC microbiology [electronic resource]
2012-12-28 02:07:44

PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Descrição: Background:In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microbiomes. Here, a bioinformatics methodology for pyrosequencing-based T-RF identification (PyroTRF-ID) was developed to combine pyrosequencing and T-RFLP approaches for the description of microbial communities. The strength of this methodology relies on the identification of T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same samples. DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. Digital T-RFLP profiles were generated from the denoised full pyrosequencing datasets, and the sequences contributing to each digital T-RF were classified to taxonomic bins using the Greengenes reference database. The method was tested both on bacterial communities found in chloroethene-contaminated groundwater samples and in aerobic granular sludge biofilms originating from wastewater treatment systems.Results:PyroTRF-ID was efficient for high-throughput mapping and digital T-RFLP profiling of pyrosequencing datasets. After denoising, a dataset comprising ca. 10[prime]000 reads of 300 to 500 bp was typically processed within ca. 20 minutes on a high-performance computing cluster, running on a Linux-related CentOS 5.5 operating system, enabling parallel processing of multiple samples. Both digital and experimental T-RFLP profiles were aligned with maximum cross-correlation coefficients of 0.71 and 0.92 for high- and low-complexity environments, respectively. On average, 63+/-18% of all experimental T-RFs (30 to 93 peaks per sample) were affiliated to phylotypes.Conclusions:PyroTRF-ID profits from complementary advantages of pyrosequencing and T-RFLP and is particularly adapted for optimizing laboratory and computational efforts to describe microbial communities and their dynamics in any biological system. The high resolution of the microbial community composition is provided by pyrosequencing, which can be performed on a restricted set of selected samples, whereas T-RFLP enables simultaneous fingerprinting of numerous samples at relatively low cost and is especially adapted for routine analysis and follow-up of microbial communities on the long run.

Identificador: doi:10.1186/1471-2180-12-306
Volume: 0
Página: 3 a


Mais informações

  • Twitter iSaúde
publicidade
Jornal Informe Saúde

Indique o portal
Fechar [X]
  • Você está indicando a notícia: http://www.isaude.net
  • Para que seu amigo(a) receba esta indicação preencha os dados abaixo:

RSS notícias do portal  iSaúde.net
Receba o newsletter do portal  iSaúde.net
Indique o portal iSaúde.net
Notícias do  iSaúde.net em seu blog ou site.
Receba notícias com assunto de seu interesse.
© 2000-2011 www.isaude.net Todos os direitos reservados.