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Collins T, Muste C, Owens KG. Identification of Microbial Strains via 2D Cross-Correlation of LC-MS Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1352-1362. [PMID: 38742647 PMCID: PMC11197091 DOI: 10.1021/jasms.4c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
Mass spectrometry is commonly used in the identification of species present in microbial samples, but the high similarity in the peptide composition between strains of a single species has made analysis at the subspecies level challenging. Prior research in this area has employed methods such as Principal Component Analysis (PCA), the k-Nearest Neighbors' (kNN) algorithm, and Pearson correlation. Previously, 1D cross-correlation of mass spectra has been shown to be useful in the classification of small molecule compounds as well as in the identification of peptide sequences via the SEQUEST algorithm and its variants. While direct application of cross-correlation to mass spectral data has been shown to aid in the identification of many other types of compounds, this type of analysis has not been demonstrated in the literature for the purpose of LC-MS based identification of microbial strains. A method of identifying microbial strains is presented here that applies the principle of 2D cross-correlation to LC-MS data. For a set of N = 30 yeast isolate samples representing 5 yeast strains (K-97, S-33, T-58, US-05, WB-06), high-resolution LC-MS-Orbitrap data were collected. Reference spectra were then generated for each strain from the combined data of each sample of that strain. Sample strains were then predicted by computing the 2D cross-correlation of each sample against the reference spectra, followed by application of correction factors measuring the asymmetry of the 2D correlation functions.
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Affiliation(s)
- Tucker
James Collins
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Cathy Muste
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Kevin G. Owens
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
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2
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Zhang J, Plowman JE, Tian B, Clerens S, On SLW. Application of MALDI-TOF analysis to reveal diversity and dynamics of winemaking yeast species in wild-fermented, organically produced, New Zealand Pinot Noir wine. Food Microbiol 2021; 99:103824. [PMID: 34119109 DOI: 10.1016/j.fm.2021.103824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 02/06/2023]
Abstract
Rapid yeast identification is of particular importance in monitoring wine fermentation and assessing strain application in winemaking. We used MALDI-TOF MS analysis supported by 26 S rRNA gene sequence analysis and Saccharomyces-specific PCR testing to differentiate reference and field strains recovered from organic wine production facilities in Waipara, New Zealand, in which Pinot Noir wine was produced by spontaneous fermentations in the vineyard and in the winery. Strains were isolated from each of four key stages of each ferment to evaluate changes in taxonomic diversity. MALDI-TOF MS analysis was confirmed as an excellent yeast identification method, with even closely related Saccharomyces species readily distinguished. A total of 13 indigenous species belonging to eight genera were identified from Pinot Noir ferments, with taxonomic diversity generally reducing as fermentation progressed. However, differences between the taxa recovered were observed between the vineyard and winery ferments, despite the grapes used being from the same batch. Furthermore, some consistent proteomic differences between strains of S. cerevisiae, Hanseniasporum uvarum, Candida californica, Pichia membranifaciens and Starmerella bacillaris correlated with the different fermentation systems used. The high speed, low cost, taxonomic resolution and ability to characterise subtle changes in phenotype that may result from variations in environmental conditions makes MALDI-TOF analysis an attractive tool for further and wider applications in the wine industry. Such applications may include monitoring wine fermentation to actively support the consistency of high-quality wine products, and potentially for the development of such products too.
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Affiliation(s)
- Junwen Zhang
- Department of Wine, Food and Molecular Biosciences, Lincoln University, PO Box 85054, Lincoln, New Zealand
| | | | - Bin Tian
- Department of Wine, Food and Molecular Biosciences, Lincoln University, PO Box 85054, Lincoln, New Zealand
| | - Stefan Clerens
- AgResearch Ltd, Lincoln Research Centre, Lincoln, New Zealand; Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, PO Box 85054, Lincoln, New Zealand.
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3
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Schmid J, Wefers D, Vogel RF, Jakob F. Analysis of Structural and Functional Differences of Glucans Produced by the Natively Released Dextransucrase of Liquorilactobacillus hordei TMW 1.1822. Appl Biochem Biotechnol 2021; 193:96-110. [PMID: 32820351 PMCID: PMC7790797 DOI: 10.1007/s12010-020-03407-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/12/2020] [Indexed: 11/26/2022]
Abstract
The properties of the glucopolymer dextran are versatile and linked to its molecular size, structure, branching, and secondary structure. However, suited strategies to control and exploit the variable structures of dextrans are scarce. The aim of this study was to delineate structural and functional differences of dextrans, which were produced in buffers at different conditions using the native dextransucrase released by Liquorilactobacillus (L.) hordei TMW 1.1822. Rheological measurements revealed that dextran produced at pH 4.0 (MW = 1.1 * 108 Da) exhibited the properties of a viscoelastic fluid up to concentrations of 10% (w/v). By contrast, dextran produced at pH 5.5 (MW = 1.86 * 108 Da) was gel-forming already at 7.5% (w/v). As both dextrans exhibited comparable molecular structures, the molecular weight primarily influenced their rheological properties. The addition of maltose to the production assays caused the formation of the trisaccharide panose instead of dextran. Moreover, pre-cultures of L. hordei TMW 1.1822 grown without sucrose were substantial for recovery of higher dextran yields, since the cells stored the constitutively expressed dextransucrase intracellularly, until sucrose became available. These findings can be exploited for the controlled recovery of functionally diverse dextrans and oligosaccharides by the use of one dextransucrase type.
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Affiliation(s)
- Jonas Schmid
- Chair of Technical Microbiology, Technical University of Munich (TUM), Freising, Germany
| | - Daniel Wefers
- Division of Food Chemistry, Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
- Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Rudi F Vogel
- Chair of Technical Microbiology, Technical University of Munich (TUM), Freising, Germany
| | - Frank Jakob
- Chair of Technical Microbiology, Technical University of Munich (TUM), Freising, Germany.
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4
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Suzuki K. Emergence of New Spoilage Microorganisms in the Brewing Industry and Development of Microbiological Quality Control Methods to Cope with This Phenomenon: A Review. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2020. [DOI: 10.1080/03610470.2020.1782101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Koji Suzuki
- Asahi Quality and Innovations, Ltd, Moriya, Ibaraki, Japan
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5
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Bucka-Kolendo J, Sokołowska B, Winiarczyk S. Influence of High Hydrostatic Pressure on the Identification of Lactobacillus by MALDI-TOF MS- Preliminary Study. Microorganisms 2020; 8:E813. [PMID: 32481763 PMCID: PMC7356497 DOI: 10.3390/microorganisms8060813] [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: 05/08/2020] [Revised: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 11/17/2022] Open
Abstract
In the present study, we assessed the ability of MALDI-TOF MS (matrix-assisted laser desorption ionization time-of-flight mass spectrometry) to identify microbial strains subjected to high hydrostatic pressure (HHP) as a stress factor. Protein changes induced by HHP can affect the identification of microorganisms when the identification technique is based on the protein profile. We evaluated two methods, namely MALDI-TOF MS and 16S rDNA sequencing, as a valuable tool to identify Lactobacillus species isolated from spoiled food, juices and beers. The data obtained from the protein mass fingerprint analysis of some of the lactobacilli strains showed differences in unpressured and pressured mass spectrum profiles (MSPs), which influenced the results of the identification. Four out of 13 strains (30%) showed different MSP results for unpressured and pressured samples and these results did not overlap with the 16S rDNA identification results. The 16S rDNA sequencing method revealed that five unpressured strains (38%) and four pressured strains (40%) were identified correctly by MALDI-TOF MS. Both methods showed compatible results in 38% of unpressured strains and in 30% of pressured strains. Stress factors, cultivation methods or the natural environment from which the bacteria were derived can affect their protein profile and thus change the mass spectrum. It is necessary to expand the database with a wide range of mass spectra dedicated to a high-throughput study of the microorganisms derived from different environments.
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Affiliation(s)
- Joanna Bucka-Kolendo
- Department of Microbiology, Institute of Agriculture and Food Biotechnology, 02-532 Warsaw, Poland;
| | - Barbara Sokołowska
- Department of Microbiology, Institute of Agriculture and Food Biotechnology, 02-532 Warsaw, Poland;
- Institute of High Pressure Physics, Polish Academy of Sciences, 01-142 Warsaw, Poland
| | - Stanisław Winiarczyk
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-612 Lublin, Poland;
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6
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Eckel VPL, Ziegler LM, Vogel RF, Ehrmann M. Bifidobacterium tibiigranuli sp. nov. isolated from homemade water kefir. Int J Syst Evol Microbiol 2020; 70:1562-1570. [PMID: 31860428 DOI: 10.1099/ijsem.0.003936] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Bifidobacterium strains, TMW 2.2057T and TMW 2.1764 were isolated from two different homemade water kefirs from Germany. Both strains were oxidase- and catalase-negative and Gram-staining-positive. Cells were non-motile, irregular rods that were aerotolerant anaerobes. On basis of fructose 6-phosphate phosphoketolase activity, they were assigned to the family Bifidobacteriaceae. Comparative analysis of 16S rRNA and concatenated housekeeping genes (clpC, dnaB, dnaG, dnaJ, hsp60 and rpoB) demonstrated that both strains represented a member of the genus Bifidobacterium, with Bifidobacterium subtile DSM 20096T as the closest phylogenetic relative (98.35 % identity). Both strains can be distinguished using randomly amplified polymorphic DNA fingerprinting. Analysis of concatenated marker gene sequences as well as average nucleotide identity by blast (ANIb) and in silico DNA-DNA hybridization (isDDH) calculations of their genome sequences confirmed Bifidobacterium subtile DSM 20096T as the closest relative (87.91 and 35.80 % respectively). All phylogenetic analyses allow differentiation of strains TMW 2.2057T and TMW 2.1764 from all hitherto described species of the genus Bifidobacterium with validly published names. We therefore propose a novel species with the name Bifidobacterium tibiigranuli, for which TMW 2.2057T (=DSM 108414T=LMG 31086T) is the type strain.
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Affiliation(s)
- Viktor P L Eckel
- Technische Universität München, Lehrstuhl fuer Technische Mikrobiologie, Gregor-Mendel-Str. 4, 85354 Freising, Germany
| | - Lisa-Marie Ziegler
- Technische Universität München, Lehrstuhl fuer Technische Mikrobiologie, Gregor-Mendel-Str. 4, 85354 Freising, Germany
| | - Rudi F Vogel
- Technische Universität München, Lehrstuhl fuer Technische Mikrobiologie, Gregor-Mendel-Str. 4, 85354 Freising, Germany
| | - Matthias Ehrmann
- Technische Universität München, Lehrstuhl fuer Technische Mikrobiologie, Gregor-Mendel-Str. 4, 85354 Freising, Germany
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7
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An improved method for MALDI-TOF analysis of wine-associated yeasts. J Microbiol Methods 2020; 172:105904. [DOI: 10.1016/j.mimet.2020.105904] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 02/04/2023]
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8
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Ly D, Mayrhofer S, Agung Yogeswara IB, Nguyen TH, Domig KJ. Identification, Classification and Screening for γ-Amino-butyric Acid Production in Lactic Acid Bacteria from Cambodian Fermented Foods. Biomolecules 2019; 9:E768. [PMID: 31766706 PMCID: PMC6995518 DOI: 10.3390/biom9120768] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 11/16/2022] Open
Abstract
Screening for various types of lactic acid bacteria (LAB) that form the biological agent γ-amino-butyric acid (GABA) is important to produce different kinds of GABA-containing fermented foods. So far, no GABA-producing LAB have been reported from Cambodian fermented foods. Most small-scale fermentations and even some industrial processes in this country still rely on indigenous LAB. The application of GABA-producing autochthonous starters would allow the production of Cambodian fermented foods with an additional nutritional value that meet the population's dietary habits and that are also more attractive for the international food market. Matrix-assisted laser desorption/ionizing time-of-flight mass spectrometry (MALDI-TOF MS) and partial 16S rDNA sequencing were used to identify 68 LAB isolates from Cambodian fermented foods. These isolates were classified and grouped with (GTG)5 rep-PCR, resulting in 50 strains. Subsequently, all strains were investigated for their ability to produce GABA by thin layer chromatography. GABA-positive strains were further analyzed by the GABase assay. Of the six GABA-positive LAB strains-one Lactobacillus futsaii, two Lactobacillus namurensis, and three Lactobacillus plantarum strains-two Lactobacillus plantarum strains produced high amounts of GABA (20.34 mM, 16.47 mM). These strains should be further investigated for their potential application as GABA-producing starter cultures in the food applications.
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Affiliation(s)
- Dalin Ly
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria; (S.M.); (I.B.A.Y.); (T.-H.N.); (K.J.D.)
- Department of Food Biotechnology, Faculty of Agro-Industry, Royal University of Agriculture, Dangkor District, P.O. Box: 2696, Phnom Penh 12400, Cambodia
| | - Sigrid Mayrhofer
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria; (S.M.); (I.B.A.Y.); (T.-H.N.); (K.J.D.)
| | - I. B. Agung Yogeswara
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria; (S.M.); (I.B.A.Y.); (T.-H.N.); (K.J.D.)
- Department of Nutrition, Universitas Dhyana Pura, Bali 80361, Indonesia
| | - Thu-Ha Nguyen
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria; (S.M.); (I.B.A.Y.); (T.-H.N.); (K.J.D.)
| | - Konrad J. Domig
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria; (S.M.); (I.B.A.Y.); (T.-H.N.); (K.J.D.)
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9
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Quéro L, Courault P, Cellière B, Lorber S, Jany JL, Puel O, Girard V, Vasseur V, Nodet P, Mounier J. Application of MALDI-TOF MS to species complex differentiation and strain typing of food related fungi: Case studies with Aspergillus section Flavi species and Penicillium roqueforti isolates. Food Microbiol 2019; 86:103311. [PMID: 31703856 DOI: 10.1016/j.fm.2019.103311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 05/29/2019] [Accepted: 08/20/2019] [Indexed: 11/26/2022]
Abstract
Filamentous fungi are one of the main causes of food losses worldwide and their ability to produce mycotoxins represents a hazard for human health. Their correct and rapid identification is thus crucial to manage food safety. In recent years, MALDI-TOF emerged as a rapid and reliable tool for fungi identification and was applied to typing of bacteria and yeasts, but few studies focused on filamentous fungal species complex differentiation and typing. Therefore, the aim of this study was to evaluate the use of MALDI-TOF to identify species of the Aspergillus section Flavi, and to differentiate Penicillium roqueforti isolates from three distinct genetic populations. Spectra were acquired from 23 Aspergillus species and integrated into a database for which cross-validation led to more than 99% of correctly attributed spectra. For P. roqueforti, spectra were acquired from 63 strains and a two-step calibration procedure was applied before database construction. Cross-validation and external validation respectively led to 94% and 95% of spectra attributed to the right population. Results obtained here suggested very good agreement between spectral and genetic data analysis for both Aspergillus species and P. roqueforti, demonstrating MALDI-TOF applicability as a fast and easy alternative to molecular techniques for species complex differentiation and strain typing of filamentous fungi.
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Affiliation(s)
- Laura Quéro
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France; BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Priscillia Courault
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Beatrice Cellière
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Sophie Lorber
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France.
| | - Jean-Luc Jany
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
| | - Olivier Puel
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France.
| | - Victoria Girard
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Valérie Vasseur
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
| | - Patrice Nodet
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
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10
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Anderson HE, Santos IC, Hildenbrand ZL, Schug KA. A review of the analytical methods used for beer ingredient and finished product analysis and quality control. Anal Chim Acta 2019; 1085:1-20. [PMID: 31522723 DOI: 10.1016/j.aca.2019.07.061] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 07/28/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022]
Abstract
Beer is an incredibly complex beverage containing more than 3000 different compounds, including carbohydrates, proteins, ions, microbes, organic acids, and polyphenols, among others. Beer becomes even more complex during storage, for over time it may undergo chemical changes that negatively affect the flavor, aroma, and appearance. Thus, it can be expected that maintaining the quality of beer throughout its lifetime is a difficult task. Since it is such a popular drink throughout the world, being familiar with proper analytical techniques for beer evaluation is useful for researchers and brewers. These techniques include, but are not limited to, gas chromatography, liquid chromatography, matrix assisted laser desorption/ionization, capillary electrophoresis, mass spectrometry, ultraviolet-visible spectroscopy, and flame ionization detection. This review aims to summarize the various ingredients and components of beer, discuss how they affect the finished product, and present some of the analytical methods used for quality control and understanding the formation of chemicals in beer during the brewing process.
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Affiliation(s)
- Hailee E Anderson
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, TX, 76019, USA
| | - Ines C Santos
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, TX, 76019, USA; Affiliate of Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Zacariah L Hildenbrand
- Affiliate of Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, 76019, USA; Inform Environmental, LLC, 6060 N. Central Expressway, Suite 500, Dallas, TX, 75206, USA
| | - Kevin A Schug
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, TX, 76019, USA; Affiliate of Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, 76019, USA.
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11
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Liu B, Han L, Liu X, Wu J, Ma Q. Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1211-1218. [PMID: 29993815 DOI: 10.1109/tcbb.2018.2816032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sigma factor, as a unit of RNA polymerase holoenzyme, is a critical factor in the process of gene transcriptional regulation. It recognizes the specific DNA sites and brings the core enzyme of RNA polymerase to the upstream regions of target genes. Therefore, the prediction of the promoters for a particular sigma factor is essential for interpreting functional genomic data and observation. This paper develops a new method to predict sigma-54 promoters in bacterial genomes. The new method organically integrates motif finding and machine learning strategies to capture the intrinsic features of sigma-54 promoters. The experiments on E. coli benchmark test set show that our method has good capability to distinguish sigma-54 promoters from surrounding or randomly selected DNA sequences. The applications of the other three bacterial genomes indicate the potential robustness and applicative power of our method on a large number of bacterial genomes. The source code of our method can be freely downloaded at https://github.com/maqin2001/PromotePredictor.
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12
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Condina MR, Dilmetz BA, Razavi Bazaz S, Meneses J, Ebrahimi Warkiani M, Hoffmann P. Rapid separation and identification of beer spoilage bacteria by inertial microfluidics and MALDI-TOF mass spectrometry. LAB ON A CHIP 2019; 19:1961-1970. [PMID: 31099359 DOI: 10.1039/c9lc00152b] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS), in combination with Biotyper software, is a rapid, high-throughput, and accurate method for the identification of microbes. Microbial outbreaks in a brewery present a major risk for companies as it can lead to cost-intensive recalls and damage to the brand reputation. MALDI-TOF MS has been implemented into a brewery setting for quality control practices and the identification of beer spoilage microorganisms. However, the applicability of this approach is hindered by compatibility issues associated with mixed cultures, requiring the use of time-consuming selective cultivation techniques prior to identification. We propose a novel, low-cost approach based on the combination of inertial microfluidics and secondary flows in a spiral microchannel for high-throughput and efficient separation of yeasts (Saccharomyces pastorianus and Saccharomyces cerevisiae) from beer spoilage microorganisms (Lactobacillus brevis and Pediococcus damnosus). Flow rates were optimised using S. pastorianus and L. brevis, leading to separation of more than 90% of the L. brevis cells from yeast. The microorganisms were then identified to the species level using the MALDI-TOF MS platform using standard sample preparation protocols. This study shows the high-throughput and rapid separation of spoilage microorganisms (0.3-3 μm) from background yeast (5 μm) from beer, subsequent identification using MALDI Biotyper, and the potential applicability of the approach for biological control in the brewing industry.
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Affiliation(s)
- Mark R Condina
- Future Industries Institute, University of South Australia, Adelaide, Australia.
| | - Brooke A Dilmetz
- Future Industries Institute, University of South Australia, Adelaide, Australia.
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Australia.
| | | | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Australia. and Institute of Molecular Medicine, Sechenov University, Moscow 119991, Russia
| | - Peter Hoffmann
- Future Industries Institute, University of South Australia, Adelaide, Australia.
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13
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Muste C, Owens KG. Cell-Free Identification of S. cerevisiae Strains by Analysis of Supernatant Using LC-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2260-2267. [PMID: 30105741 DOI: 10.1007/s13361-018-2046-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 07/13/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
Current literature shows a gap for methods which can identify yeast sub-species (strains or serovars) in samples where there are no viable cells remaining. Presented here is a technique for the analysis of yeast supernatant, including solid phase extraction, data-dependent acquisition liquid chromatography/mass spectrometry (LC-MS), and two chemometric methods to identify and classify yeast strains. Five strains of Saccharomyces cerevisiae were successfully identified in various stages of growth. In addition, peptide/protein identification was performed, without the need for additional data acquisition. Graphical Abstract ᅟ.
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Affiliation(s)
- Cathy Muste
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104-2875, USA
| | - Kevin G Owens
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104-2875, USA.
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14
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Janßen D, Eisenbach L, Ehrmann MA, Vogel RF. Assertiveness of Lactobacillus sakei and Lactobacillus curvatus in a fermented sausage model. Int J Food Microbiol 2018; 285:188-197. [DOI: 10.1016/j.ijfoodmicro.2018.04.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 04/11/2018] [Accepted: 04/16/2018] [Indexed: 11/15/2022]
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15
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Rating of the industrial application potential of yeast strains by molecular characterization. Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3088-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Giacometti F, Piva S, Vranckx K, De Bruyne K, Drigo I, Lucchi A, Manfreda G, Serraino A. Application of MALDI-TOF MS for the subtyping of Arcobacter butzleri strains and comparison with their MLST and PFGE types. Int J Food Microbiol 2018; 277:50-57. [PMID: 29684765 DOI: 10.1016/j.ijfoodmicro.2018.04.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 12/19/2022]
Abstract
For the first time, this study evaluated the use of MALDI-TOF as a typing tool for Arcobacter butzleri. A total of 104 A. butzleri strains isolated from different sources in an artisanal dairy plant in Italy were identified and typed using MALDI-TOF and compared with their multilocus sequence typing (MLST) and pulsed field gel electrophoresis (PFGE) profiles found in previous studies. MALDI-TOF correctly identified all the isolates to species level. No clearly delineated clusters appeared on dendrograms based on either the complete spectra or the significant peaks, but nine clusters were defined using the cophenetic correlation. Interestingly, MALDI-TOF proved able to discriminate A. butzleri strains below species level, confirming its potential use for epidemiological surveys. As expected, the comparative analysis with PFGE and MLST showed that the discriminatory index was lower for MALDI-TOF but roughly comparable to sequence types and pulsotypes. MALDI-TOF appears to be a relatively low cost answer to the urgent need for more rapid, less expensive typing tools suitable for source attribution studies, readily allowing multiple typing methods to be combined. This study provides insights into MALDI-TOF as potential epidemiological tool. Its application in healthcare surveillance systems awaits further exploration to encourage interaction and convergence studies between primary care in humans and animal and food veterinary authorities as part of the One Health concept.
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Affiliation(s)
- Federica Giacometti
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Silvia Piva
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | | | | | - Ilenia Drigo
- Istituto Zooprofilattico Sperimentale delle Venezie, Villorba, Treviso, Italy.
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Andrea Serraino
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
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Illikoud N, Rossero A, Chauvet R, Courcoux P, Pilet MF, Charrier T, Jaffrès E, Zagorec M. Genotypic and phenotypic characterization of the food spoilage bacterium Brochothrix thermosphacta. Food Microbiol 2018; 81:22-31. [PMID: 30910085 DOI: 10.1016/j.fm.2018.01.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/10/2018] [Accepted: 01/19/2018] [Indexed: 11/17/2022]
Abstract
Microbial food spoilage is responsible for significant economic losses. Brochothrix thermosphacta is one of the major bacteria involved in the spoilage of meat and seafood. Its growth and metabolic activities during food storage result in the production of metabolites associated with off-odors. In this study, we evaluated the genotypic and phenotypic diversity of this species. A collection of 161 B. thermosphacta strains isolated from different foods, spoiled or not, and from a slaughterhouse environment was constituted from various laboratory collections and completed with new isolates. A PCR test based on the rpoB gene was developed for a fast screening of B. thermosphacta isolates. Strains were typed by MALDI-TOF MS, rep-PCR, and PFGE. Each typing method separated strains into distinct groups, revealing significant intra-species diversity. These classifications did not correlate with the ecological origin of strains. The ability to produce acetoin and diacetyl, two molecules associated with B. thermosphacta spoilage, was evaluated in meat and shrimp juices. The production level was variable between strains and the spoilage ability on meat or shrimp juice did not correlate with the substrate origin of strains. Although the B. thermosphacta species encompasses ubiquitous strains, spoiling ability is both strain- and environment-dependent.
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Affiliation(s)
- Nassima Illikoud
- SECALIM, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France.
| | - Albert Rossero
- SECALIM, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France.
| | - Romain Chauvet
- EUROFINS, Laboratoire Microbiologie Ouest, 44300 Nantes, France.
| | - Philippe Courcoux
- Oniris, StatSC Sensometrics and Chemometrics Laboratory, Nantes F-44322, France.
| | - Marie-France Pilet
- SECALIM, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France.
| | - Thomas Charrier
- EUROFINS, Laboratoire Microbiologie Ouest, 44300 Nantes, France.
| | - Emmanuel Jaffrès
- SECALIM, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France.
| | - Monique Zagorec
- SECALIM, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France.
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Lauterbach A, Usbeck JC, Behr J, Vogel RF. MALDI-TOF MS typing enables the classification of brewing yeasts of the genus Saccharomyces to major beer styles. PLoS One 2017; 12:e0181694. [PMID: 28792944 PMCID: PMC5549903 DOI: 10.1371/journal.pone.0181694] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 07/04/2017] [Indexed: 11/19/2022] Open
Abstract
Brewing yeasts of the genus Saccharomyces are either available from yeast distributor centers or from breweries employing their own “in-house strains”. During the last years, the classification and characterization of yeasts of the genus Saccharomyces was achieved by using biochemical and DNA-based methods. The current lack of fast, cost-effective and simple methods to classify brewing yeasts to a beer type, may be closed by Matrix Assisted Laser Desorption/Ionization–Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) upon establishment of a database based on sub-proteome spectra from reference strains of brewing yeasts. In this study an extendable “brewing yeast” spectra database was established including 52 brewing yeast strains of the most important types of bottom- and top-fermenting strains as well as beer-spoiling S. cerevisiae var. diastaticus strains. 1560 single spectra, prepared with a standardized sample preparation method, were finally compared against the established database and investigated by bioinformatic analyses for similarities and distinctions. A 100% separation between bottom-, top-fermenting and S. cerevisiae var. diastaticus strains was achieved. Differentiation between Alt and Kölsch strains was not achieved because of the high similarity of their protein patterns. Whereas the Ale strains show a high degree of dissimilarity with regard to their sub-proteome. These results were supported by MDS and DAPC analysis of all recorded spectra. Within five clusters of beer types that were distinguished, and the wheat beer (WB) cluster has a clear separation from other groups. With the establishment of this MALDI-TOF MS spectra database proof of concept is provided of the discriminatory power of this technique to classify brewing yeasts into different major beer types in a rapid, easy way, and focus brewing trails accordingly. It can be extended to yeasts for specialty beer types and other applications including wine making or baking.
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Affiliation(s)
- Alexander Lauterbach
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Julia C. Usbeck
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Jürgen Behr
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
- * E-mail:
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García-Cayuela T, Requena T, Martínez-Cuesta MC, Peláez C. Rapid detection of Lactococcuslactis isolates producing the lantibiotics nisin, lacticin 481 and lacticin 3147 using MALDI-TOF MS. J Microbiol Methods 2017; 139:138-142. [PMID: 28583849 DOI: 10.1016/j.mimet.2017.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/29/2017] [Accepted: 06/01/2017] [Indexed: 01/17/2023]
Abstract
The aim of the study was to evaluate the potential use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for fast and reliable detection of strains producing the lantibiotics nisin, lacticin 481 and lacticin 3147 in a large collection of lactococci. A total of one hundred lactococcal isolates from traditional ewe's and goat's raw milk cheeses were identified to the species level as Lactococcuslactis by MALDI-TOF MS based on comparison with lactococcal entries in the BioTyper database. Mass spectra in the range 2000-4000Da of the identified isolates were compared to reference spectra of three lactococcal strains producing lacticin 481 (IFPL 330), lacticin 3147 (IFPL 105) and nisin (IFPL 503). Only eight isolates had mass spectra with peaks that could be unequivocally identified as lacticin 481 (2900.47Da) or nisin (3330.31Da). None of the assayed isolates matched the mass spectra corresponding to the two-peptide lacticin 3147 (2847.97 and 3306.29Da). The results obtained by MALDI-TOF MS were genetically validated by amplification of the corresponding structural gene coding for lacticin 481, nisin and lacticin 3147. MALDI-TOF MS can be used as a fast and reliable technique to screen a large number of lactococcal isolates for the ability to produce the lantibiotics nisin, lacticin 481 and lacticin 3147.
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Affiliation(s)
- Tomás García-Cayuela
- Departamento de Biotecnología y Microbiología de Alimentos, Instituto de Investigación en Ciencias de la Alimentación CIAL (CSIC), Madrid, Spain.
| | - Teresa Requena
- Departamento de Biotecnología y Microbiología de Alimentos, Instituto de Investigación en Ciencias de la Alimentación CIAL (CSIC), Madrid, Spain
| | - M Carmen Martínez-Cuesta
- Departamento de Biotecnología y Microbiología de Alimentos, Instituto de Investigación en Ciencias de la Alimentación CIAL (CSIC), Madrid, Spain
| | - Carmen Peláez
- Departamento de Biotecnología y Microbiología de Alimentos, Instituto de Investigación en Ciencias de la Alimentación CIAL (CSIC), Madrid, Spain
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Turvey ME, Weiland F, Keller EJ, Hoffmann P. The changing face of microbial quality control practices in the brewing industry: Introducing mass spectrometry proteomic fingerprinting for microbial identification. JOURNAL OF THE INSTITUTE OF BREWING 2017. [DOI: 10.1002/jib.428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- M. E. Turvey
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
- Singapore-MIT Alliance for Research and Technology Centre; Singapore
| | - F. Weiland
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
| | - E. J. Keller
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
| | - P. Hoffmann
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
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Foschi C, Laghi L, Parolin C, Giordani B, Compri M, Cevenini R, Marangoni A, Vitali B. Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR. PLoS One 2017; 12:e0172483. [PMID: 28207855 PMCID: PMC5312945 DOI: 10.1371/journal.pone.0172483] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/06/2017] [Indexed: 02/07/2023] Open
Abstract
Lactobacilli represent a wide range of bacterial species with several implications for the human host. They play a crucial role in maintaining the ecological equilibrium of different biological niches and are essential for fermented food production and probiotic formulation. Despite the consensus about the ‘health-promoting’ significance of Lactobacillus genus, its genotypic and phenotypic characterization still poses several difficulties. The aim of this study was to assess the integration of different approaches, genotypic (16S rRNA gene sequencing), proteomic (MALDI-TOF MS) and metabolomic (1H-NMR), for the taxonomic and metabolic characterization of Lactobacillus species. For this purpose we analyzed 40 strains of various origin (intestinal, vaginal, food, probiotics), belonging to different species. The high discriminatory power of MALDI-TOF for species identification was underlined by the excellent agreement with the genotypic analysis. Indeed, MALDI-TOF allowed to correctly identify 39 out of 40 Lactobacillus strains at the species level, with an overall concordance of 97.5%. In the perspective to simplify the MALDI TOF sample preparation, especially for routine practice, we demonstrated the perfect agreement of the colony-picking from agar plates with the protein extraction protocol. 1H-NMR analysis, applied to both culture supernatants and bacterial lysates, identified a panel of metabolites whose variations in concentration were associated with the taxonomy, but also revealed a high intra-species variability that did not allow a species-level identification. Therefore, despite not suitable for mere taxonomic purposes, metabolomics can be useful to correlate particular biological activities with taxonomy and to understand the mechanisms related to the antimicrobial effect shown by some Lactobacillus species.
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Affiliation(s)
- Claudio Foschi
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | - Luca Laghi
- Centre of Foodomics, Department of Agro-Food Science and Technology, University of Bologna, Bologna, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Barbara Giordani
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Monica Compri
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | | | | | - Beatrice Vitali
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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23
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Turvey ME, Weiland F, Meneses J, Sterenberg N, Hoffmann P. Identification of beer spoilage microorganisms using the MALDI Biotyper platform. Appl Microbiol Biotechnol 2016; 100:2761-73. [DOI: 10.1007/s00253-016-7344-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/17/2016] [Accepted: 01/19/2016] [Indexed: 10/22/2022]
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Advantages and limitations of potential methods for the analysis of bacteria in milk: a review. Journal of Food Science and Technology 2015; 53:42-9. [PMID: 26787931 DOI: 10.1007/s13197-015-1993-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/04/2015] [Accepted: 08/07/2015] [Indexed: 12/27/2022]
Abstract
Contamination concerns in the dairy industry are motivated by outbreaks of disease in humans and the inability of thermal processes to eliminate bacteria completely in processed products. HACCP principles are an important tool used in the food industry to identify and control potential food safety hazards in order to meet customer demands and regulatory requirements. Milk testing is of importance to the milk industry regarding quality assurance and monitoring of processed products by researchers, manufacturers and regulatory agencies. Due to the availability of numerous methods used for analysing the microbial quality of milk in literature and differences in priorities of stakeholders, it is sometimes confusing to choose an appropriate method for a particular analysis. The objective of this paper is to review the advantages and disadvantages of selected techniques that can be used in the analysis of bacteria in milk. SSC, HRMA, REP, and RAPD are the top four techniques which are quick and cost-effective and possess adequate discriminatory power for the detection and profiling of bacteria. The following conclusions were arrived at during this review: HRMA, REP and RFLP are the techniques with the most reproducible results, and the techniques with the most discriminatory power are AFLP, PFGE and Raman Spectroscopy.
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25
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Jadhav S, Gulati V, Fox EM, Karpe A, Beale DJ, Sevior D, Bhave M, Palombo EA. Rapid identification and source-tracking of Listeria monocytogenes using MALDI-TOF mass spectrometry. Int J Food Microbiol 2015; 202:1-9. [DOI: 10.1016/j.ijfoodmicro.2015.01.023] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 01/20/2015] [Accepted: 01/24/2015] [Indexed: 11/29/2022]
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26
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Detection of acid and hop shock induced responses in beer spoiling Lactobacillus brevis by MALDI-TOF MS. Food Microbiol 2015; 46:501-506. [DOI: 10.1016/j.fm.2014.09.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/27/2014] [Accepted: 09/28/2014] [Indexed: 11/24/2022]
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27
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Anderson AC, Sanunu M, Schneider C, Clad A, Karygianni L, Hellwig E, Al-Ahmad A. Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing. BMC Microbiol 2014; 14:312. [PMID: 25495549 PMCID: PMC4272787 DOI: 10.1186/s12866-014-0312-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 11/25/2014] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Lactobacillus represents a large genus with different implications for the human host. Specific lactobacilli are considered to maintain vaginal health and to protect from urogenital infection. The presence of Lactobacillus species in carious lesions on the other hand is associated with progressive caries. Despite their clinical significance, species-level identification of lactobacilli still poses difficulties and mostly involves a combination of different phenotypic and genotypic methods. This study evaluated rapid MALDI-TOF MS analysis of vaginal and oral Lactobacillus isolates in comparison to 16S rDNA analysis. RESULTS Both methods were used to analyze 77 vaginal and 21 oral Lactobacillus isolates. The concordance of both methods was at 96% with five samples discordantly identified. Fifteen different Lactobacillus species were found in the vaginal samples, primarily L. iners, L. crispatus, L. jensenii and L. gasseri. In the oral samples 11 different species were identified, mostly L. salivarius, L. gasseri, L. rhamnosus and L. paracasei. Overall, the species found belonged to six different phylogenetic groups. For several samples, MALDI-TOF MS analysis only yielded scores indicating genus-level identification. However, in most cases the species found agreed with the 16S rDNA analysis result. CONCLUSION MALDI-TOF MS analysis proved to be a reliable and fast tool to identify lactobacilli to the species level. Even though some results were ambiguous while 16S rDNA sequencing yielded confident species identification, accuracy can be improved by extending reference databases. Thus, mass spectra analysis provides a suitable method to facilitate monitoring clinically relevant Lactobacillus species.
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Affiliation(s)
- Annette Carola Anderson
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Hugstetter Strasse 55, Freiburg, Germany.
| | - Mohamed Sanunu
- Department of Hygiene and Microbiology, Albert-Ludwigs-University, Hermann-Herder-Str. 11, Freiburg, Germany.
| | - Christian Schneider
- Department of Hygiene and Microbiology, Albert-Ludwigs-University, Hermann-Herder-Str. 11, Freiburg, Germany.
| | - Andreas Clad
- Department for Gynaecology, Medical Center, Albert-Ludwigs-University, Hugstetter Strasse 55, Freiburg, Germany.
| | - Lamprini Karygianni
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Hugstetter Strasse 55, Freiburg, Germany.
| | - Elmar Hellwig
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Hugstetter Strasse 55, Freiburg, Germany.
| | - Ali Al-Ahmad
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Hugstetter Strasse 55, Freiburg, Germany.
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