Giovanni Widmer

At Tufts Veterinary School of Medicine Giovanni Widmer and colleagues are using Illumina technology to sequence PCR amplicons obtained from the bacterial 16S rRNA gene. The analysis of millions of short sequences obtained with this method enables them to assess the taxonomic composition of bacterial populations and the impact of experimental interventions. Some of these analyses are computer-intensive and running them on the cluster saves time. Typically, they use Clustal Omega to align sequences. On the cluster, a samples of a few thousand sequence reads can be aligned in a few minutes. They have also installed mothur on the cluster (mothur.org) and are running sequence analysis programs from this collection. These programs are used to de-noise sequence data and to compute pairwise genetic distance matrices. They visualize the genetic diversity of microbial populations using Principal Coordinate Analysis, which is also computer-intensive. They have adapted this approach to analyze populations of the eukaryotic pathogen Cryptosporidium. Several Cryptosporidium species infect the gastro-intestinal tract of human and animals. Using a similar approach as applied to the analysis of bacterial populations, they assess the diversity of Cryptosporidium parasites infecting a host and monitor the impact of various interventions on the genetic diversity of this parasites.