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Marín S, Freire L, Femenias A, Sant’Ana AS. Use of predictive modelling as tool for prevention of fungal spoilage at different points of the food chain. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2021.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cremonesi P, Garofalo C, Picozzi C, Castiglioni B, Mangieri N, Milanović V, Osimani A, Aquilanti L. Development of quantitative real-time PCR and digital droplet-PCR assays for rapid and early detection of the spoilage yeasts Saccharomycopsis fibuligera and Wickerhamomyces anomalus in bread. Food Microbiol 2021; 101:103894. [PMID: 34579854 DOI: 10.1016/j.fm.2021.103894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/27/2021] [Accepted: 08/25/2021] [Indexed: 11/26/2022]
Abstract
In the present study, for the first time, high sensitive quantitative polymerase chain reaction (qPCR) and digital droplet polymerase chain reaction (ddPCR) assays were developed to detect and quantify total eumycetes with potential application in several food matrices and to specifically determine the level of contamination by Saccharomycopsis fibuligera and Wickerhamomyces anomalus cells directly in bread. Among the candidate target genes used to develop the assays, car1 gene was chosen to detect the two spoilage yeasts S. fibuligera and W. anomalus. The specificity of the PCR assays was tested using purified genomic DNA from 36 bacterial and fungal strains. The sensitivity of the assays was defined by using tenfold serial dilutions of genomic DNA starting from 106 cfu/mL to 1 cfu/mL of S. fibuligera and W. anomalus. Validation of the assays was achieved by enumeration of S. fibuligera and W. anomalus DNA copies from samples of artificially contaminated bread homogenates detecting up to 10 cfu/mL (0.06 ± 0.01 copies/μL) of W. anomalus by using ddPCR. In conclusion, the developed qPCR and ddPCR assays demonstrate strong performance in the early detection of S. fibuligera and W. anomalus in bread, representing promising tools for applying high-throughput approaches to regularly monitor bread quality.
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Affiliation(s)
- Paola Cremonesi
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Consiglio Nazionale delle Ricerche, Via Einstein S/n, 26900, Lodi, Italy
| | - Cristiana Garofalo
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Claudia Picozzi
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Sezione di Microbiologia degli Alimenti e Bioprocessi, Via Celoria 2, 20133, Milano, Italy.
| | - Bianca Castiglioni
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Consiglio Nazionale delle Ricerche, Via Einstein S/n, 26900, Lodi, Italy
| | - Nicola Mangieri
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Sezione di Microbiologia degli Alimenti e Bioprocessi, Via Celoria 2, 20133, Milano, Italy
| | - Vesna Milanović
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Andrea Osimani
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Lucia Aquilanti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
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Debonne E, Meuninck V, Vroman A, Eeckhout M. Influence of environmental growth conditions on chalk yeasts causing bread spoilage. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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The first human report of Hyphopichia burtonii, initially misdiagnosed as sterile peritonitis in a patient on peritoneal dialysis. Med Mycol Case Rep 2021; 33:26-29. [PMID: 34377633 PMCID: PMC8326973 DOI: 10.1016/j.mmcr.2021.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 11/21/2022] Open
Abstract
This is the first human infection caused by Hyphopichia burtonii, resulting in peritonitis in a patient on peritoneal dialysis initially diagnosed as sterile peritonitis, resulting in delayed diagnosis and treatment. This pathogen posed a challenging diagnosis, causing low-grade peritonitis and difficulty to culture with standard bacterial broth. Moreover, automated platforms for pathogenic yeast identification could not specify the species, but broad-range PCR targeting rDNA followed by DNA sequencing successfully solved the etiology.
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Arfken AM, Frey JF, Ramsay TG, Summers KL. Yeasts of Burden: Exploring the Mycobiome-Bacteriome of the Piglet GI Tract. Front Microbiol 2019; 10:2286. [PMID: 31649634 PMCID: PMC6792466 DOI: 10.3389/fmicb.2019.02286] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/19/2019] [Indexed: 12/11/2022] Open
Abstract
Interactions between the bacteria and fungi in the gut microbiome can result in altered nutrition, pathogenicity of infection, and host development, making them a crucial component in host health. Associations between the mycobiome and bacteriome in the piglet gut, in the context of weaning, remain unknown. Weaning is a time of significant stress, dietary changes, microbial alterations, and a predisposition to infection. The loss of animal health and growth makes potential microbial interventions of interest to the swine industry. Recent studies have demonstrated the diversity and development of the microbiome in the gastrointestinal (GI) tract of piglets during weaning, resulting from the dietary and physiological changes. Despite these advances, the role of the mycobiota in piglet health and its contribution to overall microbiome development remains mostly unknown. In this study we investigated the bacteriome and the mycobiome after weaning in the GI tract organs and feces from 35-day old piglets. Following weaning, the α-diversity and amplicon sequence variants (ASVs) counts of the bacteriome increased, proximally to distally, from the stomach to the feces along the GI tract, while the mycobiome α-diversity and ASV counts were highest in the porcine stomach. β-diversity analyses show distinct clusters based on organ type in the bacteriome and mycobiome, but dispersion remained relatively constant in the mycobiome between organ/fecal sites. Bacteroidetes, Firmicutes, and Epsilonbacteraeota were the most abundant bacterial phyla present in the GI tract and feces based on mean taxonomic composition with high variation of composition found in the stomach. In the mycobiome, the dominant phyla were Ascomycota and Basidiomycota, and the stomach mycobiome did not demonstrate the same high level of variation observed in the bacteriome. Potential interactions between genera were found in the lower piglet GI bacteriome and mycobiome with positive correlations found between the fungus, Kazachstania, and several bacterial species, including Lactobacillus. Aspergillus demonstrated negative correlations with the short chain fatty acid-producing bacteria Butyricoccus, Subdoligranulum, and Fusicatenibacter. This study demonstrates the distinct colonization dynamics between fungi and bacteria in the GI tract and feces of piglets directly following weaning and the potential interactions of these microbes in the porcine gut ecosystem.
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Affiliation(s)
- Ann M Arfken
- Animal Biosciences and Biotechnology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Juli Foster Frey
- Animal Biosciences and Biotechnology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Timothy G Ramsay
- Animal Biosciences and Biotechnology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Katie Lynn Summers
- Animal Biosciences and Biotechnology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
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Basak S. Modelling the effect of betel leaf essential oil on germination time of Aspergillus flavus and Penicillium expansum spore population. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Hernández A, Pérez-Nevado F, Ruiz-Moyano S, Serradilla MJ, Villalobos MC, Martín A, Córdoba MG. Spoilage yeasts: What are the sources of contamination of foods and beverages? Int J Food Microbiol 2018; 286:98-110. [PMID: 30056262 DOI: 10.1016/j.ijfoodmicro.2018.07.031] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
Foods and beverages are nutrient-rich ecosystems in which most microorganisms are able to grow. Moreover, several factors, such as physicochemical characteristics, storage temperature, culinary practices, and application of technologies for storage, also define the microbial population of foods and beverages. The yeast population has been well-characterised in fresh and processed fruit and vegetables, dairy products, dry-cured meat products, and beverages, among others. Some species are agents of alteration in different foods and beverages. Since the most comprehensive studies of spoilage yeasts have been performed in the winemaking process, hence, these studies form the thread of the discussion in this review. The natural yeast populations in raw ingredients and environmental contamination in the manufacturing facilities are the main modes by which food contamination occurs. After contamination, yeasts play a significant role in food and beverage spoilage, particularly in the alteration of fermented foods. Several mechanisms contribute to spoilage by yeasts, such as the production of lytic enzymes (lipases, proteases, and cellulases) and gas, utilisation of organic acids, discolouration, and off-flavours. This review addresses the role of yeasts in foods and beverages degradation by considering the modes of contamination and colonisation by yeasts, the yeast population diversity, mechanisms involved, and the analytical techniques for their identification, primarily molecular methods.
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Affiliation(s)
- A Hernández
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain.
| | - F Pérez-Nevado
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain
| | - S Ruiz-Moyano
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain
| | - M J Serradilla
- Área de Vegetales, Centro de Investigaciones Científicas y Tecnológicas de Extremadura (CICYTEX), A5 km 372, 06187 Guadajira, Spain
| | - M C Villalobos
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain
| | - A Martín
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain
| | - M G Córdoba
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain
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Gasaluck P, Mahidsanan T. The consequences of implicit factors as cross-protective stresses on freeze-dried Bacillus subtilis SB-MYP-1 with soybean flour during storage. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.12.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Diversity of microbiota found in coffee processing wastewater treatment plant. World J Microbiol Biotechnol 2017; 33:211. [PMID: 29134289 DOI: 10.1007/s11274-017-2372-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 10/20/2017] [Indexed: 10/18/2022]
Abstract
Cultivable microbiota presents in a coffee semi-dry processing wastewater treatment plant (WTP) was identified. Thirty-two operational taxonomic units (OTUs) were detected, these being 16 bacteria, 11 yeasts and 4 filamentous fungi. Bacteria dominated the microbial population (11.61 log CFU mL- 1), and presented the highest total diversity index when observed in the WTP aerobic stage (Shannon = 1.94 and Simpson = 0.81). The most frequent bacterial species were Enterobacter asburiae, Sphingobacterium griseoflavum, Chryseobacterium bovis, Serratia marcescens, Corynebacterium flavescens, Acetobacter orientalis and Acetobacter indonesiensis; these showed the largest total bacteria populations in the WTP, with approximately 10 log CFU mL- 1. Yeasts were present at 7 log CFU mL- 1 of viable cells, with Hanseniaspora uvarum, Wickerhamomyces anomalus, Torulaspora delbrueckii, Saturnispora gosingensis, and Kazachstania gamospora being the prevalent species. Filamentous fungi were found at 6 log CFU mL- 1, with Fusarium oxysporum the most populous species. The identified species have the potential to act as a biological treatment in the WTP, and the application of them for this purpose must be better studied.
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Choo JH, Hong CP, Lim JY, Seo JA, Kim YS, Lee DW, Park SG, Lee GW, Carroll E, Lee YW, Kang HA. Whole-genome de novo sequencing, combined with RNA-Seq analysis, reveals unique genome and physiological features of the amylolytic yeast Saccharomycopsis fibuligera and its interspecies hybrid. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:246. [PMID: 27872659 PMCID: PMC5106798 DOI: 10.1186/s13068-016-0653-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/22/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Genomic studies on fungal species with hydrolytic activity have gained increased attention due to their great biotechnological potential for biomass-based biofuel production. The amylolytic yeast Saccharomycopsis fibuligera has served as a good source of enzymes and genes involved in saccharification. Despite its long history of use in food fermentation and bioethanol production, very little is known about the basic physiology and genomic features of S. fibuligera. RESULTS We performed whole-genome (WG) de novo sequencing and complete assembly of S. fibuligera KJJ81 and KPH12, two isolates from wheat-based Nuruk in Korea. Intriguingly, the KJJ81 genome (~38 Mb) was revealed as a hybrid between the KPH12 genome (~18 Mb) and another unidentified genome sharing 88.1% nucleotide identity with the KPH12 genome. The seven chromosome pairs of KJJ81 subgenomes exhibit highly conserved synteny, indicating a very recent hybridization event. The phylogeny inferred from WG comparisons showed an early divergence of S. fibuligera before the separation of the CTG and Saccharomycetaceae clades in the subphylum Saccharomycotina. Reconstructed carbon and sulfur metabolic pathways, coupled with RNA-Seq analysis, suggested a marginal Crabtree effect under high glucose and activation of sulfur metabolism toward methionine biosynthesis under sulfur limitation in this yeast. Notably, the lack of sulfate assimilation genes in the S. fibuligera genome reflects a unique phenotype for Saccharomycopsis clades as natural sulfur auxotrophs. Extended gene families, including novel genes involved in saccharification and proteolysis, were identified. Moreover, comparative genome analysis of S. fibuligera ATCC 36309, an isolate from chalky rye bread in Germany, revealed that an interchromosomal translocation occurred in the KPH12 genome before the generation of the KJJ81 hybrid genome. CONCLUSIONS The completely sequenced S. fibuligera genome with high-quality annotation and RNA-Seq analysis establishes an important foundation for functional inference of S. fibuligera in the degradation of fermentation mash. The gene inventory facilitates the discovery of new genes applicable to the production of novel valuable enzymes and chemicals. Moreover, as the first gapless genome assembly in the genus Saccharomycopsis including members with desirable traits for bioconversion, the unique genomic features of S. fibuligera and its hybrid will provide in-depth insights into fungal genome dynamics as evolutionary adaptation.
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Affiliation(s)
- Jin Ho Choo
- Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea
| | - Chang Pyo Hong
- Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea
| | - Jae Yun Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 South Korea
| | - Jeong-Ah Seo
- School of Systems Biomedical Science, Soongsil University, Seoul, 06978 South Korea
| | - Young-Suk Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760 South Korea
| | - Dong Wook Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea
| | - Sin-Gi Park
- Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea
| | - Gir Won Lee
- Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea
| | - Emily Carroll
- School of Systems Biomedical Science, Soongsil University, Seoul, 06978 South Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 South Korea
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea
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Giannone V, Pitino I, Pecorino B, Todaro A, Spina A, Lauro MR, Tomaselli F, Restuccia C. Effects of innovative and conventional sanitizing treatments on the reduction of Saccharomycopsis fibuligera defects on industrial durum wheat bread. Int J Food Microbiol 2016; 235:71-6. [DOI: 10.1016/j.ijfoodmicro.2016.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/21/2016] [Accepted: 07/10/2016] [Indexed: 10/21/2022]
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