Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg | Wisconsin Institute for Discovery

Browsing Posts tagged Datasets

A couple of days ago, a paper I have co-authored describing an ITS sequence dataset for chimera control in fungi went online as an advance online publication in Microbes and Environments. There are several software tools available for chimera detection (e.g. Henrik Nilsson’s fungal chimera checker (1) and UCHIME (2)), but these generally rely on the presence of a chimera-free reference dataset. Until now, there was no such dataset is for the fungal ITS region, and we in this paper (3) introduce a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database (4). This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. We estimated the dataset performance on a large set of artificial chimeras to be above 99.5%, and also used the dataset to remove nearly 1,000 chimeric fungal ITS sequences from the UNITE database. The dataset can be downloaded from the UNITE repository. Thereby, it is also possible for users to curate the dataset in the future through the UNITE interactive editing tools.

References:

  1. Nilsson RH, Abarenkov K, Veldre V, Nylinder S, Wit P de, Brosché S, Alfredsson JF, Ryberg M, Kristiansson E: An open source chimera checker for the fungal ITS region. Molecular Ecology Resources, 10, 1076–1081 (2010).
  2. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27, 16, 2194-2200 (2011). doi:10.1093/bioinformatics/btr381
  3. Nilsson RH, Tedersoo L, Ryberg M, Kristiansson E, Hartmann M, Unterseher M, Porter TM, Bengtsson-Palme J, Walker D, de Sousa F, Gamper HA, Larsson E, Larsson K-H, Kõljalg U, Edgar R, Abarenkov K: A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts. Microbes and Environments, Advance Online Publication (2015). doi: 10.1264/jsme2.ME14121
  4. Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TT, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Senés C, Smith ME, Suija A, Taylor DE, Telleria MT, Weiß M, Larsson KH: Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology, 22, 21, 5271–5277 (2013). doi: 10.1111/mec.12481

I just got word from BMC Genomics that my most recent paper has just been published (in provisional form; we still have not seen the edited proofs). In this paper (1), which I have co-authored with Anders Blomberg, Magnus Alm Rosenblad and Mikael Molin, we utilize metagenomic data from the GOS-expedition (2) together with fully sequenced bacterial genomes to show that:

  1. Detoxification genes in general are underrepresented in marine planktonic bacteria
  2. Surprisingly, the detoxification that show a differential distribution are more abundant in open ocean water than closer to the coast
  3. Peroxidases and peroxiredoxins seem to be the main line of defense against oxidative stress for bacteria in the marine milieu, rather than e.g. catalases
  4. The abundance of detoxification genes does not seem to increase with estimated pollution.

From this we conclude that other selective pressures than pollution likely play the largest role in shaping marine planktonic bacterial communities, such as for example nutrient limitations. This suggests substantial streamlining of gene copy number and genome sizes, in line with observations made in previous studies (3). Along the same lines, our findings indicate that the majority of marine bacteria would have a low capacity to adapt to increased pollution, which is relevant as large amounts of human pollutants and waste end up in the oceans every year. The study exemplifies the use of metagenomics data in ecotoxicology, and how we can examine anthropogenic consequences on life in the sea using approaches derived from genomics. You can read the paper in its entirety here.

References:

  1. Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A: Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities. BMC Genomics. Volume 15, Issue 749 (2014). doi: 10.1186/1471-2164-15-749 [Paper link]

  2. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, Van Belle C, Chandonia J-M, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, et al: The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biology. 5:e16 (2007).
  3. Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, Johnson J, Montgomery R, Ferriera S, Beeson KY, Williamson SJ, Tovchigrechko A, Allen AE, Zeigler LA, Sutton G, Eisenstadt E, Rogers Y-H, Friedman R, Frazier M, Venter JC: Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature. 468:60–66 (2010).

In an interesting development, Nature Publishing Group has launched a new initiative: Scientific Data – a online-only open access journal that publishes data sets without the demand of testing scientific hypotheses in connection to the data. That is, the data itself is seen as the valuable product, not any findings that might result from it. There is an immediate upside of this; large scientific data sets might be accessible to the research community in a way that enables proper credit for the sample collection effort. Since there is no demand for a full analysis of the data, the data itself might quicker be of use to others, without worrying that someone else might steal the bang of the data per se. I also see a possible downside, though. It would be easy to hold on to the data until you have analyzed it yourself, and then release it separately just about when you submit the paper on the analysis, generating extra papers and citation counts. I don’t know if this is necessarily bad, but it seems it could contribute to “publishing unit dilution”. Nevertheless, I believe that this is overall a good initiative, although how well it actually works will be up to us – the scientific community. Some info copied from the journal website:

Scientific Data’s main article-type is the Data Descriptor: peer-reviewed, scientific publications that provide an in-depth look at research datasets. Data Descriptors are a combination of traditional scientific publication content and structured information curated in-house, and are designed to maximize reuse and enable searching, linking and data mining. (…) Scientific Data aims to address the increasing need to make research data more available, citable, discoverable, interpretable, reusable and reproducible. We understand that wider data-sharing requires credit mechanisms that reward scientists for releasing their data, and peer evaluation mechanisms that account for data quality and ensure alignment with community standards.