Metabolic Fingerprint Analysis of Cytochrome b5-producing E. coli N4830-1 Using FT-IR Spectroscopy

Optimization of recombinant protein expression in bacteria is an important task in order to increase protein yield while maintaining the structural fidelity of the product. In this study, we employ Fourier transform infrared (FT-IR) spectroscopy as a high throughput metabolic fingerprinting approach to optimize and monitor cytochrome b 5 (CYT b 5) production in Escherichia coli N4830-1, as the heterologous host. Cyt b5 was introduced as a plasmid with between 0 and 6 copies under a strong promoter. The FT-IR spectroscopy results combined with multivariate chemometric analysis illustrated discriminations among culture conditions as well as revealing features that correlated to the different cytb 5 gene copy numbers. The second derivative of the FT-IR spectral data allowed for the quantitative detection of Cyt b5 directly inside the intact cells without the need for extraction, and highlighted changes in protein secondary structure that was directly correlated to the cytb 5 gene copy number and protein content, and was in complete agreement with quantitative findings of standard traditional techniques such as SDS-PAGE and western blot analysis

The role of salivary metabolomics in chronic periodontitis: bridging oral and systemic diseases

Background: Chronic periodontitis is a condition impacting approximately 50% of the world’s population. As chronic periodontitis progresses, the bacteria in the oral cavity change resulting in new microbial interactions which in turn influence metabolite production. Chronic periodontitis manifests with inflammation of the periodontal tissues, which is progressively developed due to bacterial infection and prolonged bacterial interaction with the host immune response. The bi-directional relationship between periodontitis and systemic diseases has been reported in many previous studies. Traditional diagnostic methods for chronic periodontitis and systemic diseases such as chronic kidney diseases (CKD) have limitations due to their invasiveness, requiring practised individuals for sample collection, frequent blood collection, and long waiting times for the results. More rapid methods are required to detect such systemic diseases, however, the metabolic profiles of the oral cavity first need to be determined. Aim of review: In this review, we explored metabolomics studies that have investigated salivary metabolic profiles associated with chronic periodontitis and systemic illnesses including CKD, oral cancer, Alzheimer’s disease, Parkinsons’s disease, and diabetes to highlight the most recent methodologies that have been applied in this field. Key scientific concepts of the review: Of the rapid, high throughput techniques for metabolite profiling, Nuclear magnetic resonance (NMR) spectroscopy was the most applied technique, followed by liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS). Furthermore, Raman spectroscopy was the most used vibrational spectroscopic technique for comparison of the saliva from periodontitis patients to healthy individuals, whilst Fourier Transform Infra-Red Spectroscopy (FT-IR) was not utilised as much in this field. A recommendation for cultivating periodontal bacteria in a synthetic medium designed to replicate the conditions and composition of saliva in the oral environment is suggested to facilitate the identification of their metabolites. This approach is instrumental in assessing the potential of these metabolites as biomarkers for systemic illnesses

Through-container, extremely low concentration detection of multiple chemical markers of counterfeit alcohol using a handheld SORS device

Major food adulteration incidents occur with alarming frequency and are episodic, with the latest incident, involving the adulteration of meat from 21 producers in Brazil supplied to 60 other countries, reinforcing this view. Food fraud and counterfeiting involves all types of foods, feed, beverages, and packaging, with the potential for serious health, as well as significant economic and social impacts. In the spirit drinks sector, counterfeiters often ‘recycle’ used genuine packaging, or employ good quality simulants. To prove that suspect products are non-authentic ideally requires accurate, sensitive, analysis of the complex chemical composition while still in its packaging. This has yet to be achieved. Here, we have developed handheld spatially offset Raman spectroscopy (SORS) for the first time in a food or beverage product, and demonstrate the potential for rapid in situ through-container analysis; achieving unequivocal detection of multiple chemical markers known for their use in the adulteration and counterfeiting of Scotch whisky, and other spirit drinks. We demonstrate that it is possible to detect a total of 10 denaturants/additives in extremely low concentrations without any contact with the sample; discriminate between and within multiple well-known Scotch whisky brands, and detect methanol concentrations well below the maximum human tolerable level

Portable through Bottle SORS for the Authentication of Extra Virgin Olive Oil

The authenticity of olive oil has been a significant long-term challenge. Extra virgin olive oil (EVOO) is the most desirable of these products and commands a high price, thus unscrupulous individuals often alter its quality by adulteration with a lower grade oil. Most analytical methods employed for the detection of food adulteration require sample collection and transportation to a central laboratory for analysis. We explore the use of portable conventional Raman and spatially-offset Raman spectroscopy (SORS) technologies as non-destructive approaches to assess the adulteration status of EVOO quantitatively and for SORS directly through the original container, which means that after analysis the bottle is intact and the oil would still be fit for use. Three sample sets were generated, each with a different adulterant and varying levels of chemical similarity to EVOO. These included EVOO mixed with sunflower oil, pomace olive oil, or refined olive oil. Authentic EVOO samples were stretched/diluted from 0% to 100% with these adulterants and measured using two handheld Raman spectrometers (excitation at 785 or 1064 nm) and handheld SORS (830 nm). The PCA scores plots displayed clear trends which could be related to the level of adulteration for all three mixtures. Conventional Raman (at 785 or 1064 nm) and SORS (at 830 nm with a single spatial offset) conducted in sample vial mode resulted in prediction errors for the test set data ranging from 1.9–4.2% for sunflower oil, 6.5–10.7% for pomace olive oil and 8.0–12.8% for refined olive oil; with the limit of detection (LOD) typically being 3–12% of the adulterant. Container analysis using SORS produced very similar results: 1.4% for sunflower, 4.9% for pomace, and 10.1% for refined olive oil, with similar LODs ranging from 2–14%. It can be concluded that Raman spectroscopy, including through-container analysis using SORS, has significant potential as a rapid and accurate analytical method for the non-destructive detection of adulteration of extra virgin olive oil

A systematic analysis of TCA Escherichia coli mutants reveals suitable genetic backgrounds for enhanced hydrogen and ethanol production using glycerol as main carbon source

Biodiesel has emerged as an environmentally friendly alternative to fossil fuels; however, the low price of glycerol feed-stocks generated from the biodiesel industry has become a burden to this industry. A feasible alternative is the microbial biotransformation of waste glycerol to hydrogen and ethanol. Escherichia coli, a microorganism commonly used for metabolic engineering, is able to biotransform glycerol into these products. Nevertheless, the wild type strain yields can be improved by rewiring the carbon flux to the desired products by genetic engineering. Due to the importance of the central carbon metabolism in hydrogen and ethanol synthesis, E. coli single null mutant strains for enzymes of the TCA cycle and other related reactions were studied in this work. These strains were grown anaerobically in a glycerol-based medium and the concentrations of ethanol, glycerol, succinate and hydrogen were analysed by HPLC and GC. It was found that the reductive branch is the more relevant pathway for the aim of this work, with malate playing a central role. It was also found that the putative C4-transporter dcuD mutant improved the target product yields. These results will contribute to reveal novel metabolic engineering strategies for improving hydrogen and ethanol production by E. coli

Metabolomics of Escherichia coli for Disclosing Novel Metabolic Engineering Strategies for Enhancing Hydrogen and Ethanol Production

The biological production of hydrogen is an appealing approach to mitigating the environmental problems caused by the diminishing supply of fossil fuels and the need for greener energy. Escherichia coli is one of the best-characterized microorganisms capable of consuming glycerol—a waste product of the biodiesel industry—and producing H2 and ethanol. However, the natural capacity of E. coli to generate these compounds is insufficient for commercial or industrial purposes. Metabolic engineering allows for the rewiring of the carbon source towards H2 production, although the strategies for achieving this aim are difficult to foresee. In this work, we use metabolomics platforms through GC-MS and FT-IR techniques to detect metabolic bottlenecks in the engineered ΔldhΔgndΔfrdBC::kan (M4) and ΔldhΔgndΔfrdBCΔtdcE::kan (M5) E. coli strains, previously reported as improved H2 and ethanol producers. In the M5 strain, increased intracellular citrate and malate were detected by GC-MS. These metabolites can be redirected towards acetyl-CoA and formate by the overexpression of the citrate lyase (CIT) enzyme and by co-overexpressing the anaplerotic human phosphoenol pyruvate carboxykinase (hPEPCK) or malic (MaeA) enzymes using inducible promoter vectors. These strategies enhanced specific H2 production by up to 1.25- and 1.49-fold, respectively, compared to the reference strains. Other parameters, such as ethanol and H2 yields, were also enhanced. However, these vectors may provoke metabolic burden in anaerobic conditions. Therefore, alternative strategies for a tighter control of protein expression should be addressed in order to avoid undesirable effects in the metabolic network

Bacterial discrimination by Fourier transform infrared spectroscopy, MALDI-mass spectrometry and whole-genome sequencing

Aim: Proof-of-concept study, highlighting the clinical diagnostic ability of FT-IR compared with MALDI-TOF MS, combined with WGS. Materials & methods: 104 pathogenic isolates of Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus were analyzed. Results: Overall prediction accuracy was 99.6% in FT-IR and 95.8% in MALDI-TOF-MS. Analysis of N. meningitidis serogroups was superior in FT-IR compared with MALDI-TOF-MS. Phylogenetic relationship of S. pyogenes was similar by FT-IR and WGS, but not S. aureus or S. pneumoniae. Clinical severity was associated with the zinc ABC transporter and DNA repair genes in S. pneumoniae and cell wall proteins (biofilm formation, antibiotic and complement permeability) in S. aureus via WGS. Conclusion: FT-IR warrants further clinical evaluation as a promising diagnostic tool

Application of Rapid Evaporative Ionization Mass Spectrometry (REIMS) to Identify Antimicrobial Resistance in Uropathogenic <i>Escherichia coli</i> (UPEC) Isolates via Deuterium Isotope Probing.

Antimicrobial resistance (AMR) continues to pose a significant threat to global health, undermining advances in modern medicine and increasing mortality from previously treatable infections. Rapid and accurate antimicrobial susceptibility testing (AST) is critical, both for effective judicious treatment and controlling the spread of AMR. For the first time, we demonstrate the application of rapid evaporative ionization mass spectrometry (REIMS), combined with deuterium isotope probing (DIP), as a novel approach for identifying AMR in uropathogenic Escherichia coli (UPEC) isolates within only a 1 h incubation period. By directly analyzing bacterial samples without extensive preparation, REIMS serves as a rapid fingerprinting tool, employing DIP and multivariate statistical analysis to provide AST profiling of UPEC isolates. Distinct clustering patterns were observed between trimethoprim-susceptible and trimethoprim-resistant UPEC isolates grown in media containing 10% deuterium oxide (D2O). TMP-susceptible isolates treated with trimethoprim displayed no significant deuterium incorporation, serving as an indicator of a lower metabolic activity resulting from antimicrobial action. We also demonstrated the ability to differentiate the origin of heavy water, confirming that deuterium incorporation was a biological process rather than of extracellular origin resulting from chemical processes. Several mass spectral bins showed patterns consistent with deuterated phospholipid species, including those in the expected mass range for phosphatidylethanolamine (PE) and phosphatidylglycerol (PG), which are the most abundant phospholipids in E. coli. However, these annotations remain tentative, as no structural confirmation (e.g., MS/MS) was performed. These findings suggest that REIMS, combined with DIP and multivariate statistical analysis, serves as an efficient fast workflow for the rapid detection of AMR