Application of gas chromatography mass spectrometry (GC-MS)-based metabolomics for the study of fermented cereal and legume foods:a review

A new era of cutting-edge technologies and advancements in analytical platforms and omics sciences is disruptively bringing a paradigm shift in fundamental and translational research. Metabolomics is one of the omics strategies that yields big data and has gained popularity in a wide spectrum of applications. Among various analytical platforms used in metabolomics, gas chromatography mass spectrometry (GC-MS) allows the measurement of thermally stable (volatiles and semi-volatiles) metabolites, with an advantage of spectral reproducibility. Cereal and legume-based fermented foods are part of the food culture in various countries throughout the world. Thus, this review provides an overview of recent applications of GC-MS-based metabolomics in the food fermentation field, specifically cereal and legume-based fermented foods. This emerging use of metabolomics in food fermentation studies illustrates the potentials of this omics science to elucidate metabolome landscapes of fermented foods. Such insights would advance our predictive understanding of fermentation processes and molecular descriptions of resultant food products; a necessary step for improvements and sustainability in food industry. Furthermore, the review echoes the current need of collaborative efforts in the scientific community (in this field) to harness and maximise the potentials of metabolomics in food fermentation studies

Influence of Fermentation Conditions (Temperature and Time) on the Physicochemical Properties and Bacteria Microbiota of Amasi

The aim of this present study was to optimize the fermentation conditions (time and temperature) of amasi (a Southern African fermented dairy product) using response surface methodology (RSM), and to determine the physicochemical properties, as well as the microbial composition, using next generation sequencing. Fermentation time and temperature were optimized to produce different amasi samples and different parameters, including pH, total soluble solids (TSS), total titratable acids (TTA), and consistency. All the variables studied were found to show significant (p ≤ 0.05) changes with increasing fermentation time and temperature. Numerical optimization was used to obtain the optimal fermentation conditions for amasi; based on RSM, it was 32 °C for 140 h, while with k-means clustering, it was 25 °C for 120 h. Under both conditions for the optimal samples, the pH reduced from 6.64 to 3.99, TTA increased from 0.02 to 0.11 (% lactic acid), TSS decreased from 9.47 to 6.67 °Brix, and the consistency decreased from 23 to 15.23 cm/min. Most of the identified bacteria were linked to lactic acid bacteria, with the family Lactobacillaceae being the most predominant in amasi, while in raw milk, Prevotellaceae was the most abundant. The fermentation conditions (time and temperature) had a significant influence on the parameters investigated in this study. Results of this study could provide information for the commercialization of quality amasi

Enhanced stability and local structure in biologically relevant amorphous materials containing pyrophosphate

There is increasing evidence that amorphous inorganic materials play a key role in biomineralisation in many organisms, however the inherent instability of synthetic analogues in the absence of the complex in vivo matrix limits their study and clinical exploitation. To address this, we report here an approach that enhances long-term stability to >1 year of biologically relevant amorphous metal phosphates, in the absence of any complex stabilisers, by utilising pyrophosphates (P2O7 4-); species themselves ubiquitous in vivo. Ambient temperature precipitation reactions were employed to synthesise amorphous Ca2P2O7.nH2O and Sr2P2O7.nH2O (3.8 < n < 4.2) and their stability and structure were investigated. Pair distribution functions (PDF) derived from synchrotron X-ray data indicated a lack of structural order beyond ~8 A° in both phases, with this local order found to resemble crystalline analogues. Further studies, including 1H and 31P solid state NMR, suggest the unusually high stability of these purely inorganic amorphous phases is partly due to disorder in the P–O–P bond angles within the P2O7 units, which impede crystallization, and to water molecules, which are involved in H-bonds of various strengths within the structures and hamper the formation of an ordered network. In situ high temperature powder X-ray diffraction data indicated that the amorphous nature of both phases surprisingly persisted to ~450° C. Further NMR and TGA studies found that above ambient temperature some water molecules reacted with P2O7 anions, leading to the hydrolysis of some P–O–P linkages and the formation of HPO4 2- anions within the amorphous matrix. The latter anions then recombined into P2O7 ions at higher temperatures prior to crystallization. Together, these findings provide important new materials with unexplored potential for enzyme-assisted resorption and establish factors crucial to isolate further stable amorphous inorganic materials

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways.

Primary biliary cirrhosis (PBC) is a classical autoimmune liver disease for which effective immunomodulatory therapy is lacking. Here we perform meta-analyses of discovery data sets from genome-wide association studies of European subjects (n=2,764 cases and 10,475 controls) followed by validation genotyping in an independent cohort (n=3,716 cases and 4,261 controls). We discover and validate six previously unknown risk loci for PBC (Pcombined<5 × 10(-8)) and used pathway analysis to identify JAK-STAT/IL12/IL27 signalling and cytokine-cytokine pathways, for which relevant therapies exist

Adjunctive rifampicin for Staphylococcus aureus bacteraemia (ARREST): a multicentre, randomised, double-blind, placebo-controlled trial.

BACKGROUND: Staphylococcus aureus bacteraemia is a common cause of severe community-acquired and hospital-acquired infection worldwide. We tested the hypothesis that adjunctive rifampicin would reduce bacteriologically confirmed treatment failure or disease recurrence, or death, by enhancing early S aureus killing, sterilising infected foci and blood faster, and reducing risks of dissemination and metastatic infection. METHODS: In this multicentre, randomised, double-blind, placebo-controlled trial, adults (≥18 years) with S aureus bacteraemia who had received ≤96 h of active antibiotic therapy were recruited from 29 UK hospitals. Patients were randomly assigned (1:1) via a computer-generated sequential randomisation list to receive 2 weeks of adjunctive rifampicin (600 mg or 900 mg per day according to weight, oral or intravenous) versus identical placebo, together with standard antibiotic therapy. Randomisation was stratified by centre. Patients, investigators, and those caring for the patients were masked to group allocation. The primary outcome was time to bacteriologically confirmed treatment failure or disease recurrence, or death (all-cause), from randomisation to 12 weeks, adjudicated by an independent review committee masked to the treatment. Analysis was intention to treat. This trial was registered, number ISRCTN37666216, and is closed to new participants. FINDINGS: Between Dec 10, 2012, and Oct 25, 2016, 758 eligible participants were randomly assigned: 370 to rifampicin and 388 to placebo. 485 (64%) participants had community-acquired S aureus infections, and 132 (17%) had nosocomial S aureus infections. 47 (6%) had meticillin-resistant infections. 301 (40%) participants had an initial deep infection focus. Standard antibiotics were given for 29 (IQR 18-45) days; 619 (82%) participants received flucloxacillin. By week 12, 62 (17%) of participants who received rifampicin versus 71 (18%) who received placebo experienced treatment failure or disease recurrence, or died (absolute risk difference -1·4%, 95% CI -7·0 to 4·3; hazard ratio 0·96, 0·68-1·35, p=0·81). From randomisation to 12 weeks, no evidence of differences in serious (p=0·17) or grade 3-4 (p=0·36) adverse events were observed; however, 63 (17%) participants in the rifampicin group versus 39 (10%) in the placebo group had antibiotic or trial drug-modifying adverse events (p=0·004), and 24 (6%) versus six (2%) had drug interactions (p=0·0005). INTERPRETATION: Adjunctive rifampicin provided no overall benefit over standard antibiotic therapy in adults with S aureus bacteraemia. FUNDING: UK National Institute for Health Research Health Technology Assessment

Screening and Production of Industrially Relevant Enzymes by <i>Bacillus paranthracis</i> Strain MHDS3, a Potential Probiotic

The digestive process and intestinal protein absorption are influenced by a variety of factors. Due to their numerous health advantages, including potential favorable effects on protein digestion and absorption, probiotics have gained increased attention in recent years. Probiotics can control the intestinal microflora, which in turn affects the intestinal bacteria responsible for proteolysis. Additionally, certain probiotics can release exoenzymes that aid in the digestion of proteins and others can stimulate the host’s digestive protease and peptidase activity. By boosting transport and enhancing the epithelium’s capacity for absorption, probiotics can also improve the absorption of tiny peptides and amino acids as well as lessen detrimental protein fermentation, which lowers the toxicity of metabolites. The present study explored the production of enzymes by Bacillus paranthracis strain MHDS3, a probiotic candidate isolated from Pellaea calomelanos. Bacillus paranthracis displayed enzyme activities of amylase (31,788.59 IU), cellulase (4487.486 IU), and pectinase (13.98986 IU) through submerged fermentation. The CAZyme analysis of B. paranthracis revealed 16 CAZyme gene clusters associated with cellulose, amylase, and pectinase activity. Thus, B. paranthracis is a promising probiotic strain that can produce enzymes with biotechnological applications

Screening of Bacillus spp. bacterial endophytes for protease production, and application in feather degradation and bio-detergent additive

Research on proteases and secondary metabolites from endophytes is an area that requires attention from researchers. In this study, proteases from Bacillus sp. strain MHSD16 and Bacillus sp. strain MHSD17 endophytes were characterised, and their potential biotechnological applications were investigated. Optimum protease production was achieved when isolates were grown in media containing (g/L): glucose 10g, casein 5g, yeast extract 5g, KH2PO4 2g, Na2CO3 10g at pH 9. The crude protease extracts were active in alkaline environments, thus referred to as alkaline proteases with optimal pH of 10. Additionally, Bacillus sp. strain MHSD 16 and Bacillus sp. strain MHSD17 proteases were active at high temperatures, with optimum enzyme activity at 50 °C. Thermostability profiles of these proteases showed that the enzymes were highly stable between (40–60 °C), maintaining over 85 % stability after 120 min incubation at 60 °C. Furthermore, the enzymes were stable and compatible with various household and laundry detergents. In the presence of commercial laundry detergent, OMO® 68 % and 72 % activity was retained for Bacillus sp. strain MHSD16 and Bacillus sp. strain MHSD17, respectively, while 67 % and 68 % activity were retained in the presence of Sunlight®. The potential application for use in detergents was investigated through the removal of blood stains with the crude alkaline extracts displaying efficient stain removal abilities. Feather degradation was also investigated and Bacillus sp. MHSD17 exhibited feather keratin degrading properties more effectively than Bacillus sp. MHSD16

Influence of Fermentation Conditions (Temperature and Time) on the Physicochemical Properties and Bacteria Microbiota of Amasi

The aim of this present study was to optimize the fermentation conditions (time and temperature) of amasi (a Southern African fermented dairy product) using response surface methodology (RSM), and to determine the physicochemical properties, as well as the microbial composition, using next generation sequencing. Fermentation time and temperature were optimized to produce different amasi samples and different parameters, including pH, total soluble solids (TSS), total titratable acids (TTA), and consistency. All the variables studied were found to show significant (p &le; 0.05) changes with increasing fermentation time and temperature. Numerical optimization was used to obtain the optimal fermentation conditions for amasi; based on RSM, it was 32 &deg;C for 140 h, while with k-means clustering, it was 25 &deg;C for 120 h. Under both conditions for the optimal samples, the pH reduced from 6.64 to 3.99, TTA increased from 0.02 to 0.11 (% lactic acid), TSS decreased from 9.47 to 6.67 &deg;Brix, and the consistency decreased from 23 to 15.23 cm/min. Most of the identified bacteria were linked to lactic acid bacteria, with the family Lactobacillaceae being the most predominant in amasi, while in raw milk, Prevotellaceae was the most abundant. The fermentation conditions (time and temperature) had a significant influence on the parameters investigated in this study. Results of this study could provide information for the commercialization of quality amasi

The structure of an archaeal homodimeric ligase which has RNA circularization activity

The genome of Pyrococcus abyssi contains two open reading frames encoding proteins which had been previously predicted to be DNA ligases, Pab2002 and Pab1020. We show that while the former is indeed a DNA ligase, Pab1020 had no effect on the substrate deoxyoligo-ribonucleotides tested. Instead, Pab1020 catalyzes the nucleotidylation of oligo-ribonucleotides in an ATP-dependent reaction, suggesting that it is an RNA ligase. We have solved the structure of Pab1020 in complex with the ATP analog AMPPNP by single-wavelength anomalous dispersion (SAD), elucidating a structure with high structural similarity to the catalytic domains of two RNA ligases from the bacteriophage T4. Additional carboxy-terminal domains are also present, and one of these mediates contacts with a second protomer, which is related by noncrystallographic symmetry, generating a homodimeric structure. These C-terminal domains are terminated by short domain swaps which themselves end within 5 Å of the active sites of the partner molecules. Additionally, we show that the protein is indeed capable of circularizing RNA molecules in an ATP-dependent reaction. These structural and biochemical results provide an insight into the potential physiological roles of Pab1020