Last week, a preprint describing a study which I have played a small part in was posted on bioRxiv. This paper (1) uses the Metaxa2 database (2) to tease out how much of an effect mitochondrial rRNA sequences have on studies of bacterial diversity in corals. And it turns out that it matters… a lot. Importantly, by supplementing the taxonomic databases with diverse mitochondrial rRNA sequences from the Metaxa2 database, ~97% of unique unclassified sequences could be resolved as mitochondrial, without increasing the level of misannotation in mock communities. Thus the study not only points to a problem, but also to its solution! You can read it all here.
- Sonnet D, Brown T, Bengtsson-Palme J, Padilla-Gamiño J, Zaneveld JR: The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome Analysis. bioRxiv, 431501 (2021). doi: 10.1101/2021.02.23.431501 [Link]
- 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 [Paper link]
The Microbiology Lab Pod is back with season two. This first episode was recorded on February 4 and has the theme of global change and effects on microbes. The crew (Johan Bengtsson-Palme, Emil Burman, Anna Abramova, Marcus Wenne, Sebastian Wettersten and Mahbuba Lubna Akter) is joined by two guests – Shumaila Malik and Emilio Rudbeck – and talks about the lab’s most recent publication, the one-year covid anniversary, the effects of global warming and other global change factors on soil microbial communities, and thawing permafrost.
The specific papers discussed in the pod (with approximate timings) are as follows:
- 5:45 – Abramova, A., Osińska, A., Kunche, H., Burman, E., Bengtsson-Palme, J., 2021. CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa1086
- 8:00 – Bengtsson, J., 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, 471–475. https://doi.org/10.1007/s10482-011-9598-6
- 29:30 – Donhauser, J., Niklaus, P.A., Rousk, J., Larose, C., Frey, B., 2020. Temperatures beyond the community optimum promote the dominance of heat-adapted, fast growing and stress resistant bacteria in alpine soils. Soil Biology and Biochemistry 148, 107873. https://doi.org/10.1016/j.soilbio.2020.107873
- 54:30 – Zhou, Z., Wang, C., Luo, Y., 2020. Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality. Nat Commun 11, 3072. https://doi.org/10.1038/s41467-020-16881-7
- 60:45 – Bahram, M., et al., 2018. Structure and function of the global topsoil microbiome. Nature 320, 1039. https://doi.org/10.1038/s41586-018-0386-6
- 68:15 – Lozano, G.L., et al., 2019. Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior. mBio 10. https://doi.org/10.1128/mBio.02846-18
- 70:15 – Bengtsson-Palme, J., 2020. Microbial model communities: To understand complexity, harness the power of simplicity. Computational and Structural Biotechnology Journal 18, 3987–4001. https://doi.org/10.1016/j.csbj.2020.11.043
- 72:00 – Sajjad, W., et al., 2020. Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth? Science of The Total Environment 735, 139275. https://doi.org/10.1016/j.scitotenv.2020.139275
- 74:00 – Yashina, S., et al., 2012. Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in Siberian permafrost. Proceedings of the National Academy of Sciences 109, 4008–4013. https://doi.org/10.1073/pnas.1118386109
- 74:30 – Pikuta, E.V., et al., 2005. Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska. International Journal of Systematic and Evolutionary Microbiology 55, 473–478. https://doi.org/10.1099/ijs.0.63384-0
- 75:00 – Bidle, K.D., Lee, S., Marchant, D.R., Falkowski, P.G., 2007. Fossil genes and microbes in the oldest ice on Earth. Proceedings of the National Academy of Sciences 104, 13455–13460. https://doi.org/10.1073/pnas.0702196104
- 75:15 – Timofeev, V., et al., 2019. Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia. PLoS ONE 14, e0209140. https://doi.org/10.1371/journal.pone.0209140
- 83:15 – Bengtsson-Palme, J., Boulund, F., Fick, J., Kristiansson, E., Larsson, D.G.J., 2014. Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in microbiology 5, 648. https://doi.org/10.3389/fmicb.2014.00648
- 84:00 – Bengtsson-Palme, J., Larsson, D.G.J., 2015. Antibiotic resistance genes in the environment: prioritizing risks. Nature reviews Microbiology 13, 396. https://doi.org/10.1038/nrmicro3399-c1
The podcast was recorded on February 4, 2021. If you want to reach out to us with comments, suggestions, or other feedback, please send an e-mail to podcast at microbiology dot se or contact @bengtssonpalme via Twitter. The music that can be heard on the pod is composed by Johan Bengtsson-Palme and is taken from the album Cafe Phonocratique.
Yes, Saturdays are somewhat weird days for software updates, but if you’re doing weekend work anyway, why wait to push bug fixes to the community? A very minor bug-fix update to Metaxa2 was released today, bringing the software to version 2.2.3.
Two things have changed in this version, both related to the genome mode. 1) We fixed a file reading bug in the ‘genome’ mode of the software. This bug caused the last sequence in an input FASTA file not to be read unless there was a newline after it. Since the ‘genome’ mode is rarely used by most users, we suspect not a lot of users have been affected by this bug.
2) While we were at it, we changed the behavior of the ‘genome’ mode to mirror that of the ‘auto’ mode, as the strict genome mode dropped sequences shorter than 2500 bp. We considered this behavior counter-intuitive to what most users would want, and has now changed the ‘genome’ mode to behave the same as the ‘auto’ mode and not drop short sequences.
No other changes have been made in this version. The update can be found at the Metaxa2 software page.
A new version of ITSx is released today. This minor update contains two minor bug fixes and two small new features.
The first bug was that ITSx returned empty sequences in the FASTA file for no detections for large input files. This has now been fixed.
The second bug fix is a bit more fuzzy and involved some fine-tuning of how large input files are handled in ITSx to stabilise E-value and score cut-offs.
The two new features are:
- The possbility to put the temporary directory in a custom location using the
- ITSx now warns when the input file contains sequences with identical identifiers, which usually leads to sequences being dropped from the input file.
The new update brings ITSx to version 1.1.3. Thanks for the users who have spotted bugs and suggested new features! Happy barcoding everyone!
I am happy to report that today a preprint on a recent collaboration with Christian Wurzbacher‘s group came out on bioRxiv. In the preprint study, we explore microbial communities in stormwater runoff from roads in terms of microbial composition and the potential for these settings to disseminate and select for antibiotic resistance, as well as metal resistance. My part of this study is quite small; I mostly provided the analysis of resistance genes on integrons, but it was a fun study and I look forward to work more with Christian and his excellent team!
We start the new year with a bang, or at least a new paper published. Bioinformatics put our paper (1) describing the software package CAFE online today (although it was accepted late last year). The CAFE package is a combination of Perl and R tools that can analyze data from paired transposon mutant sequencing experiments (2-4), generate fitness coefficients for each gene and condition, and perform appropriate statistical testing on these fitness coefficients. The paper is short, but shows that CAFE performs as good as the best competing tools (5-7) while being superior at controlling for false positives (you’ll have to dig into the supplement to find the data for that though).
Importantly, this is a collaborative effort by basically the entire research group from last spring: me, Haveela, Emil, Anna and our visiting student Adriana. A big thanks to all of you for working on this short but important paper! You can read the full paper here.
- Abramova A, Osińska A, Kunche H, Burman E, Bengtsson-Palme J (2021) CAFE: A software suite for analysis of paired-sample transposon insertion sequencing data. Bioinformatics, advance article doi: 10.1093/bioinformatics/btaa1086
- Chao,M.C. et al. (2016) The design and analysis of transposon insertion sequencing experiments. Nature reviews Microbiology, 14, 119–128.
- van Opijnen,T. and Camilli,A. (2013) Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nature reviews Microbiology, 11, 435–442.
- Goodman,A.L. et al. (2011) Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries. Nature Protocols, 6, 1969–1980.
- McCoy,K.M. et al. (2017) MAGenTA: a Galaxy implemented tool for complete Tn- Seq analysis and data visualization. Bioinformatics, 33, 2781– 2783.
- Zhao,L. et al. (2017) TnseqDiff: identification of conditionally essential genes in transposon sequencing studies. BMC Bioinformatics, 18.
- Zomer,A. et al. (2012) ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data. PLoS ONE, 7, e43012.
In the sixth episode of the Microbiology Lab Pod, recorded on December 17, the crew (Johan Bengtsson-Palme, Emil Burman, Haveela Kunche, Anna Abramova, Marcus Wenne, Sebastian Wettersten and Mahbuba Lubna Akter) talks about Haveela’s master thesis, virtual conferences and bring three Christmas themed papers.
The specific papers discussed in the pod (with approximate timings) are as follows:
- 13:00 – Fulcher, M.R., Bolton, M.L., Millican, M.D., et al., 2020. Broadening Participation in Scientific Conferences during the Era of Social Distancing. Trends in Microbiology. https://doi.org/10.1016/j.tim.2020.08.004
- 25:15 – de Clercq, N.C., Frissen, M.N., Levin, E., et al., 2019. The effect of having Christmas dinner with in-laws on gut microbiota composition. Human Microbiome Journal 13, 100058. https://doi.org/10.1016/j.humic.2019.100058
- 44:00 – Garcia-Lemos, A.M., Gobbi, A., et al., 2020. Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development. Frontiers in Microbiology 11. https://doi.org/10.3389/fmicb.2020.00198
- 56:15 – Halverson, L.J., Clayton, M.K., Handelsman, J., 1993. Population biology of Bacillus cereus UW85 in the rhizosphere of field-grown soybeans. Soil Biology and Biochemistry 25, 485–493. https://doi.org/10.1016/0038-0717(93)90074-L
- 65:00 – Glendinning, L., Genç, B., Wallace, R.J., Watson, M., 2020. Metagenomic analysis of the cow, sheep, reindeer and red deer rumen. bioRxiv. https://doi.org/10.1101/2020.02.12.945139
The podcast was recorded on December 17, 2020. If you want to reach out to us with comments, suggestions or other feedback, please send an e-mail to podcast at microbiology dot se or contact @bengtssonpalme via Twitter. The music that can be heard on the pod is composed by Johan Bengtsson-Palme and is taken from the album Cafe Phonocratique.
This is the fifth episode of the Microbiology Lab Pod and has been lying around on my computer almost finished for way too long. It was recorded on September 23, and the bigger-than-ever-before crew (Johan Bengtsson-Palme, Emil Burman, Haveela Kunche, Anna Abramova, Marcus Wenne, Sebastian Wettersten and Mahbuba Lubna Akter) is joined by Fanny Berglund to discuss computational discovery of novel resistance genes. We also discuss antibiotic resistance mechanisms, particularly in Pseudomonas aeruginosa.
The specific papers discussed in the pod (with approximate timings) are as follows:
- 5:30 – Berglund, F., Johnning, A., Larsson, D.G.J., Kristiansson, E., 2020. An updated phylogeny of the metallo-b-lactamases. Journal of Antimicrobial Chemotherapy 7. https://doi.org/10.1093/jac/dkaa392
- 5:45 – Berglund, F., Österlund, T., Boulund, F., Marathe, N.P., Larsson, D.G.J., Kristiansson, E., 2019. Identification and reconstruction of novel antibiotic resistance genes from metagenomes. Microbiome 7, 52. https://doi.org/10.1186/s40168-019-0670-1
- 6:00 – Berglund, F., Marathe, N.P., Österlund, T., Bengtsson-Palme, J., Kotsakis, S., Flach, C.-F., Larsson, D.G.J., Kristiansson, E., 2017. Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data. Microbiome 5, i29. https://doi.org/10.1186/s40168-017-0353-8
- 6:15 – Boulund, F., Berglund, F., Flach, C.-F., Bengtsson-Palme, J., Marathe, N.P., Larsson, D.G.J., Kristiansson, E., 2017. Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets. BMC Genomics 18, 438. https://doi.org/10.1186/s12864-017-4064-0
- 37:15 – Crippen, C.S., Jr., M.J.R., Sanchez, S., Szymanski, C.M., 2020. Multidrug Resistant Acinetobacter Isolates Release Resistance Determinants Through Contact-Dependent Killing and Bacteriophage Lysis. Frontiers in Microbiology 11. https://doi.org/10.3389/fmicb.2020.01918
- 52:15 – Leonard, A.F.C., Zhang, L., Balfour, A.J., Garside, R., Hawkey, P.M., Murray, A.K., Ukoumunne, O.C., Gaze, W.H., 2018. Exposure to and colonisation by antibiotic-resistant E. coli in UK coastal water users: Environmental surveillance, exposure assessment, and epidemiological study (Beach Bum Survey). Environment International 114, 326–333. https://doi.org/10.1016/j.envint.2017.11.003
- 53:30 – Bengtsson-Palme, J., Kristiansson, E., Larsson, D.G.J., 2018. Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews 42, 25. https://doi.org/10.1093/femsre/fux053
- 54:30 – Leonard, A.F.C., Zhang, L., Balfour, A.J., Garside, R., Gaze, W.H., 2015. Human recreational exposure to antibiotic resistant bacteria in coastal bathing waters. Environment International 82, 92–100. https://doi.org/10.1016/j.envint.2015.02.013
- 55:30 – Ahmed, M.N., Abdelsamad, A., Wassermann, T., et al., 2020. The evolutionary trajectories of P. aeruginosa in biofilm and planktonic growth modes exposed to ciprofloxacin: beyond selection of antibiotic resistance. npj Biofilms and Microbiomes 6. https://doi.org/10.1038/s41522-020-00138-8
- 69:30 – Rezzoagli, C., Archetti, M., Mignot, I., Baumgartner, M., Kümmerli, R., 2020. Combining antibiotics with antivirulence compounds can have synergistic effects and reverse selection for antibiotic resistance in Pseudomonas aeruginosa. PLOS Biology 18, e3000805. https://doi.org/10.1371/journal.pbio.3000805
- 79:45 – Allen, R.C., Popat, R., Diggle, S.P., Brown, S.P., 2014. Targeting virulence: can we make evolution-proof drugs? Nature reviews Microbiology 12, 300–308. https://doi.org/10.1038/nrmicro3232
- 80:45 – Köhler, T., Perron, G.G., Buckling, A., van Delden, C., 2010. Quorum Sensing Inhibition Selects for Virulence and Cooperation in Pseudomonas aeruginosa. PLoS Pathogens 6, e1000883. https://doi.org/10.1371/journal.ppat.1000883
The podcast was recorded on September 23, 2020. If you want to reach out to us with comments, suggestions or other feedback, please send an e-mail to podcast at microbiology dot se or contact @bengtssonpalme via Twitter. The music that can be heard on the pod is composed by Johan Bengtsson-Palme and is taken from the album Cafe Phonocratique.
This week, in a stroke of luck coinciding with my conference presentation on the same topic, my review paper on microbial model communities came out in Computational and Structural Biotechnology Journal. The paper (1) provides an overview of the existing microbial model communities that have been developed for different purposes and makes some recommendations on when to use what kind of community. I also make a deep-dive into community intrinsic-properties and how to capture and understand how microbes growing together interact in a way that is not predictable from how they grow in isolation.
The main take-home messages of the paper are that 1) there already exists a quite diverse range of microbial model communities – we probably don’t need a wealth of additional model systems, 2) there need to be better standardization and description of the exact protocols used – this is more important in multi-species communities than when species are grown in isolation, and 3) the researchers working with microbial model communities need to settle on a ‘gold standard’ set of model communities, as well as common definitions, terms and frameworks, or the complexity of the universe of model systems itself may throw a wrench into the research made using these model systems.
The paper was inspired by the work I did in Jo Handelsman‘s lab on the THOR model community (2), which I then have brought with me to the University of Gothenburg. In the lab, we are also setting up other model systems for microbial interactions, and in this process I thought it would be useful to make an overview of what is already out there. And that overview then became this review paper.
The paper is fully open-access, so there is really not much need to go into the details here. Go and read the entire thing instead (or just get baffled by Table 1, listing the communities that are already out there!)
- Bengtsson-Palme J: Microbial model communities: To understand complexity, harness the power of simplicity. Computational and Structural Biotechnology Journal, in press (2020). doi: 10.1016/j.csbj.2020.11.043
- Lozano GL, Bravo JI, Garavito Diago MF, Park HB, Hurley A, Peterson SB, Stabb EV, Crawford JM, Broderick NA, Handelsman J: Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior. mBio, 10, 2, e02846-18 (2019). doi: 10.1128/mBio.02846-18
I am very happy to share the news that our starting grant application to the Swedish Research Council has been granted 3.3 million SEK of funding for four years! This is fantastic news, as it allows us to further explore the interactions between bacteria in the human microbiome that are important for community stability and resilience to being colonized by pathogens. In the granted project, we will investigate environmental and genetic factors that are important for bacterial invasiveness and community stability in the human gastrointestinal tract.
Within the scope of the project, we will establish model bacterial communities and experimental systems for the human stomach and intestine. We will then investigate how disturbances, such as antibiotic exposure, change the interactions in these microbial communities and their long-term stability. Finally, we aim to identify genes that contribute to successful bacterial colonization or resilience to invasion of established communities in the human microbiome.
Aside from myself, Prof. Sara Lindén and Dr. Kaisa Thorell from the University of Gothenburg as well as Prof. Ed Moore at the university’s Culture Collection will be involved in this project in different ways. We will also collaborate with my former postdoc supervisor Prof. Jo Handelsman as well as Dr. Ophelia Venturelli at the University of Wisconsin-Madison. Finally, we will also collaborate with Dr. Åsa Sjöling at the Karolinska Institute. I look forward to work with you all over the coming four years! A big thanks to the Swedish Research Council for believing in this research and investing in making it happen!