Our work on metagenomic data to understand community functioning of microbes dates back to 2008, when we started to analyze the Global Ocean Sampling dataset for detoxification systems. Through the work with metagenomics projects, the lab has been involved in several software development efforts aiming to better extract and visualize information from the enormous datasets produced (Metaxa, Megraft, TriMetAss, PETKit, FARAO, Mumame). Currently, we use metagenomic sequencing data to analyze different environments for antibiotic resistance genes, and thereby try to uncover which risks for environmental resistance development and dissemination we should be most concerned about, as well as possible secondary effects of antibiotics on microbial communities.
Metagenomics is intertwined into some aspect of nearly all projects the lab is pursuing. For example, we have used metagenomic sequencing to study bacterial detoxification mechanisms in marine milieus, for deciphering the taxonomic and functional diversity of marine periphyton, for studying antibiotic resistance genes in diverse environments (including a polluted lake, sewage treatment plants, the human gut and artificial laboratory settings), and for charting out the relationships between the gastric microbiome and cancer development. Thus, metagenomics forms an integral part of our research activities, providing the foundation for studies on antibiotic resistance, the ecology of pathogens, microbial taxonomy, and ecosystem perturbations in various environments.
Open questions of interest
- How can we better derive useful information and identify meaningful differences between sample types using shotgun metagenomics?
- How to improve metagenomic sequence assembly for highly conserved regions, found in multiple contexts (a common problem for resistance genes)?
- How can metagenomics be used to target specific research questions, moving from being a hypothesis-generating tool to a hypothesis-driven one?
- Bengtsson-Palme J, Larsson DGJ, Kristiansson E: Using metagenomics to investigate human and environmental resistomes. Journal of Antimicrobial Chemotherapy, 72, 2690–2703 (2017). doi: 10.1093/jac/dkx199 [Paper link]
- Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A: Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities. BMC Genomics, 15, 749 (2014). doi: 10.1186/1471-2164-15-749 [Paper link]
- 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 [Paper link]
- 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]
- Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: The human gut microbiome as a transporter of antibiotic resistance genes between continents. Antimicrobial Agents and Chemotherapy, 59, 10, 6551-6560 (2015). doi: 10.1128/AAC.00933-15 [Paper link]
- 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, 85, 10, e00031-17 (2017). doi: 10.1128/IAI.00031-17 [Paper link]