Microbiology, Metagenomics and Bioinformatics

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

Browsing Posts in Thoughts

I just wanted to notify anyone who might be interested in following my more personal reflections on my month in Wisconsin (and in Michigan over EDAR4) that I will be updating my Wisconsin Blog at this site (hopefully) regularly. The blog updates are not visible on the first page, so you will have to actively go to the Wisconsin Blog page by clicking in the upper right of the page.

Mitochondrial DNA Part B today published a mitochondrial genome announcement paper (1) in which I was involved in doing the assemblies and annotating them. The paper describes the mitogenome of Calanus glacialis, a marine planktonic copepod, which is a keystone species in the Arctic Ocean. The mitogenome is 20,674 bp long, and includes 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. While this is of course note a huge paper, we believe that this new resource will be of interest in understanding the structure and dynamics of C. glacialis populations. The main work in this paper has been carried out by Marvin Choquet at Nord University in Bodø, Norway. So hats off to him for great work, thanks Marvin! The paper can be read here.


  1. Choquet M, Alves Monteiro HJ, Bengtsson-Palme J, Hoarau G: The complete mitochondrial genome of the copepod Calanus glacialis. Mitochondrial DNA Part B, 2, 2, 506–507 (2017). doi: 10.1080/23802359.2017.1361357 [Paper link]

Today, I started my new position at the University of Gothenburg as a non-tenured assistant professor (forskarassistent)*. In essence, this means that I have a position funded by my own grant until the end of 2020, although I will be on a leave-of-absence while doing my PostDoc with Jo Handelsman in Wisconsin. Speaking of which, I will be leaving to the US on Thursday next week for a month of setting things up at her lab (and also going to the EDAR4 conference in Lansing). I will return to Sweden in mid-September and leave for the US for real early next year.

In terms of actual work, this change of position will not mean very much at the moment. I will continue to do the same things for some time, and I will remain closely associated with Joakim Larsson’s lab at the Dept. of Infectious Diseases. And luckily, I will retain my lovely roommates for at least the time being. In the long run, however, this means that I will shift my research focus slightly, away from antibiotic resistance risk management towards interactions in microbial communities (still related to antibiotics though). Exciting times ahead!

* For some reason, the university administration refuses to call this position assistant professor in English at this time, instead referring to the position as “Postdoctoral research fellow”. I guess that it might be bloody annoying explaining that this is not the same as “postdoctoral researcher” and virtually everywhere else would be called “(non-tenured) assistant professor”, but then on the other hand, who cares about titles anyway?

I have just returned from a week of vacation in Sicily (almost without internet access), so I am a tad late to this news, but earlier this week Infection and Immunity published our paper on the Helicobacter pylori transcriptome in gastric infection (and early stages of carcinogenesis), and how that relates to the transcriptionally active microbiota in the stomach environment (1). This paper has been long in the making (an earlier version of it was included in Kaisa Thorell’s PhD thesis (2)), but some late additional analyses did substantially strengthen our confidence in the suggestions we got from the original data.

In the paper (1) we use metatranscriptomic RNAseq to investigate the composition of the viable microbial community, and at the same time study H. pylori gene expression in stomach biopsies. The biopsies were sampled from individuals with different degrees of H. pylori infection and/or pre-malignant tissue changes. We found that H. pylori completely dominates the microbiota in infected individuals, but (somewhat surprisingly) also in the majority of individuals classified as H. pylori uninfected using traditional methods. This confirms previous reports that have detected minute quantities of H. pylori also in presumably uninfected individuals (3-6), and raises the question of how large part of the human population (if any) that is truly not infected/colonized by H. pylori. The abundance of H. pylori was correlated with the abundance of Campylobacter, Deinococcus, and Sulfurospirillum. It is unclear, however, if these genera only share the same habitat preferences as Helicobacter, or if they are specifically promoted by the presence of H. pylori (or tissue changes induced by it). We also found that genes involved in pH regulation and nickel transport were highly expressed in H. pylori, regardless of disease stage. As far as we know, this study is the first to use metatranscriptomics to study the viable microbiota of the human stomach, and we think that this is a promising approach for future studies on pathogen-microbiota interactions. The paper (in unedited format) can be read here.


  1. Thorell K, Bengtsson-Palme J, Liu OH, Gonzales RVP, Nookaew I, Rabeneck L, Paszat L, Graham DY, Nielsen J, Lundin SB, Sjöling Å: In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis. Infection and Immunity, accepted manuscript (2017). doi: 10.1128/IAI.00031-17 [Paper link]
  2. Thorell K: Multi-level characterization of host and pathogen in Helicobacter pylori-associated gastric carcinogenesis. Doctoral thesis, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg (2014). [Link]
  3. Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Reman DA: Molecular analysis of the bacterial microbiota in the human stomach. PNAS, 103:732-737 (2006).
  4. Dicksved J, Lindberg M, Rosenquist M, Enroth H, Jansson JK, Engstrand L: Molecular characterization of the stomach microbiota in patients with gastric cancer and in controls. Journal of Medical Microbiology, 58:509-516 (2009).
  5. Maldonado-Contreras A, Goldfarb KC, Godoy-Vitorino F, Karaoz U, Contreras M, Blaser MJ, Brodie EL, Dominguez-Bello MG: Structure of the human gastric bacterial community in relation to Helicobacter pylori status. ISME Journal, 5:574-579 (2011).
  6. Li TH, Qin Y, Sham PC, Lau KS, Chu KM, Leung WK: Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis. Scientific Reports, 7:44935 (2017).

In two weeks time, on the 15th of June, I will participate in a seminar organised by Landstingens nätverk för läkemedel och miljö (the Swedish county council network for pharmaceuticals and environment; the seminar will be held in Swedish) in Stockholm. I will give a talk on our proposed emission limits for antibiotics published last year (the paper is available here), but there will also be talks on wastewater treatment, sustainable pharmaceutical usage and environmental standards for pharmaceuticals. The full program can be found here, and you may register here until June 9. The seminar is free of charge.

And if you are interested in this, I can also recommend the webinar given by Healthcare Without Harm next week (on June 8), which will deal with sustainable procurement as a means to deal with pharmaceutical pollution in the environment. I will at least tune in to hear how the discussion goes here.

In March, I attended a workshop on the role of NGS technologies in the coordinated action plan against antimicrobial resistance, organised by JRC in Italy. I was, together with 14 other experts, invited to discuss where and how sequencing can be used to investigate and manage antibiotic resistance. The report from the workshop has just recently been published, and is available here. There will be follow-up activities on this workshop, which I also hope that I will be able to participate in, since this is an important and very interesting pet topic of mine.


  • Angers A, Petrillo P, Patak, A, Querci M, Van den Eede G: The Role and Implementation of Next-Generation Sequencing Technologies in the Coordinated Action Plan against Antimicrobial Resistance. JRC Conference and Workshop Report, EUR 28619 (2017). doi: 10.2760/745099 [Link]
  • This morning as I was leaving my daughter at daycare, I got asked by one of the other kids at kindergarten what I do for work. Trying to communicate what you do as a researcher to a five-year-old is a quite interesting task. Five-year-olds are smart – but not very knowledgeable, which leads to very interesting turns to the conversation. Here’s the entire dialogue, transcribed from memory and translated to English:

    – What do you do for work?
    – I work at the hospital, but I’m not a doctor.
    – So you are a psychologist?
    – No, I am something called a researcher. I try to understand why bacteria turn evil and make us sick.
    – Does someone need to do that?
    – Not really. But if we can understand why bugs go bad, we may be able to be sick for much shorter in the future. Or perhaps not get sick at all.
    – Okay. Isn’t that hard?
    – Yes it is.
    – Okay. Bye!

    A few things I learned from this conversation: 1) explaining your research to young kids really makes you think about how to present what you do. 2) Kids really question the usefulness of your work (“Does someone need to do that?”). This is actually quite cool, because you need to think about how useful your work really is, in terms that a five-year-old can understand. 3) Society is awesome! To some extent, my work is a “luxury job”, i.e. maybe someone does not need to do my work, but it something we can afford because we share responsibilities and work together as a society, improving (hopefully) the world for all of us. In some sense, nobody strictly needs to be building houses; everyone could just build their own cottage. But building houses improve the standards for everyone, setting time aside for curing diseases, making music, researching microbial interactions, gardening, coffee roasting… Society is awesome.

    First of all, I am happy to announce that the webinar I participated in on the (un)recognised pathways of AMR: Air pollution and food, organised by Healthcare Without Harm is now put online so that you can view it, in case you missed out on this event. To be honest it is probably not one of my best public appearances, but the topic is highly interesting.

    Second, next week I am taking part in Vetenskapsfestivalen – the Science Festival in Gothenburg. Specifically, I will be on of the researchers participating in the Science Roulette, taking place in the big ferris wheel at Liseberg. This will take place between 17.00 and 18.00 on May 11th. The idea is that people will be paired with researchers in diverse subjects, of which I am one, and then have a 20 minute chat while the wheel is spinning. Sounds like potential for lot of fun, and I hope to see you there! I will discuss antibiotic resistance, and for how much longer we can trust that our antibiotics will work.

    Sorry for the late notice, but if you have half an hour to spare later today I will discuss our findings on resistance genes in Beijing air on a webinar organised by Healthcare Without Harm on “The (un)recognised pathways of AMR: Air pollution and food“. Tune in a few minutes before 16.00 CEST!

    I am happy to announce that the opinion/review piece I wrote for Current Opinion in Food Science has been published. The paper (1) extends on some of my thoughts on how high-throughput sequencing and metagenomics can aid in risk assessment of antibiotic resistant bacteria that I outlined in my PhD thesis (2), but specifically focuses on the food supply chain and its role in resistance dissemination and selection.

    In the paper, I argue for that the food supply chain is a special type of setting in the resistance puzzle, as it not only serves as a connection between environmental habitats for bacteria and humans, but also sometimes presents a substantial selection for resistance, due to use of antibiotics in agri- and aquaculture. International food standards are clear that both selection and dissemination of foodborne resistance should be considered in the risk analysis of food production (3). However, the current main use of DNA sequencing in food safety is whole genome sequencing to delineate which specific strains that are involved in foodborne disease outbreaks, including the resistance factors they may carry (4,5). Further, I argue that while shotgun metagenomics could be used to screen samples for a large number of genes involved in resistance and virulence in the food supply chain, it would at present be very costly and therefore of doubtful benefit to employ in routine screening programs. Still, metagenomics can contribute knowledge that can be used in quantitative risk assessment of antibiotic resistance in the food supply chain.

    The entire paper can be read here.


    1. Bengtsson-Palme J: Antibiotic resistance in the food supply chain: Where can sequencing and metagenomics aid risk assessment? Current Opinion in Food Science, in press (2017). doi: 10.1016/j.cofs.2017.01.010 [Paper link]
    2. Bengtsson-Palme J: Antibiotic resistance in the environment: a contribution from metagenomic studies. Doctoral thesis (medicine), Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 2016. [Link]
    3. Codex Alimentarius Commission: Guidelines for risk analysis of foodborne antimicrobial resistance. Food and Agriculture Organization of the United Nations & World Health Organization2011. [Link]
    4. Franz E, Gras LM, Dallman T: Significance of whole genome sequencing for surveillance, source attribution and microbial risk assessment of foodborne pathogens. Current Opinion in Food Science, 8, 74-79 (2016). doi: 10.1016/j.cofs.2016.04.004
    5. Stasiewicz MJ, Bakker den HC, Wiedmann M: Genomics tools in microbial food safety. Current Opinion in Food Science, 4, 105-110 (2015). doi: 10.1016/j.cofs.2015.06.002