Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg

I have tried to put together a list of talks I find interesting at ISME14 next week (oh, well going through the program book I find virtually all talks interesting, but some of them more so than others). I didn’t get there quite yet, but I have a list for monday and tuesday. I have realized that monday morning will likely run smoothly (a tough call between von Mering and Gilbert at 11.30, but otherwise the choices were not too hard). Monday afternoon I will probably spend in Session Room B3, where the Microbial Community Diversity: 16S and Beyond session will take place (many sessions have really silly, non-informative, names at this conference – what would not fit into the concept “16S and beyond“?). I will really miss the talk by Otto X. Cordero on bacteria act as socially cohesive units and antibiotic resistance, but I simply don’t think there will be time for a trip to Hall A2 and back just for that talk.

Tuesday is a lot messier, and can not have been planned with my interests in mind. Everything seems to happen at once here. I guess I will spend the morning discussing Mobility of genes and the species concept in Auditorium 12, but then I’ll be missing out talks on dormancy and genes under selection pressure I really would have liked to hear. But it gets even worse in the afternoon. Here I would really have needed Hermione’s time-turner. I’ll try to start the afternoon with Effects of loss of rare microbes on soil ecosystem services by Gera Hol in Auditorium 10, but will then miss at least two other diversity talks. Then, I will largely prioritize the Auditorium 12 talks on mobility of genes, with a small trip to Hall A2, where Kristian Koefoed Brandt will discuss antibiotic and metal resistance. Sadly, I will miss so many important talks this afternoon.

Another tough call is the round table discussions on Monday evening. Here, however, I feel that I have a duty to attend to the Unraveling the bacterial mobilome: Potentials and limitations of the present methodology session in Auditorium 11, which also might be the most relevant one for my current research projects.

Below you find my list of interesting talks at ISME14, sorted by time. Times in bold are the ones I will aim to attend in case I have to make a choice. Also, of course I will attend my own poster presentation on Monday afternoon (poster board number 267A). Hope to see you there!

Monday

Morning session

1000 – 1030 Cross-biome comparisons of soil microbial communities and their functional potentials
Noah Fierer, University of Colorado at Boulder, USA (Hall A2)

1030 – 1100 Experimental biogeography of bacteria in miniature ecosystems
Thomas Bell, Imperial College, London, UK (Hall A2)

1130 – 1200 Tracking OTUs around the environment – a challenge for clustering algorithms and interpretation
Christian von Mering, University of Zurich, Switzerland (Hall A1)

1130 – 1200   The Earth Microbiome Project: A new paradigm in geospatial and temporalstudies of microbial ecology
Jack A. Gilbert, Argonne National Laboratory and University of Chicago, USA (Hall A2)

Afternoon session

1330 – 1345 What makes a bacterium fresh? Genome wide functional comparison of marine and freshwater SAR11
Alexander Eiler [Sweden] (Auditorium 15)

1330 – 1345 Rarity and the problem of measuring diversity
Bart Haegeman [France] (Session Room B3)

1345 – 1400 Complexity does not necessarily create diversity
Tom Curtis [United Kingdom] (Session Room B3)

1345 – 1400 Depletion of the rare bacterial biosphere in expanding oceanic oxygen minimum zones
J. Michael Beman [USA] (Session Room B4)

1400 – 1415 Selection history affects the predictability of microbial ecosystem development
Andrew Free [United Kingdom] (Session Room B3)

1415 – 1430 Can we use microbial life strategies to understand the response of microbial communities to moisture stress?
Sarah Evans [USA] (Session Room B3)

1430 – 1445 Towards a unified taxonomy for ribosomal RNA databases
Pelin Yilmaz [Germany] (Session Room B3)

1445 – 1500 Systematic design of 18S rDNA primers for assessing eukaryotic diversity
Luisa Hugerth [Sweden] (Session Room B3)

1445 – 1500 Either Of yeast, grapes and wasps: Saccharomyces cerevisiae ecology revised
Irene Stefanini [Italy] (Hall A1)

1500 – 1515 Soil bacterial biogeography: a taxonomic and functional perspective
Rob Griffiths [United Kingdom] (Hall A1)

1500 – 1515 Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance in the wild
Otto X. Cordero [USA] (Hall A2)

1515 – 1530 Micro-scale drivers of bacterial diversity and biogeography
George Kowalchuk [Netherlands] (Hall A1)

1515 – 1530 Time and space resolved deep metagenomics to investigate selection pressures on low abundant species in complex environments
Mads Albertsen [Denmark] (Session Room B3)

1515 – 1530 Bacterial community structure and composition in high arsenic contaminated ground water from West Bengal and microbial role in subsurface arsenic release
Pinaki Sar [India] (Auditorium 10)

Evening session (round-table discussions)

17:30 – 19:30  RT11: Microbial Network Ecology: Deciphering Complex Network Interactions in Microbial Communities (Hall A3)

17:30 – 19:30 RT16: Unraveling the bacterial mobilome: Potentials and limitations of the present methodology (Auditorium 11)

17:30 – 19:30  RT17: Microbial invasions: What defines whether a microorganism is an invasive species? (Auditorium 12)

Tuesday

Morning session

08:30 – 09:20 You are what you eat but not always what omics predicts: On the importance of single cell ecophysiology of microbes
Michael Wagner, Department of Microbial Ecology, University of Vienna, Austria (Hall A1)

1000 – 1030 Can dormancy theory help us retrieve rare and uncultured microbes?
Jay Lennon, Indiana University, USA (Hall A3)

1000 – 1030 A critical review of mean metabolic rates of subsurface microbial communities
Bo Barker Jørgensen, University of Aarhus, Denmark (Auditorum 11)

1000 – 1030 Horizontal genetic transfer and the origin of species in bacteria
Frederick M. Cohan, Wesleyan University, USA (Auditorum 12)

1030 – 1100 Phylogenomic networks reveal mechanisms for lateral gene transfer during microbial evolution
Tal Dagan, Heinrich Heine University Düsseldorf, Germany (Auditorum 12)

1100 – 1130 Coevolution between plasmids and their hosts: consequences for the persistence of drug resistance
Eva Top, University of Idaho, USA (Auditorum 12)

1130 – 1200 The communal gene pool in natural environments
Søren J. Sørensen, University of Copenhagen, Denmark (Auditorum 12)

1130 – 1200 Let genomes do the talking: Using genomics to unravel genes under selection in archaeal populations
Rachel Whitaker, University of Illinois, USA (Auditorum 15)

Afternoon session

1330 – 1345 Spatial patterns of microbial communities at a soil microscale
Florentin Constancias [France] (Hall A2)

1330 – 1345 Microbial biofilm biodiversity distribution in a stream network
Katharina Besemer [Austria] (Session Room B3)

1330 – 1345 Effects of loss of rare microbes on soil ecosystem services
Gera Hol [Netherlands] (Auditorium 10)

1345 – 1400 Targeted recovery of novel phylogenetic diversity from next-generation sequence data
Josh D. Neufeld [Canada] (Auditorium 10)

1345 – 1400 Functionally relevant microdiversity of Nitrospira-like bacteria in activated sludge
Christiane Dorninger [Austria] (Hall A3)

1345 – 1400 Hot spot of horizontal gene transfer: high abundance and diversity of mobile genetic elements in bacterial communities of on-farm pesticide biopurification systems
Kornelia Smalla [Germany] (Auditorium 12)

1400 – 1415 Transcriptional dynamics of catabolic genes in soil – fine-scale analysis for a deeper understanding of soil functioning
Mette H Nicolaisen [Denmark] (Hall A1)

1400 – 1415 Seasonal synchronicity and specificity of microbial community and population dynamics across four alpine lakes
Ryan Mueller [Spain] (Session Room B3)

1400 – 1415 Mapping genotypic diversity onto niche adaptation
Yutaka Yawata [USA] (Auditorium 12)

1415 – 1430 Soil bacterial community shift after chitin enrichment: an integrative metagenomic approach
Samuel Jacquiod [France] (Hall A3)

1415 – 1430 MetaGenomic Species: adding structure to metagenomics data
H. Bjørn Nielsen [Denmark] (Auditorium 12)

1430 – 1445 Impact of diet on human gut microbial communities
Cindy Nakatsu [USA] (Hall A3)

1430 – 1445 Insights into the bovine rumen plasmidome
Itzhak Mizrahi [Israel] (Auditorium 12)

1445 – 1500 Mechanisms of biocide-induced antibiotic resistance: from single cell to community
Seungdae Oh [USA] (Hall A3)

1445 – 1500 Antibiotic resistance in soil bacterial communities: comparison of metals and antibiotic residues as selecting agents and spatial heterogeneity of coselected resistance patterns
Kristian Koefoed Brandt [Denmark] (Hall A2)

1445 – 1500 Viruses, a controlling force on Prokaryotic diversity?
Ruth-Anne Sandaa [Norway] (Session Room B4)

1445 – 1500 Regulation of transfer of the ICEclc element of Pseudomonas
Jan Roelof van der Meer [Switzerland] (Auditorium 12)

1500 – 1515 Pathogen removal in slow sand filters as revealed by stable isotope probing coupled with next generation sequencing
Sarah Haig [United Kingdom] (Hall A3)

1500 – 1515 Development of zinc tolerance by the ammonia oxidising community is restricted to ammonia oxidising Bacteria, rather than Archaea
Stefan Ruyters [Belgium] (Hall A2)

1500 – 1515 Survival strategies of plasmids in chemostats and biofilms: effect of hostrange and competition
Jan-Ulrich Kreft [United Kingdom] (Auditorium 12)

1515 – 1530 Evaluating process-related and seasonal changes in bacterial community in drinking water treatment and distribution systems
Ameet Pinto [USA] (Hall A3)

1515 – 1530 Distribution, diversity, and evolution of cyclic peptide secondary metabolites in natural populations of marine picocyanobacteria
Andres Cubillos-Ruiz [USA] (Hall A1)

1515 – 1530 Permissiveness of soil microbial communities toward receipt of mobile genetic elements
Sanin Musovic [Denmark] (Auditorium 12)

Evening session

1830 Víctor de Lorenzo, Molecular Environmental Microbiology Laboratory, the Spanish National Research Council, Spain
Conflict management and division of labor in bacterial populations degrading recacitrant aromatics

1915  Stephen J. Giovannoni, Oregon State University, USA
Outliers: Extreme Selection for Minimalism in Ocean Microbial Plankton

I am on my way to Copenhagen for the ISME14 conference that begins today. I’m myself quite excited about this event, and will present three posters (two as first author), and give a short talk on antibiotic resistance gene identification and metagenomics. My talk will be in the Bioinformatics in Microbial Ecology session on Thursday afternoon (at 13.30).

If you’d like to talk about Metaxa and Megraft, I will present an SSU-oriented poster in the Monday afternoon poster section (board number 267A). My antibiotic resistance gene poster will be presented on Thursday afternoon (board number 002A), and I really encourage everyone interested in metagenomics (especially metagenomic assembly) to come talk to me then! Finally, I am also partially responsible for a poster on periphyton metagenomics with Martin Eriksson as its main author. This poster is also presented on Monday, in the Microbial Dispersion and Biogeography session (board number 021A).

I hope to be able to make another post later tonight on what are the “essential” sessions for me on this conference. Hope to see you there soon!

I am married

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As many of you probably know, I have gotten married, which of course is a huge step for me. In short, I think the main way it will affect my scientific life is that I am changing my surname. So from now on, I am going to publish under the name “Johan Bengtsson-Palme” instead of just “Johan Bengtsson”. Not that much of a change, but it could still be nice to know that Bengtsson-Palme J, and Bengtsson J might very well be the same person.

On a side note, we just recently got a paper accepted on guidelines for quality control of ITS barcode sequences. More on that to follow soon.

Yesterday, our paper on Megraft – a software tool to graft ribosomal small subunit (16S/18S) fragments onto full-length SSU sequences – became available as an accepted online early article in Research in Microbiology. Megraft is built upon the notion that when examining the depth of a community sequencing effort, researchers often use rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in a metagenome. However, the SSU sequences in metagenomic libraries generally are present as fragmentary, non-overlapping entries, which poses a great problem for this analysis. Megraft aims to remedy this problem by grafting the input SSU fragments from the metagenome (obtained by e.g. Metaxa) onto full-length SSU sequences. The software also uses a variability model which accounts for observed and unobserved variability. This way, Megraft enables accurate assessment of species richness and sequencing depth in metagenomic datasets.

The algorithm, efficiency and accuracy of Megraft is thoroughly described in the paper. It should be noted that this is not a panacea for species richness estimates in metagenomics, but it is a huge step forward over existing approaches. Megraft shares some similarities with EMIRGE (Miller et al., 2011), which is a software package for reconstruction of full-length ribosomal genes from paired-end Illumina sequences. Megraft, however, is set apart in that it has a strong focus on rarefaction, and functions also when the number of sequences is small, which is often the case in 454 and Sanger-based metagenomics studies. Thus, EMIRGE and Megraft seek to solve a roughly similar problem, but for different sequencing technologies and sequencing scales.

Megraft is available for download here, and the paper can be read here.

  1. Bengtsson, J., Hartmann, M., Unterseher, M., Vaishampayan, P., Abarenkov, K., Durso, L., Bik, E.M., Garey, J.R., Eriksson, K.M., Nilsson R.H. (2012). Megraft: A software package to graft
  2. Miller, C. S., Baker, B. J., Thomas, B. C., Singer, S. W., & Banfield, J. F. (2011). EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biology, 12(5), R44. doi:10.1186/gb-2011-12-5-r44

I realized that I have been using a newer version of Metaxa than most of you for the last couple of months. This bug fix was written sometime in February or March, and we have kept it internal to make sure it works as it should. Then other things came across and we never got around to actually release it. But with testing passed and upcoming versions of Metaxa in the pipeline, I think it is about time that everyone gets their hands on the latest Metaxa version.

It’s only two small things this time:

  • Slight tweaks to the new HMM scoring system, making Metaxa just a little bit faster
  • Fixed a rarely occurring bug causing the –heuristics options to be ignored in certain circumstances

Download the Metaxa 1.1.1 package here

For the last months I have been (part time) struggling with getting Metaxa to eat Illumina paired-end data. This is a pretty tricky task, mainly due to the fact that Illumina reads are so much shorter than those obtained by Sanger and 454 sequencing. Therefore, I am more than happy to inform the community that today (the day before I go on vacation) I have a working prototype up and running. In fact, calling it a prototype is unfair, it is a quite far gone piece of software by now. Currently, I am running it on test data sets, and I will try to keep it running over the next couple of weeks. Thereafter, I hope to be able to release it sometime this autumn (but don’t expect a September release!), harnessing the power of Illumina sequencing for SSU identification. Stayed tuned, and have a great summer!

For those of you who like to listen to (or look at) me, I will be giving a presentation at this year’s SocBiN conference in Stockholm. My presentation has the long and quite informative title: Comprehensive Analysis of Antibiotic Resistance Genes in River Sediment, Well Water and Soil Microbial Communities Using Metagenomic DNA Sequencing. The talk is scheduled in the Using Next generation sequence data session, right after Jeroen Raes and Christopher Quince… It’s a short talk, so I will probably need to keep it simple, but it will be the first time I present results generated in relation with my present position, which I personally feel is very nice. We’re moving forward!

I was recently involved as an adviser in a report by the County Administrative Board in Västra Götaland (Länsstyrelsen) which has now been published [1]. [UPDATE: The PDF link at Länsstyrelsen's page does not seem to work, but leads to another report in Swedish. I have reported this error to the web admin, we'll see what happens. Once again, the PDF seems to work.] The report aims to identify gaps in the current monitoring system of hazardous substances in the Swedish environment. The report deals with effect based monitoring tools and their usefulness for predicting and/or observing effects of hazardous substances in the environment. The overall conclusion of the report is that there are several gaps in both knowledge and techniques, and a need for developing new resources. However, Sweden still has a good potential to adapt the monitoring system to fill the needs. I have been involved in one of the last chapters, describing the use of metagenomics if study ecosystem function (chapter 30.3). For people with an interest in environmental monitoring, the report is an interesting read in its entirety. For those more interested in applications for metagenomics I recommend turning to page 285 and continue to the end of the report (it’s only five pages on metagenomics, so you’ll manage).

  1. Länsstyrelsen i Västra Götalands län. (2012). Swedish monitoring of hazardous substances in the aquatic environment (No. 2012:23). (A.-S. Wernersson, Ed.) Current vs required monitoring and potential developments (pp. 1–291). Länsstyrelsen i Västra Götalands län, vattenvårdsenheten.

The guys at Pfam recently introduced a new database, called AntiFam, which will provide HMM profiles for some groups of sequences that seemingly formed larger protein families, although they were not actually real proteins. For example, rRNA sequences could contain putative ORFs, that seems to be conserved over broad lineages; with the only problem being that they are not translated into proteins in real life, as they are part of an rRNA [1].

With this initiative the Xfam team wants to “reduce the number of spurious proteins that make their way into the protein sequence databases.” I have run into this problem myself at some occasions with suspicious sequences in GenBank, and I highly encourage this development towards consistency and correctness in sequence databases. It is of extreme importance that databases remain reliable if we want bioinformatics to tell us anything about organismal or community functions. The Antifam database is a first step towards such a cleanup of the databases, and as such I would like to applaud Pfam for taking actions in this direction.

To my knowledge, GenBank are doing what they can with e.g. barcoding data (SSU, LSU, ITS sequences), but for bioinformatics and metagenomics (and even genomics) to remain viable, these initiatives needs to come quickly; and automated (but still very sensitive) tools for this needs to get our focus immediately. For example, Metaxa [2] could be used as a tool to clean up SSU sequences of misclassified origin. More such tools are needed, and a lot of work remains to be done in the area of keeping databases trustworthy in the age of large-scale sequencing.

References

  1. Tripp, H. J., Hewson, I., Boyarsky, S., Stuart, J. M., & Zehr, J. P. (2011). Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies. Nucleic Acids Research, 39(20), 8792–8802. doi:10.1093/nar/gkr576
  2. Bengtsson, J., Eriksson, K. M., Hartmann, M., Wang, Z., Shenoy, B. D., Grelet, G.-A., Abarenkov, K., et al. (2011). Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie van Leeuwenhoek, 100(3), 471–475. doi:10.1007/s10482-011-9598-6

The newly formed bioinformatics network for PhD students in Gothenburg (GoBiG), will have an introductory meeting next week, on thursday the 26th at Chalmers. See this page for more info.