IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms.

Development of user-friendly, high throughput screening for ligands and inhibitors of carbohydrate modifying enzymes

This paper describes the impact of cloud computing and the use of GPUs on the performance of Autodock and Gromacs respectively. Cloud computing was applicable to reducing the ‘‘tail’’ seen in running Autodock on desktop grids and the GPU version of Gromacs showed significant improvement over the CPU version. A large (200,000 compounds) library of small molecules, seven sialic acid analogues of the putative substrate and 8000 sugar molecules were converted into pdbqt format and used to interrogate the Trichomonas vaginalis neuraminidase using Autodock Vina. Good binding energy was noted for some of the small molecules (~-9 kcal/mol), but the sugars bound with affinity of less than -7.6 kcal/mol. The screening of the sugar library resulted in a ‘‘top hit’’ with a-2,3-sialyllacto-N-fucopentaose III, a derivative of the sialyl Lewisx structure and a known substrate of the enzyme. Indeed in the top 100 hits 8 were related to this structure. A comparison of Autodock Vina and Autodock 4.2 was made for the high affinity small molecules and in some cases the results were superimposable whereas in others, the match was less good. The validation of this work will require extensive ‘‘wet lab’’ work to determine the utility of the workflow in the prediction of potential enzyme inhibitors.

Cinnamaldehyde increases the susceptibility of quorum-sensing-mediated biofilms to conventional antibiotics

The role of bacterial communication, also known as quorum sensing is an important mechanism in biofilm formation which is fundamental to the development of anti-biofilm strategies. In this current study, the synergy between a quorum sensing inhibitor (cinnamaldehyde) and two antibiotics (ceftazidime and levofloxacin) was evaluated in an attempt to develop a strategy for biofilm disruption using the high-throughput minimum biofilm eliminating concentration (MBEC) assay. Klebsiella pneumoniae and Proteus mirabilis biofilms of initial broth suspensions of 108 colony forming units (CFU) per mL, cultivated on the pegs of the MBEC device were challenged with 5120 µg/ml of ceftazidime and levofloxacin in a double dilution assay in the presence of 500 µM cinnamaldehyde. The minimum inhibitory concentrations (MIC) in the presence of cinnamaldehyde for ceftazidime and levofloxacin were 0.125% (640 µg/mL) and 0.0625% (320 µg/mL) respectively with no significant bacterial growth on LB agar. The MBECs for ceftazidime and levofloxacin were above 5120 and 2560 µg/mL respectively which yielded over 70% reduction in both Klebsiella pneumoniae and Proteus mirabilis biofilms. The above results indicate the possibility that the synergy between antimicrobial agents may lead to biofilm eradication.