scholarly journals Population Dynamics and Yeast Diversity in Early Winemaking Stages without Sulfites Revealed by Three Complementary Approaches

2021 ◽  
Vol 11 (6) ◽  
pp. 2494
Author(s):  
Sara Windholtz ◽  
Lucie Dutilh ◽  
Marine Lucas ◽  
Julie Maupeu ◽  
Amélie Vallet-Courbin ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Protein Extraction ◽  
Wine Yeast ◽  
Yeast Identification ◽  
Maldi Tof Ms ◽  
Operational Taxonomic Units ◽  
Maldi Tof ◽  
Hanseniaspora Uvarum ◽  
Standard Procedures ◽  
Tof Ms

Nowadays, the use of sulfur dioxide (SO2) during the winemaking process is a controversial societal issue. In order to reduce its use, various alternatives are emerging, in particular bioprotection by adding yeasts, with different impacts on yeast microbiota in early winemaking stages. In this study, quantitative-PCR and metabarcoding high-throughput sequencing (HTS) were combined with MALDI-TOF-MS to monitor yeast population dynamic and diversity in the early stages of red winemaking process without sulfites and with bioprotection by Torulaspora delbrueckii and Metschnikowia pulcherrima addition. By using standard procedures for yeast protein extraction and a laboratory-specific database of wine yeasts, identification at species level of 95% of the isolates was successfully achieved by MALDI-TOF-MS, thus confirming that it is a promising method for wine yeast identification. The different approaches confirmed the implantation and the niche occupation of bioprotection leading to the decrease of fungal communities (HTS) and Hanseniaspora uvarum cultivable population (MALDI-TOF MS). Yeast and fungi diversity was impacted by stage of maceration and, to a lesser extent, by bioprotection and SO2, resulting in a modification of the nature and abundance of the operational taxonomic units (OTUs) diversity.

scholarly journals Development and Validation of an in-House Library of Colombian Candida auris Strains with MALDI-TOF MS to Improve Yeast Identification

2020 ◽  
Vol 6 (2) ◽  
pp. 72 ◽  
Author(s):  
Andrés Ceballos-Garzon ◽  
Daniela Amado ◽  
Norida Vélez ◽  
María José Jiménez-A ◽  
Crescencio Rodríguez ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Candida Auris ◽  
Yeast Identification ◽  
Great Opportunity ◽  
Maldi Tof Ms ◽  
Identification Process ◽  
Clinical Strains ◽  
Maldi Tof ◽  
Development And Validation ◽  
Tof Ms

Background: Candida auris is characterized for having a high genetic variability among species. MALDI-TOF MS library contains spectra from only three strains of C. auris, which makes difficult the identification process and gives low scores at the species level. Our aim was to construct and validate an internal library to improve C. auris identification with Colombian clinical strains. Methods: From 30 clinical strains, 770 mass spectra were obtained for the construction of the database. The validation was performed with 300 strains to compare the identification results in the BDAL and C. auris Colombia libraries. Results: Our library allowed a complete, 100% identification of the evaluated strains and a significant improvement in the scores obtained, showing a better performance compared to the Bruker BDAL library. Conclusions: The strengthening of the database is a great opportunity to improve the scoring and C. auris identification. Library data are available via ProteomeXchange with identifier PXD016387.

scholarly journals Mass Spectrometry Based-Proteomic Analysis of Anisakis spp.: A Preliminary Study towards a New Diagnostic Tool

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 693 ◽  
Author(s):  
Valeria Marzano ◽  
Stefania Pane ◽  
Gianluca Foglietta ◽  
Stefano Levi Mortera ◽  
Pamela Vernocchi ◽  
...  
Keyword(s):  
Diagnostic Tool ◽  
Protein Extraction ◽  
Shotgun Proteomics ◽  
Diagnostic Tools ◽  
Routine Practice ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Proteomics Approach ◽  
Anisakis Spp ◽  
Tof Ms

Anisakiasis is nowadays a well-known infection, mainly caused by the accidental ingestion of Anisakis larvae, following the consumption of raw or undercooked fishes and cephalopods. Due to the similarity of symptoms with those of common gastrointestinal disorders, this infection is often underestimated, and the need for new specific diagnostic tools is becoming crucial. Given the remarkable impact that MALDI–TOF MS biotyping had in the last decade in clinical routine practice for the recognition of bacterial and fungi strains, a similar scenario could be foreseen for the identification of parasites, such as nematodes. In this work, a MALDI–TOF MS profiling of Anisakis proteome was pursued with a view to constructing a first spectral library for the diagnosis of Anisakis infections. At the same time, a shotgun proteomics approach by LC–ESI–MS/MS was performed on the two main fractions obtained from protein extraction, to evaluate the protein species enriched by the protocol. A set of MALDI–TOF MS signals associated with proteins originating in the ribosomal fraction of the nematode extract was selected as a potential diagnostic tool for the identification of Anisakis spp.

scholarly journals Identification of Nocardia species using Autof MS 1000 and Bruker MALDI-TOF MS systems: A comparison

2021 ◽  
Author(s):  
Bing Ma ◽  
Yunqi Tian ◽  
Yungang Han ◽  
Lifang Ban ◽  
Junwen Yang ◽  
...  
Keyword(s):  
Species Identification ◽  
Protein Extraction ◽  
Reference Method ◽  
Invasive Disease ◽  
Species Level ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Significant Difference ◽  
Tof Ms

ABSTRACTNocardia is an important cause of clinically invasive disease, but for most clinical laboratories, identification of these isolates to the species level is challenging. Recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used for identification of most bacterial and fungal isolates. In this multicenter study, we evaluated the identification of Nocardia isolates using Autof MS1000 and Bruker Biotyper. A total of 86 non-duplicate Nocardia isolates from 7 hospital laboratories were evaluated. Further, we carried out sequence analysis of 16S rRNA, gyrB, secA1, hsp65, and rpoB genes as a reference method for Nocardia species identification. The 86 isolates were directly spotted on the target plate and plate protein extraction was performed. Data were analyzed by SPSS 19.0. In total, 72 (83.7%) strains (score ≥ 9.0) and 70 (81.4%) strains (score ≥ 2.0) were correctly identified by the Autof MS1000 and Bruker Biotyper systems, respectively, at the species level. There was no significant difference (P > 0.05) between the two systems using the same protein extraction method. In conclusion, the Autof MS 1000 and Bruker MALDI-TOF systems showed no difference in identification of Nocardia spp. to the species level and could meet the most important clinical requirement for species identification.

scholarly journals Evaluation of Two Protein Extraction Protocols Based on Freezing and Mechanical Disruption for Identifying Nontuberculous Mycobacteria by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry from Liquid and Solid Cultures

2018 ◽  
Vol 56 (4) ◽  
Author(s):  
David Rodriguez-Temporal ◽  
Daniel Perez-Risco ◽  
Eduardo A. Struzka ◽  
Mireia Mas ◽  
Fernando Alcaide
Keyword(s):  
Protein Extraction ◽  
Nontuberculous Mycobacteria ◽  
Laser Desorption Ionization ◽  
Liquid Media ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Mechanical Disruption ◽  
Tof Ms

ABSTRACTMatrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has proved to be a useful diagnostic method for identifying conventional bacteria. In the case of mycobacteria, a good protein extraction protocol is essential in order to obtain reliable identification results. To date, no such protocol has been definitively established. The aim of this study was to compare the manufacturer's recommended protein extraction protocol (protocol A) with two novel protocols (protocols B and C), which apply different freezing temperatures and mechanical disruption times using an automatic tissue homogenizer. A total of 302 clinical isolates, comprising 41 nontuberculous mycobacteria (NTM) species, were grown in parallel on solid and liquid media and analyzed: 174 isolates were slow-growing mycobacteria (SGM) and 128 isolates were rapid-growing mycobacteria (RGM). Overall, MALDI-TOF MS identified a higher number of NTM isolates from solid than from liquid media, especially with protocol C (83.4 and 68.2%, respectively;P< 0.05). From solid media, this protein extraction method identified 57.9 and 3.9% more isolates than protocols A (P< 0.001) and B (P< 0.05), respectively. In the case of liquid media, protocol C identified 49.7 and 6.3% more isolates than protocols A and B, respectively (P< 0.001). With regard to the growth rate, MALDI-TOF MS identified more RGM isolates than SGM isolates in all of the protocols studied. In conclusion, the application of freezing and automatic tissue homogenizer improved protein extraction of NTM and boosted identification rates. Consequently, MALDI-TOF MS, which is a cheap and simple method, could be a helpful tool for identifying NTM species in clinical laboratories.

Wine yeast typing by MALDI-TOF MS

2014 ◽  
Vol 98 (8) ◽  
pp. 3737-3752 ◽  
Author(s):  
Julia C. Usbeck ◽  
Caroline Wilde ◽  
Dave Bertrand ◽  
Jürgen Behr ◽  
Rudi F. Vogel
Keyword(s):  
Wine Yeast ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

scholarly journals Evaluation of four pretreatment procedures for MALDI-TOF MS yeast identification in the routine clinical laboratory

2013 ◽  
Vol 51 (4) ◽  
pp. 371-377 ◽  
Author(s):  
Carole Cassagne ◽  
Anne-Laure Cella ◽  
Pierre Suchon ◽  
Anne-Cecile Normand ◽  
Stephane Ranque ◽  
...  
Keyword(s):  
Clinical Laboratory ◽  
Yeast Identification ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Routine Clinical Laboratory ◽  
Tof Ms

scholarly journals Yeast identification by sequencing, biochemical kits, MALDI–TOF MS and rep-PCR DNA fingerprinting

2017 ◽  
Vol 56 (7) ◽  
pp. 816-827 ◽  
Author(s):  
Ying Zhao ◽  
Chi-Ching Tsang ◽  
Meng Xiao ◽  
Jasper F W Chan ◽  
Susanna K P Lau ◽  
...  
Keyword(s):  
Dna Fingerprinting ◽  
Yeast Identification ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

Rapid one-step protein extraction method for the identification of mycobacteria using MALDI-TOF MS

2019 ◽  
Vol 94 (4) ◽  
pp. 355-360 ◽  
Author(s):  
Suwatchareeporn Rotcheewaphan ◽  
Jamie K. Lemon ◽  
Uma U. Desai ◽  
Christina M. Henderson ◽  
Adrian M. Zelazny
Keyword(s):  
Extraction Method ◽  
Protein Extraction ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
One Step ◽  
Tof Ms
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