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What do I do with my metagenomes? A comparison of three online metagenomic analysis platforms

Authors:
Christos Christakis at Foundation for Research and Technology - Hellas
Christos Christakis
Paraskevi Polymenakou at Hellenic Centre of Marine Research Crete
Paraskevi Polymenakou
  • Hellenic Centre of Marine Research Crete
Stephanos P. Kilias at National and Kapodistrian University of Athens
Stephanos P. Kilias
Jon Bent Kristoffersen at Hellenic Centre for Marine Research
Jon Bent Kristoffersen
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Christakis et al. “What do I do with my metagenomes?”
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What do I do with my metagenomes? A comparison of three online metagenomic
analysis platforms
ø not for oral presentation, poster only
Christos Christakis (author 1, corresponding)
Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and
Aquaculture, 71500 Heraklion, Crete, Greece
Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens,
Panepistimioupoli Zografou, 15784 Athens, Greece
Paraskevi N. Polymenakou (author 2)
Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and
Aquaculture, 71500 Heraklion, Crete, Greece
Stephanos P. Kilias (author 3)
Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens,
Panepistimioupoli Zografou, 15784 Athens, Greece
Jon Bent Kristoffersen (author 4)
Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and
Aquaculture, 71500 Heraklion, Crete, Greece
Torben Nielsen (author 5)
IMG Group, DOE Joint Genome Institute 2800 Mitchell Drive Walnut Creek, CA 94598
Paraskevi Nomikou (author 6)
Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens,
Panepistimioupoli Zografou, 15784 Athens, Greece
Georgios Kotoulas (author 7)
Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and
Aquaculture, 71500 Heraklion, Crete, Greece
Antonios Magoulas (author 8)
Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and
Aquaculture, 71500 Heraklion, Crete, Greece
email: christakis@hcmr.gr
Abstract
Metagenomics has become indispensable in microbial ecology, allowing the study of whole
microbial communities by sequencing the total DNA material from environmental samples
and without the need of culturing. Microbial communities are highly diverse and with their
Christakis et al. “What do I do with my metagenomes?”
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unique metabolic functions, they play key-roles in ecosystem functioning and
biogeochemical element cycling. While the vast amount of data produced with shotgun
metagenomics can assess the diversity and functioning of entire microbial communities, the
subsequent bioinformatics analyses are technically challenging and computationally
demanding. Thus, different online software tools for metagenomics data analysis like
IMG/MER1, MG-RAST2 and EBI MGnify3 have been developed.
Here, we performed shotgun sequencing on two samples from the Kallisti Limnes, CO2-
accumulating subsea pools, a unique hydrothermal vent ecosystem situated at 200m in the
Santorini caldera. Three separate MiSeq runs were performed for each sample. The resulting
sequences were assembled using MIRA4. Subsequently, we submitted the unassembled
sequences to MGnify and the assembled sequences to MG-RAST and IMG/MER. We then
compared each analysis in three levels: a taxonomic comparison at the phylum level, a
comparison of the major functional categories and a comparison of genes associated with the
biogeochemical cycles of C, S, N and Fe.
The analysis showed that MGnify performs quality control on each run separately and
provides detailed taxonomic information with limited functional information. MG-RAST,
while rapid and user-friendly, provides limited information about assembled data. Despite the
cumbersome platform and outdated handbooks, IMG/MER provides detailed functional
analyses with extractable data that can easily be used in downstream analysis.
Keywords: shotgun metagenomics, MiSeq sequencing, microbial communities, hydrothermal
vent, web resources
References
1. Markowitz, V. M. et al. IMG: the integrated microbial genomes database and
comparative analysis system. Nucleic Acids Res. 40, D115–D122 (2012).
2. Meyer, F. et al. The metagenomics RAST server – a public resource for the automatic
phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9, 386
(2008).
3. Mitchell, A. L. et al. EBI Metagenomics in 2017: Enriching the analysis of microbial
communities, from sequence reads to assemblies. Nucleic Acids Res. 46, D726–D735
(2018).
4. Chevreux, B., Wetter, T. & Suhai, S. Genome Sequence Assembly Using Trace
Signals and Additional Sequence Information. in Computer Science and Biology:
Proceedings of the German Conference on Bioinformatics (GCB) 45–56 (1999).
ResearchGate has not been able to resolve any citations for this publication.
EBI Metagenomics in 2017: Enriching the analysis of microbial communities, from sequence reads to assemblies
Article
Full-text available
  • Oct 2017
  • NUCLEIC ACIDS RES
EBI metagenomics ( http://www.ebi.ac.uk/metagenomics ) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.
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IMG: The Integrated Microbial Genomes database and comparative analysis system
Article
Full-text available
  • Jan 2012
  • NUCLEIC ACIDS RES
The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. IMG's data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp).
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The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
Article
Full-text available
  • Oct 2008
  • BMC BIOINFORMATICS
Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers. A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats. The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis - the availability of high-performance computing for annotating the data. http://metagenomics.nmpdr.org.
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Genome Sequence Assembly Using Trace Signals and Additional Sequence Information
Conference Paper
  • Dec 1999
Motivation: This article presents a method for assembling shotgun sequences which primarily uses high confidence regions whilst taking advantage of additional available information such as low confidence regions, quality values or repetitive region tags. Conflict situations are resolved with routines for analysing trace signals.
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