{"title":"Strain-level typing of Wickerhamomyces anomalus using Fourier transform infrared spectroscopy and whole-genome sequencing.","authors":"Asuka Kashiwaba, Asako Mitani, Takumi Sonoda, Naofumi Shigemune, Hiroki Takahashi","doi":"10.1016/j.mimet.2025.107184","DOIUrl":null,"url":null,"abstract":"<p><p>In industrial settings, identifying the source of microbial contamination is crucial for effective microbiological risk assessment. While various strain identification technologies exist, many struggle with practicality, accuracy, and reproducibility. Fourier Transform Infrared Spectroscopy (FT-IR) has emerged as a rapid method, demonstrating a strong correlation with whole-genome sequencing (WGS) for certain bacteria. However, its accuracy for identifying yeast strains has been limited. This study focuses on improving the accuracy of FT-IR for yeast strain identification by optimizing pretreatment conditions. We conducted phylogenetic analyses on Wickerhamomyces anomalus using both WGS single-nucleotide polymorphisms (SNPs) and FT-IR. Although initial FT-IR results were less accurate than WGS, refining the culture and sample preparation conditions led to significant improvements. We tested 16 different conditions, using Euclidean Distances (EDs) and dendrogram comparisons to evaluate discrimination ability, including metrics like the F-measure and adjusted Rand index (ARI). The most accurate and reproducible FT-IR results were achieved with incubation in Sabouraud dextrose (SD) broth aligning closely with WGS results. This optimized FT-IR protocol now allows for rapid and precise strain-level discrimination of W. anomalus, offering a practical tool for tracking contamination sources in industrial environments.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107184"},"PeriodicalIF":1.7000,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of microbiological methods","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1016/j.mimet.2025.107184","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
In industrial settings, identifying the source of microbial contamination is crucial for effective microbiological risk assessment. While various strain identification technologies exist, many struggle with practicality, accuracy, and reproducibility. Fourier Transform Infrared Spectroscopy (FT-IR) has emerged as a rapid method, demonstrating a strong correlation with whole-genome sequencing (WGS) for certain bacteria. However, its accuracy for identifying yeast strains has been limited. This study focuses on improving the accuracy of FT-IR for yeast strain identification by optimizing pretreatment conditions. We conducted phylogenetic analyses on Wickerhamomyces anomalus using both WGS single-nucleotide polymorphisms (SNPs) and FT-IR. Although initial FT-IR results were less accurate than WGS, refining the culture and sample preparation conditions led to significant improvements. We tested 16 different conditions, using Euclidean Distances (EDs) and dendrogram comparisons to evaluate discrimination ability, including metrics like the F-measure and adjusted Rand index (ARI). The most accurate and reproducible FT-IR results were achieved with incubation in Sabouraud dextrose (SD) broth aligning closely with WGS results. This optimized FT-IR protocol now allows for rapid and precise strain-level discrimination of W. anomalus, offering a practical tool for tracking contamination sources in industrial environments.
期刊介绍:
The Journal of Microbiological Methods publishes scholarly and original articles, notes and review articles. These articles must include novel and/or state-of-the-art methods, or significant improvements to existing methods. Novel and innovative applications of current methods that are validated and useful will also be published. JMM strives for scholarship, innovation and excellence. This demands scientific rigour, the best available methods and technologies, correctly replicated experiments/tests, the inclusion of proper controls, calibrations, and the correct statistical analysis. The presentation of the data must support the interpretation of the method/approach.
All aspects of microbiology are covered, except virology. These include agricultural microbiology, applied and environmental microbiology, bioassays, bioinformatics, biotechnology, biochemical microbiology, clinical microbiology, diagnostics, food monitoring and quality control microbiology, microbial genetics and genomics, geomicrobiology, microbiome methods regardless of habitat, high through-put sequencing methods and analysis, microbial pathogenesis and host responses, metabolomics, metagenomics, metaproteomics, microbial ecology and diversity, microbial physiology, microbial ultra-structure, microscopic and imaging methods, molecular microbiology, mycology, novel mathematical microbiology and modelling, parasitology, plant-microbe interactions, protein markers/profiles, proteomics, pyrosequencing, public health microbiology, radioisotopes applied to microbiology, robotics applied to microbiological methods,rumen microbiology, microbiological methods for space missions and extreme environments, sampling methods and samplers, soil and sediment microbiology, transcriptomics, veterinary microbiology, sero-diagnostics and typing/identification.