Comparison of Fiber Optic and Conduit Attenuated Total Reflection (ATR) Fourier Transform Infrared (FT-IR) Setup for In-Line Fermentation Monitoring

On-line untargeted metabolomics monitoring of an E. coli succinate fermentation process

The real‐time monitoring of metabolites (RTMet) is instrumental for the industrial production of biobased fermentation products. This study shows the first application of untargeted on‐line metabolomics for the monitoring of undiluted fermentation broth samples taken automatically from a 5 L bioreactor every 5 min via flow injection mass spectrometry. The travel time from the bioreactor to the mass spectrometer was 30 s. Using mass spectrometry allows, on the one hand, the direct monitoring of targeted key process compounds of interest and, on the other hand, provides information on hundreds of additional untargeted compounds without requiring previous calibration data. In this study, this technology was applied in an Escherichia coli succinate fermentation process and 886 different m/z signals were monitored, including key process compounds (glucose, succinate, and pyruvate), potential biomarkers of biomass formation such as (R)‐2,3‐dihydroxy‐isovalerate and (R)‐2,3‐dihydroxy‐3‐methylpentanoate and compounds from the pentose phosphate pathway and nucleotide metabolism, among others. The main advantage of the RTMet technology is that it allows the monitoring of hundreds of signals without the requirement of developing partial least squares regression models, making it a perfect tool for bioprocess monitoring and for testing many different strains and process conditions for bioprocess development.

In Situ Quantification of Polyhydroxybutyrate in Photobioreactor Cultivations of Synechocystis sp. Using an Ultrasound-Enhanced ATR-FTIR Spectroscopy Probe

Polyhydroxybutyrate (PHB) is a very promising alternative to most petroleum-based plastics with the huge advantage of biodegradability. Biotechnological production processes utilizing cyanobacteria as sustainable source of PHB require fast in situ process analytical technology (PAT) tools for sophisticated process monitoring. Spectroscopic probes supported by ultrasound particle traps provide a powerful technology for in-line, nondestructive, and real-time process analytics in photobioreactors. This work shows the great potential of using ultrasound particle manipulation to improve spectroscopic attenuated total reflection Fourier-transformed mid-infrared (ATR-FTIR) spectra as a monitoring tool for PHB production processes in photobioreactors.

Monitoring E. coli Cell Integrity by ATR-FTIR Spectroscopy and Chemometrics: Opportunities and Caveats

During recombinant protein production with E. coli, the integrity of the inner and outer membrane changes, which leads to product leakage (loss of outer membrane integrity) or lysis (loss of inner membrane integrity). Motivated by current Quality by Design guidelines, there is a need for monitoring tools to determine leakiness and lysis in real-time. In this work, we assessed a novel approach to monitoring E. coli cell integrity by attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. Various preprocessing strategies were tested in combination with regression (partial least squares, random forest) or classification models (partial least squares discriminant analysis, linear discriminant analysis, random forest, artificial neural network). Models were validated using standard procedures, and well-performing methods were additionally scrutinized by removing putatively important features and assessing the decrease in performance. Whereas the prediction of target compound concentration via regression was unsuccessful, possibly due to a lack of samples and low sensitivity, random forest classifiers achieved prediction accuracies of over 90% within the datasets tested in this study. However, strong correlations with untargeted spectral regions were revealed by feature selection, thereby demonstrating the need to rigorously validate chemometric models for bioprocesses, including the evaluation of feature importance.

Polarimetric Balanced Detection: Background-Free Mid-IR Evanescent Field Laser Spectroscopy for Low-Noise, Long-term Stable Chemical Sensing

In this work, we introduce polarimetric balanced detection as a new attenuated total reflection (ATR) infrared (IR) sensing scheme, leveraging unequal effective thicknesses achieved with laser light of different polarizations. We combined a monolithic widely tunable Vernier quantum cascade laser (QCL-XT) and a multibounce ATR IR spectroscopy setup for analysis of liquids in a process analytical setting. Polarimetric balanced detection enables simultaneous recording of background and sample spectra, significantly reducing long-term drifts. The root-mean-square noise could be improved by a factor of 10 in a long-term experiment, compared to conventional absorbance measurements obtained via the single-ended optical channel. The sensing performance of the device was further evaluated by on-site measurements of ethanol in water, leading to an improved limit of detection (LOD) achieved with polarimetric balanced detection. Sequential injection analysis was employed for automated injection of samples into a custom-built ATR flow cell mounted above a zinc sulfide multibounce ATR element. The QCL-XT posed to be suitable for mid-IR-based sensing in liquids due to its wide tunability. Polarimetric balanced detection proved to enhance the robustness and long-term stability of the sensing device, along with improving the LOD by a factor of 5. This demonstrates the potential for new polarimetric QCL-based ATR mid-IR sensing schemes for in-field measurements or process monitoring usually prone to a multitude of interferences.

Monitoring and control of E. coli cell integrity

Soluble expression of recombinant proteins in E. coli is often done by translocation of the product across the inner membrane (IM) into the periplasm, where it is retained by the outer membrane (OM). While the integrity of the IM is strongly coupled to viability and impurity release, a decrease in OM integrity (corresponding to increased "leakiness") leads to accumulation of product in the extracellular space, strongly impacting the downstream process. Whether leakiness is desired or not, differential monitoring and control of IM and OM integrity are necessary for an efficient E. coli bioprocess in compliance with the guidelines of Quality by Design and Process Analytical Technology. In this review, we give an overview of relevant monitoring tools, summarize the research on factors affecting E. coli membrane integrity and provide a brief discussion on how the available monitoring technology can be implemented in real-time control of E. coli cultivations.

On-line analysis and in situ pH monitoring of mixed acid fermentation by Escherichia coli using combined FTIR and Raman techniques

We introduce an experimental setup allowing continuous monitoring of bacterial fermentation processes by simultaneous optical density (OD) measurements, long-path FTIR headspace monitoring of CO2, acetaldehyde and ethanol, and liquid Raman spectroscopy of acetate, formate, and phosphate anions, without sampling. We discuss which spectral features are best suited for detection, and how to obtain partial pressures and concentrations by integrations and least squares fitting of spectral features. Noise equivalent detection limits are about 2.6 mM for acetate and 3.6 mM for formate at 5 min integration time, improving to 0.75 mM for acetate and 1.0 mM for formate at 1 h integration. The analytical range extends to at least 1 M with a standard deviation of percentage error of about 8%. The measurement of the anions of the phosphate buffer allows the spectroscopic, in situ determination of the pH of the bacterial suspension via a modified Henderson-Hasselbalch equation in the 6-8 pH range with an accuracy better than 0.1. The 4 m White cell FTIR measurements provide noise equivalent detection limits of 0.21 μbar for acetaldehyde and 0.26 μbar for ethanol in the gas phase, corresponding to 3.2 μM acetaldehyde and 22 μM ethanol in solution, using Henry's law. The analytical dynamic range exceeds 1 mbar ethanol corresponding to 85 mM in solution. As an application example, the mixed acid fermentation of Escherichia coli is studied. The production of CO2, ethanol, acetaldehyde, acids such as formate and acetate, and the changes in pH are discussed in the context of the mixed acid fermentation pathways. Formate decomposition into CO2 and H2 is found to be governed by a zeroth-order kinetic rate law, showing that adding exogenous formate to a bioreactor with E. coli is expected to have no beneficial effect on the rate of formate decomposition and biohydrogen production.

Production of Active Recombinant Hyaluronidase Inclusion Bodies from Apis mellifera in E. coli Bl21(DE3) and characterization by FT-IR Spectroscopy

The bacterium E. coli is one of the most important hosts for recombinant protein production. The benefits are high growth rates, inexpensive media, and high protein titers. However, complex proteins with high molecular weight and many disulfide bonds are expressed as inclusion bodies (IBs). In the last decade, the overall perception of these IBs being not functional proteins changed, as enzyme activity was found within IBs. Several applications for direct use of IBs are already reported in literature. While fluorescent proteins or protein tags are used for determination of IB activity to date, direct measurements of IB protein activity are scacre. The expression of recombinant hyaluronidase from Apis mellifera in E. coli BL21(DE3) was analyzed using a face centered design of experiment approach. Hyaluronidase is a hard to express protein and imposes a high metabolic burden to the host. Conditions giving a high specific IB titer were found at 25 °C at low specific substrate uptake rates and induction times of 2 to 4 h. The protein activity of hyaluronidase IBs was verified using (Fourier transform) FT-IR spectroscopy. Degradation of the substrate hyaluronan occurred at increased rates with higher IB concentrations. Active recombinant hyaluronidase IBs can be immediately used for direct degradation of hyaluronan without further down streaming steps. FT-IR spectroscopy was introduced as a method for tracking IB activity and showed differences in degradation behavior of hyaluronan dependent on the applied active IB concentration.

The Danger of Relying on Database Spectra

With the availability of easy-to-use commercial instrumentation for infrared (IR) and Raman spectroscopy, the number of users is growing very fast. Even in labs in which no personnel with experience in spectroscopy is around, spectra can be recorded and analyzed. However, for an inexperienced person it is virtually impossible to check whether a spectrum is plausible. In this Note, it is demonstrated that even comparing an experimental spectrum with data from a database may lead to significant errors. The vibrational spectrum of dimethyl sulfoxide (DMSO) is presented as an example.

Vibrational Spectroscopy as a Promising Toolbox for Analyzing Functionalized Ceramic Membranes

Ceramic materials find use in many fields including the life sciences and environmental engineering. For example, ceramic membranes have shown to be promising filters for water treatment and virus retention. The analysis of such materials, however, remains challenging. In the present study, the potential of three vibrational spectroscopic methods for characterizing functionalized ceramic membranes for water treatment is evaluated. For this purpose, Raman scattering, infrared (IR) absorption, and solvent infrared spectroscopy (SIRS) were employed. The data were analyzed with respect to spectral changes as well as using principal component analysis (PCA). The Raman spectra allow an unambiguous discrimination of the sample types. The IR spectra do not change systematically with functionalization state of the material. Solvent infrared spectroscopy allows a systematic distinction and enables studying the molecular interactions between the membrane surface and the solvent.