New gene technology reveals the evolution of bacteria
Technical developments in recent decades have made it possible to characterize the genomes of every living thing. The study of the genomes of micro-organisms that have adapted to humans, animals and plants is adding further pieces to the puzzle. New DNA sequencing techniques are making it possible for Siv Andersson, professor of molecular evolution and Faculty at SciLifeLab, to make revolutionary discoveries about the origins and evolution of bacteria.
What is it that determines the onset and course of a disease? Decades of sequencing bacterial genomes are casting light upon the important role played by bacteria in health and the environment. Increased knowledge of the kinds of bacteria which cause diseases in humans and animals will help us to diagnose, cure and predict epidemic outbreaks in future, according to Siv Andersson.
“I want to understand the ecological and evolutionary history of bacteria. Where do they come from and how do disease-causing bacteria spread? Many of them originate from bacteria which have adapted well to other animal groups. There they don’t cause diseases but then the bacteria are transferred to humans by insects or ticks and before you know it we’ve been hit by various infectious diseases.”
Her research team at the Uppsala Biomedical Centre (BMC) has examined the genes of the typhus bacterium among others. Its genetic structure was the first to be completely mapped in Sweden and the results were published in the journal Nature in 1998. These days, the focus is upon putting the knowledge of bacterial genomes she has built up to practical use.
“For a long time, I’ve researched bacteria which interact with humans, animals, insects and other types of cells. Some of them are dangerous, others not at all and yet others are totally necessary for their hosts. Every possible variant exists. Where is the difference between deadly dangerous and necessary bacteria?”
The research team has studied one of these groups of bacteria, Bartonella, which has been isolated from people, dogs, cats and cattle as well as mice, elks and kangaroos. In order to discover a reason for the world-wide spread of these bacteria, Siv Andersson is presently studying related bacteria found in ants. She points out that there are many factors which determine whether bacteria will succeed in becoming established in humans.
“Human genes play an important part in deciding whether people are receptive to these infections. Bacteria can find their way in quite easily but whether they survive and what happens after this depends very heavily on the immune system. It also depends on whether they can spread to other people through air, water, food or via insects. Hygiene plays an important part in this.”
One group of bacteria which are believed to benefit their hosts are lactobacilli which are part of the lactic acid bacteria group. Researchers from Lund have isolated lactobacilli from the honey stomachs of bees. They recently began collaborating with Siv Andersson’s team and this has helped towards an understanding of how the genomes of lactic acid bacteria have evolved and adapted to their environment.
“The genetic structure of these bacteria is unique. The genes needed for what we call the housework – forming new cells and taking care of everything inside cells – make up one half of the genome and the genes needed to interact with the surrounding world are in the other half,” says Siv Andersson.
“The latter half also secretes products which we believe can eliminate competing bacteria. In the long term, perhaps it will be possible to find new alternatives to antibiotics using these bacteria.”
According to Siv Andersson, many bacteria with extremely small genomes cannot be cultured in laboratories. The key to studying these bacteria is called single-cell genomics.
“These days, one cell from a bacterium is enough to characterize most of its genome. In the past, if you wanted to study bacteria in aphids, you would have to collect several thousand aphids, dissect them under a microscope and pick out the bacteria from each one in order to get enough material to determine their genetic structure.”
At SciLifeLab at BMC, there is both advanced equipment for DNA sequencing and the expertise needed to analyse the data. The Bioinformatics Platform is part of a major programme for a national infrastructure financed by the Knut & Alice Wallenberg Foundation, the Swedish Research Council and SciLifeLab.
“Here, there is a pool of experts who take part in projects all over the country. It can take ten years to train a really good bioinformatician. Their expertise is needed to collate and analyse the enormous amount of data available these days and to pose complex, biological questions.
Facts Siv Andersson
Title: Professor of molecular evolution
Selected awards and achievements: Göran Gustafsson Prize for Molecular Biology 2005, member of the Royal Swedish Academy of Sciences 2005, Wallenberg Scholar 2011
Connection to SciLifeLab: SciLifeLab faculty and Head of Facility at Bioinformatics Long-term Support (WABI).
Lives: By the Dalälven river in southern Dalarna. Has commuted to Uppsala every day for almost 30 years, a journey of one and a half hours each way. I do a lot of thinking in my car, about ideas and which projects to do. This might be good in a way. It gives you some perspective and distance to things.
Exercise: Cycling, running and skiing. I started training when I was 45 with the goal of doing a Swedish classic five times before I was 50. Once I’d achieved this, I got a more sophisticated bicycle and did a couple of competitions on it. In the past, the high-speed groups at the cycle race Vätternrundan consisted almost exclusively of men. Before Vätternrundan 2012, another woman and I started a high-speed girls’ cycling team called SubXX after the female chromosomes. The first year, about 20 of us finished in less than nine hours. Since then, SubXX has become a cycle club, which have had a high-speed female group among the many male groups cycling around lake Vättern every year.
Like: Writing. It’s one of my favourite things to do. I analyse data, sit and think about what the research team has studied and then I write it down. When I was young, I dreamed of being a poet. This felt like my greatest strength. But then I chose natural sciences at high school. However, I intend to be a poet when I retire.