Quantitative assessment of strain isolates and microbiomes using fast MS/MS-free metaproteomics

Kazakova, E. M.; Ivanov, M. V.; Kusainova, T.; Bubis, J. A.; Polivtseva, V. N.; Petrikov, K. V.; Gorshkov, V.; Kjeldsen, F.; Gorshkov, M. V.; Delegan, Y. A.; Solyanikova, I. P.; Tarasova, I. A.

doi:10.1101/2024.04.15.589175

bioRxiv · 10.1101/2024.04.15.589175

Quantitative assessment of strain isolates and microbiomes using fast MS/MS-free metaproteomics

Kazakova, E. M.·Ivanov, M. V.·Kusainova, T.·Bubis, J. A.·Polivtseva, V. N.·Petrikov, K. V.·Gorshkov, V.·Kjeldsen, F.·Gorshkov, M. V.·Delegan, Y. A.·Solyanikova, I. P.·Tarasova, I. A.

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Abstract

BACKGROUNDMicrobial communities play a crucial role in human health and environmental regulation, but present an especial challenge for the analytical science due to their diversity and dynamic range. Tandem mass spectrometry provides functional insights on microorganisms life cycle, but still lacks throughput and sensitivity. MALDI TOF is widely used for ultrafast identification of species, but does not assess their functional activity. Development of ultrafast mass spectrometry methods and bioinformatic approaches applicable for both accurate identification and functional assessment of microbial communities based on their protein content is of high interest. RESULTSWe show for the first time that both identity and functional activity of microorganisms and their communities can be accurately determined in experiments as short as 7 minutes per sample, using the basic Orbitrap MS configuration without peptide fragmentation. The approach was validated using strain isolates, mock microbiomes composed of bacteria spiked at known concentrations and human fecal microbiomes. Our new bioinformatic algorithm identifies the bacterial species with an accuracy of 95 %, when no prior information on the sample is available. Microbiome composition was resolved at the genus level with the mean difference between the actual and identified components of 12 %. For mock microbiomes, Pearson coefficient of up to 0.97 was achieved in estimates of strain biomass change. By the example of Rhodococcus biodegradation of n-alkanes, phenols and its derivatives, we showed the accurate assessment of functional activity of strain isolates, compared with the standard label-free and label-based approaches. SIGNIFICANCEOur approach makes microbial proteomics fast, functional and insightful using the Orbitrap instruments even without employing peptide fragmentation technology. The approach can be applied to any microorganisms and can take a niche in routine functional assessment of microbial pathogens and consortiums in clinical diagnostics together with MALDI TOF MS and 16S rRNA gene sequencing.

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Kazakova, E. M., Ivanov, M. V., Kusainova, T., Bubis, J. A., Polivtseva, V. N., Petrikov, K. V., Gorshkov, V., Kjeldsen, F., Gorshkov, M. V., Delegan, Y. A., Solyanikova, I. P., Tarasova, I. A.. 2024-04-15. Quantitative assessment of strain isolates and microbiomes using fast MS/MS-free metaproteomics. https://doi.org/10.1101/2024.04.15.589175

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