Microbiology, Metagenomics and Bioinformatics

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

Welcome

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My name is Johan Bengtsson-Palme. I am currently a postdoctoral associate to Jo Handelsman’s lab at the Wisconsin Institute for Discovery, part of the University of Wisconsin-Madison. While in the US, I am on a temporary leave from my position as assistant professor at the Sahlgrenska Academy at University of Gothenburg, Sweden. My research concerns microbiology and microbial ecology, primarily focusing on investigating antibiotic resistance and interactions in bacterial communities through metagenomics and bioinformatics. I also have an interest in molecular taxonomy and improving the quality of reference databases. I work closely with the groups of Joakim Larsson, Jo Handelsman, Erik Kristiansson and Henrik Nilsson. To contact me, feel free to send an e-mail to my firstname.lastname@microbiology.se

A few days ago, my attention was turned to a duplicate in the COI database bundled with Metaxa2 2.2. While this duplicate sequence should not cause any troubles for Metaxa2 itself, it has created issues for people using the database itself together with, e.g., QIIME. Therefore, I have today issued a very very minor update to the Metaxa2 2.2 package as well as the entry in the Metaxa2 Database Repository, removing the duplicate sequence. I deemed that this was not significant enough to issue a new version, particularly as no code was changed and it did not cause issues for the software itself, so the version will stay at 2.2 for the time being. Happy barcoding!

Time flies, and my first 2019 publication (wait what?) is now out! It’s a chapter in the book “Management of Emerging Public Health Issues and Risks: Multidisciplinary Approaches to the Changing Environment(1), edited by Benoit Roig, Karine Weiss and Véronique Thireau. I have to confess to not having read the other chapters in the book yet, but I think the subject is exciting and hope for a lot of good reading over Christmas here!

My chapter deals with assessment and management of risks associated with antibiotic resistance in the environment (2), and particularly I make an attempt at clarifying the different types of risks and how to deal with them. In short, I partition resistance risks into two categories: dissemination risks and risks for acquisition of new types of resistance (see also 3). While the former category largely encompasses quantifiable risks, the latter is to a large extent impossible (or at least extremely hard) to quantify with current means. This means that we need to be a bit more creative in assessing, prioritizing and managing these risks. Some lessons can be learnt from other fields dealing with very uncertain (and rare) risks, such as asteroid impact assessment, nuclear energy accidents and ecosystem destabilization (4,5). Incorporating elements from such risk management schemes will be necessary to understand and delay emergence of novel resistance in the future.

All these aspects are further discussed in the book chapter (2), which I encourage everyone working with environmental antibiotic resistance risks to read!

References

  1. Roig B, Weiss K, Thoreau V (Eds.) Management of Emerging Public Health Issues and Risks: Multidisciplinary Approaches to the Changing Environment. Academic Press/Elsevier, UK (2019). doi: 10.1016/C2016-0-00995-6
  2. Bengtsson-Palme J: Assessment and management of risks associated with antibiotic resistance in the environment. In: Roig B, Weiss K, Thoreau V (Eds.) Management of Emerging Public Health Issues and Risks: Multidisciplinary Approaches to the Changing Environment, 243–263. Elsevier, UK (2019). doi: 10.1016/B978-0-12-813290-6.00010-X
  3. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews, 42, 1, 68–80 (2018). doi: 10.1093/femsre/fux053
  4. WBGU GACOGC: World in Transition: Strategies for Managing Global Environmental Risks. Springer
    Berlin Heidelberg, Berlin, Heidelberg (2000).
  5. Government Office for Science: Blackett Review of High Impact Low Probability Events. Department for
    Business, Innovation and Skills, London (2011).

Due to updates to PHP I have been forced into updating the backbone of this website (i.e. the WordPress installation). Since I have a few custom modifications to the site, there might be a few hours of unscheduled downtime over the next couple of weeks. I apologize for this (but the alternative would be to take the site down, which is not really a better option…) I hope you will have patience.

In the 2019 database issue, Nucleic Acids Research will include a new paper on the UNITE database for molecular identification of fungi (1). I have been involved in the development of UNITE in different ways since 2012, most prominently via the ITSx (2) and Atosh software which are ticking under the hood of the database.

In this update paper, we introduce a redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems. The database now contains around one million fungal ITS sequences that can be used for reference, which are clustered into roughly 459,000 species hypotheses (3). Each species hypothesis is assigned a digital object identifier (DOI), which enables unambiguous reference across studies. The paper is available as open access and the UNITE database is available open source from here.

References

  1. Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K: The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, Advance article, gky1022 (2018). doi: 10.1093/nar/gky1022
  2. Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Souza F, Amend AS, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson KM, Vik U, Veldre V, Nilsson RH: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing. Methods in Ecology and Evolution, 4, 10, 914–919 (2013). doi: 10.1111/2041-210X.12073
  3. 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

Let me get straight to something somewhat besides the point here: summer students can achieve amazing things! One such student I had the pleasure to work with this summer is Shruthi Magesh, and a preprint based on work she did with me at the Wisconsin Institute for Discovery this summer just got published on bioRxiv (1). The preprint describes a software tool called Mumame, which uses database information on mutations in DNA or protein sequences to search metagenomic datasets and quantifies the relative proportion of resistance mutations over wild type sequences.

In the preprint (1), we first of all show that Mumame works on amplicon data where we already knew the true outcome (2). Second, we show that we can detect differences in mutation frequencies in controlled experiments (2,3). Lastly, we use the tool to gain some further information about resistance patterns in sediments from polluted environments in India (4,5). Together these analyses show that one of the most central aspects for Mumame to be able to find mutations is having a very high number of sequenced reads in all libraries (preferably more than 50 million per library), because these mutations are generally rare – even in polluted environments and microcosms exposed to antibiotics. We expect Mumame to be a useful addition to metagenomic studies of e.g. antibiotic resistance, and to increase the detail by which metagenomes can be screened for phenotypically important differences.

While I did write the code for the software (with a lot of input from Viktor Jonsson, who also is a coauthor on the preprint, on the statistical analysis), Shruthi did the software testing and evaluations, and the paper would not have been possible hadn’t she wanted a bioinformatic summer project related to metagenomics, aside from her laboratory work. The resulting preprint is available from bioRxiv and the Mumame software is freely available from this site.

References

  1. Magesh S, Jonsson V, Bengtsson-Palme JQuantifying point-mutations in metagenomic data. bioRxiv, 438572 (2018). doi: 10.1101/438572 [Link]
  2. Kraupner N, Ebmeyer S, Bengtsson-Palme J, Fick J, Kristiansson E, Flach C-F, Larsson DGJ: Selective concentration for ciprofloxacin in Escherichia coli grown in complex aquatic bacterial biofilms. Environment International, 116, 255–268 (2018). doi: 10.1016/j.envint.2018.04.029 [Paper link]
  3. Lundström S, Östman M, Bengtsson-Palme J, Rutgersson C, Thoudal M, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach C-F, Larsson DGJ: Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms. Science of the Total Environment, 553, 587–595 (2016). doi: 10.1016/j.scitotenv.2016.02.103 [Paper link]
  4. Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in Microbiology, 5, 648 (2014). doi: 10.3389/fmicb.2014.00648 [Paper link]
  5. Kristiansson E, Fick J, Janzon A, Grabic R, Rutgersson C, Weijdegård B, Söderström H, Larsson DGJ: Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS ONE, Volume 6, e17038 (2011). doi:10.1371/journal.pone.0017038.

This week, a paper by my former roommate Katariina Pärnänen was published by Nature Communications. In the paper (1), we use shotgun metagenomics to show that infants carry more resistant bacteria in their gut than adults do, irrespective of whether they themselves have been treated with antibiotics or not. We also found that the antibiotic resistance gene and mobile genetic element profiles of infant feces are more similar to those of their own mothers than to those of unrelated mothers. This is suggestive of a pathway of transmission of resistance genes from the mothers, and importantly we find that the mobile genetic elements in breastmilk are shared with those of the infant feces, despite vast differences in their microbiota composition. Finally, we find that termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers are associated with higher abundances of specific ARGs in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but that the taxonomic composition of the microbiota still strongly dictates the overall load of resistance genes.

I am not going to dwell in to details of the study here, but I instead encourage you to read the paper (hey, it’s open access!) or the excellent popular summary that Katariina has already written. Finally, I want to emphasize the great work Katariina has put into this (I would know, since I shared room with her) and congratulate her on her own little infant!

Reference

  1. Pärnänen K, Karkman A, Hultman J, Lyra C, Bengtsson-Palme J, Larsson DGJ, Rautava S, Isolauri E, Salminen S, Kumar H, Satokari R, Virta M: Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. Nature Communications, 9, 3891 (2018). doi: 10.1038/s41467-018-06393-w [Paper link]

On Friday, Molecular Ecology Resources put online Christian Wurzbacher‘s latest paper, of which I am also a coauthor. The paper presents three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats, covering all the ribosomal markers (ETS, SSU, ITS1, 5.8S, ITS2, LSU, and IGS) (1). This paper is important because it introduces a technique to utilize third generation sequencing (PacBio and Nanopore) to generate high‐quality reference data (equivalent or better than Sanger sequencing) in a high‐throughput manner. The paper shows that the quality of the Nanopore generated sequences was 99.85%, which is comparable with the 99.78% accuracy described for Sanger sequencing.

My main contribution to this paper is the consensus sequence generation script – Consension – which is available from my software page. Importantly, there are huge gaps in the reference databases we use for taxonomic classification and this method will facilitate the integration of reference data from all of the ribosomal markers. We hope that this work will stimulate large-scale generation of ribosomal reference data covering several marker genes, linking previously spread-out information together.

Reference

  1. Wurzbacher C, Larsson E, Bengtsson-Palme J, Van den Wyngaert S, Svantesson S, Kristiansson E, Kagami M, Nilsson RH: Introducing ribosomal tandem repeat barcoding for fungi. Molecular Ecology Resources, Accepted article (2018). doi: 10.1111/1755-0998.12944 [Paper link]

Last week, I uploaded a new database to the Metaxa2 Database Repository, called DAIRYdb. DAIRYdb (1) is a manually curated reference database for 16S rRNA amplicon sequences from dairy products. Significant efforts have been put into improving annotation algorithms, such as Metaxa2 (2), while less attention has been put into curation of reliable and consistent databases (3). Previous studies have shown that databases restricted to the studied environment improve unambiguous taxonomy annotation to the species level, thanks to consistent taxonomy, lack of blanks and reduced competition between different reference taxonomies (4-5). The usage of DAIRYdb in combination with different classification tools allows taxonomy annotation accuracy of over 90% at species level for microbiome samples from dairy products, where species identification is mandatory due to the affiliation to few closely related genera of most dominant lactic acid bacteria.

The database can be added to your Metaxa2 (version 2.2 or later) installation by using the following command:

metaxa2_install_database -g SSU_DAIRYdb_v1.1.2

Further adaptations of the DAIRYdb can be found on GitHub and the preprint has been deposited in BioRxiv (1). DAIRYdb was developed by Marco Meola, Etienne Rifa and their collaborators, who also provided most of the text for this post. Thanks Marco for this excellent addition to the database collection!

References

  1. Meola M, Rifa E, Shani N, Delbes C, Berthoud H, Chassard C: DAIRYdb: A manually curated gold standard reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products. bioRxiv, 386151 (2018). doi: 10.1101/386151
  2. Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources, 15, 6, 1403–1414 (2015). doi: 10.1111/1755-0998.12399
  3. Edgar RC: Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences. PeerJ, 6, e4652 (2018). doi: 10.7717/peerj.4652
  4. Ritari J, Salojärvi J, Last L, de Vos WM: Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database. BMC Genomics, 16, 1, 1056 (2015). doi: 10.1186/s12864-015-2265-y
  5. Newton ILG, Roeselers G: The effect of training set on the classification of honey bee gut microbiota using the naïve bayesian classifier. BMC Microbiology, 12, 1, 221 (2012). doi: 10.1186/1471-2180-12-221

I’m really late at this ball for a number of reasons, but last week Nature published our paper on the structure and function of the global topsoil microbiome (1). This paper has a long story, but in short I got contacted by Mohammad Bahram (the first author) about two years ago about a project using metagenomic sequencing to look at a lot of soil samples for patterns of antibiotic resistance gene abundances and diversity. The project had made the interesting discovery that resistance gene abundances were linked to the ratio of fungi and bacteria (so that more fungi was linked to more resistance genes). During the following year, we together worked on deciphering these discoveries, which are now published in Nature. The paper also deals with the taxonomic patterns linked to geography (1), but as evident from the above, my main contribution here has been on the antibiotic resistance side.

In short, we find that:

  • Bacterial diversity is highest in temperate habitats, and lower both closer to the equator and the poles
  • For bacteria, the diversity of biological functions follows the same pattern, but for fungi, the functional diversity is higher closer to the poles and the equator
  • Higher abundance of fungi is linked to higher abundance and diversity of antibiotic resistance genes. Specifically, this is related to known antibiotic producing fungal lineages, such as Penicillium and Oidiodendron. There also seems to be a link between the Actinobacteria, encompassing the antibiotic-producing bacterial genus of Streptomyces and higher resistance gene diversity.
  • Similar relationships between the fungus-like Oomycetes and resistance genes was also found in ocean samples from the Tara Oceans project (2)

The results of this study indicate that both environmental filtering and niche differentiation determine soil microbial composition, and that the role of dispersal limitation is minor at this scale. Soil pH and precipitation seems to be the strongest drivers of community composition. Furthermore, we interpret our data to reveal that inter-kingdom antagonism is important in structuring microbial communities. This speaks against the notion put forward that antibiotic resistance genes might not have a resistance function in natural settings (3). That said, the most likely explanation here is probably a bit of both warfare and repurposing of genes. Soil seems to be the largest untapped source of resistance genes for human pathogens (4), and the finding that natural antagonism may be driving resistance gene diversification and enrichment may be important for future management of environmental antibiotic resistance (5,6).

It was really great to work with Mohammad and his team, and I sure hope that we will collaborate again in the future. The entire paper can be found in the issue of Nature coming out this week, and is already online at Nature’s website.

References

  1. Bahram M°, Hildebrand F°, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P: Structure and function of the global topsoil microbiome. Nature, 560, 233–237 (2018). doi: 10.1038/s41586-018-0386-6
  2. Sunagawa S et al. Structure and function of the global ocean microbiome. Science 348, 6237, 1261359 (2015). doi: 10.1126/science.1261359
  3. Aminov RI: The role of antibiotics and antibiotic resistance in nature. Environmental Microbiology, 11, 12, 2970-2988 (2009). doi: 10.1111/j.1462-2920.2009.01972.x
  4. Bengtsson-Palme J: The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants – but not always. Microbiome, 6, 125 (2018). doi: 10.1186/s40168-018-0508-2
  5. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews, 42, 1, 68–80 (2018). doi: 10.1093/femsre/fux053
  6. Larsson DGJ, Andremont A, Bengtsson-Palme J, Brandt KK, de Roda Husman AM, Fagerstedt P, Fick J, Flach C-F, Gaze WH, Kuroda M, Kvint K, Laxminarayan R, Manaia CM, Nielsen KM, Ploy M-C, Segovia C, Simonet P, Smalla K, Snape J, Topp E, van Hengel A, Verner-Jeffreys DW, Virta MPJ, Wellington EM, Wernersson A-S: Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. Environment International, 117, 132–138 (2018).

I have just published a popular-science-for-scientists type of post at the Nature Microbiology Community about my recent paper published in Microbiome. I personally think that it might be worth a read, so feel free to head over here and read it!