R+D CSIC

Scientists develop a device to quickly identify micro-organisms in an environmental sample

The device, tested in Antarctica, optimises the efficient collection of samples and allows them to be analysed in situ. The breakthrough has been made possible by combining technologies that include the use of portable equipment to obtain and analyse DNA sequences, and proprietary analysis software, which has been patented. This development may also have applications in the clinical setting and in industry.

It is a field portable laboratory that allows obtaining information from samples very quickly and thus improving sampling design. It is a novel experimental approach, the success of which was demonstrated during the last Spanish Antarctic campaign by studying micro-organism communities of terrestrial ecosystems on Livingston and Deception Islands. It has been developed by scientists from the Centro Nacional de Biotecnología (CNB) and  the Museo Nacional de Ciencias Naturales (MNCN), both from the CSIC, in the framework of the Rock-Eaters project (Agencia Estatal de Investigación, Ministerio de Ciencia e Innovación).

CNB researcher Javier Tamames, who has implemented the system, explains that "the combination of technologies allows us to extract microbial DNA, purify it and also sequence it with a small commercial sequencer, directly at the sampling site".

A portable lab

The scientists have deployed a portable laboratory capable of operating autonomously in the field, and "the key to this has been a reliable bioinformatics analysis tool developed by us, the SqueezeMeta software, with which we have managed to streamline and automate the entire process of identifying microorganisms from their DNA sequences". 

"Never before has it been possible to generate such complete information on the composition and function of a microbial community in such a short time. This opens the door to numerous applications where speed of analysis is essential," adds Tamames.

In Antarctica there are unexplored regions inhabited by microorganisms, many of them still unknown, such as those that colonise the rocks that are exposed after the retreat of ice in glaciers or volcanic lavas. To identify them, samples are usually collected and subsequently analysed in laboratories using massive genome sequencing techniques and bioinformatics analysis.

In contrast, "this methodology has allowed us to process the sequencing data during the field work and thus design the samples and experiments in a dynamic and more accurate way, making decisions quickly, without having to wait for our return to Spain to finalise the process," says MNCN researcher Asunción de los Ríos.

"In previous campaigns, you had an intuition about where to take samples and you expected to get good results. With this system, you know if you are on the right track from the beginning and, based on that, you can select the sampling areas and guarantee that you are obtaining the data you need," de los Ríos highlights.

The results obtained are of great interest for understanding the role of microorganisms in Antarctic terrestrial ecosystems. "By identifying the microorganisms present in Antarctic rocks, we can better assess their contribution to the functioning of the ecosystem," concludes Fernando Garrido, also from the MNCN.

The device can be used also to the detection of antibiotic resistance profiles in urgent clinical situations or the rapid monitoring of biotechnological systems where microbiomes are involved

From Antarctica to the clinic and industry

The strategy may find applications in other sectors and fields, such as the detection of antibiotic resistance profiles in clinical situations where speed is crucial, explains Javier Tamames. Or, for example, in serious clinical cases where the most appropriate antibiotic treatment needs to be determined quickly.

In the agro-food industry, it could be applied for rapid monitoring in biotechnological systems, such as fermenters or bioreactors where the composition or capabilities of the microbiomes involved are key and can change rapidly. Other examples are sewage treatment plants, bioleaching systems, food fermentation, rapid monitoring of water or pathogen emergence.

The laboratory equipment used by the researchers is commercial equipment, as well as the usual DNA isolation and sequencing protocols. In this part, what the scientists have contributed is the refinement and optimisation of the procedures for the samples analysed based on their previous experience with the study system and laboratory procedures. The centrepiece is the SqueezeMeta analysis software, which is already patented. "It is entirely our own development and what makes the difference, which makes it possible to obtain results in such a short time and using such small and inexpensive equipment."

Reference articles:

Tamames J, Puente-Sánchez F. SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline. Front Microbiol. 2019 Jan 24;9:3349. doi: 10.3389/fmicb.2018.03349.

Puente-Sánchez F, García-García N, Tamames J. SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o. BMC Bioinformatics. 2020 Aug 14;21(1):358. doi: 10.1186/s12859-020-03703-2.

Javier Tamames, Diego Jiménez, Álvaro Redondo, Sandra Martínez, Asunción de los Rios. In-situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day. bioRxiv 2023.01.25.525498; doi: https://doi.org/10.1101/2023.01.25.525498

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