A simple strategy based on ATR-FTIR difference spectroscopy to monitor substrate intake and metabolite release by growing bacteria

High throughput parameter estimation and uncertainty analysis applied to the production of mycoprotein from synthetic lignocellulosic hydrolysates

The current global food system produces substantial waste and carbon emissions while exacerbating the effects of global hunger and protein deficiency. This study aims to address these challenges by exploring the use of lignocellulosic agricultural residues as feedstocks for microbial protein fermentation, focusing on Fusarium venenatum A3/5, a mycelial strain known for its high protein yield and nutritional quality. We propose a high throughput microlitre batch fermentation system paired with analytical chemistry to generate time series data of microbial growth and substrate utilisation. An unstructured biokinetic model was developed using a bootstrap sampling approach to quantify uncertainty in the parameter estimates. The model was validated against an independent data set of a different glucose-xylose composition to assess the predictive performance. Our results indicate a robust model fit with high coefficients of determination and low root mean squared errors for biomass, glucose, and xylose concentrations. Estimated parameter values provided insights into the resource utilisation strategies of Fusarium venenatum A3/5 in mixed substrate cultures, aligning well with previous research findings. Significant correlations between estimated parameters were observed, highlighting challenges in parameter identifiability. The high throughput workflow presents a novel, rapid methodology for biokinetic model development, enabling efficient exploration of microbial growth dynamics and substrate utilisation. This innovative method directly supports the development of a foundational model for optimising microbial protein production from lignocellulosic hydrolysates, contributing to a more sustainable global food system.

Antimicrobial susceptibility testing using infrared attenuated total reflection (IR-ATR) spectroscopy to monitor metabolic activity

Fast and accurate detection of antimicrobial resistance in pathogens remains a challenge, and with the increase in antimicrobial resistance due to mis- and overuse of antibiotics, it has become an urgent public health problem. We demonstrate how infrared attenuated total reflection (IR-ATR) can be used as a simple method for assessment of bacterial susceptibility to antibiotics. This is achieved by monitoring the metabolic activities of bacterial cells via nutrient consumption and using this as an indicator of bacterial viability. Principal component analysis of the obtained spectra provides a tool for fast and simple discrimination of antimicrobial resistance in the acquired data. We demonstrate this concept using four bacterial strains and four different antibiotics, showing that the change in glucose concentration in the growth medium after 2 h, as monitored by IR-ATR, can be used as a spectroscopic diagnostic technique, to reduce detection time and to improve quality in the assessment of antimicrobial resistance in pathogens.

Applications of Fourier Transform-Infrared spectroscopy in microbial cell biology and environmental microbiology: advances, challenges, and future perspectives

Microorganisms play pivotal roles in shaping ecosystems and biogeochemical cycles. Their intricate interactions involve complex biochemical processes. Fourier Transform-Infrared (FT-IR) spectroscopy is a powerful tool for monitoring these interactions, revealing microorganism composition and responses to the environment. This review explores the diversity of applications of FT-IR spectroscopy within the field of microbiology, highlighting its specific utility in microbial cell biology and environmental microbiology. It emphasizes key applications such as microbial identification, process monitoring, cell wall analysis, biofilm examination, stress response assessment, and environmental interaction investigation, showcasing the crucial role of FT-IR in advancing our understanding of microbial systems. Furthermore, we address challenges including sample complexity, data interpretation nuances, and the need for integration with complementary techniques. Future prospects for FT-IR in environmental microbiology include a wide range of transformative applications and advancements. These include the development of comprehensive and standardized FT-IR libraries for precise microbial identification, the integration of advanced analytical techniques, the adoption of high-throughput and single-cell analysis, real-time environmental monitoring using portable FT-IR systems and the incorporation of FT-IR data into ecological modeling for predictive insights into microbial responses to environmental changes. These innovative avenues promise to significantly advance our understanding of microorganisms and their complex interactions within various ecosystems.