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Shanmugasundaram S, Agrawal R, Gupta D. Electron impact partial ionization cross sections: R-carvone, 2-butanol, imidazole, and 2-nitroimidazole. J Chem Phys 2024; 160:094310. [PMID: 38445738 DOI: 10.1063/5.0193517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
We calculate electron impact partial and total ionization cross sections of R-carvone (C10H14O), 2-butanol (C4H10O), imidazole (C3H4N2), and 2-nitroimidazole (C3H3N3O2). We have used the Binary Encounter Bethe (BEB) model to obtain total electron impact ionization cross sections (TICSs). The modified BEB method in combination with mass spectrum data of the molecules is used to calculate the partial ionization cross section (PICS) of the cationic fragments dissociating from the parent molecule. Our PICS data for R-carvone and 2-butanol are in good agreement with the experimental data for all the cation fragments along with the TICS data. For imidazole and 2-nitroimidazole, the estimates of the PICS are reported for the first time in the present study. We have found that both the modified BEB method and the mass spectrum dependence method work effectively to estimate PICS if we have information about the appearance energies and relative abundance data of the target under investigation.
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Affiliation(s)
- Suriyaprasanth Shanmugasundaram
- Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Katpadi, Vellore 632014, Tamil Nadu, India
| | - Rounak Agrawal
- School of Computer Science and Engineering, Vellore Institute of Technology, Katpadi, Vellore 632014, Tamil Nadu, India
| | - Dhanoj Gupta
- Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Katpadi, Vellore 632014, Tamil Nadu, India
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Poirier S, Coeuret G, Champomier-Vergès MC, Desmonts MH, Werner D, Feurer C, Frémaux B, Guillou S, Luong NDM, Rué O, Loux V, Zagorec M, Chaillou S. Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios. Front Microbiol 2023; 14:1286661. [PMID: 37920261 PMCID: PMC10619683 DOI: 10.3389/fmicb.2023.1286661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023] Open
Abstract
Background The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics. Methods Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers. Results Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism. Conclusion We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.
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Affiliation(s)
- Simon Poirier
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
| | - Gwendoline Coeuret
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
| | | | | | | | | | | | | | | | - Olivier Rué
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Valentin Loux
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Stéphane Chaillou
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
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Faricha A, Yoshida S, Chakraborty P, Okamoto K, Chang TFM, Sone M, Nakamoto T. Array of Miniaturized Amperometric Gas Sensors Using Atomic Gold Decorated Pt/PANI Electrodes in Room Temperature Ionic Liquid Films. SENSORS (BASEL, SWITZERLAND) 2023; 23:4132. [PMID: 37112472 PMCID: PMC10141993 DOI: 10.3390/s23084132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 06/19/2023]
Abstract
Miniaturized sensors possess many advantages, such as rapid response, easy chip integration, a possible lower concentration of target compound detection, etc. However, a major issue reported is a low signal response. In this study, a catalyst, the atomic gold clusters of Aun where n = 2, was decorated at a platinum/polyaniline (Pt/PANI) working electrode to enhance the sensitivity of butanol isomers gas measurement. Isomer quantification is challenging because this compound has the same chemical formula and molar mass. Furthermore, to create a tiny sensor, a microliter of room-temperature ionic liquid was used as an electrolyte. The combination of the Au2 clusters decorated Pt/PANI and room temperature ionic liquid with several fixed electrochemical potentials was explored to obtain a high solubility of each analyte. According to the results, the presence of Au2 clusters increased the current density due to electrocatalytic activity compared to the electrode without Au2 clusters. In addition, the Au2 clusters on the modified electrode had a more linear concentration dependency trend than the modified electrode without atomic gold clusters. Finally, the separation among butanol isomers was enhanced using different combination of room-temperature ionic liquids and fixed potentials.
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Affiliation(s)
- Anifatul Faricha
- Department of Information and Communications Engineering, Tokyo Institute of Technology, Yokohama 226-8503, Kanagawa, Japan
| | - Shohei Yoshida
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama 226-8503, Kanagawa, Japan
| | - Parthojit Chakraborty
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Kanagawa, Japan
| | - Keisuke Okamoto
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama 226-8503, Kanagawa, Japan
| | - Tso-Fu Mark Chang
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Kanagawa, Japan
| | - Masato Sone
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Kanagawa, Japan
| | - Takamichi Nakamoto
- Department of Information and Communications Engineering, Tokyo Institute of Technology, Yokohama 226-8503, Kanagawa, Japan
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Kanagawa, Japan
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4
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Liu B, Nakagawa Y, Li C, Yabushita M, Tomishige K. Selective C–O Hydrogenolysis of Terminal C–OH Bond in 1,2-Diols over Rutile-Titania-Supported Iridium-Iron Catalysts. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Ben Liu
- Department of Applied Chemistry, School of Engineering, Tohoku University, 6-6-07 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Yoshinao Nakagawa
- Department of Applied Chemistry, School of Engineering, Tohoku University, 6-6-07 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
- Research Center for Rare Metal and Green Innovation, Tohoku University, 468-1, Aoba, Aramaki, Aoba-ku, Sendai 980-0845, Japan
| | - Congcong Li
- Department of Applied Chemistry, School of Engineering, Tohoku University, 6-6-07 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Mizuho Yabushita
- Department of Applied Chemistry, School of Engineering, Tohoku University, 6-6-07 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
- Research Center for Rare Metal and Green Innovation, Tohoku University, 468-1, Aoba, Aramaki, Aoba-ku, Sendai 980-0845, Japan
| | - Keiichi Tomishige
- Department of Applied Chemistry, School of Engineering, Tohoku University, 6-6-07 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
- Research Center for Rare Metal and Green Innovation, Tohoku University, 468-1, Aoba, Aramaki, Aoba-ku, Sendai 980-0845, Japan
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
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5
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Hocq R, Sauer M. An artificial coculture fermentation system for industrial propanol production. FEMS MICROBES 2022. [DOI: 10.1093/femsmc/xtac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Converting plant biomass into biofuels and biochemicals via microbial fermentation has received considerable attention in the quest for finding renewable energies and materials. Most approaches have so far relied on cultivating a single microbial strain, tailored for a specific purpose. However, this contrasts to how nature works, where microbial communities rather than single species perform all tasks. In artificial coculture systems, metabolic synergies are rationally designed by carefully selecting and simultaneously growing different microbes, taking advantage of the broader metabolic space offered by the use of multiple organisms.
1-propanol and 2-propanol, as biofuels and precursors for propylene, are interesting target molecules to valorize plant biomass. Some solventogenic Clostridia can naturally produce 2-propanol in the so-called Isopropanol-Butanol-Ethanol (IBE) fermentation, by coupling 2-propanol synthesis to acetate and butyrate reduction into ethanol and 1-butanol.
In this work, we hypothesized propanoate would be converted into 1-propanol by the IBE metabolism, while driving at the same time 2-propanol synthesis. We first verified this hypothesis and chose two propionic acid bacteria (PAB) strains as propanoate producers. While consecutive PAB and IBE fermentations only resulted in low propanol titers, coculturing Propionibacterium freudenreichii and Clostridium beijerinckii at various inoculation ratios yielded much higher solvent concentrations, with as much as 21 g/L of solvents (58% increase compared to C. beijerinckii monoculture) and 12 g/L of propanol (98% increase). Taken together, our results underline how artificial cocultures can be used to foster metabolic synergies, increasing fermentative performances and orienting the carbon flow towards a desired product.
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Affiliation(s)
- Rémi Hocq
- CD-Laboratory for Biotechnology of Glycerol, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael Sauer
- CD-Laboratory for Biotechnology of Glycerol, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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Oberg TS, McMahon DJ, Culumber MD, McAuliffe O, Oberg CJ. Invited review: Review of taxonomic changes in dairy-related lactobacilli. J Dairy Sci 2022; 105:2750-2770. [DOI: 10.3168/jds.2021-21138] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/13/2021] [Indexed: 11/19/2022]
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Ibrahim MF, Shaharuddin NA, Alias NH, Jenol MA, Abd‐Aziz S, Phang L. Biobutanol Production from Oil Palm Biomass. BIOREFINERY OF OIL PRODUCING PLANTS FOR VALUE‐ADDED PRODUCTS 2022:307-324. [DOI: 10.1002/9783527830756.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Peculiar Response in the Co-Culture Fermentation of Leuconostoc mesenteroides and Lactobacillus plantarum for the Production of ABE Solvents. FERMENTATION 2021. [DOI: 10.3390/fermentation7040212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Two bacterial strains (CL11A and CL11D) that are capable of ABE fermentation, identified as Leuconostoc mesenteroides and Weissella cibari, were isolated from the soil surrounding the roots of bean plants. Another strain (ZM 3A), identified as Lactobacillus plantarum, which is capable of purely ethanolic fermentation was isolated from sugarcane. Glucose was used as a standard substrate to investigate the performance of these strains in mono—and co-culture fermentation for ABE production. The performance parameters employed in this study were substrate degradation rates, product and metabolite yields, pH changes and microbial growth rates. Both ABE isolates were capable of producing the three solvents but Leuconostoc mesenteroides had a higher specificity for ethanol than Weissella cibari. The co-culturing of Leuconostoc mesenteroides and Lactobacillus plantarum enhanced ethanol production at the expense of both acetone and butanol, and also influenced the final substrate consumption rate and product yield. The experiments indicated the potential of these niche environments for the isolation of ABE-producing microorganisms. This study contributes to the formulation of ideal microbial co-culture and consortia fermentation, which seeks to maximize the yield and production rates of favored products.
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9
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Dorau R, Liu J, Solem C, Jensen PR. Metabolic Engineering of Lactic Acid Bacteria. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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C4 Bacterial Volatiles Improve Plant Health. Pathogens 2021; 10:pathogens10060682. [PMID: 34072921 PMCID: PMC8227687 DOI: 10.3390/pathogens10060682] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/10/2021] [Accepted: 05/24/2021] [Indexed: 02/04/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) associated with plant roots can trigger plant growth promotion and induced systemic resistance. Several bacterial determinants including cell-wall components and secreted compounds have been identified to date. Here, we review a group of low-molecular-weight volatile compounds released by PGPR, which improve plant health, mostly by protecting plants against pathogen attack under greenhouse and field conditions. We particularly focus on C4 bacterial volatile compounds (BVCs), such as 2,3-butanediol and acetoin, which have been shown to activate the plant immune response and to promote plant growth at the molecular level as well as in large-scale field applications. We also disc/ uss the potential applications, metabolic engineering, and large-scale fermentation of C4 BVCs. The C4 bacterial volatiles act as airborne signals and therefore represent a new type of biocontrol agent. Further advances in the encapsulation procedure, together with the development of standards and guidelines, will promote the application of C4 volatiles in the field.
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Yoo JI, Sohn YJ, Son J, Jo SY, Pyo J, Park SK, Choi JI, Joo JC, Kim HT, Park SJ. Recent advances in the microbial production of C4 alcohols by metabolically engineered microorganisms. Biotechnol J 2021; 17:e2000451. [PMID: 33984183 DOI: 10.1002/biot.202000451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND The heavy global dependence on petroleum-based industries has led to serious environmental problems, including climate change and global warming. As a result, there have been calls for a paradigm shift towards the use of biorefineries, which employ natural and engineered microorganisms that can utilize various carbon sources from renewable resources as host strains for the carbon-neutral production of target products. PURPOSE AND SCOPE C4 alcohols are versatile chemicals that can be used directly as biofuels and bulk chemicals and in the production of value-added materials such as plastics, cosmetics, and pharmaceuticals. C4 alcohols can be effectively produced by microorganisms using DCEO biotechnology (tools to design, construct, evaluate, and optimize) and metabolic engineering strategies. SUMMARY OF NEW SYNTHESIS AND CONCLUSIONS In this review, we summarize the production strategies and various synthetic tools available for the production of C4 alcohols and discuss the potential development of microbial cell factories, including the optimization of fermentation processes, that offer cost competitiveness and potential industrial commercialization.
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Affiliation(s)
- Jee In Yoo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Yu Jung Sohn
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Seo Young Jo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jiwon Pyo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Su Kyeong Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jong-Il Choi
- Department of Biotechnology and Engineering, Interdisciplinary Program of Bioenergy and Biomaterials, Chonnam National University, Gwangju, Republic of Korea
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Gyenggi-do, Republic of Korea
| | - Hee Taek Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
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Monedeiro F, Railean-Plugaru V, Monedeiro-Milanowski M, Pomastowski P, Buszewski B. Metabolic Profiling of VOCs Emitted by Bacteria Isolated from Pressure Ulcers and Treated with Different Concentrations of Bio-AgNPs. Int J Mol Sci 2021; 22:4696. [PMID: 33946710 PMCID: PMC8124631 DOI: 10.3390/ijms22094696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/22/2021] [Accepted: 04/27/2021] [Indexed: 12/30/2022] Open
Abstract
Considering the advent of antibiotic resistance, the study of bacterial metabolic behavior stimulated by novel antimicrobial agents becomes a relevant tool to elucidate involved adaptive pathways. Profiling of volatile metabolites was performed to monitor alterations of bacterial metabolism induced by biosynthesized silver nanoparticles (bio-AgNPs). Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae and Proteus mirabilis were isolated from pressure ulcers, and their cultures were prepared in the presence/absence of bio-AgNPs at 12.5, 25 and 50 µg mL-1. Headspace solid phase microextraction associated to gas chromatography-mass spectrometry was the employed analytical platform. At the lower concentration level, the agent promoted positive modulation of products of fermentation routes and bioactive volatiles, indicating an attempt of bacteria to adapt to an ongoing suppression of cellular respiration. Augmented response of aldehydes and other possible products of lipid oxidative cleavage was noticed for increasing levels of bio-AgNPs. The greatest concentration of agent caused a reduction of 44 to 80% in the variety of compounds found in the control samples. Pathway analysis indicated overall inhibition of amino acids and fatty acids routes. The present assessment may provide a deeper understanding of molecular mechanisms of bio-AgNPs and how the metabolic response of bacteria is untangled.
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Affiliation(s)
- Fernanda Monedeiro
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, 4 Wileńska St., 87-100 Toruń, Poland; (F.M.); (V.R.-P.); (M.M.-M.); (P.P.)
| | - Viorica Railean-Plugaru
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, 4 Wileńska St., 87-100 Toruń, Poland; (F.M.); (V.R.-P.); (M.M.-M.); (P.P.)
| | - Maciej Monedeiro-Milanowski
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, 4 Wileńska St., 87-100 Toruń, Poland; (F.M.); (V.R.-P.); (M.M.-M.); (P.P.)
| | - Paweł Pomastowski
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, 4 Wileńska St., 87-100 Toruń, Poland; (F.M.); (V.R.-P.); (M.M.-M.); (P.P.)
| | - Bogusław Buszewski
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, 4 Wileńska St., 87-100 Toruń, Poland; (F.M.); (V.R.-P.); (M.M.-M.); (P.P.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarina St., 87-100 Toruń, Poland
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Lactic acid bacteria: little helpers for many human tasks. Essays Biochem 2021; 65:163-171. [PMID: 33739395 DOI: 10.1042/ebc20200133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/26/2022]
Abstract
Lactic acid bacteria (LAB) are a group of highly specialised bacteria specifically adapted to a diverse range of habitats. They are found in the gut of humans and other animals, in many food fermentations, and on plants. Their natural specialisation in close relation to human activities make them particularly interesting from an industrial point of view. They are relevant not only for traditional food fermentations, but also as probiotics, potential therapeutics and cell factories for the production of many different products. Many new tools and methods are being developed to analyse and modify these microorganisms. This review shall give an overview highlighting some of the most striking characteristics of lactic acid bacteria and our approaches to harness their potential in many respects - from home made food to industrial chemical production, from probiotic activities to the most modern cancer treatments and vaccines.
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Liu S, Qureshi N, Bischoff K, Darie CC. Proteomic Analysis Identifies Dysregulated Proteins in Butanol-Tolerant Gram-Positive Lactobacillus mucosae BR0713-33. ACS OMEGA 2021; 6:4034-4043. [PMID: 33644533 PMCID: PMC7906490 DOI: 10.1021/acsomega.0c06028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Butanol can be produced biologically through fermentation of lignocellulosic biomass-derived sugars by Gram-positive Clostridium species. For cost-effective production, increased butanol fermentation titers are desired. However, the currently available butanol-fermenting microbes do not tolerate sufficiently high butanol concentrations; thus, new butanol-tolerant strains are desired. One promising strategy is to genetically modify Clostridium species by introducing stress tolerance-associated genes. This study was aimed to seek butanol tolerance genes from other Gram-positive species, which might be better suited than those from Gram-negative E. coli or eukaryotic Saccharomyces cerevisiae. Several butanol-tolerant lactobacilli were reported previously, and Lactobacillus mucosae BR0713-33, which showed the most robust anaerobic growth in 4% butanol, was used here for proteomics analyses. Cellular proteins that responded to 2, 3, and 4% butanol were characterized. Twenty-nine proteins that were identified were dysregulated in response to increased concentrations of butanol in L. mucosae . Seventeen genes involved in coding for stress-tolerant proteins GroES, GroEL, and DnaK and genes involved in substrate utilization, fatty acid metabolism, and nucleotide synthesis were induced by increased butanol, and 12 genes involving energy production (F0F1ATP synthases) and redox balance preservation were repressed by increased butanol. These results can help guide targeted engineering strategies to improve tolerance and production of biobutanol.
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Affiliation(s)
- Siqing Liu
- Renewable
Product Technology Research Unit, National Center for Agricultural
Utilization Research, Agricultural Research Service, U.S. Department
of Agriculture, Peoria, Illinois 61604, United States
| | - Nasib Qureshi
- Bioenery
Research Unit, National Center for Agricultural Utilization Research,
Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604, United States
| | - Kenneth Bischoff
- Renewable
Product Technology Research Unit, National Center for Agricultural
Utilization Research, Agricultural Research Service, U.S. Department
of Agriculture, Peoria, Illinois 61604, United States
| | - Costel C. Darie
- Biochemistry
& Proteomics Group, Department of Chemistry & Biomolecular
Science, Clarkson University, Potsdam, New York 13699, United States
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Evaluation of salivary VOC profile composition directed towards oral cancer and oral lesion assessment. Clin Oral Investig 2021; 25:4415-4430. [PMID: 33387033 DOI: 10.1007/s00784-020-03754-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/18/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Endogenous substances have been analyzed in biological samples in order to be related with metabolic dysfunctions and diseases. The study aimed to investigate profiles of volatile organic compounds (VOCs) from fresh and incubated saliva donated by healthy controls, individuals with oral tissue lesions and with oral cancer, in order to assess case-specific biomarkers of oxidative stress. MATERIALS AND METHODS VOCs were pre-concentrated using headspace-solid phase microextraction and analyzed using gas chromatography-mass spectrometry. Then, VOCs positively modulated by incubation process were subtracted, yielding profiles with selected features. Principal component analysis and hierarchical cluster analysis were used to inspect data distribution, while univariate statistics was applied to indicate potential markers of oral cancer. Machine learning algorithm was implemented, aiming multiclass prediction. RESULTS The removal of bacterial contribution to VOC profiles allowed the obtaining of more specific case-related patterns. Artificial neural network model included 9 most relevant compounds (1-octen-3-ol, hexanoic acid, E-2-octenal, heptanoic acid, octanoic acid, E-2-nonenal, nonanoic acid, 2,4-decadienal and 9-undecenoic acid). Model performance was assessed using 10-fold cross validation and receiver operating characteristic curves. Obtained overall accuracy was 90%. Oral cancer cases were predicted with 100% of sensitivity and specificity. CONCLUSIONS The selected VOCs were ascribed to lipid oxidation mechanism and presented potential to differentiate oral cancer from other inflammatory conditions. CLINICAL RELEVANCE These results highlight the importance of interpretation of saliva composition and the clinical value of salivary VOCs. Elucidated metabolic alterations have the potential to aid the early detection of oral cancer and the monitoring of oral lesions.
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How to outwit nature: Omics insight into butanol tolerance. Biotechnol Adv 2020; 46:107658. [PMID: 33220435 DOI: 10.1016/j.biotechadv.2020.107658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022]
Abstract
The energy crisis, depletion of oil reserves, and global climate changes are pressing problems of developed societies. One possibility to counteract that is microbial production of butanol, a promising new fuel and alternative to many petrochemical reagents. However, the high butanol toxicity to all known microbial species is the main obstacle to its industrial implementation. The present state of the art review aims to expound the recent advances in modern omics approaches to resolving this insurmountable to date problem of low butanol tolerance. Genomics, transcriptomics, and proteomics show that butanol tolerance is a complex phenomenon affecting multiple genes and their expression. Efflux pumps, stress and multidrug response, membrane transport, and redox-related genes are indicated as being most important during butanol challenge, in addition to fine-tuning of global regulators of transcription (Spo0A, GntR), which may further improve tolerance. Lipidomics shows that the alterations in membrane composition (saturated lipids and plasmalogen increase) are very much species-specific and butanol-related. Glycomics discloses the pleiotropic effect of CcpA, the role of alternative sugar transport, and the production of exopolysaccharides as alternative routes to overcoming butanol stress. Unfortunately, the strain that simultaneously syntheses and tolerates butanol in concentrations that allow its commercialization has not yet been discovered or produced. Omics insight will allow the purposeful increase of butanol tolerance in natural and engineered producers and the effective heterologous expression of synthetic butanol pathways in strains hereditary butanol-resistant up to 3.2 - 4.9% (w/v). Future breakthrough can be achieved by a detailed study of the membrane proteome, of which 21% are proteins with unknown functions.
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Ferreira S, Pereira R, Wahl SA, Rocha I. Metabolic engineering strategies for butanol production in Escherichia coli. Biotechnol Bioeng 2020; 117:2571-2587. [PMID: 32374413 DOI: 10.1002/bit.27377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 04/03/2020] [Accepted: 05/04/2020] [Indexed: 11/06/2022]
Abstract
The global market of butanol is increasing due to its growing applications as solvent, flavoring agent, and chemical precursor of several other compounds. Recently, the superior properties of n-butanol as a biofuel over ethanol have stimulated even more interest. (Bio)butanol is natively produced together with ethanol and acetone by Clostridium species through acetone-butanol-ethanol fermentation, at noncompetitive, low titers compared to petrochemical production. Different butanol production pathways have been expressed in Escherichia coli, a more accessible host compared to Clostridium species, to improve butanol titers and rates. The bioproduction of butanol is here reviewed from a historical and theoretical perspective. All tested rational metabolic engineering strategies in E. coli to increase butanol titers are reviewed: manipulation of central carbon metabolism, elimination of competing pathways, cofactor balancing, development of new pathways, expression of homologous enzymes, consumption of different substrates, and molecular biology strategies. The progress in the field of metabolic modeling and pathway generation algorithms and their potential application to butanol production are also summarized here. The main goals are to gather all the strategies, evaluate the respective progress obtained, identify, and exploit the outstanding challenges.
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Affiliation(s)
- Sofia Ferreira
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Rui Pereira
- SilicoLife Lda, Braga, Portugal.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - S A Wahl
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Isabel Rocha
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
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Mar MJ, Andersen JM, Kandasamy V, Liu J, Solem C, Jensen PR. Synergy at work: linking the metabolism of two lactic acid bacteria to achieve superior production of 2-butanol. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:45. [PMID: 32180827 PMCID: PMC7065357 DOI: 10.1186/s13068-020-01689-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/26/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND The secondary alcohol 2-butanol has many important applications, e.g., as a solvent. Industrially, it is usually made by sulfuric acid-catalyzed hydration of butenes. Microbial production of 2-butanol has also been attempted, however, with little success as witnessed by the low titers and yields reported. Two important reasons for this, are the growth-hampering effect of 2-butanol on microorganisms, and challenges associated with one of the key enzymes involved in its production, namely diol dehydratase. RESULTS We attempt to link the metabolism of an engineered Lactococcus lactis strain, which possesses all enzyme activities required for fermentative production of 2-butanol from glucose, except for diol dehydratase, which acts on meso-2,3-butanediol (mBDO), with that of a Lactobacillus brevis strain which expresses a functional dehydratase natively. We demonstrate growth-coupled production of 2-butanol by the engineered L. lactis strain, when co-cultured with L. brevis. After fine-tuning the co-culture setup, a titer of 80 mM (5.9 g/L) 2-butanol, with a high yield of 0.58 mol/mol is achieved. CONCLUSIONS Here, we demonstrate that it is possible to link the metabolism of two bacteria to achieve redox-balanced production of 2-butanol. Using a simple co-cultivation setup, we achieved the highest titer and yield from glucose in a single fermentation step ever reported. The data highlight the potential that lies in harnessing microbial synergies for producing valuable compounds.
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Affiliation(s)
- Mette J. Mar
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Joakim M. Andersen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Vijayalakshmi Kandasamy
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Jianming Liu
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Peter R. Jensen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
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