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Nascimento ALF, de Medeiros AGJ, Neves ACO, de Macedo ABN, Rossato L, Assis Santos D, dos Santos ALS, Lima KMG, Bastos RW. Near-infrared spectroscopy and multivariate analysis as effective, fast, and cost-effective methods to discriminate Candida auris from Candida haemulonii. Front Chem 2024; 12:1412288. [PMID: 39050373 PMCID: PMC11266292 DOI: 10.3389/fchem.2024.1412288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/10/2024] [Indexed: 07/27/2024] Open
Abstract
Candida auris and Candida haemulonii are two emerging opportunistic pathogens that have caused an increase in clinical cases in the recent years worldwide. The differentiation of some Candida species is highly laborious, difficult, costly, and time-consuming depending on the similarity between the species. Thus, this study aimed to develop a new, faster, and less expensive methodology for differentiating between C. auris and C. haemulonii based on near-infrared (NIR) spectroscopy and multivariate analysis. C. auris CBS10913 and C. haemulonii CH02 were separated in 15 plates per species, and three isolated colonies of each plate were selected for Fourier transform near-infrared (FT-NIR) analysis, totaling 90 spectra. Subsequently, principal component analysis (PCA) and variable selection algorithms, including the successive projections algorithm (SPA) and genetic algorithm (GA) coupled with linear discriminant analysis (LDA), were employed to discern distinctive patterns among the samples. The use of PCA, SPA, and GA algorithms associated with LDA achieved 100% sensitivity and specificity for the discriminations. The SPA-LDA and GA-LDA algorithms were essential in selecting the variables (infrared wavelengths) of most importance for the models, which could be attributed to binding of cell wall structures such as polysaccharides, peptides, proteins, or molecules resulting from yeasts' metabolism. These results show the high potential of combined FT-NIR and multivariate analysis techniques for the classification of Candida-like fungi, which can contribute to faster and more effective diagnosis and treatment of patients affected by these microorganisms.
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Affiliation(s)
- Ayrton L. F. Nascimento
- Laboratório de Química Biológica e Quimiometria, Instituto de Química, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Anthony G. J. de Medeiros
- Laboratório de Uso Comum, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Ana C. O. Neves
- Laboratório de Química Biológica e Quimiometria, Instituto de Química, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Ana B. N. de Macedo
- Laboratório de Uso Comum, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Luana Rossato
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados, Brazil
| | - Daniel Assis Santos
- Laboratório de Micologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- National Institute of Science and Technology in Human Pathogenic Fungi, Ribeirão Preto, Brazil
| | - André L. S. dos Santos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro-RJ, Brazil
| | - Kássio M. G. Lima
- Laboratório de Química Biológica e Quimiometria, Instituto de Química, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Rafael W. Bastos
- Laboratório de Uso Comum, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
- National Institute of Science and Technology in Human Pathogenic Fungi, Ribeirão Preto, Brazil
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2
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Fransson P, Robertson AHJ, Campbell CD. Carbon availability affects already large species-specific differences in chemical composition of ectomycorrhizal fungal mycelia in pure culture. MYCORRHIZA 2023; 33:303-319. [PMID: 37824023 PMCID: PMC10752919 DOI: 10.1007/s00572-023-01128-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
Although ectomycorrhizal (ECM) contribution to soil organic matter processes receives increased attention, little is known about fundamental differences in chemical composition among species, and how that may be affected by carbon (C) availability. Here, we study how 16 species (incl. 19 isolates) grown in pure culture at three different C:N ratios (10:1, 20:1, and 40:1) vary in chemical structure, using Fourier transform infrared (FTIR) spectroscopy. We hypothesized that C availability impacts directly on chemical composition, expecting increased C availability to lead to more carbohydrates and less proteins in the mycelia. There were strong and significant effects of ECM species (R2 = 0.873 and P = 0.001) and large species-specific differences in chemical composition. Chemical composition also changed significantly with C availability, and increased C led to more polysaccharides and less proteins for many species, but not all. Understanding how chemical composition change with altered C availability is a first step towards understanding their role in organic matter accumulation and decomposition.
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Affiliation(s)
- Petra Fransson
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, PO Box 7026, SE-750 07, Uppsala, Sweden.
| | - A H Jean Robertson
- The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, Scotland
| | - Colin D Campbell
- The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, Scotland
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3
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Yang H, Shi H, Feng B, Wang L, Chen L, Alvarez-Ordóñez A, Zhang L, Shen H, Zhu J, Yang S, Ding C, Prietod M, Yang F, Yu S. Protocol for bacterial typing using Fourier transform infrared spectroscopy. STAR Protoc 2023; 4:102223. [PMID: 37061919 PMCID: PMC10130498 DOI: 10.1016/j.xpro.2023.102223] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/16/2023] [Accepted: 03/14/2023] [Indexed: 04/17/2023] Open
Abstract
The Fourier transform infrared (FT-IR) signals obtained from bacterial samples are specific and reproducible, making FT-IR an efficient tool for bacterial typing at a subspecies level. However, the typing accuracy could be affected by many factors, including sample preparation and spectral acquisition. Here, we present a unified protocol for bacterial typing based on FT-IR spectroscopy. We describe sample preparation from bacterial culture and FT-IR spectrum collection. We then detail FT-IR spectrum preprocessing and multivariate analysis of spectral data for bacterial typing.
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Affiliation(s)
- Huayan Yang
- Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315211, China; Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Haimei Shi
- Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315211, China; Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Bin Feng
- Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315211, China; Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Li Wang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China
| | | | | | - Li Zhang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Hao Shen
- Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315211, China; Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jianhua Zhu
- Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315211, China
| | - Shouning Yang
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chuanfan Ding
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Miguel Prietod
- Institute of Food Science and Technology, University of León, 24071 León, Spain.
| | - Fan Yang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | - Shaoning Yu
- Department of Intensive Care Unit, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315211, China; Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
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Gupte AP, Pierantoni DC, Conti A, Donati L, Basaglia M, Casella S, Favaro L, Corte L, Cardinali G. Renewing Lost Genetic Variability with a Classical Yeast Genetics Approach. J Fungi (Basel) 2023; 9:jof9020264. [PMID: 36836378 PMCID: PMC9958831 DOI: 10.3390/jof9020264] [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: 12/28/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Due to their long domestication time course, many industrial Saccharomyces cerevisiae strains are adopted in numerous processes mostly for historical reasons instead of scientific and technological needs. As such, there is still significant room for improvement for industrial yeast strains relying on yeast biodiversity. This paper strives to regenerate biodiversity with the innovative application of classic genetic methods to already available yeast strains. Extensive sporulation was indeed applied to three different yeast strains, specifically selected for their different origins as well as backgrounds, with the aim of clarifying how new variability was generated. A novel and easy method to obtain mono-spore colonies was specifically developed, and, to reveal the extent of the generated variability, no selection after sporulation was introduced. The obtained progenies were then tested for their growth in defined mediums with high stressor levels. A considerable and strain-specific increase in both phenotypic and metabolomic variability was assessed, and a few mono-spore colonies were found to be of great interest for their future exploitation in selected industrial processes.
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Affiliation(s)
- Ameya Pankaj Gupte
- Department of Agronomy Food natural Resources Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | | | - Angela Conti
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy
| | - Leonardo Donati
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy
| | - Marina Basaglia
- Department of Agronomy Food natural Resources Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Sergio Casella
- Department of Agronomy Food natural Resources Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Lorenzo Favaro
- Department of Agronomy Food natural Resources Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
- Correspondence: (L.F.); (L.C.)
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy
- Correspondence: (L.F.); (L.C.)
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy
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5
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Wang J, Meng S, Lin K, Yi X, Sun Y, Xu X, He N, Zhang Z, Hu H, Qie X, Zhang D, Tang Y, Huang WE, He J, Song Y. Leveraging single-cell Raman spectroscopy and single-cell sorting for the detection and identification of yeast infections. Anal Chim Acta 2023; 1239:340658. [PMID: 36628751 DOI: 10.1016/j.aca.2022.340658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022]
Abstract
Invasive fungal infection serves as a great threat to human health. Discrimination between fungal and bacterial infections at the earliest stage is vital for effective clinic practice; however, traditional culture-dependent microscopic diagnosis of fungal infection usually requires several days, meanwhile, culture-independent immunological and molecular methods are limited by the detectable type of pathogens and the issues with high false-positive rates. In this study, we proposed a novel culture-independent phenotyping method based on single-cell Raman spectroscopy for the rapid discrimination between fungal and bacterial infections. Three Raman biomarkers, including cytochrome c, peptidoglycan, and nucleic acid, were identified through hierarchical clustering analysis of Raman spectra across 12 types of most common yeast and bacterial pathogens. Compared to those of bacterial pathogens, the single cells of yeast pathogens demonstrated significantly stronger Raman peaks for cytochrome c, but weaker signals for peptidoglycan and nucleic acid. A two-step protocol combining the three biomarkers was established and able to differentiate fungal infections from bacterial infections with an overall accuracy of 94.9%. Our approach was also used to detect ten raw urinary tract infection samples. Successful identification of fungi was achieved within half an hour after sample obtainment. We further demonstrated the accurate fungal species taxonomy achieved with Raman-assisted cell ejection. Our findings demonstrate that Raman-based fungal identification is a novel, facile, reliable, and with a breadth of coverage approach, that has a great potential to be adopted in routine clinical practice to reduce the turn-around time of invasive fungal disease (IFD) diagnostics.
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Affiliation(s)
- Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Kaicheng Lin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xiaofei Yi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 20040, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yixiang Sun
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 20040, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Na He
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhiqiang Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Huijie Hu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China
| | - Xingwang Qie
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Jian He
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China.
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6
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Mendoza-Reyes DF, Gómez-Gaviria M, Mora-Montes HM. Candida lusitaniae: Biology, Pathogenicity, Virulence Factors, Diagnosis, and Treatment. Infect Drug Resist 2022; 15:5121-5135. [PMID: 36068831 PMCID: PMC9441179 DOI: 10.2147/idr.s383785] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/25/2022] [Indexed: 12/30/2022] Open
Abstract
The incidence of fungal infections is increasing at an alarming rate and has posed a great challenge for science in recent years. The rise in these infections has been related to the increase in immunocompromised patients and the resistance of different species to antifungal drugs. Infections caused by the different Candida species, especially Candida albicans, are one of the most common mycoses in humans, and the etiological agents are considered opportunistic pathogens associated with high mortality rates when disseminated infections occur. Candida lusitaniae is considered an emerging opportunistic pathogen that most frequently affects immunocompromised patients with some comorbidity. Although it is a low-frequency pathogen, and the mortality rate of C. lusitaniae-caused candidemia does not exceed 5%, some isolates are known to be resistant to antifungals such as amphotericin B, 5-fluorocytosine, and fluconazole. In this paper, a detailed review of the current literature on this organism and its different aspects, such as its biology, possible virulence factors, pathogen-host interaction, diagnosis, and treatment of infection, is provided. Of particular interest, through Blastp analysis we predicted possible virulence factors in this species.
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Affiliation(s)
- Diana F Mendoza-Reyes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Guanajuato, Gto, C.P. 36050, México
| | - Manuela Gómez-Gaviria
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Guanajuato, Gto, C.P. 36050, México
- Correspondence: Manuela Gómez-Gaviria; Héctor M Mora-Montes, Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, Guanajuato, Gto, C.P. 36050, México, Tel +52 473-7320006 Ext. 8193, Fax +52 473-7320006 Ext. 8153, Email ;
| | - Héctor M Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Guanajuato, Gto, C.P. 36050, México
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7
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Romano P, Siesto G, Capece A, Pietrafesa R, Lanciotti R, Patrignani F, Granchi L, Galli V, Bevilacqua A, Campaniello D, Spano G, Caridi A, Poiana M, Foschino R, Vigentini I, Blaiotta G, Corich V, Giacomini A, Cardinali G, Corte L, Toffanin A, Agnolucci M, Comitini F, Ciani M, Mannazzu I, Budroni M, Englezos V, Rantsiou K, Iacumin L, Comi G, Capozzi V, Grieco F, Tufariello M. Validation of a Standard Protocol to Assess the Fermentative and Chemical Properties of Saccharomyces cerevisiae Wine Strains. Front Microbiol 2022; 13:830277. [PMID: 35359728 PMCID: PMC8963721 DOI: 10.3389/fmicb.2022.830277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/13/2022] [Indexed: 11/13/2022] Open
Abstract
This paper reports on a common experiment performed by 17 Research Units of the Italian Group of Microbiology of Vine and Wine (GMVV), which belongs to the Scientific Society SIMTREA, with the aim to validate a protocol for the characterization of wine strains of Saccharomyces cerevisiae. For this purpose, two commercial S. cerevisiae strains (EC 1118 and AWRI796) were used to carry out inter-laboratory-scale comparative fermentations using both synthetic medium and grape musts and applying the same protocol to obtain reproducible, replicable, and statistically valid results. Ethanol yield, production of acetic acid, glycerol, higher alcohols, and other volatile compounds were assessed. Moreover, the Fourier transform infrared spectroscopy was also applied to define the metabolomic fingerprint of yeast cells from each experimental trial. Data were standardized as unit of compounds or yield per gram of sugar (glucose and fructose) consumed throughout fermentation, and analyzed through parametric and non-parametric tests, and multivariate approaches (cluster analysis, two-way joining, and principal component analysis). The results of experiments carried out by using synthetic must showed that it was possible to gain comparable results from three different laboratories by using the same strains. Then, the use of the standardized protocol on different grape musts allowed pointing out the goodness and the reproducibility of the method; it showed the main traits of the two yeast strains and allowed reducing variability amongst independent batches (biological replicates) to acceptable levels. In conclusion, the findings of this collaborative study contributed to the validation of a protocol in a specific synthetic medium and in grape must and showed how data should be treated to gain reproducible and robust results, which could allow direct comparison of the experimental data obtained during the characterization of wine yeasts carried out by different research laboratories.
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Affiliation(s)
| | | | - Angela Capece
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Rocchina Pietrafesa
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Rosalba Lanciotti
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Cesena, Italy
| | - Francesca Patrignani
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Cesena, Italy
| | - Lisa Granchi
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Viola Galli
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Antonio Bevilacqua
- Department of Agriculture, Food, Natural Resources and Engineering, University of Foggia, Foggia, Italy
| | - Daniela Campaniello
- Department of Agriculture, Food, Natural Resources and Engineering, University of Foggia, Foggia, Italy
| | - Giuseppe Spano
- Department of Agriculture, Food, Natural Resources and Engineering, University of Foggia, Foggia, Italy
| | - Andrea Caridi
- Department of Agriculture, Mediterranea University of Reggio Calabria, Reggio Calabria, Italy
| | - Marco Poiana
- Department of Agriculture, Mediterranea University of Reggio Calabria, Reggio Calabria, Italy
| | - Roberto Foschino
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Ileana Vigentini
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Giuseppe Blaiotta
- Department of Agricultural Sciences, Division of Grape and Wine Sciences, University of Naples Federico II, Naples, Italy
| | - Viviana Corich
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | - Alessio Giacomini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Annita Toffanin
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Monica Agnolucci
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Francesca Comitini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Maurizio Ciani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Ilaria Mannazzu
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
| | - Marilena Budroni
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
| | - Vasileios Englezos
- Department of Agricultural, Forest, and Food Science, University of Turin, Turin, Italy
| | - Kalliopi Rantsiou
- Department of Agricultural, Forest, and Food Science, University of Turin, Turin, Italy
| | - Lucilla Iacumin
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Giuseppe Comi
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Vittorio Capozzi
- Institute of Sciences of Food Production, National Research Council of Italy, c/o CS-DAT, Foggia, Italy
| | - Francesco Grieco
- Institute of Sciences of Food Production, National Research Council of Italy, Lecce, Italy
| | - Maria Tufariello
- Institute of Sciences of Food Production, National Research Council of Italy, Lecce, Italy
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8
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Pham DQ, Bryant SJ, Cheeseman S, Huang LZY, Bryant G, Dupont MF, Chapman J, Berndt CC, Vongsvivut JP, Crawford RJ, Truong VK, Ang ASM, Elbourne A. Micro- to nano-scale chemical and mechanical mapping of antimicrobial-resistant fungal biofilms. NANOSCALE 2020; 12:19888-19904. [PMID: 32985644 DOI: 10.1039/d0nr05617k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A fungal biofilm refers to the agglomeration of fungal cells surrounded by a polymeric extracellular matrix (ECM). The ECM is composed primarily of polysaccharides that facilitate strong surface adhesion, proliferation, and cellular protection from the surrounding environment. Biofilms represent the majority of known microbial communities, are ubiquitous, and are found on a multitude of natural and synthetic surfaces. The compositions, and in-turn nanomechanical properties, of fungal biofilms remain poorly understood, because these systems are complex, composed of anisotropic cellular and extracellular material, and importantly are species and environment dependent. Therefore, genomic variation, and/or mutations, as well as environmental and growth factors can change the composition of a fungal cell's biofilm. In this work, we probe the physico-mechanical and biochemical properties of two fungal species, Candida albicans (C. albicans) and Cryptococcus neoformans (C. neoformans), as well as two antifungal resistant sub-species of C. neoformans, fluconazole-resistant C. neoformans (FlucRC. neoformans) and amphotericin B-resistant C. neoformans (AmBRC. neoformans). A new experimental methodology of characterization is proposed, employing a combination of atomic force microscopy (AFM), instrumented nanoindentation, and Synchrotron ATR-FTIR measurements. This allowed the nano-mechanical and chemical characterisation of each fungal biofilm.
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Affiliation(s)
- Duy Quang Pham
- Surface Engineering for Advanced Materials (SEAM), Department of Mechanical and Production Design Engineering, Swinburne University of Technology, Hawthorn, Australia.
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9
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Roscini L, Conti A, Casagrande Pierantoni D, Robert V, Corte L, Cardinali G. Do Metabolomics and Taxonomic Barcode Markers Tell the Same Story about the Evolution of Saccharomyces sensu stricto Complex in Fermentative Environments? Microorganisms 2020; 8:microorganisms8081242. [PMID: 32824262 PMCID: PMC7463906 DOI: 10.3390/microorganisms8081242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/08/2020] [Accepted: 08/13/2020] [Indexed: 01/07/2023] Open
Abstract
Yeast taxonomy was introduced based on the idea that physiological properties would help discriminate species, thus assuming a strong link between physiology and taxonomy. However, the instability of physiological characteristics within species configured them as not ideal markers for species delimitation, shading the importance of physiology and paving the way to the DNA-based taxonomy. The hypothesis of reconnecting taxonomy with specific traits from phylogenies has been successfully explored for Bacteria and Archaea, suggesting that a similar route can be traveled for yeasts. In this framework, thirteen single copy loci were used to investigate the predictability of complex Fourier Transform InfaRed spectroscopy (FTIR) and High-performance Liquid Chromatography–Mass Spectrometry (LC-MS) profiles of the four historical species of the Saccharomyces sensu stricto group, both on resting cells and under short-term ethanol stress. Our data show a significant connection between the taxonomy and physiology of these strains. Eight markers out of the thirteen tested displayed high correlation values with LC-MS profiles of cells in resting condition, confirming the low efficacy of FTIR in the identification of strains of closely related species. Conversely, most genetic markers displayed increasing trends of correlation with FTIR profiles as the ethanol concentration increased, according to their role in the cellular response to different type of stress.
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Affiliation(s)
- Luca Roscini
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (L.R.); (A.C.); (D.C.P.); (G.C.)
| | - Angela Conti
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (L.R.); (A.C.); (D.C.P.); (G.C.)
| | - Debora Casagrande Pierantoni
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (L.R.); (A.C.); (D.C.P.); (G.C.)
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (L.R.); (A.C.); (D.C.P.); (G.C.)
- Correspondence: ; Tel.: +39-0755856478
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (L.R.); (A.C.); (D.C.P.); (G.C.)
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10
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Câmara AA, Nguyen TD, Saurel R, Sandt C, Peltier C, Dujourdy L, Husson F. Biophysical Stress Responses of the Yeast Lachancea thermotolerans During Dehydration Using Synchrotron-FTIR Microspectroscopy. Front Microbiol 2020; 11:899. [PMID: 32477306 PMCID: PMC7235352 DOI: 10.3389/fmicb.2020.00899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/16/2020] [Indexed: 01/17/2023] Open
Abstract
During industrial yeast production, cells are often subjected to deleterious hydric variations during dehydration, which reduces their viability and cellular activity. This study is focused on the yeast Lachancea thermotolerans, particularly sensitive to dehydration. The aim was to understand the modifications of single-cells biophysical profiles during different dehydration conditions. Infrared spectra of individual cells were acquired before and after dehydration kinetics using synchrotron radiation-based Fourier-transform infrared (S-FTIR) microspectroscopy. The cells were previously stained with fluorescent probes in order to measure only viable and active cells prior to dehydration. In parallel, cell viability was determined using flow cytometry under identical conditions. The S-FTIR analysis indicated that cells with the lowest viability showed signs of membrane rigidification and modifications in the amide I (α-helix and β-sheet) and amide II, which are indicators of secondary protein structure conformation and degradation or disorder. Shift of symmetric C–H stretching vibration of the CH2 group upon a higher wavenumber correlated with better cell viability, suggesting a role of plasma membrane fluidity. This was the first time that the biophysical responses of L. thermotolerans single-cells to dehydration were explored with S-FTIR. These findings are important for clarifying the mechanisms of microbial resistance to stress in order to improve the viability of sensitive yeasts during dehydration.
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Affiliation(s)
| | - Thanh Dat Nguyen
- Univ. Bourgogne Franche-Comt, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
| | - Rémi Saurel
- Univ. Bourgogne Franche-Comt, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
| | | | - Caroline Peltier
- Univ. Bourgogne Franche-Comt, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
| | | | - Florence Husson
- Univ. Bourgogne Franche-Comt, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
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11
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Delta-Integration of Single Gene Shapes the Whole Metabolomic Short-Term Response to Ethanol of Recombinant Saccharomyces cerevisiae Strains. Metabolites 2020; 10:metabo10040140. [PMID: 32260275 PMCID: PMC7241245 DOI: 10.3390/metabo10040140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/25/2020] [Accepted: 04/01/2020] [Indexed: 02/06/2023] Open
Abstract
In yeast engineering, metabolic burden is often linked to the reprogramming of resources from regular cellular activities to guarantee recombinant protein(s) production. Therefore, growth parameters can be significantly influenced. Two recombinant strains, previously developed by the multiple δ-integration of a glucoamylase in the industrial Saccharomyces cerevisiae 27P, did not display any detectable metabolic burden. In this study, a Fourier Transform InfraRed Spectroscopy (FTIR)-based assay was employed to investigate the effect of δ-integration on yeast strains’ tolerance to the increasing ethanol levels typical of the starch-to-ethanol industry. FTIR fingerprint, indeed, offers a holistic view of the metabolome and is a well-established method to assess the stress response of microorganisms. Cell viability and metabolomic fingerprints have been considered as parameters to detecting any physiological and/or metabolomic perturbations. Quite surprisingly, the three strains did not show any difference in cell viability but metabolomic profiles were significantly altered and different when the strains were incubated both with and without ethanol. A LC/MS untargeted workflow was applied to assess the metabolites and pathways mostly involved in these strain-specific ethanol responses, further confirming the FTIR fingerprinting of the parental and recombinant strains. These results indicated that the multiple δ-integration prompted huge metabolomic changes in response to short-term ethanol exposure, calling for deeper metabolomic and genomic insights to understand how and, to what extent, genetic engineering could affect the yeast metabolome.
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12
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Influence of the Sample Preparation Method in Discriminating Candida spp. Using ATR-FTIR Spectroscopy. Molecules 2020; 25:molecules25071551. [PMID: 32231044 PMCID: PMC7180699 DOI: 10.3390/molecules25071551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/08/2023] Open
Abstract
Several studies have investigated the capacity of ATR-FTIR spectroscopy for fungal species discrimination. However, preparation methods vary among studies. This study aims to ascertain the effect of sample preparation on the discriminatory capacity of ATR-FTIR spectroscopy. Candida species were streaked to obtain colonies and spectra were collected from each preparation type, which included: (a) untreated colonies being directly transferred to the ATR crystal, (b) following washing and (c) following 24-h fixation in formalin. Spectra were pre-processed and principal component analysis (PCA) and K-means cluster analysis (KMC) were performed. Results showed that there was a clear discrimination between preparation types. Groups of spectra from untreated and washed isolates clustered separately due to intense protein, DNA and polysaccharide bands, whilst fixed spectra clustered separately due to intense polysaccharide bands. This signified that sample preparation had influenced the chemical composition of samples. Nevertheless, across preparation types, significant species discrimination was observed, and the polysaccharide (1200-900 cm-1) region was a common critical marker for species discrimination. However, different discriminatory marker bands were observed across preparation methods. Thus, sample preparation appears to influence the chemical composition of Candida samples; however, does not seem to significantly impact the species discrimination potential for ATR-FTIR spectroscopy.
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13
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Favaro L, Cagnin L, Corte L, Roscini L, De Pascale F, Treu L, Campanaro S, Basaglia M, van Zyl WH, Casella S, Cardinali G. Metabolomic Alterations Do Not Induce Metabolic Burden in the Industrial Yeast M2n[pBKD2- Pccbgl1]-C1 Engineered by Multiple δ-Integration of a Fungal β-Glucosidase Gene. Front Bioeng Biotechnol 2019; 7:376. [PMID: 31850332 PMCID: PMC6893308 DOI: 10.3389/fbioe.2019.00376] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/14/2019] [Indexed: 11/13/2022] Open
Abstract
In the lignocellulosic yeast development, metabolic burden relates to redirection of resources from regular cellular activities toward the needs created by recombinant protein production. As a result, growth parameters may be greatly affected. Noteworthy, Saccharomyces cerevisiae M2n[pBKD2-Pccbgl1]-C1, previously developed by multiple δ-integration of the β-glucosidase BGL3, did not show any detectable metabolic burden. This work aims to test the hypothesis that the metabolic burden and the metabolomic perturbation induced by the δ-integration of a yeast strain, could differ significantly. The engineered strain was evaluated in terms of metabolic performances and metabolomic alterations in different conditions typical of the bioethanol industry. Results indicate that the multiple δ-integration did not affect the ability of the engineered strain to grow on different carbon sources and to tolerate increasing concentrations of ethanol and inhibitory compounds. Conversely, metabolomic profiles were significantly altered both under growing and stressing conditions, indicating a large extent of metabolic reshuffling involved in the maintenance of the metabolic homeostasis. Considering that four copies of BGL3 gene have been integrated without affecting any parental genes or promoter sequences, deeper studies are needed to unveil the mechanisms implied in these metabolomic changes, thus supporting the optimization of protein production in engineered strains.
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Affiliation(s)
- Lorenzo Favaro
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Lorenzo Cagnin
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Laura Corte
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia, Perugia, Italy
| | - Luca Roscini
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia, Perugia, Italy
| | | | - Laura Treu
- Department of Biology, University of Padova, Padova, Italy
| | | | - Marina Basaglia
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Matieland, South Africa
| | - Sergio Casella
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences-Microbiology, University of Perugia, Perugia, Italy.,Department of Chemistry, Biology and Biotechnology, Centre of Excellence on Nanostructured Innovative Materials (CEMIN), University of Perugia, Perugia, Italy
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14
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Spectroscopic Characterization of Bovine, Avian and Johnin Purified Protein Derivative (PPD) with High-Throughput Fourier Transform InfraRed-Based Method. Pathogens 2019; 8:pathogens8030136. [PMID: 31470609 PMCID: PMC6789744 DOI: 10.3390/pathogens8030136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/24/2019] [Accepted: 08/26/2019] [Indexed: 11/16/2022] Open
Abstract
Tuberculins purified protein derivatives (PPDs) are obtained by precipitation from heat treated mycobacteria. PPDs are used in diagnosis of mycobacterial infections in humans and animals. Bovine PPD (PPDB) is obtained from Mycobacterium bovis (Mycobacterium tuberculosis complex), while Avian PPD (PPDA) and Johnin PPD (PPDJ) are extracted, respectively, from Mycobacterium avium and M. avium subsp. paratuberculosis (M. avium complex). PPDB and PPDA are used for bovine tuberculosis diagnosis, while PPDJ is experimentally used in the immunodiagnosis of paratuberculosis. Although PPDs date back to the 19th Century, limited knowledge about their composition is currently available. The goal of our study was to evaluate Fourier Transform InfraRed (FTIR) spectroscopy as a tool to differentiate PPDB, PPDA, and three PPDJs. The results highlighted that the three PPDs have specific profiles, correlated with phylogenetic characteristics of mycobacteria used for their production. This analysis is eligible as a specific tool for different PPDs batches characterization and for the assessment of their composition. The entire PPD production may be efficiently controlled, since the N content of each preparation is related to IR spectra, with a reference spectrum for each PPD and a standardized analysis protocol.
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15
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Taha M, Hassan M, Essa S, Tartor Y. Use of Fourier transform infrared spectroscopy (FTIR) spectroscopy for rapid and accurate identification of Yeasts isolated from human and animals. Int J Vet Sci Med 2019. [DOI: 10.1016/j.ijvsm.2013.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- M. Taha
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Cairo, Egypt
| | - M. Hassan
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Cairo, Egypt
| | - S. Essa
- Department of Microbiology, Research Institute of Animal Health, Dokki, Giza, Egypt
| | - Y. Tartor
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Cairo, Egypt
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16
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Potocki L, Depciuch J, Kuna E, Worek M, Lewinska A, Wnuk M. FTIR and Raman Spectroscopy-Based Biochemical Profiling Reflects Genomic Diversity of Clinical Candida Isolates That May Be Useful for Diagnosis and Targeted Therapy of Candidiasis. Int J Mol Sci 2019; 20:ijms20040988. [PMID: 30823514 PMCID: PMC6412866 DOI: 10.3390/ijms20040988] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 12/11/2022] Open
Abstract
Despite the fact that Candida albicans is documented to be the main cause of human candidiasis, non-C. albicans Candida (NCAC) species, such as Candida glabrata and Candida tropicalis, are also suggested to be implicated in the etiopathogenesis of opportunistic fungal infections. As biology, epidemiology, pathogenicity, and antifungal resistance of NCAC species may be affected as a result of genomic diversity and plasticity, rapid and unambiguous identification of Candida species in clinical samples is essential for proper diagnosis and therapy. In the present study, 25 clinical isolates of C. albicans, C. glabrata, and C. tropicalis species were characterized in terms of their karyotype patterns, DNA content, and biochemical features. Fourier transform infrared (FTIR) spectra- and Raman spectra-based molecular fingerprints corresponded to the diversity of chromosomal traits and DNA levels that provided correct species identification. Moreover, Raman spectroscopy was documented to be useful for the evaluation of ergosterol content that may be associated with azole resistance. Taken together, we found that vibrational spectroscopy-based biochemical profiling reflects the variability of chromosome patterns and DNA content of clinical Candida species isolates and may facilitate the diagnosis and targeted therapy of candidiasis.
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Affiliation(s)
- Leszek Potocki
- Department of Genetics, Faculty of Biotechnology, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland.
| | - Joanna Depciuch
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Poland.
| | - Ewelina Kuna
- Department of Genetics, Faculty of Biotechnology, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland.
| | - Mariusz Worek
- Department of Microbiology, Faculty of Medicine, University of Rzeszow, 35-959 Rzeszow, Poland.
| | - Anna Lewinska
- Department of Cell Biochemistry, Faculty of Biotechnology, University of Rzeszow, 35-310 Rzeszow, Poland.
| | - Maciej Wnuk
- Department of Genetics, Faculty of Biotechnology, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland.
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17
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Shi QY, Câmara CRS, Schlegel V. Biochemical alterations of Candida albicans during the phenotypic transition from yeast to hyphae captured by Fourier transform mid-infrared-attenuated reflectance spectroscopy. Analyst 2019; 143:5404-5416. [PMID: 30302456 DOI: 10.1039/c8an01452c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Candida albicans is an opportunistic human pathogen that can become virulent due to its ability to switch from a benign yeast to virulent hyphae phenotype. The emergence of C. albicans resistant to commonly used antifungal agents has necessitated the development of innovative treatments, which must be accompanied by an understanding of the molecular changes that occur during the phenotypic shift. For this purpose, Fourier transform mid-infrared spectroscopy in attenuated total reflectance mode (FT-mIR-ATR) was applied to monitor the structural and compositional changes in C. albicans during the yeast-to-hyphae transition. FT-mIR-ATR measurements were completed on the whole cell of C. albicans (SC5314) during hyphal formation induced by N-acetylglucosamine at 0, 1, 2, 3, 6 and 24 h. Principal component analysis separated the FT-mIR-ATR spectra into four groups that were aligned with the morphological changes captured by microscopic imaging. Spectral signatures indicating the structural and compositional modifications during the transition were identified mainly in the fatty acid region (3100-2800 cm-1), the protein and peptide region (1800-1500 cm-1), the mixed region (1500-1200 cm-1) and the polysaccharide region (1200-900 cm-1). A spectral fingerprint of the transition via a heat map was generated based on the peak shift in position. Quantitative evaluation of the spectra by curve fitting further revealed the dynamics of the cell's main components during the transition. This work provides valuable structural and functional information on the C. albicans phenotypic transition to hyphae, which has diagnostic implications.
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Affiliation(s)
- Qin-Yin Shi
- Department of Food Science and Technology, 1901 N 21st St, Food Innovation Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-6205, USA.
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18
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Roscini L, Favaro L, Corte L, Cagnin L, Colabella C, Basaglia M, Cardinali G, Casella S. A yeast metabolome-based model for an ecotoxicological approach in the management of lignocellulosic ethanol stillage. ROYAL SOCIETY OPEN SCIENCE 2019; 6:180718. [PMID: 30800340 PMCID: PMC6366221 DOI: 10.1098/rsos.180718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 11/30/2018] [Indexed: 05/07/2023]
Abstract
Lignocellulosic bioethanol production results in huge amounts of stillage, a potentially polluting by-product. Stillage, rich in heavy metals and, mainly, inhibitors, requires specific toxicity studies to be adequately managed. To this purpose, we applied an FTIR ecotoxicological bioassay to evaluate the toxicity of lignocellulosic stillage. Two weak acids and furans, most frequently found in lignocellulosic stillage, have been tested in different mixtures against three Saccharomyces cerevisiae strains. The metabolomic reaction of the test microbes and the mortality induced at various levels of inhibitor concentration showed that the strains are representative of three different types of response. Furthermore, the relationship between concentrations and FTIR synthetic stress indexes has been studied, with the aim of defining a model able to predict the concentrations of inhibitors in stillage, resulting in an optimized predictive model for all the strains. This approach represents a promising tool to support the ecotoxicological management of lignocellulosic stillage.
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Affiliation(s)
- Luca Roscini
- Department of Pharmaceutical Sciences-Microbiology, CEMIN, Centre of Excellence on Nanostructured Innovative Materials, University of Perugia, Perugia, Italy
| | - Lorenzo Favaro
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
- Author for correspondence: Lorenzo Favaro e-mail:
| | - Laura Corte
- Department of Pharmaceutical Sciences-Microbiology, CEMIN, Centre of Excellence on Nanostructured Innovative Materials, University of Perugia, Perugia, Italy
| | - Lorenzo Cagnin
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Claudia Colabella
- Department of Pharmaceutical Sciences-Microbiology, CEMIN, Centre of Excellence on Nanostructured Innovative Materials, University of Perugia, Perugia, Italy
| | - Marina Basaglia
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences-Microbiology, CEMIN, Centre of Excellence on Nanostructured Innovative Materials, University of Perugia, Perugia, Italy
- Department of Chemistry, Biology and Biotechnology, CEMIN, Centre of Excellence on Nanostructured Innovative Materials, University of Perugia, Perugia, Italy
| | - Sergio Casella
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
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19
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Tafintseva V, Vigneau E, Shapaval V, Cariou V, Qannari EM, Kohler A. Hierarchical classification of microorganisms based on high-dimensional phenotypic data. JOURNAL OF BIOPHOTONICS 2018; 11:e201700047. [PMID: 29119695 DOI: 10.1002/jbio.201700047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 09/25/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
The classification of microorganisms by high-dimensional phenotyping methods such as FTIR spectroscopy is often a complicated process due to the complexity of microbial phylogenetic taxonomy. A hierarchical structure developed for such data can often facilitate the classification analysis. The hierarchical tree structure can either be imposed to a given set of phenotypic data by integrating the phylogenetic taxonomic structure or set up by revealing the inherent clusters in the phenotypic data. In this study, we wanted to compare different approaches to hierarchical classification of microorganisms based on high-dimensional phenotypic data. A set of 19 different species of molds (filamentous fungi) obtained from the mycological strain collection of the Norwegian Veterinary Institute (Oslo, Norway) is used for the study. Hierarchical cluster analysis is performed for setting up the classification trees. Classification algorithms such as artificial neural networks (ANN), partial least-squared discriminant analysis and random forest (RF) are used and compared. The 2 methods ANN and RF outperformed all the other approaches even though they did not utilize predefined hierarchical structure. To our knowledge, the RF approach is used here for the first time to classify microorganisms by FTIR spectroscopy.
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Affiliation(s)
- Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | | | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | | | | | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
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20
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Colabella C, Corte L, Roscini L, Shapaval V, Kohler A, Tafintseva V, Tascini C, Cardinali G. Merging FT-IR and NGS for simultaneous phenotypic and genotypic identification of pathogenic Candida species. PLoS One 2017; 12:e0188104. [PMID: 29206226 PMCID: PMC5714347 DOI: 10.1371/journal.pone.0188104] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/18/2017] [Indexed: 01/27/2023] Open
Abstract
The rapid and accurate identification of pathogen yeast species is crucial for clinical diagnosis due to the high level of mortality and morbidity induced, even after antifungal therapy. For this purpose, new rapid, high-throughput and reliable identification methods are required. In this work we described a combined approach based on two high-throughput techniques in order to improve the identification of pathogenic yeast strains. Next Generation Sequencing (NGS) of ITS and D1/D2 LSU marker regions together with FTIR spectroscopy were applied to identify 256 strains belonging to Candida genus isolated in nosocomial environments. Multivariate data analysis (MVA) was carried out on NGS and FT-IR data-sets, separately. Strains of Candida albicans, C. parapsilosis, C. glabrata and C. tropicalis, were identified with high-throughput NGS sequencing of ITS and LSU markers and then with FTIR. Inter- and intra-species variability was investigated by consensus principal component analysis (CPCA) which combines high-dimensional data of the two complementary analytical approaches in concatenated PCA blocks normalized to the same weight. The total percentage of correct identification reached around 97.4% for C. albicans and 74% for C. parapsilosis while the other two species showed lower identification rates. Results suggested that the identification success increases with the increasing number of strains actually used in the PLS analysis. The absence of reliable FT-IR libraries in the current scenario is the major limitation in FTIR-based identification of strains, although this metabolomics fingerprint represents a valid and affordable aid to rapid and high-throughput to clinical diagnosis. According to our data, FT-IR libraries should include some tens of certified strains per species, possibly over 50, deriving from diverse sources and collected over an extensive time period. This implies a multidisciplinary effort of specialists working in strain isolation and maintenance, molecular taxonomy, FT-IR technique and chemo-metrics, data management and data basing.
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Affiliation(s)
- Claudia Colabella
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Laura Corte
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Luca Roscini
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Volha Shapaval
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Achim Kohler
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Valeria Tafintseva
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Carlo Tascini
- Azienda Ospedaliera dei Colli—Ospedale Cotugno, Napoli, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials—Department of Chemistry, Biology and Biotechnology—University of Perugia, Perugia, Italy
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21
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Wohlmeister D, Vianna DRB, Helfer VE, Calil LN, Buffon A, Fuentefria AM, Corbellini VA, Pilger DA. Differentiation of Candida albicans , Candida glabrata , and Candida krusei by FT-IR and chemometrics by CHROMagar™ Candida. J Microbiol Methods 2017; 141:121-125. [DOI: 10.1016/j.mimet.2017.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 10/19/2022]
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22
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Shapaval V, Møretrø T, Wold Åsli A, Suso H, Schmitt J, Lillehaug D, Kohler A. A novel library-independent approach based on high-throughput cultivation in Bioscreen and fingerprinting by FTIR spectroscopy for microbial source tracking in food industry. Lett Appl Microbiol 2017; 64:335-342. [DOI: 10.1111/lam.12691] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/28/2016] [Accepted: 10/23/2016] [Indexed: 12/01/2022]
Affiliation(s)
- V. Shapaval
- Faculty of Science and Technology; Norwegian University of Life Sciences; Ås Norway
- Nofima AS; Ås Norway
| | | | | | | | | | | | - A. Kohler
- Faculty of Science and Technology; Norwegian University of Life Sciences; Ås Norway
- Nofima AS; Ås Norway
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23
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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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24
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Vibrational spectroscopies to investigate concretions and ectopic calcifications for medical diagnosis. CR CHIM 2016. [DOI: 10.1016/j.crci.2016.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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25
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Mohammed YF, Salem EZ, Shahin IMI, Abdo HM, Emam HE, Fawzy M, Abdel Salam MF. Applicability of Fourier transform infrared (FTIR) spectroscopy in rapid identification of some Candida and dermatophyte species infections in humans. Int J Dermatol 2016; 55:1164-71. [PMID: 27337493 DOI: 10.1111/ijd.4957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2009] [Revised: 08/15/2010] [Accepted: 09/23/2010] [Indexed: 11/26/2022]
Abstract
Traditional systems of identifying yeasts and dermatophytes have many disadvantages. Preliminary data on a radically different approach based on optical spectroscopic techniques suggest that these techniques may offer some advantages. We conducted a trial to verify the practical applicability of Fourier transform infrared (FTIR) spectroscopy in the identification of some yeast and dermatophyte species, in which samples from 50 patients with superficial fungal infections were cultured on Sabouraud dextrose agar with chloramphenicol and cycloheximide (actidione) and studied using FTIR microspectroscopy. Spectra of the same species were identical, whereas spectra of different species did not show similarity. This study showed that FTIR microspectroscopy is promising and can be used to obtain, with a single measurement, a "molecular fingerprint" of Candida and dermatophyte species. It can be improved further in terms of reliability.
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Affiliation(s)
- Yaser F Mohammed
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt.
| | - Elsayed Z Salem
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Ibrahim M I Shahin
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Hamed M Abdo
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Hanaa E Emam
- Department of Dermatology and Venereology, National Research Center, Cairo, Egypt
| | - Mahmoud Fawzy
- Department of Dermatology and Venereology, National Research Center, Cairo, Egypt
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26
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Laser induced breakdown spectroscopy for the discrimination of Candida strains. Talanta 2016; 155:101-6. [PMID: 27216662 DOI: 10.1016/j.talanta.2016.04.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/11/2016] [Accepted: 04/14/2016] [Indexed: 01/13/2023]
Abstract
The present study reports the evaluation of Laser Induced Breakdown Spectroscopy (LIBS) and Neural Networks (NN) for the discrimination of different strains of various species of Candida. This genus of yeast was selected due to its medical relevance as it is commonly found in cases of fungal infection in humans. Twenty one strains belonging to seven species of Candida were included in the study. Scanning Electron Microscopy with Energy-Dispersive X-ray Spectroscopy (SEM-EDS) was employed as a complementary technique to provide information about elemental composition of Candida cells. The use of LIBS spectra in combination with optimized NN models provided reliable discrimination among the distinct Candida strains with a high spectral correlation index for the samples analyzed, without any false positive or false negative. Therefore, this study indicates that LIBS-NN based methodology has the potential to be used as fast fungal identification or even diagnostic method.
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27
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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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28
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Silva S, Tobaldini-Valerio F, Costa-de-Oliveira S, Henriques M, Azeredo J, Ferreira EC, Lopes JA, Sousa C. Discrimination of clinically relevant Candida species by Fourier-transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). RSC Adv 2016. [DOI: 10.1039/c6ra16769a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Accurate Candida species identification remains a challenge due to their phenotypic and genotypic similarity.
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Affiliation(s)
- Sónia Silva
- CEB-Centro de Engenharia Biológica
- Universidade do Minho
- Braga
- Portugal
| | - Flávia Tobaldini-Valerio
- CEB-Centro de Engenharia Biológica
- Universidade do Minho
- Braga
- Portugal
- Departamento de Análises Clínicas e Biomedicina
| | | | - Mariana Henriques
- CEB-Centro de Engenharia Biológica
- Universidade do Minho
- Braga
- Portugal
| | - Joana Azeredo
- CEB-Centro de Engenharia Biológica
- Universidade do Minho
- Braga
- Portugal
| | | | - João A. Lopes
- Research Institute for Medicines (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- Lisboa
- Portugal
| | - Clara Sousa
- LAQV/REQUIMTE
- Departamento de Ciências Químicas
- Faculdade de Farmácia
- Universidade do Porto
- 4050-313 Porto
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29
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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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30
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Grangeteau C, Gerhards D, Terrat S, Dequiedt S, Alexandre H, Guilloux-Benatier M, von Wallbrunn C, Rousseaux S. FT-IR spectroscopy: A powerful tool for studying the inter- and intraspecific biodiversity of cultivable non-Saccharomyces yeasts isolated from grape must. J Microbiol Methods 2015; 121:50-8. [PMID: 26688103 DOI: 10.1016/j.mimet.2015.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/10/2015] [Accepted: 12/10/2015] [Indexed: 11/28/2022]
Abstract
The efficiency of the FT-IR technique for studying the inter- and intra biodiversity of cultivable non-Saccharomyces yeasts (NS) present in different must samples was examined. In first, the capacity of the technique FT-IR to study the global diversity of a given sample was compared to the pyrosequencing method, used as a reference technique. Seven different genera (Aureobasidium, Candida, Cryptococcus, Hanseniaspora, Issatchenkia, Metschnikowia and Pichia) were identified by FT-IR and also by pyrosequencing. Thirty-eight other genera were identified by pyrosequencing, but together they represented less than 6% of the average total population of 6 musts. Among the species identified, some of them present organoleptic potentials in winemaking, particularly Starmerella bacillaris (synonym Candidazemplinina). So in a second time, we evaluated the capacity of the FT-IR technique to discriminate the isolates of this species because few techniques were able to study intraspecific NS yeast biodiversity. The results obtained were validated by using a classic method as ITS sequencing. Biodiversity at strain level was high: 19 different strains were identified from 58 isolates. So, FT-IR spectroscopy seems to be an accurate and reliable method for identifying major genera present in the musts. The two biggest advantages of the FT-IR are the capacity to characterize intraspecific biodiversity of non-Saccharomyces yeasts and the possibility to discriminate a lot of strains.
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Affiliation(s)
- Cédric Grangeteau
- UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), AgroSup Dijon - Université de Bourgogne/Franche-Comté, IUVV, Rue Claude Ladrey, BP 27877, 21000 Dijon, France
| | - Daniel Gerhards
- Institut für Mikrobiologie und Biochemie Zentrum Analytische Chemie und Mikrobiologie - Hochschule Geisenheim University, Geisenheim, Germany
| | - Sebastien Terrat
- INRA, UMR 1347 Agroécologie-Plateforme Genosol, 17, rue Sully, BP 86510, 21000 Dijon, France
| | - Samuel Dequiedt
- INRA, UMR 1347 Agroécologie-Plateforme Genosol, 17, rue Sully, BP 86510, 21000 Dijon, France
| | - Hervé Alexandre
- UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), AgroSup Dijon - Université de Bourgogne/Franche-Comté, IUVV, Rue Claude Ladrey, BP 27877, 21000 Dijon, France
| | - Michèle Guilloux-Benatier
- UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), AgroSup Dijon - Université de Bourgogne/Franche-Comté, IUVV, Rue Claude Ladrey, BP 27877, 21000 Dijon, France
| | - Christian von Wallbrunn
- Institut für Mikrobiologie und Biochemie Zentrum Analytische Chemie und Mikrobiologie - Hochschule Geisenheim University, Geisenheim, Germany
| | - Sandrine Rousseaux
- UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), AgroSup Dijon - Université de Bourgogne/Franche-Comté, IUVV, Rue Claude Ladrey, BP 27877, 21000 Dijon, France.
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31
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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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32
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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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33
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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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34
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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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35
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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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36
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Lima-Neto R, Santos C, Lima N, Sampaio P, Pais C, Neves RP. Application of MALDI-TOF MS for requalification of a Candida clinical isolates culture collection. Braz J Microbiol 2014; 45:515-22. [PMID: 25242936 PMCID: PMC4166277 DOI: 10.1590/s1517-83822014005000044] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 09/09/2013] [Indexed: 11/22/2022] Open
Abstract
Microbial culture collections underpin biotechnology applications and are important resources for clinical microbiology by supplying reference strains and/or performing microbial identifications as a service. Proteomic profiles by MALDI-TOF MS have been used for Candida spp. identification in clinical laboratories and demonstrated to be a fast and reliable technique for the routine identification of pathogenic yeasts. The main aim of this study was to apply MALDI-TOF MS combined with classical phenotypic and molecular approaches to identify Candida clinical isolates preserved from 1 up to 52 years in a Brazilian culture collection and assess its value for the identification of yeasts preserved in this type of collections. Forty Candida spp. clinical isolates were identified by morphological and biochemical analyses. Identifications were also performed by the new proteomic approach based on MALDI-TOF MS. Results demonstrated 15% discordance when compared with morphological and biochemical analyses. Discordant isolates were analysed by ITS sequencing, which confirmed the MALDI-TOF MS identifications and these strains were renamed in the culture collection catalogue. In conclusion, proteomic profiles by MALDI-TOF MS represents a rapid and reliable method for identifying clinical Candida species preserved in culture collections and may present clear benefits when compared with the performance of existing daily routine methods applied at health centres and hospitals.
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Affiliation(s)
- Reginaldo Lima-Neto
- Department of Mycology Centre of Biological Sciences Federal University of Pernambuco RecifePE Brazil Department of Mycology, Centre of Biological Sciences, Federal University of Pernambuco, Recife, PE, Brazil. ; Micoteca da Universidade do Minho Centre of Biological Engineering University of Minho Braga Portugal Micoteca da Universidade do Minho, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Cledir Santos
- Micoteca da Universidade do Minho Centre of Biological Engineering University of Minho Braga Portugal Micoteca da Universidade do Minho, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Nelson Lima
- Micoteca da Universidade do Minho Centre of Biological Engineering University of Minho Braga Portugal Micoteca da Universidade do Minho, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Paula Sampaio
- Department of Biology Centre of Molecular and Environmental Biology University of Minho Braga Portugal Department of Biology, Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Célia Pais
- Department of Biology Centre of Molecular and Environmental Biology University of Minho Braga Portugal Department of Biology, Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Rejane P Neves
- Department of Mycology Centre of Biological Sciences Federal University of Pernambuco RecifePE Brazil Department of Mycology, Centre of Biological Sciences, Federal University of Pernambuco, Recife, PE, Brazil
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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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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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Candida identification: a journey from conventional to molecular methods in medical mycology. World J Microbiol Biotechnol 2014; 30:1437-51. [PMID: 24379160 DOI: 10.1007/s11274-013-1574-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/02/2013] [Indexed: 12/17/2022]
Abstract
The incidence of Candida infections have increased substantially in recent years due to aggressive use of immunosuppressants among patients. Use of broad-spectrum antibiotics and intravascular catheters in the intensive care unit have also attributed with high risks of candidiasis among immunocompromised patients. Among Candida species, C. albicans accounts for the majority of superficial and systemic infections, usually associated with high morbidity and mortality often caused due to increase in antimicrobial resistance and restricted number of antifungal drugs. Therefore, early detection of candidemia and correct identification of Candida species are indispensable pre-requisites for appropriate therapeutic intervention. Since blood culture based methods lack sensitivity, and species-specific identification by conventional method is time-consuming and often leads to misdiagnosis within closely related species, hence, molecular methods may provide alternative for accurate and rapid identification of Candida species. Although, several molecular approaches have been developed for accurate identification of Candida species but the internal transcribed spacer 1 and 2 (ITS1 and ITS2) regions of the rRNA gene are being used extensively in a variety of formats. Of note, ITS sequencing and PCR-RFLP analysis of ITS region seems to be promising as a rapid, easy, and cost-effective method for identification of Candida species. Here, we review a number of existing techniques ranging from conventional to molecular approaches currently in use for the identification of Candida species. Further, advantages and limitations of these methods are also discussed with respect to their discriminatory power, reproducibility, and ease of performance.
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40
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Wenning M, Scherer S. Identification of microorganisms by FTIR spectroscopy: perspectives and limitations of the method. Appl Microbiol Biotechnol 2013; 97:7111-20. [PMID: 23860713 DOI: 10.1007/s00253-013-5087-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/26/2013] [Accepted: 06/27/2013] [Indexed: 11/29/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy was introduced in 1991 as a technique to identify and classify microbes. Since then, it has gained growing interest and has undergone a remarkable evolution. Highly sophisticated spectrometers have been developed, enabling a high sample throughput. Today, the generation of high-quality data in a short time and the application of the technique for rapid and reliable identification of microbes to the species level are well documented. What makes FTIR spectroscopy even more attractive is the fact that spectral information can also be exploited for strain typing purposes, which is particularly important for epidemiological analyses and some technological applications. Accordingly, in recent years, FTIR spectroscopy has been increasingly used for typing and classifying microorganisms below the species level. The intention of this review is to give an overview over current knowledge and strategies of using FTIR spectroscopy for species identification and to describe different approaches for strain typing.
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Affiliation(s)
- Mareike Wenning
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung-ZIEL, Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany.
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Bhat R. Potential Use of Fourier Transform Infrared Spectroscopy for Identification of Molds Capable of Producing Mycotoxins. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2013. [DOI: 10.1080/10942912.2011.609629] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Rajeev Bhat
- a Food Technology Division, School of Industrial Technology , Universiti Sains Malaysia , Penang , Malaysia
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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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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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Wang J, Yue T, Yuan Y, Lu X, Shin JH, Rasco B. Discrimination of Alicyclobacillus Strains Using Nitrocellulose Membrane Filter and Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy. J Food Sci 2011; 76:M137-42. [DOI: 10.1111/j.1750-3841.2010.02034.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Putignani L, Del Chierico F, Onori M, Mancinelli L, Argentieri M, Bernaschi P, Coltella L, Lucignano B, Pansani L, Ranno S, Russo C, Urbani A, Federici G, Menichella D. MALDI-TOF mass spectrometry proteomic phenotyping of clinically relevant fungi. MOLECULAR BIOSYSTEMS 2010; 7:620-9. [PMID: 20967323 DOI: 10.1039/c0mb00138d] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteomics is particularly suitable for characterising human pathogens with high life cycle complexity, such as fungi. Protein content and expression levels may be affected by growth states and life cycle morphs and correlate to species and strain variation. Identification and typing of fungi by conventional methods are often difficult, time-consuming and frequently, for unusual species, inconclusive. Proteomic phenotypes from MALDI-TOF MS were employed as analytical and typing expression profiling of yeast, yeast-like species and strain variants in order to achieve a microbial proteomics population study. Spectra from 303 clinical isolates were generated and processed by standard pattern matching with a MALDI-TOF Biotyper (MT). Identifications (IDs) were compared to a reference biochemical-based system (Vitek-2) and, when discordant, MT IDs were verified with genotyping IDs, obtained by sequencing the 25-28S rRNA hypervariable D2 region. Spectra were converted into virtual gel-like formats, and hierarchical clustering analysis was performed for 274 Candida profiles to investigate species and strain typing correlation. MT provided 257/303 IDs consistent with Vitek-2 ones. However, amongst 26/303 discordant MT IDs, only 5 appeared "true". No MT identification was achieved for 20/303 isolates for incompleteness of database species variants. Candida spectra clustering agreed with identified species and topology of Candida albicans and Candida parapsilosis specific dendrograms. MT IDs show a high analytical performance and profiling heterogeneity which seems to complement or even outclass existing typing tools. This variability reflects the high biological complexity of yeasts and may be properly exploited to provide epidemiological tracing and infection dispersion patterns.
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Affiliation(s)
- Lorenza Putignani
- Microbiology Unit, Children's Hospital and Research Institute Bambino Gesù, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
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Abstract
Abstract
Introduction
Candida albicans and Candida glabrata are the two most common opportunistic pathogens which are part of the normal flora in humans. Clinical diagnosis of infection by these organisms is still largely based on culturing of these organisms. In order to identify species-specific protein expression patterns, we carried out a comparative proteomic analysis of C. albicans and C. glabrata.
Methods
We used “isobaric tag for relative and absolute quantitation” (iTRAQ) labeling of cell homogenates of C. albicans and C. glabrata followed by LC-MS/MS analysis using a quadrupole time-of-flight mass spectrometer. The MS/MS data was searched against a protein database comprised of known and predicted proteins reported from these two organisms. Subsequently, we carried out a bioinformatics analysis to group orthologous proteins across C. albicans and C. glabrata and calculated protein abundance changes between the two species.
Results and Conclusions
We identified 500 proteins from these organisms, the large majority of which corresponded to predicted transcripts. A number of proteins were observed to be significantly differentially expressed between the two species including enolase (Eno1), fructose-bisphosphate aldolase (Fba1), CCT ring complex subunit (Cct2), pyruvate kinase (Cdc19), and pyruvate carboxylase (Pyc2). This study illustrates a strategy for investigating protein expression patterns across closely related organisms by combining orthology information with quantitative proteomics.
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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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Fourier transform infrared as a powerful technique for the identification and characterization of filamentous fungi and yeasts. Res Microbiol 2010; 161:168-75. [DOI: 10.1016/j.resmic.2009.12.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 10/27/2009] [Accepted: 12/21/2009] [Indexed: 11/17/2022]
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50
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Corte L, Rellini P, Roscini L, Fatichenti F, Cardinali G. Development of a novel, FTIR (Fourier transform infrared spectroscopy) based, yeast bioassay for toxicity testing and stress response study. Anal Chim Acta 2010; 659:258-65. [DOI: 10.1016/j.aca.2009.11.035] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 11/11/2009] [Accepted: 11/13/2009] [Indexed: 10/20/2022]
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