New software tool MARTi fast-tracks identification and response to microbial threats.

Metagenomics is the study of all organisms present in a particular environment, such as soil, water, or the human body. A key part of metagenomic analysis is understanding what species are present (classification), how much of each there is (abundance), and the function of the microorganisms present.

Real-time metagenomics - the immediate analysis of data while sequencing is in progress - holds the potential to speed up the detection, monitoring, and response to microbial threats in a multitude of settings, including agricultural, environmental, and biosecurity.

However, one of the key barriers to realising the full potential of real-time metagenomics is the lack of flexibility in current tools available, increasing the time it takes for sample analysis to be returned to the site of application. 

MARTi (Metagenomic Analysis in Real Time), published today in Genome Research, is an open-source software tool that powers real-time analysis and visualisation of metagenomic data. The team have created an accessible interface which increases the usability and accessibility of metagenomic analysis.

Dr Ned Peel, first-author and postdoctoral research scientist at the Earlham Institute said: “It’s operationally very lightweight, you can use it in-field for taxonomic classification on a standard laptop, or undertake larger, complex analysis using high-performance computing.”

“One of the key impacts of MARTi is the immediacy of analysis results - it could be very useful in situations where a quick identification is essential.”  added Ned.

In clinical environments this could allow clinicians to rapidly speed up the identification and targeted treatments of pathogen infection.

Dr Richard Leggett, Group Leader and author said: “MARTi has its origins in software we developed for really rapid identification of pathogens in preterm infants, but we’ve since adapted it to use in a wide range of settings including on board research vessels in the antarctic, in agriculture, and in biosurveillance and security.

“MARTi is now our first line analysis tool for any metagenomic project and we’re using MARTi in several current collaborations. Through testing both simulated and real data we have demonstrated the robustness of results.”

The in-field analysis MARTi provides underpins the group’s work sequencing the air for pathogen threats.

AirSeq - a technology developed by the Earlham Institute, along with collaborators at the Natural History Museum, London, takes in samples of air and extracts and purifies the tiny amounts of DNA present. This is then sequenced and analysed using the MARTi software. 

“One end-goal in agricultural settings would be to have a box in a farmer's field that could continually sample the air, analysing the data onboard with MARTi and then providing the farmer with an alert in real time.” added Richard.

MARTi has two components: the MARTi Engine, which analyses the sequencing data and can be installed on either a local machine, such as a desktop or laptop, or a high-performance compute (HPC) system; and the MARTi GUI (graphical user interface), a web-based tool allowing users to view and compare results, as well as generate graphs and figures for scientific publications and presentations. 

MARTi is highly customisable and users can tune parameters and databases to the needs of their particular research. “We’ve created a user-friendly tool that should be flexible, customisable, and easy to install,” added Ned. 

At the Earlham Institute we are passionate about developing, adapting, and applying the latest technologies to answer complex biological questions. From new workflows and bespoke software, Earlham Institute scientists are constantly creating and refining technological methods in order to maintain the pace of discovery.