Siv Andersson lab

The research in Siv Andersson´s group aims at understanding how intracellular bacteria and organelles evolve. Knowledge about host-adapted bacterial genomes is important for our understanding of the interplay between bacteria and higher organisms. Which gene functions are required for life within and outside already existing cells? How should these genes be organized and embedded inside the cell to provide beneficial functions for the host? A long-term goal is to have such a deep knowledge of these processes that we can design bacterial genomes with new, host-beneficial functions.
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Research projects
Evolution of host-adapted bacteria
The research in Siv Andersson´s group aims at understanding how intracellular bacteria and organelles evolve. A long-term goal is to design novel intracellular bacterial genomes with beneficial functions using synthetic biology. To achieve this goal we need a basic understanding of the interplay between bacteria and hosts, and why organelles and mutualistic bacteria need a distinct genome. Below are a few examples of ongoing projects.
Why do some organisms need bacteria?
Many host-adapted bacterial populations produce nutrients that the host cannot get from its diet. Others produce antimicrobials to defend the host against pathogens and other invading microbes. The secreted compounds benefit the whole bacterial population and/or the host, but are costly to make for the individual bacterial cell. Hence there is a risk that cheaters arise that benefit from the secreted compounds without contributing to their production. In this project, we use bacteria adapted to mammals and insects as model systems to study how the production of the public good is organized and how cheaters are avoided in the bacterial population.
Why do some cells need internal compartments?
Eukaryotic cells contain several membrane-bound compartments, such as for example mitochondria. Bacterial cells do not normally contain internal membranes. But there are exceptions. To understand why and how complex cellular architectures arise we study bacterial cells that contain a network of internal membranes and connected vesicles. In this project, we use comparative, functional and ecological genomics to learn more about cellular compartmentalization.
Why do some compartments need a genome?
We have recently published results that support the hypothesis that mitochondria need a genome to avoid that the encoded proteins are transported to the Endoplasmatic Reticulum. Transporting proteins between compartments inside the cell requires a multitude of signals to ensure that each protein reaches its final destination. In this project, we use bioinformatics and experimental methods to learn more about why mitochondria need a distinct genome.
This work is supported by the Swedish Research Council (VR) and the Knut and Alice Wallenberg Foundation (KAW). In addition, we participate in several collaborative projects: Uppsala Center for Evolutionary Genomics (supported by VR), the Human Microbiome in Health and Disease (supported by KAW) and Inland Water Ecosystems in the Global Carbon Cycle – Towards a Mechanistic Understanding (supported by KAW).
Group members
Publications
Folded Alpha Helical Putative New Proteins from Apilactobacillus kunkeei
Part of Journal of Molecular Biology, 2024
- DOI for Folded Alpha Helical Putative New Proteins from Apilactobacillus kunkeei
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Part of Genome Biology and Evolution, 2024
- DOI for Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota
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TADA: Taxonomy-Aware Dataset Aggregator
Part of Bioinformatics, 2023
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Genome Evolution of a Symbiont Population for Pathogen Defense in Honeybees
Part of Genome Biology and Evolution, 2022
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Antibiotics should not be used for back/leg pain
Part of Acta Orthopaedica, p. 244-246, 2021
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Part of The spine journal, p. 1233-1235, 2021
Part of Frontiers in Microbiology, 2021
- DOI for The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns
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Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum
Part of Genome Biology and Evolution, p. 1528-1548, 2020
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Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures
Part of Molecular biology and evolution, p. 1020-1040, 2020
Rethinking microbial symbioses
Part of FEMS Microbiology Letters, 2020
Bacteria: back pain, leg pain and Modic sign-a surgical multicentre comparative study
Part of European spine journal, p. 2981-2989, 2019
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Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
Part of The ISME Journal, p. 742-755, 2018
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Genome Evolution of Bartonellaceae Symbionts of Ants at the Opposite Ends of the Trophic Scale
Part of Genome Biology and Evolution, p. 1687-1704, 2018
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Origin and evolution of the Bartonella Gene Transfer Agent
Part of Molecular biology and evolution, p. 451-464, 2018
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Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere
Part of Fungal Biology, p. 231-240, 2018
Part of Genome Biology and Evolution, p. 2560-2579, 2017
- DOI for Switches in Genomic GC Content Drive Shifts of Optimal Codons under Sustained Selection on Synonymous Sites
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Part of International Journal of Systematic and Evolutionary Microbiology, p. 4923-4929, 2017
- DOI for Tuwongella immobilis gen. nov., sp nov., a novel non-motile bacterium within the phylum Planctomycetes
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Why mitochondria need a genome revisited
Part of FEBS Letters, p. 65-75, 2017
Stress management strategies in single bacterial cells
Part of Proceedings of the National Academy of Sciences of the United States of America, p. 3921-3923, 2016
Part of Scientific Reports, p. 1-11, 2016
- DOI for The genome of Rhizobiales bacteria in predatory ants reveals urease gene functions but no genes for nitrogen fixation
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Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria
Part of The ISME Journal, p. 1902-1914, 2016
Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut
Part of BMC Genomics, 2015
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Part of Genome Biology and Evolution, p. 1455-1473, 2015
- DOI for Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees
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Mitochondrial genomes are retained by selective constraints on protein targeting
Part of Proceedings of the National Academy of Sciences of the United States of America, p. 10154-10161, 2015
Part of The ISME Journal, p. 2373-2385, 2015
Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae
Part of BMC Genomics, p. 1097, 2014
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Part of Genome Biology and Evolution, p. 2240-2257, 2014
- DOI for Missing Genes, Multiple ORFs, and C-to-U Type RNA Editing in Acrasis kona (Heterolobosea, Excavata) Mitochondrial DNA
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Part of Environmental Microbiology, p. 2682-2698, 2014
- DOI for Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics
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Single cell genomics of deep ocean bacteria
Part of Trends in Microbiology, p. 233-234, 2014
Part of PLOS Genetics, 2013
- DOI for A Gene Transfer Agent and a Dynamic Repertoire of Secretion Systems Hold the Keys to the Explosive Radiation of the Emerging Pathogen Bartonella
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Part of PLOS ONE, 2013
- DOI for Adaptive Mutations and Replacements of Virulence Traits in the Escherichia coli O104:H4 Outbreak Population
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Part of PLOS ONE, 2013
- DOI for Comparative and Phylogenomic Evidence that the Alphaproteobacterium HIMB59 is not a Member of the Oceanic SAR11 Clade
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Comparative Genomics of Wolbachia and the Bacterial Species Concept
Part of PLOS Genetics, 2013
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No Ancient DNA Damage in Actinobacteria from the Neanderthal Bone
Part of PLOS ONE, 2013
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Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade
Part of Genome Biology, 2013
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Part of PLOS ONE, 2013
- DOI for Testing the Reproducibility of Multiple Displacement Amplification on Genomes of Clonal Endosymbiont Populations
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The Diversity and Evolution of Wolbachia Ankyrin Repeat Domain Genes
Part of PLOS ONE, 2013
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A genome-wide study of recombination rate variation in Bartonella henselae
Part of BMC Evolutionary Biology, p. 65, 2012
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Bacterial genomes: Next generation sequencing technologies for studies of bacterial ecosystems
Part of Current Opinion in Microbiology, p. 603-604, 2012
Genomic diversity of the 2011 European outbreaks of Escherichia coli O104:H4
Part of Proceedings of the National Academy of Sciences of the United States of America, 2012
Part of PLOS Genetics, 2012
- DOI for Large-Scale Introgression Shapes the Evolution of the Mating-Type Chromosomes of the Filamentous Ascomycete Neurospora tetrasperma
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Part of PLOS ONE, 2011
Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade
Part of Molecular biology and evolution, p. 599-615, 2011
Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents
Part of BMC Genomics, p. 152, 2010
genoPlotR: comparative gene and genome visualization in R
Part of Bioinformatics, p. 2334-2335, 2010
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Part of Molecular Ecology, p. 2241-2255, 2010
Part of Journal of Bacteriology, p. 3352-3367, 2010
Computational Resources in Infectious Disease: Limitations and Challenges
Part of PloS Computational Biology, 2009
Part of PLoS genetics, 2009
The alpha-proteobacteria: the Darwin finches of the bacterial world
Part of Biology Letters, p. 429-432, 2009