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Decision tree-based identification of Staphylococcus aureus via infrared spectral analysis of ambient gas. Anal Bioanal Chem 2021; 414:1049-1059. [PMID: 34686896 PMCID: PMC8724094 DOI: 10.1007/s00216-021-03729-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/10/2021] [Accepted: 10/11/2021] [Indexed: 12/02/2022]
Abstract
In this study, eight types of bacteria were cultivated, including Staphylococcus aureus. The infrared absorption spectra of the gas surrounding cultured bacteria were recorded at a resolution of 0.5 cm−1 over the wavenumber range of 7500–500 cm−1. From these spectra, we searched for the infrared wavenumbers at which characteristic absorptions of the gas surrounding Staphylococcus aureus could be measured. This paper reports two wavenumber regions, 6516–6506 cm−1 and 2166–2158 cm−1. A decision tree–based machine learning algorithm was used to search for these wavenumber regions. The peak intensity or the absorbance difference was calculated for each region, and the ratio between them was obtained. When these ratios were used as training data, decision trees were created to classify the gas surrounding Staphylococcus aureus and the gas surrounding other bacteria into different groups. These decision trees show the potential effectiveness of using absorbance measurement at two wavenumber regions in finding Staphylococcus aureus.
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2
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Shahid S, Corroler D, Mosrati R, Amiel C, Gaillard JL. New model development for qualitative and quantitative analysis of microbial polyhydroxyalkanoates: A comparison of Fourier Transform Infrared Spectroscopy with Gas Chromatography. J Biotechnol 2021; 329:38-48. [PMID: 33539895 DOI: 10.1016/j.jbiotec.2021.01.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 02/04/2023]
Abstract
FT-IR spectroscopy is a non-destructive testing technique that requires minimal sample preparation time and allows the rapid characterization of structural features of complex, polymeric material. This technique has been frequently used in the past for the detection of PHA (Polyhydroxyalkanoates) but rarely for their quantification. In this work, by using cluster and discriminant statistical analysis of FT-IR data, different models are proposed for rapid identification of PHA monomers produced under different growth conditions by bacterial strains, and for their semi quantification. The results on the ability to produce large amounts of PHA (of 21 strains) in different environmental conditions of medium, substrates and deficiency of nutrients are presented. The spectral data analysis gives qualitative and semi quantitative information about the PHA produced in the samples. Models are proposed to test a large number of cultural conditions of strains and substrates in the field of screening and for identifying best conditions of PHA production in lab scale bioreactor and on industrial scale.
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Affiliation(s)
- Salma Shahid
- Department of Biochemistry, Govt College Women University Faisalabad, Pakistan.
| | - David Corroler
- Unité de Recherche ABTE, (Alimentation-Bioprocédés-Toxicologie-Environnements), EA 4651, Esplanade de la Paix, Université de Caen Normandie, 14032 Caen Cedex 5, France
| | - Ridha Mosrati
- Unité de Recherche ABTE, (Alimentation-Bioprocédés-Toxicologie-Environnements), EA 4651, Esplanade de la Paix, Université de Caen Normandie, 14032 Caen Cedex 5, France
| | - Caroline Amiel
- Unité de Recherche ABTE, (Alimentation-Bioprocédés-Toxicologie-Environnements), EA 4651, Esplanade de la Paix, Université de Caen Normandie, 14032 Caen Cedex 5, France
| | - Jean-Luc Gaillard
- Unité de Recherche ABTE, (Alimentation-Bioprocédés-Toxicologie-Environnements), EA 4651, Esplanade de la Paix, Université de Caen Normandie, 14032 Caen Cedex 5, France
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3
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Lin J, Huang Z, Lin X, Wu Q, Quan K, Cheng Y, Zheng M, Xu J, Dai Y, Qiu H, Lin D, Feng S. Rapid and label-free urine test based on surface-enhanced Raman spectroscopy for the non-invasive detection of colorectal cancer at different stages. BIOMEDICAL OPTICS EXPRESS 2020; 11:7109-7119. [PMID: 33408983 PMCID: PMC7747921 DOI: 10.1364/boe.406097] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/29/2020] [Accepted: 11/02/2020] [Indexed: 05/09/2023]
Abstract
The concept of being able to urinate in a cup and screen for colorectal cancer (CRC) is fascinating to the public at large. Here, a simple and label-free urine test based on surface-enhanced Raman spectroscopy (SERS) was employed for CRC detection. Significant spectral differences among normal, stages I-II, and stages III-IV CRC urines were observed. Using discriminant function analysis, the diagnostic sensitivities of 95.8%, 80.9%, and 84.3% for classification of normal, stages I-II, and stages III-IV CRC were achieved in training model, indicating the great promise of urine SERS as a rapid, convenient and noninvasive method for CRC staging detection.
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Affiliation(s)
- Jinyong Lin
- Radiation Oncology Department, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Digital Fujian Internet-of-Things Laboratory of Environment Monitoring, Fujian Normal University, Fuzhou, 350007, China
- These authors contributed equally to this work
| | - Zongwei Huang
- Radiation Oncology Department, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
- These authors contributed equally to this work
| | - Xueliang Lin
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Digital Fujian Internet-of-Things Laboratory of Environment Monitoring, Fujian Normal University, Fuzhou, 350007, China
| | - Qiong Wu
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Digital Fujian Internet-of-Things Laboratory of Environment Monitoring, Fujian Normal University, Fuzhou, 350007, China
| | - Kerun Quan
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China
| | - Yanming Cheng
- Radiation Oncology Department, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Mingzhi Zheng
- Radiation Oncology Department, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Jiaying Xu
- Radiation Oncology Department, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Yitao Dai
- Radiation Oncology Department, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Hejin Qiu
- Radiation Oncology Department, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Duo Lin
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Digital Fujian Internet-of-Things Laboratory of Environment Monitoring, Fujian Normal University, Fuzhou, 350007, China
| | - Shangyuan Feng
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Digital Fujian Internet-of-Things Laboratory of Environment Monitoring, Fujian Normal University, Fuzhou, 350007, China
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Shahid S, Razzaq S, Farooq R, Nazli ZIH. Polyhydroxyalkanoates: Next generation natural biomolecules and a solution for the world's future economy. Int J Biol Macromol 2020; 166:297-321. [PMID: 33127548 DOI: 10.1016/j.ijbiomac.2020.10.187] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 02/08/2023]
Abstract
Petrochemical plastics have become a cause of pollution for decades and finding alternative plastics that are environmental friendly. Polyhydroxyalkanoate (PHA), a biopolyester produced by microbial cells, has characteristics (biocompatible, biodegradable, non-toxic) that make it appropriate as a biodegradable plastic substance. The different forms of PHA make it suitable to a wide choice of products, from packaging materials to biomedical applications. The major challenge in commercialization of PHA is the cost of manufacturing. There are a lot of factors that could affect the efficiency of a development method. The development of new strategic parameters for better synthesis, including consumption of low cost carbon substrates, genetic modification of PHA-producing strains, and fermentational strategies are discussed. Recently, many efforts have been made to develop a method for the cost-effective production of PHAs. The isolation, analysis as well as characterization of PHAs are significant factors for any developmental process. Due to the biodegradable and biocompatible properties of PHAs, they are majorly used in biomedical applications such as vascular grafting, heart tissue engineering, skin tissue repairing, liver tissue engineering, nerve tissue engineering, bone tissue engineering, cartilage tissue engineering and therapeutic carrier. The emerging and interesting area of research is the development of self-healing biopolymer that could significantly broaden the operational life and protection of the polymeric materials for a broad range of uses. Biodegradable and biocompatible polymers are considered as the green materials in place of petroleum-based plastics in the future.
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Affiliation(s)
- Salma Shahid
- Department of Biochemistry, Government College Women University Faisalabad, Pakistan.
| | - Sadia Razzaq
- Department of Chemistry, Government College Women University Faisalabad, Pakistan
| | - Robina Farooq
- Department of Chemistry, Government College Women University Faisalabad, Pakistan
| | - Zill-I-Huma Nazli
- Department of Chemistry, Government College Women University Faisalabad, Pakistan
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5
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Meng F, Ma S, Muhammad Y, Li J, Sahibzada M, Chi F. Analysis of Virgin Asphalt Brands via the Integrated Application of FTIR and Gel Permeation Chromatography. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2020. [DOI: 10.1007/s13369-020-04539-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Park KY, Yu YJ, Yun SJ, Kweon JH. Natural organic matter removal from algal-rich water and disinfection by-products formation potential reduction by powdered activated carbon adsorption. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 235:310-318. [PMID: 30703645 DOI: 10.1016/j.jenvman.2019.01.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/24/2018] [Accepted: 01/22/2019] [Indexed: 05/25/2023]
Abstract
Algal blooms intensified operational problems in water treatment due to the increases of taste- and odor-causing compounds and natural organic matter (NOM). Effects of powdered activated carbon (PAC) addition during algal blooms on NOM removal was investigated in this study using an algal-rich water. Water quality analyses including dissolved organic carbon (DOC), ultraviolet absorbance at 254 nm (UV254) and specific UV absorbance (SUVA) were performed to elucidate characteristics of NOM removal by PAC adsorption. Variations of MW distributions and emission/excitation matrix (EEM) spectra with increasing PAC dosages were also measured. In addition, formation potential (FP) of trihalomethanes (THMs), haloacetic acids (HAAs), and haloacetonitriles (HANs) was evaluated with increasing PAC dosage. The correlations between disinfection by-products formation potential (DBPFP) and water qualities such as DOC, UV254, SUVA, and EEM spectra were also investigated to identify factors associated with DBPFP. The PAC addition was effective to remove NOM, especially low molecular weights NOM and proteinaceous substances with weak aromatics. The PAC addition showed the consistent reduction of THMFPs, HAAFPs, and HANFPs with increasing PAC dosage while the greater reduction of HAN precursors was eminent compared to the other two FPs. The close correlations between UV254 and the three DBPFPs were obtained. The low molecular weight (i.e., 1-700 Da) NOM and three fluorescence spectra peaks, i.e., T1, A and C peaks, also showed high correlation factors with the three DBPFPs. Those analyses with high correlations with DBPFPs would provide useful information to reduce DBPs during algal blooms.
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Affiliation(s)
- Keun-Young Park
- Konkuk University, Department of Environmental Engineering, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea
| | - Young-Jae Yu
- Konkuk University, Department of Environmental Engineering, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea
| | - Soon-Jin Yun
- Korea University, Department of Environmental Science and Ecological Engineering, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea
| | - Ji-Hyang Kweon
- Konkuk University, Department of Environmental Engineering, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea.
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Analytical study of effective biodegradation of p-cresol using Serratia marcescens ABHI001: application in bioremediation. 3 Biotech 2017; 7:384. [PMID: 29142804 DOI: 10.1007/s13205-017-1006-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 10/09/2017] [Indexed: 10/18/2022] Open
Abstract
This study evaluated the capability of Serratia marcescens ABHI001 to effectively degrade p-cresol through different techniques. The molecular identity of the laboratory isolate S. marcescens ABHI001 was confirmed through the 16S ribosomal DNA gene pattern, and its morphological features were investigated through field-emission scanning electron microscopy. In addition, the degradation behavior of the isolate for cresol was verified using several techniques, including UV-visible spectroscopy, followed by high-performance liquid chromatography (HPLC), gas chromatography, and Fourier transform infrared spectroscopy. The maximum degradation percentage of 85% for p-cresol could be achieved after 18 h of incubation with S. marcescens ABHI001. The formation of p-hydroxybenzaldehyde, p-hydroxybenzoate, and protocatechuate metabolites was confirmed through HPLC. The study results indicate that S. marcescens ABHI001 may have applications in the bioremediation of organic pollutants, such as p-cresol.
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Conte C, Roscini L, Sardella R, Mariucci G, Scorzoni S, Beccari T, Corte L. Toll Like Receptor 4 Affects the Cerebral Biochemical Changes Induced by MPTP Treatment. Neurochem Res 2017; 42:493-500. [PMID: 28108849 DOI: 10.1007/s11064-016-2095-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/17/2016] [Accepted: 10/27/2016] [Indexed: 02/06/2023]
Abstract
The etiology and pathogenesis of Parkinson's disease (PD) are still unclear. However, multiple lines of evidence suggest a critical role of the toll like receptor 4 (TLR4) in inflammatory response and neuronal death. Neuroinflammation may be associated with the misfolding and aggregation of proteins accompanied by a change in their secondary structure. Recent findings also suggest that biochemical perturbations in cerebral lipid content could contribute to the pathogenesis of central nervous system (CNS) disorders, including PD. Thus, it is of great importance to determine the biochemical changes that occur in PD. In this respect, Fourier Transform Infrared (FTIR) spectroscopy represents a useful tool to detect molecular alterations in biological systems in response to stress stimuli. By relying upon FTIR approach, this study was designed to elucidate the potential role of TLR4 in biochemical changes induced by methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) neurotoxin in a mouse model of PD. The analysis of the FTIR spectra was performed in different brain regions of both wild type (WT) and toll like receptor 4-deficient (TLR4-/-) mice. It revealed that each brain region exhibited a characteristic molecular fingerprint at baseline, with no significant differences between genotypes. Conversely, WT and TLR4-/- mice showed differential biochemical response to MPTP toxicity, principally related to lipid and protein composition. These differences appeared to be characteristic for each brain area. Furthermore, the present study showed that WT mice resulted more vulnerable than TLR4-/- animals to striatal dopamine (DA) depletion following MPTP treatment. These results support the hypothesis of a possible involvement of TLR4 in biochemical changes occurring in neurodegeneration.
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Affiliation(s)
- Carmela Conte
- Department of Pharmaceutical Sciences, Section of Biochemical and Health Sciences, University of Perugia, Via del Giochetto, 06123, Perugia, Italy.
| | - Luca Roscini
- Department of Pharmaceutical Sciences, Section of Biochemical and Health Sciences, University of Perugia, Via del Giochetto, 06123, Perugia, Italy
| | - Roccaldo Sardella
- Department of Pharmaceutical Sciences, Section of Biochemical and Health Sciences, University of Perugia, Via del Giochetto, 06123, Perugia, Italy
| | - Giuseppina Mariucci
- Department of Pharmaceutical Sciences, Section of Biochemical and Health Sciences, University of Perugia, Via del Giochetto, 06123, Perugia, Italy
| | - Stefania Scorzoni
- Department of Pharmaceutical Sciences, Section of Biochemical and Health Sciences, University of Perugia, Via del Giochetto, 06123, Perugia, Italy.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tommaso Beccari
- Department of Pharmaceutical Sciences, Section of Biochemical and Health Sciences, University of Perugia, Via del Giochetto, 06123, Perugia, Italy
| | - Laura Corte
- Department of Pharmaceutical Sciences, Section of Biochemical and Health Sciences, University of Perugia, Via del Giochetto, 06123, Perugia, Italy
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Tiecco M, Roscini L, Corte L, Colabella C, Germani R, Cardinali G. Ionic Conductivity as a Tool To Study Biocidal Activity of Sulfobetaine Micelles against Saccharomyces cerevisiae Model Cells. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1101-1110. [PMID: 26752694 DOI: 10.1021/acs.langmuir.5b04077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Zwitterionic sulfobetaine surfactants are used in pharmaceutical or biomedical applications for the solubilization and delivery of hydrophobic molecules in aqueous medium or in biological environments. In a screening on the biocidal activity of synthetic surfactants on microbial cells, remarkable results have emerged with sulfobetaine amphiphiles. The interaction between eight zwitterionic sulfobetaine amphiphiles and Saccharomyces cerevisiae model cells was therefore analyzed. S. cerevisiae yeast cells were chosen, as they are a widely used unicellular eukaryotic model organism in cell biology. Conductivity measurements were used to investigate the interaction between surfactant solution and cells. Viable counts measurements were performed, and the mortality data correlated with the conductivity profiles very well, in terms of the inflection points (IPs) observed in the curves and in terms of supramolecular properties of the aggregates. A Fourier transform infrared (FTIR)-based bioassay was then performed to determine the metabolomic stress-response of the cells subjected to the action of zwitterionic surfactants. The surfactants showed nodal concentration (IPs) with all the techniques in their activities, corresponding to the critical micellar concentrations of the amphiphiles. This is due to the pseudocationic behavior of sulfobetaine micelles, because of their charge distribution and charge densities. This behavior permits the interaction of the micellar aggregates with the cells, and the structure of the surfactant monomers has impact on the mortality and the metabolomic response data observed. On the other hand, the concentrations that are necessary to provoke a biocidal activity do not promote these amphiphiles as potential antimicrobial agents. In fact, they are much higher than the ones of cationic surfactants.
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Affiliation(s)
- Matteo Tiecco
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia , Borgo XX Giugno 74, I-06121 Perugia, Italy
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials, Department of Chemistry, Biology and Biotechnology, University of Perugia , via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Luca Roscini
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia , Borgo XX Giugno 74, I-06121 Perugia, Italy
| | - Laura Corte
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia , Borgo XX Giugno 74, I-06121 Perugia, Italy
| | - Claudia Colabella
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia , Borgo XX Giugno 74, I-06121 Perugia, Italy
| | - Raimondo Germani
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials, Department of Chemistry, Biology and Biotechnology, University of Perugia , via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia , Borgo XX Giugno 74, I-06121 Perugia, Italy
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials, Department of Chemistry, Biology and Biotechnology, University of Perugia , via Elce di Sotto 8, I-06123 Perugia, Italy
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Favaro L, Corte L, Roscini L, Cagnin L, Tiecco M, Colabella C, Berti A, Basaglia M, Cardinali G, Casella S. A novel FTIR-based approach to evaluate the interactions between lignocellulosic inhibitory compounds and their effect on yeast metabolism. RSC Adv 2016. [DOI: 10.1039/c6ra08859g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
FTIR analysis revealed antagonistic effects between lignocellulosic inhibitory compounds through the metabolomic alterations induced on differentS. cerevisiaestrains.
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Affiliation(s)
- Lorenzo Favaro
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE)
- University of Padova
- Italy
| | - Laura Corte
- Department of Pharmaceutical Sciences-Microbiology
- University of Perugia
- I-06121 Perugia
- Italy
| | - Luca Roscini
- Department of Pharmaceutical Sciences-Microbiology
- University of Perugia
- I-06121 Perugia
- Italy
| | - Lorenzo Cagnin
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE)
- University of Padova
- Italy
| | - Matteo Tiecco
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials
- Department of Chemistry, Biology and Biotechnology
- University of Perugia
- Italy
| | - Claudia Colabella
- Department of Pharmaceutical Sciences-Microbiology
- University of Perugia
- I-06121 Perugia
- Italy
| | - Antonio Berti
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE)
- University of Padova
- Italy
| | - Marina Basaglia
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE)
- University of Padova
- Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences-Microbiology
- University of Perugia
- I-06121 Perugia
- Italy
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials
| | - Sergio Casella
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE)
- University of Padova
- Italy
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Moktaduzzaman M, Galafassi S, Vigentini I, Foschino R, Corte L, Cardinali G, Piškur J, Compagno C. Strain-dependent tolerance to acetic acid in Dekkera bruxellensis. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1115-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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12
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Corte L, di Cagno R, Groenewald M, Roscini L, Colabella C, Gobbetti M, Cardinali G. Phenotypic and molecular diversity of Meyerozyma guilliermondii strains isolated from food and other environmental niches, hints for an incipient speciation. Food Microbiol 2015; 48:206-15. [PMID: 25791010 DOI: 10.1016/j.fm.2014.12.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 11/17/2014] [Accepted: 12/16/2014] [Indexed: 10/24/2022]
Abstract
Meyerozyma guilliermondii is a yeast species widely isolated from several natural environments and from fruit; in medical microbiology it is known as the teleomorph of the opportunistic pathogen Candida guilliermondii, which causes about 2% of the human blood infections. This yeast is also promising in a variety of biotechnological applications as vitamins production and post-harvest control. The question if isolates from different sources are physiologically and genetically similar, or if the various environments induced significant differences, is crucial for the understanding of this species structure and to select strains appropriate for each application. This question was addressed using LSU and ITS sequencing for taxonomic assignment, i-SSR (GACA4) for the molecular characterization and FTIR for the metabolomic fingerprint. All data showed that fruit and environmental isolates cluster separately with a general good agreement between metabolomics and molecular analysis. An additional RAPD analysis was able to discriminate strains according to the isolation position within the pineapple fruit. Although all strains are members of the M. guilliermondii species according to the current standards, the distribution of large variability detected suggests that some specialization occurred in the niches inhabited by this yeast and that food related strains can be differentiated from the medical isolates.
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Affiliation(s)
- Laura Corte
- Department of Pharmaceutical Sciences - Microbiology, University of Perugia, Borgo 20 Giugno 74, 06121 Perugia, Italy
| | - Raffaella di Cagno
- Department of Plant Protection and Applied Microbiology, University of Bari, via Amendola 165/a, 70126 Bari, Italy
| | | | - Luca Roscini
- Department of Pharmaceutical Sciences - Microbiology, University of Perugia, Borgo 20 Giugno 74, 06121 Perugia, Italy
| | - Claudia Colabella
- Department of Pharmaceutical Sciences - Microbiology, University of Perugia, Borgo 20 Giugno 74, 06121 Perugia, Italy
| | - Marco Gobbetti
- Department of Plant Protection and Applied Microbiology, University of Bari, via Amendola 165/a, 70126 Bari, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences - Microbiology, University of Perugia, Borgo 20 Giugno 74, 06121 Perugia, Italy; CEMIN, Centre of Excellence on Nanostructured Innovative Materials, Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, I-06123 Perugia, Italy.
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13
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Corte L, Tiecco M, Roscini L, De Vincenzi S, Colabella C, Germani R, Tascini C, Cardinali G. FTIR metabolomic fingerprint reveals different modes of action exerted by structural variants of N-alkyltropinium bromide surfactants on Escherichia coli and Listeria innocua cells. PLoS One 2015; 10:e0115275. [PMID: 25588017 PMCID: PMC4294686 DOI: 10.1371/journal.pone.0115275] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/23/2014] [Indexed: 12/05/2022] Open
Abstract
Surfactants are extremely important agents to clean and sanitize various environments. Their biocidal activity is a key factor determined by the interactions between amphiphile structure and the target microbial cells. The object of this study was to analyze the interactions between four structural variants of N-alkyltropinium bromide surfactants with the Gram negative Escherichia coli and the Gram positive Listeria innocua bacteria. Microbiological and conductometric methods with a previously described FTIR bioassay were used to assess the metabolomic damage exerted by these compounds. All surfactants tested showed more biocidal activity in L. innocua than in E. coli. N-tetradecyltropinium bromide was the most effective compound against both species, while all the other variants had a reduced efficacy as biocides, mainly against E. coli cells. In general, the most prominent metabolomic response was observed for the constituents of the cell envelope in the fatty acids (W1) and amides (W2) regions and at the wavenumbers referred to peptidoglycan (W2 and W3 regions). This response was particularly strong and negative in L. innocua, when cells were challenged by N-tetradecyltropinium bromide, and by the variant with a smaller head and a 12C tail (N-dodecylquinuclidinium bromide). Tail length was critical for microbial inhibition especially when acting against E. coli, maybe due the complex nature of Gram negative cell envelope. Statistical analysis allowed us to correlate the induced mortality with the metabolomic cell response, highlighting two different modes of action. In general, gaining insights in the interactions between fine structural properties of surfactants and the microbial diversity can allow tailoring these compounds for the various operative conditions.
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Affiliation(s)
- Laura Corte
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Borgo XX Giugno 74, I-06121 Perugia, Italy
- * E-mail:
| | - Matteo Tiecco
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials, Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Luca Roscini
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Borgo XX Giugno 74, I-06121 Perugia, Italy
| | - Sergio De Vincenzi
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Borgo XX Giugno 74, I-06121 Perugia, Italy
| | - Claudia Colabella
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Borgo XX Giugno 74, I-06121 Perugia, Italy
| | - Raimondo Germani
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials, Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Carlo Tascini
- U.O. Malattie Infettive, Azienda Ospedaliera Universitaria Pisana, Via Paradisa 2, Cisanello, 56100 Pisa, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Borgo XX Giugno 74, I-06121 Perugia, Italy
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials, Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, I-06123 Perugia, Italy
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14
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Cardellini F, Germani R, Cardinali G, Corte L, Roscini L, Spreti N, Tiecco M. Room temperature deep eutectic solvents of (1S)-(+)-10-camphorsulfonic acid and sulfobetaines: hydrogen bond-based mixtures with low ionicity and structure-dependent toxicity. RSC Adv 2015. [DOI: 10.1039/c5ra03932k] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Preparation, properties and toxicity of room temperature deep eutectic solvents formed by (1S)-(+)-10-camphorsulfonic acid and aromatic, aliphatic and amphiphilic sulfobetaines.
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Affiliation(s)
- Fabio Cardellini
- CEMIN
- Centre of Excellence on Nanostructured Innovative Materials
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
| | - Raimondo Germani
- CEMIN
- Centre of Excellence on Nanostructured Innovative Materials
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
| | - Gianluigi Cardinali
- CEMIN
- Centre of Excellence on Nanostructured Innovative Materials
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
| | - Laura Corte
- Department of Pharmaceutical Sciences – Microbiology
- University of Perugia
- Perugia
- Italy
| | - Luca Roscini
- Department of Pharmaceutical Sciences – Microbiology
- University of Perugia
- Perugia
- Italy
| | - Nicoletta Spreti
- Department of Physical and Chemical Sciences
- University of L'Aquila
- L'Aquila
- Italy
| | - Matteo Tiecco
- CEMIN
- Centre of Excellence on Nanostructured Innovative Materials
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
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15
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Cardellini F, Tiecco M, Germani R, Cardinali G, Corte L, Roscini L, Spreti N. Novel zwitterionic deep eutectic solvents from trimethylglycine and carboxylic acids: characterization of their properties and their toxicity. RSC Adv 2014. [DOI: 10.1039/c4ra10628h] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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16
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Corte L, Tiecco M, Roscini L, Germani R, Cardinali G. FTIR analysis of the metabolomic stress response induced by N-alkyltropinium bromide surfactants in the yeasts Saccharomyces cerevisiae and Candida albicans. Colloids Surf B Biointerfaces 2014; 116:761-71. [DOI: 10.1016/j.colsurfb.2014.01.054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 01/27/2014] [Accepted: 01/30/2014] [Indexed: 10/25/2022]
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17
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Corte L, Dell'abate MT, Magini A, Migliore M, Felici B, Roscini L, Sardella R, Tancini B, Emiliani C, Cardinali G, Benedetti A. Assessment of safety and efficiency of nitrogen organic fertilizers from animal-based protein hydrolysates--a laboratory multidisciplinary approach. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:235-245. [PMID: 23712286 DOI: 10.1002/jsfa.6239] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/10/2013] [Accepted: 05/24/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND Protein hydrolysates or hydrolysed proteins (HPs) are high-N organic fertilizers allowing the recovery of by-products (leather meal and fluid hydrolysed proteins) otherwise disposed of as polluting wastes, thus enhancing matter and energy conservation in agricultural systems while decreasing potential pollution. Chemical and biological characteristics of HPs of animal origin were analysed in this work to assess their safety, environmental sustainability and agricultural efficacy as fertilizers. Different HPs obtained by thermal, chemical and enzymatic hydrolytic processes were characterized by Fourier transform infrared spectroscopy and sodium dodecyl sulfate polyacrylamide gel electrophoresis, and their safety and efficacy were assessed through bioassays, ecotoxicological tests and soil biochemistry analyses. RESULTS HPs can be discriminated according to their origin and hydrolysis system by proteomic and metabolomic methods. Three experimental systems, soil microbiota, yeast and plants, were employed to detect possible negative effects exerted by HPs. The results showed that these compounds do not significantly interfere with metabolomic activity or the reproductive system. CONCLUSION The absence of toxic and genotoxic effects of the hydrolysates prepared by the three hydrolytic processes suggests that they do not negatively affect eukaryotic cells and soil ecosystems and that they can be used in conventional and organic farming as an important nitrogen source derived from otherwise highly polluting by-products.
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Affiliation(s)
- Laura Corte
- Department of Applied Biology-Microbiology, University of Perugia, Borgo XX Giugno 74, I-06121, Perugia, Italy
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18
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Copper enhanced monooxygenase activity and FT-IR spectroscopic characterisation of biotransformation products in trichloroethylene degrading bacterium: Stenotrophomonas maltophilia PM102. BIOMED RESEARCH INTERNATIONAL 2013; 2013:723680. [PMID: 24083236 PMCID: PMC3780474 DOI: 10.1155/2013/723680] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/13/2013] [Accepted: 07/15/2013] [Indexed: 11/17/2022]
Abstract
Stenotrophomonas maltophilia PM102 (NCBI GenBank Acc. no. JQ797560) is capable of growth on trichloroethylene as the sole carbon source. In this paper, we report the purification and characterisation of oxygenase present in the PM102 isolate. Enzyme activity was found to be induced 10.3-fold in presence of 0.7 mM copper with a further increment to 14.96-fold in presence of 0.05 mM NADH. Optimum temperature for oxygenase activity was recorded at 36°C. The reported enzyme was found to have enhanced activity at pH 5 and pH 8, indicating presence of two isoforms. Maximum activity was seen on incubation with benzene compared to other substrates like TCE, chloroform, toluene, hexane, and petroleum benzene. K(m) and V(max) for benzene were 3.8 mM and 340 U/mg/min and those for TCE were 2.1 mM and 170 U/mg/min. The crude enzyme was partially purified by ammonium sulphate precipitation followed by dialysis. Zymogram analysis revealed two isoforms in the 70% purified enzyme fraction. The activity stain was more prominent when the native gel was incubated in benzene as substrate in comparison to TCE. Crude enzyme and purified enzyme fractions were assayed for TCE degradation by the Fujiwara test. TCE biotransformation products were analysed by FT-IR spectroscopy.
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Shakirova L, Grube M, Gavare M, Auzina L, Zikmanis P. Lactobacillus acidophilus La5 and Bifidobacterium lactis Bb12 cell surface hydrophobicity and survival of the cells under adverse environmental conditions. J Ind Microbiol Biotechnol 2012; 40:85-93. [PMID: 23053348 DOI: 10.1007/s10295-012-1204-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 09/21/2012] [Indexed: 11/29/2022]
Abstract
Changes in the cell surface hydrophobicity (CSH) of probiotic bacteria Lactobacillus acidophilus La5 and Bifidobacterium lactis Bb12 and the survival of these cells were examined in response to varied cultivation conditions and adverse environmental conditions. An inverse linear relationship (P < 0.01) was detected between the CSH of intact L. acidophilus La5 and B. lactis Bb12 and survival of cells subjected to subsequent freezing/thawing, long-term storage or exposure to mineral and bile acids. The observed relationships were supported by significant correlations between the CSH and changes in composition of the cell envelopes (proteins, lipids and carbohydrates) of L. acidophilus La5 and B. lactis Bb12 examined using FT-IR spectroscopy and conventional biochemical analysis methods. The results also suggest that the estimates of hydrophobicity, being a generalized characteristic of cell surfaces, are important parameters to predict the ability of intact probiotic bacteria to endure extreme environments and therefore should be monitored during cultivation. A defined balance of cell components, which can be characterized by the reduced CSH values, apparently helps to ensure the resistance, improved viability and hence the overall probiotic properties of bacteria.
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Affiliation(s)
- Laisana Shakirova
- Institute of Microbiology and Biotechnology, University of Latvia, Kronvalda Boulevard 4, Riga 1010, Latvia.
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Ribeiro M, Monteiro FJ, Ferraz MP. Infection of orthopedic implants with emphasis on bacterial adhesion process and techniques used in studying bacterial-material interactions. BIOMATTER 2012; 2:176-94. [PMID: 23507884 PMCID: PMC3568104 DOI: 10.4161/biom.22905] [Citation(s) in RCA: 424] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Staphylococcus comprises up to two-thirds of all pathogens in orthopedic implant infections and they are the principal causative agents of two major types of infection affecting bone: septic arthritis and osteomyelitis, which involve the inflammatory destruction of joint and bone. Bacterial adhesion is the first and most important step in implant infection. It is a complex process influenced by environmental factors, bacterial properties, material surface properties and by the presence of serum or tissue proteins. Properties of the substrate, such as chemical composition of the material, surface charge, hydrophobicity, surface roughness and the presence of specific proteins at the surface, are all thought to be important in the initial cell attachment process. The biofilm mode of growth of infecting bacteria on an implant surface protects the organisms from the host immune system and antibiotic therapy. The research for novel therapeutic strategies is incited by the emergence of antibiotic-resistant bacteria. This work will provide an overview of the mechanisms and factors involved in bacterial adhesion, the techniques that are currently being used studying bacterial-material interactions as well as provide insight into future directions in the field.
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Affiliation(s)
- Marta Ribeiro
- Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal.
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21
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Effect of pH on potassium metabisulphite biocidic activity against yeast and human cell cultures. Food Chem 2012; 134:1327-36. [DOI: 10.1016/j.foodchem.2012.03.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 01/23/2012] [Accepted: 03/06/2012] [Indexed: 02/08/2023]
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22
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Ojeda JJ, Dittrich M. Fourier transform infrared spectroscopy for molecular analysis of microbial cells. Methods Mol Biol 2012; 881:187-211. [PMID: 22639215 DOI: 10.1007/978-1-61779-827-6_8] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A rapid and inexpensive method to characterise chemical cell properties and identify the functional groups present in the cell wall is Fourier transform infrared spectroscopy (FTIR). Infrared spectroscopy is a well-established technique to identify functional groups in organic molecules based on their vibration modes at different infrared wave numbers. The presence or absence of functional groups, their protonation states, or any changes due to new interactions can be monitored by analysing the position and intensity of the different infrared absorption bands. Additionally, infrared spectroscopy is non-destructive and can be used to monitor the chemistry of living cells. Despite the complexity of the spectra, the elucidation of functional groups on Gram-negative and Gram-positive bacteria has been already well documented in the literature. Recent advances in detector sensitivity have allowed the use of micro-FTIR spectroscopy as an important analytical tool to analyse biofilm samples without the need of previous treatment. Using FTIR spectroscopy, the infrared bands corresponding to proteins, lipids, polysaccharides, polyphosphate groups, and other carbohydrate functional groups on the bacterial cells can now be identified and compared along different conditions. Despite some differences in FTIR spectra among bacterial strains, experimental conditions, or changes in microbiological parameters, the IR absorption bands between approximately 4,000 and 400 cm(-1) are mainly due to fundamental vibrational modes and can often be assigned to the same particular functional groups. In this chapter, an overview covering the different sample preparation protocols for infrared analysis of bacterial cells is given, alongside the basic principles of the technique, the procedures for calculating vibrational frequencies based on simple harmonic motion, and the advantages and disadvantages of FTIR spectroscopy for the analysis of microorganisms.
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Affiliation(s)
- Jesús J Ojeda
- Experimental Techniques Centre, Brunel University, Uxbridge, Middlesex, UK.
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Corte L, Antonielli L, Roscini L, Fatichenti F, Cardinali G. Influence of cell parameters in Fourier transform infrared spectroscopy analysis of whole yeast cells. Analyst 2011; 136:2339-49. [PMID: 21494743 DOI: 10.1039/c0an00515k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fourier Transform InfraRed spectroscopy (FTIR) is an emerging technique in biology. One of the analytical problems inherent with this approach is the extreme variability typical of biological systems. Extrinsic fonts of variations are the growth media and the growth phase of the microbial culture. In order to gain knowledge on the relations between these two factors and the spectral variability, metabolomic changes in Saccharomyces cerevisiae cells during growth were analyzed with FTIR spectroscopy. Spectral variations reflected the changes occurring in all cellular compartments and components during the different growth stages and describe the metabolomic evolution of cell cultures during growth. Three different media were tested. Different mathematical and statistical treatments were used to describe and evaluate the changes occurring during growth. Variations were mainly concentrated in the exponential phase, whereas fewer changes occurred in stationary phase cells. The three different media caused different metabolomic behaviours during growth. The mathematical distance between the peak areas of amide I, amide II and of two distinct peaks in the carbohydrates region could give a synthetic description of growth and produced similar trends in all the conditions tested. The distance between the two carbohydrate peaks could be used to determine the mid exponential phase and the entrance in the stationary phase. Growth phase was shown to influence the sensitivity of a FTIR-based cell stress bioassay. The knowledge of the metabolomic variations during growth could be used in the future to optimize FTIR applications in microbiology.
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Affiliation(s)
- Laura Corte
- Department Applied Biology-Microbiology, University of Perugia, Borgo 20 Giugno, 74, I-06121 Perugia, Italy
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Wharfe ES, Jarvis RM, Winder CL, Whiteley AS, Goodacre R. Fourier transform infrared spectroscopy as a metabolite fingerprinting tool for monitoring the phenotypic changes in complex bacterial communities capable of degrading phenol. Environ Microbiol 2011; 12:3253-63. [PMID: 20649644 DOI: 10.1111/j.1462-2920.2010.02300.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The coking process produces great volumes of wastewater contaminated with pollutants such as cyanides, sulfides and phenolics. Chemical and physical remediation of this wastewater removes the majority of these pollutants; however, these processes do not remove phenol and thiocyanate. The removal of these compounds has been effected during bioremediation with activated sludge containing a complex microbial community. In this investigation we acquired activated sludge from an industrial bioreactor capable of degrading phenol. The sludge was incubated in our laboratory and monitored for its ability to degrade phenol over a 48 h period. Multiple samples were taken across the time-course and analysed by Fourier transform infrared (FT-IR) spectroscopy. FT-IR was used as a whole-organism fingerprinting approach to monitor biochemical changes in the bacterial cells during the degradation of phenol. We also investigated the ability of the activated sludge to degrade phenol following extended periods (2-131 days) of storage in the absence of phenol. A reduction was observed in the ability of the microbial community to degrade phenol and this was accompanied by a detectable biochemical change in the FT-IR fingerprint related to cellular phenotype of the microbial community. In the absence of phenol a decrease in thiocyanate vibrations was observed, reflecting the ability of these communities to degrade this substrate. Actively degrading communities showed an additional new band in their FT-IR spectra that could be attributed to phenol degradation products from the ortho- and meta-cleavage of the aromatic ring. This study demonstrates that FT-IR spectroscopy when combined with chemometric analysis is a very powerful high throughput screening approach for assessing the metabolic capability of complex microbial communities.
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Affiliation(s)
- Emma S Wharfe
- School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7ND, UK
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Phenotypic characterization of Shewanella oneidensis MR-1 under aerobic and anaerobic growth conditions by using fourier transform infrared spectroscopy and high-performance liquid chromatography analyses. Appl Environ Microbiol 2010; 76:6266-76. [PMID: 20675447 DOI: 10.1128/aem.00912-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shewanella oneidensis is able to conserve energy for growth by reducing a wide variety of terminal electron acceptors during anaerobic respiration, including several environmentally hazardous pollutants. This bacterium employs various electron transfer mechanisms for anaerobic respiration, including cell-bound reductases and secreted redox mediators. The aim of this study was to develop rapid tools for profiling the key metabolic changes associated with these different growth regimes and physiological responses. Initial experiments focused on comparing cells grown under aerobic and anaerobic conditions. Fourier transform infrared (FT-IR) spectroscopy with cluster analysis showed that there were significant changes in the metabolic fingerprints of the cells grown under these two culture conditions. FT-IR spectroscopy clearly differentiated cells of S. oneidensis MR-1 cultured at various growth points and cells grown using different electron acceptors, resulting in different phenotypic trajectories in the cluster analysis. This growth-related trajectory analysis is applied successfully for the first time, here with FT-IR spectroscopy, to investigate the phenotypic changes in contrasting S. oneidensis cells. High-performance liquid chromatography (HPLC) was also used to quantify the concentrations of flavin compounds, which have been identified recently as extracellular redox mediators released by a range of Shewanella species. The partial least-squares regression (PLSR) multivariate statistical technique was combined with FT-IR spectroscopy to predict the concentrations of the flavins secreted by cells of S. oneidensis MR-1, suggesting that this combination could be used as a rapid alternative to conventional chromatographic methods for analysis of flavins in cell cultures. Furthermore, coupling of the FT-IR spectroscopy and HPLC techniques appears to offer a potentially useful tool for rapid characterization of the Shewanella cell metabolome in various process environments.
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Roscini L, Corte L, Antonielli L, Rellini P, Fatichenti F, Cardinali G. Influence of cell geometry and number of replicas in the reproducibility of whole cell FTIR analysis. Analyst 2010; 135:2099-105. [PMID: 20523945 DOI: 10.1039/c0an00127a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fourier Transform InfraRed (FTIR) spectroscopy is an increasingly used technique in biology, especially for whole cell metabolomic fingerprint. The reproducibility of this technique is influenced by a large number of factors such as the physiological state of cells, sample manipulation and growth conditions. Evidence exists suggesting that the cell shape and dimension can be further elements to consider in whole cell FTIR analysis. In this study we aimed to address the effect of cell geometry on the FTIR spectra and to define the extent of variability occurring between machine and biological replicas with a standardized protocol. The yeast species Saccharomyces cerevisiae (large oval-shaped cells) and Debaryomyces hansenii (small round shaped cells) were employed for their different morphology. Thirty machine replicas of each were analyzed separately and after averaging in groups of three, showing a three to four-fold reduction of the variability. Similarly, a two-fold reduction of variability was observed when thirty biological replicas of the two yeast species were analyzed. The optimal number of replicas to average was then estimated with a bootstrap-like procedure in which biological and machine replicas were randomly resampled 2000 times and averaged in groups spanning from 2 to 12 replicas. This simulation has shown that little if any advantage can be obtained by increasing the number of replicas over five and that the variability exhibited by the small regular cells of D. hansenii was always roughly half of that displayed by the large S. cerevisiae cells, confirming the results obtained with standard non-bootstrapped averages.
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Affiliation(s)
- Luca Roscini
- Department Applied Biology-Microbiology, University of Perugia, Borgo 20 Giugno, 74, I-06121 Perugia, Italy
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Ojeda JJ, Romero-González ME, Banwart SA. Analysis of Bacteria on Steel Surfaces Using Reflectance Micro-Fourier Transform Infrared Spectroscopy. Anal Chem 2009; 81:6467-73. [DOI: 10.1021/ac900841c] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jesús J. Ojeda
- Cell-Mineral Research Center, Kroto Research Institute, The University of Sheffield, Broad Lane, Sheffield S3 7HQ, U.K
| | - María E. Romero-González
- Cell-Mineral Research Center, Kroto Research Institute, The University of Sheffield, Broad Lane, Sheffield S3 7HQ, U.K
| | - Steven A. Banwart
- Cell-Mineral Research Center, Kroto Research Institute, The University of Sheffield, Broad Lane, Sheffield S3 7HQ, U.K
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Nagase A, Sakae T, Sato Y, Sato I. 532nm Laser Raman Analysis of Intraoral Bacterium. J HARD TISSUE BIOL 2007. [DOI: 10.2485/jhtb.16.205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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