Posts Tagged ‘microbiome’

Functions and ecology of the plant microbiome

December 24th, 2011

28th New Phytologist Symposium: Functions and ecology of the plant microbiome  

Rhodes, Greece, 18–21 May 2012

http://www.newphytologist.org/microbiome/default.htm

 

International Human Microbiome Congress in Paris

October 23rd, 2011

The next International Human Microbiome Congress, organized by the European consortium MetaHIT will take place in Paris, March 19-21, 2012 at the Palais Brongniart.

Social network wants to sequence your gut

September 10th, 2011

 

 

The non-profit programme MyMicrobes, launched today, is inviting people to have their gut bacteria sequenced for about €1,500 (US$2,100). Read more

28th NPS

July 15th, 2011

454 vs. Illumina for microbiota amplicon profiling

July 14th, 2011

To survey the soil bacterial and fungal communities in forest ecosystems, we have extensively used 454 Titanium pyrosequencing (Buée et al., 2009, Uroz et al., 2010), but we are currently comparing this approach to the paired-end Illumina read sequencing of the rRNA internal transcribed spacer (ITS). We are expecting the first datasets in a few weeks. The later approach sounds very promising, but in their recent analysis of the intestinal microbiota Claesson et al. (2010) showed that this approach has still important limitations. A very large proportion of the Illumina 16 rRNA reads could not be classified down to genus level as a result of their shorter length and higher error rates beyond 60 nt. Let’s see what we get with the ITS. See abstract below.

[Abstract. High-throughput molecular technologies can profile microbial communities at high resolution even in complex environments like the intestinal microbiota. Recent improvements in next-generation sequencing technologies allow for even finer resolution. We compared phylogenetic profiling of both longer (454 Titanium) sequence reads with shorter, but more numerous, paired-end reads (Illumina). For both approaches, we targeted six tandem combinations of 16S rRNA gene variable regions, in microbial DNA extracted from a human faecal sample, in order to investigate their limitations and potentials. In silico evaluations predicted that the V3/V4 and V4/V5 regions would provide the highest classification accuracies for both technologies. However, experimental sequencing of the V3/V4 region revealed significant amplification bias compared to the other regions, emphasising the necessity for experimental validation of primer pairs. The latest developments of 454 and Illumina technologies offered higher resolution compared to their previous versions, and showed relative consistency with each other. However, the majority of the Illumina reads could not be classified down to genus level due to their shorter length and higher error rates beyond 60 nt. Nonetheless, with improved quality and longer reads, the far greater coverage of Illumina promises unparalleled insights into highly diverse and complex environments such as the human gut].

Claesson et al. (2010) Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res. 38:e200. Epub 2010 Sep 29.

Buée et al. (2009) 454 pyrosequencing analysis of soil fungal diversity as affected by forest management. New Phytologist 184: 452–459.

Uroz et al. (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environmental Microbiology Reports 2: 281–288.