Researchers at the EMBL European Biotechnology Institute (EMBL-EBI) have combined their knowledge of bacterial genetics and web search algorithms to build a DNA search engine for microbial data. The search engine, described in a paper published in Nature Biotechnology, enables researchers and public health agencies to use genome sequence data to monitor the spread of antibiotic resistance genes. By making this vast amount of data that could not be discovered, the search engine could also allow researchers to learn more about bacteria and viruses.
Search engine for microbes
The search engine, from the name Bitsliced Genomic Signature Index (BIGSI), achieves a similar purpose for internet search engines, such as Google.
The amount of subsequent microbial DNA doubles every two years. So far, there was no practical way to search this data.
This type of search could be extremely useful for understanding diseases. Take, for example, a cause of food poisoning, where the Salmonella case contains drug resistant plasmid (DNA & hitchhiking element) which can spread drug resistance across different bacterial species). For the first time, BIGSI allows researchers to see easily if and when the flasmid was seen.
Google and other search engines use natural language processing to search through millions of websites. They can take advantage of the fact that human language is relatively unchanged. By contrast, microbial DNA shows billions of years of evolution, so each genome of new microbes can include language & # 39; new never seen before. The key to doing BIGSI's work was to find a way to build a search index that could cope with a variety of microbial DNA.
Monitor infectious diseases
"We have been motivated by the problem of controlling antibiotic and infectious disease," explained Zamin Iqbal, the EMBL-EBI Research Group Leader. "We know that bacteria can be resistant to antibiotics either through mutations or with the help of plasmids. We also know that we can use mutations in bacterial DNA as an historical record of bacterial antiquity. This allows us to find it to some extent, how bacteria could spread across the hospital, country or world ward. BIGSI helps us to study all of these things on a massive scale. For the first time, & # 39 ; n allow scientists to ask questions such as this strain that was seen before and if this drug resistance gene has been spread to a new species? & # 39; . "
Quick and easy search
"This search engine supports other existing devices and offers a solution that can graduate the vast amounts of data that we are now producing," explained Phelim Bradley, EMBL-EBI Bioconductor. "This means that the search will continue to work as the amount of data continues to grow. In fact, this is one of the biggest challenges we have to overcome. We developed search engine that anyone with an internet can use connection. "
"As DNA progression becomes cheaper, we will see a host of new users outside basic research, and a rapid increase in the number of data generated," continues Iqbal.
"It's very likely to see a DNA sequence used in clinics, or in the field, to diagnose patients and prescribe treatment, but we could also see it being used for a range of other things, such as checking what kind of meat is in burger. Making genomic data currently searchable is essential and will enable us to learn a huge amount of biology, evolution, spread of diseases, and much more. "
Why do we worry about microbes?
Microbes are a very small living thing that they see with the naked eye and they need a microscope. The general term is microbial; which is used to describe the forms of different types of life, including bacteria, viruses, fungi, and more.
A small fraction of microbes, mainly certain types of bacteria and viruses, is responsible for infectious diseases. When bacteria can handle "antiviral" of antibiotic treatment, they become extremely dangerous for patients. This is increasingly happening around the world and is known as an antibiotic collision.
By comparing the DNA of multiple bacterial species, we can begin to understand how they belong and study antibiotic resistant dynamics as it spreads – geographically and across species. For example, a DNA analysis can help us predict how dangerous a tuberculosis is, and what types of drugs that a particular stress may respond to.