Paper out: Are pangenomes adaptive or not?

I have been interested in bacterial pan genomes for some time: apart from acquiring mutations in genes shared between strains, bacteria are able to pick up genes (via several Lateral Gene Transfer processes), duplicate genes and also lose genes. These processes can take place rapidly, and could potentially have large effects on fitness. Together with Adam Eyre-Walker and several co-authors, I wrote an Opinion piece exploring both the rate  at which these accessory genome changes can occur and their evolutionary fate (see this post). Earlier this year, I published a short meta-analysis with Nadia Andreani and Elze Hesse (see this post) explicitly demonstrating that species with genetically more diverse core genomes also have more diverse accessory genomes. This pattern is inconsistent with predominantly strongly deleterious effects and consistent with slightly deleterious or neutral fitness effects. A recent Opinion piece in Nature Microbiology by McInerney etal argued that most observed accessory genome changes are actually adaptive. This prompted Jesse Shapiro to write a short letter to Nature Microbiology contrasting these findings with ours, prompting Adam and myself to write a critique of the McInerney paper and McInerney to write a response. I feel that the evolution of accessory genomes is one of the least understood but most pressing issues in evolutionary microbiology. Hopefully the present discussion will help to stir up debate.

M. Vos and A. Eyre-Walker (2017) Are pangenomes adaptive or not? Nature Microbiology 2, 1576 DOIdoi:10.1038/s41564-017-0067-5

Prospective PhD’s: please see the blog post below!

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PhD opportunities

The BBSRC GW4 Universities Doctoral Training Program is currently advertising PhD projects. This is a slightly complicated process, but basically comes down to prospective students picking a project offered by scientists working at participating universities and institutions and applying to the program. I (Dr Michiel Vos, m.vos@exeter.ac.uk) offer one of these projects as part of a team of  GW4 colleagues (Prof Ed Feil, University of Bath, Dr Ben Temperton, University of Exeter and with collaborator Prof Adam Eyre-Walker, University of Sussex). Below the project description:

Quantifying the rate and fate of bacterial gene content evolution

Bacteria are the most abundant and diverse life forms on earth, vital to the functioning of all ecosystems and to human health and wellbeing. Bacteria rely on a highly diverse array of mechanisms to create genomic changes which, combined with usually enormous population sizes, can result in rapid evolutionary change. Most bacterial species have ‘fluid’ genomes, where a stable core genome is complemented by an accessory set of genes that can be rapidly taken up through lateral transfer and lost through deletion (1). Such Gene Content Changes (GCC) have been estimated to occur at rates similar to nucleotide substitution in the core genome and are likely to have more significant effects on fitness (2). Despite its importance to bacterial evolution, the rate of gene content turnover and the selective effects of GCC are not well-understood. Some researchers argue that most changes have only small effects on fitness (3), whereas others argue that most variation in accessory genes is adaptive (4). As the tempo and mode of bacterial evolution is fundamental to a wide range of fields, from molecular epidemiology to biotechnology, this controversy needs to be resolved. This project takes a comparative genomics approach to 1) explicitly measure the rate of GCC in a range of different bacteria and 2) develop novel tests of selection to quantify the selective effects of gene content change.

  1. Ochman H, Davalos LM. The nature and dynamics of bacterial genomes. Science. 2006; 311(5768):1730-3
  2. Vos M, Hesselman MC, te Beek TA, van Passel MW, Eyre-Walker A. Rates of Lateral Gene Transfer in Prokaryotes: High but Why? Trends in microbiology. 2015; 23(10):598-605
  3. Andreani, E. Hesse and M. Vos. Prokaryote genome fluidity is dependent on effective population size. 2017 ISME J doi:10.1038/ismej.2017.36
  4. McInerney, James O., Alan McNally, and Mary J. O’Connell. “Why prokaryotes have pangenomes.” Nature Microbiology. 2017 28; 2:17040. doi:10.1038/nmicrobiol.2017.40

I am second supervisor (along with Prof Sam Sheppard at Bath) on a project led by Prof Ben Raymond at the University of Exeter:

Clone wars in niche space: exploring the evolutionary and genetic basis for bacterial species

Understanding the forces that shape bacterial genetic variation is a fundamental problem in microbiology.  Classifying bacteria into meaningful species groups is also essential for applied microbiology and ecology. Many bacterial species have been shown to exhibit extensive variation in gene repertoires, where a set of core genes shared by all strains are supplemented with a set of accessory genes that are only present in a subset of strains.  The ability to exploit particular niches is thought to depend on the acquisition of a range of accessory genes, typically acquired via horizontal gene transfer (Vos et al. 2015).  However, genetic variation in core genes shared between different strains is often associated with ecological niche (Raymond et al 2010, Zheng et al 2017)(Figure 1), suggesting that variation in core genes may be ecologically significant.

This project will explore the extent to which core genetic variation arises from neutral genetic drift process and from positive selection in distinct habitats, a question with broad importance for understanding bacterial biology and evolution.  For instance, many isolates of economic and therapeutic importance (Bacillus thuringiensis biopesticides, Escherichia coli probiotics etc) are closely related to isolates capable of causing disease.  In both these cases, humans consume large doses of viable microbes in food or as therapeutic agents.  Understanding the potential of beneficial bacteria to cause harm or acquire harmful genes is particularly important for assessing the safety of these uses.   If core genetic variation limits virulence or niche shifts then the risk of these applications will be substantially reduced  (Raymond & Federici 2017).

Bacillus thuringiensis, in particular, has an excellent safety record and is the most widely applied microbial insecticide, facilitating environmentally friendly mosquito control and pest management.  Nevertheless, disagreements regarding its ecological niche, and it taxonomic status relative to Bacillus cereus, a causative agent of diarrhea, have threatened its continued use in the European Union.  In this project, the student will (1) carry out genome sequencing and phenotypic characterization of isolates from natural populations (2) apply experimental evolution and re-sequencing approaches to look for convergent adaptive mutations in novel niches (3) use CRISPR-Cas9 genome editing to introduce putative adaptive alleles into different genetic backgrounds.

Raymond, B., & Federici, B.A. (2017).FEMS Microbiology and Ecology.  doi: 10.1093/femsec/fix084

Zheng, J., Gao, Q., Liu, L., Liu, H., Wang, Y., Peng, D., Ruan, L., Raymond, B., & Sun., M.  (2017) mBio 8:e 00822-17. doi: 10.1128/mBio.00822-17.

Raymond, B., Wyres, K., Sheppard, S., Ellis, R.J., Wright, D.J., & Bonsall, M.B (2010). PLoS Pathogens 6(5): e1000905.

Vos, M., Hesselman, M., Te Beek, T., van Passel, M.,Eyre-Walker, A. (2015) Trends Microbiol 23.10: 598-605

If this seems of interest, please check the BBSRC SW BioSciences DTP website. The application deadline is Midnight, Monday 4th December 2017.

 

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Group Update

High time for another Group Update, as I have a great bunch of (inter)national students working in the lab at the moment. Back left on the photo is Rafael Hernandez (USA), who is a second year Medical Student at Stony Brook University in New York. He has obtained funding for a two-month summer project and he is busy injecting environmental samples in Galleria wax moth larvae to detect pathogenic strains. (Scruffy person back right is yours truly). At the front from left to right: Nika Lo (Hong Kong) who is a CLES MSc student but working with us in the Medical School. In collaboration with Prof. Will Gaze, Prof. Tamara Galloway and Research Fellow Uli Klumper, Nika is testing for interactions of microplastic contamination and antibiotic contamination. Tiffany Morcom (Kernow, UK), an MSc by Research student who is looking at the relationship between seaweed colonization and bacterial antibiotic resistance (co-supervised by Will Gaze). Claudia Cappello (Italy) is an MSc student at the University of Padua who is visiting under the ERASMUS program to look at the effects of bacterial interactions on the production of antimicrobials. Daria Swigon (Poland) is a BSc student at the University of Gdansk who is also visiting under the ERASMUS program and will also look at antimicrobial production by interacting bacteria. All will endeavour to write a short blog post on their projects  in the near future.

Michiel Vos

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Michael Mosley vs The Superbugs

Last night the documentary “Michael Mosley vs The Superbugs aired on BBC4 (still available for a month on iPlayer for people in the UK). Anne Leonard, PhD and now postdoc with Will Gaze, is featured with her ‘Beach Bum‘ study (see also here). I can very briefly be seen too, collecting seaweeds for antimicrobial assays (something we need to finally publish this year!). I found being filmed for tv pretty brutal (trying to explain pretty complex science whilst squatting in a rock pool in a downpour with just an hour of filming), so that the interview did not make the final cut was probably for the best! Anyway, have a look, there is lots of interesting research that could hopefully help solve one of the most pressing health care problems of our time.

Michiel

P.S. a photo I made years ago of the cooperative soil bacterium Myxococcus xanthus (see this post) was used as part of the cover image for a new, very in-depth review on antibiotics produced by gram-negative bacteria by Masschelein, Jenner and Challis:

Presentation1

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Paper Out: Prokaryote genome fluidity is dependent on effective population size

Last year, I had the pleasure to host (now Dr.) Nadia Andreani from the University of Padua in Italy for a six-month visit in 2015. She did lab work on blue, food-spoiling Pseudomonas but we also did a population genomics meta-analysis, together with BioSciences/ESI Research Associate Dr. Elze Hesse. We tried to figure out what determines ‘genomic fluidity‘, or the degree to which different strains differ in gene content, using data on many species. From the Abstract:

Many prokaryote species are known to have fluid genomes, with different strains varying markedly in accessory gene content through the combined action of gene loss, gene gain via lateral transfer, as well as gene duplication. However, the evolutionary forces determining genome fluidity are not yet well understood. We here for the first time systematically analyse the degree to which this distinctive genomic feature differs between bacterial species. We find that genome fluidity is positively correlated with synonymous nucleotide diversity of the core genome, a measure of effective population size Ne. No effects of genome size, phylogeny or homologous recombination rate on genome fluidity were found. Our findings are consistent with a scenario where accessory gene content turnover is for a large part dictated by neutral evolution.

Michiel

The paper is Open Access:

Nadia Andrea Andreani, Elze Hesse and Michiel Vos. Prokaryote genome fluidity is dependent on effective population size. The ISME Journal advance online publication 31 March 2017; doi: 10.1038/ismej.2017.36

P.S. If you are interested in more on the background of genomic fluidity, please check out an Opinion paper from 2015 on the topic mentioned in this post.

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visit to the StrAda lab at the University of Nancy

Streptomyces producing the blue pigment actinorhodin

Last week I visited the ‘StrAda’ (Streptomyces Adaptation) lab of Pierre Leblond at the University of Nancy in France. Pierre and his colleagues, including Cyril Bontemps, have been isolating and genome-sequencing Streptomyces from very fine spatial scales which formed the basis of a good day of discussion. There are some interesting parallels between Streptomycetes and Myxobacteria: both are important components of soil communities (but also occur in marine environments), have large genomes with high GC content, partly multicellular life cycles which includes spore formation, and a rich diversity in secondary metabolites. There are many differences as well, Streptomyces for instance have linear chromosomes.  We discussed a plan to apply for a grant, combining our interests in the evolution of soil bacteria and recombination, which I hope to post about in the future. All in all a very stimulating trip, with great hosts, great discussion and some great French food as well!

Michiel

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Pipelines for bacterial evolutionary genomic analysis meeting in Bath

dsc_0223I attended a small, but very nice meeting last week at the University of Bath. The topic was the development of software to measure all important parameters in bacterial population genomics datasets. It was organized by Daniel Falush, who is very well known in the field of statistical genetics, developing methods such as STRUCTURE (used to study genomes from bacteria to humans). He has recently moved from Swansea to Bath along with Sam Sheppard and so with Ed Feil already there, this means Bath is now a world class centre of bacterial genomics. Unfortunately collaborators Adam Eyre-Walker and Xavier Didelot (see this and this recent paper) could not make it, but it was extremely useful to meet new people.

Michiel

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