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Mugo-Kamiri L, Imungi JK, Njue L, Diiro G, Ombura FLO, Akutse KS, Chrysantus TM, Khamis FM, Subramanian S. Vendors' handling practices of edible long-horned grasshoppers ( Ruspolia differens) products and implications on microbial safety. Front Microbiol 2024; 15:1385433. [PMID: 38770022 PMCID: PMC11102984 DOI: 10.3389/fmicb.2024.1385433] [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: 02/12/2024] [Accepted: 04/08/2024] [Indexed: 05/22/2024] Open
Abstract
Edible grasshopper, Ruspolia ruspolia, has nutritional and cherished cultural and economic importance to people from diverse cultures, particularly in over 20 African countries. It is consumed at home or commercially traded as sautéed, deep-fried, or boiled products. However, there is limited information on the hygiene practices of the vendors and the implications on the microbial safety of the final product. This research aimed at assessing the food safety knowledge, handling practices and shelf life of edible long-horned grasshopper products among vendors and the microbial safety of ready-to-eat products sold in 12 different markets in Uganda. Samples of raw, deep-fried and boiled grasshoppers were randomly collected from 74 vendors (62% street and 38% market vendors) and subjected to microbial analysis. Over 85% of the vendors surveyed had no public health food handler's certificate and >95% had limited post-harvest handling knowledge. Total aerobic bacteria (7.30-10.49 Log10 cfu/g), Enterobacteriaceae (5.53-8.56 Log10 cfu/g), yeasts and molds (4.96-6.01 Log10 cfu/g) total counts were significantly high and above the acceptable Codex Alimentarius Commission and Food Safety Authority of Ireland (FSAI) limits for ready-to-eat food products. Eight key pathogenic bacteria responsible for foodborne diseases were detected and these isolates were characterized as Bacillus cereus, Hafnia alvei, Serratia marcescens, Staphylococcus aureus, S. xylosus, S. scuiri, S. haemolyticus, and Pseudomonas aeruginosa. Findings from this study highlight the urgent need to create local and national food safety policies for the edible grasshopper "nsenene" subsector to regulate and guide street and market vending along the value chain, to prevent the transmission of foodborne diseases to consumers.
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Affiliation(s)
- Loretta Mugo-Kamiri
- International Centre for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
- Department of Food Science Nutrition and Technology, Faculty of Agriculture, University of Nairobi, Nairobi, Kenya
| | - Jasper K. Imungi
- Department of Food Science Nutrition and Technology, Faculty of Agriculture, University of Nairobi, Nairobi, Kenya
| | - Lucy Njue
- Department of Food Science Nutrition and Technology, Faculty of Agriculture, University of Nairobi, Nairobi, Kenya
| | - Gracious Diiro
- International Centre for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | | | - Komivi S. Akutse
- International Centre for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Tanga M. Chrysantus
- International Centre for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Fathiya M. Khamis
- International Centre for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Sevgan Subramanian
- International Centre for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
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Rosa CA, Lachance MA, Limtong S, Santos ARO, Landell MF, Gombert AK, Morais PB, Sampaio JP, Gonçalves C, Gonçalves P, Góes-Neto A, Santa-Brígida R, Martins MB, Janzen DH, Hallwachs W. Yeasts from tropical forests: Biodiversity, ecological interactions, and as sources of bioinnovation. Yeast 2023; 40:511-539. [PMID: 37921426 DOI: 10.1002/yea.3903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023] Open
Abstract
Tropical rainforests and related biomes are found in Asia, Australia, Africa, Central and South America, Mexico, and many Pacific Islands. These biomes encompass less than 20% of Earth's terrestrial area, may contain about 50% of the planet's biodiversity, and are endangered regions vulnerable to deforestation. Tropical rainforests have a great diversity of substrates that can be colonized by yeasts. These unicellular fungi contribute to the recycling of organic matter, may serve as a food source for other organisms, or have ecological interactions that benefit or harm plants, animals, and other fungi. In this review, we summarize the most important studies of yeast biodiversity carried out in these biomes, as well as new data, and discuss the ecology of yeast genera frequently isolated from tropical forests and the potential of these microorganisms as a source of bioinnovation. We show that tropical forest biomes represent a tremendous source of new yeast species. Although many studies, most using culture-dependent methods, have already been carried out in Central America, South America, and Asia, the tropical forest biomes of Africa and Australasia remain an underexplored source of novel yeasts. We hope that this review will encourage new researchers to study yeasts in unexplored tropical forest habitats.
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Affiliation(s)
- Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Savitree Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Biodiversity Center Kasetsart University, Kasetsart University, Bangkok, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok, Thailand
| | - Ana R O Santos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Melissa F Landell
- Setor de Genética, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Andreas K Gombert
- Department of Engineering and Food Technology, School of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Paula B Morais
- Laboratório de Microbiologia Ambiental e Biotecnologia, Campus de Palmas, Universidade Federal do Tocantins, Palmas, Tocantins, Brazil
| | - José P Sampaio
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Carla Gonçalves
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Aristóteles Góes-Neto
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Francisco EC, Ribeiro FDC, Almeida Junior JN, Pedoni DB, da Matta DA, Dolande M, Melo ASDA, Lima RF, Aquino VR, Corzo-León DE, Zurita J, Cortes JA, Nucci M, Colombo AL. Emergence of cryptic species and clades of Meyerozyma guilliermondii species complex exhibiting limited in vitro susceptibility to antifungals in patients with candidemia. Microbiol Spectr 2023; 11:e0511522. [PMID: 37698428 PMCID: PMC10580822 DOI: 10.1128/spectrum.05115-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/11/2023] [Indexed: 09/13/2023] Open
Abstract
Members of the Meyerozyma guilliermondii species complex are able to cause superficial and life-threatening systemic infections with low susceptibility to azoles and echinocandins. We tested 130 bloodstream M. guilliermondii complex isolates collected from eight Latin American medical centers over 18 years (period 1 = 2000-2008 and period 2 = 2009-2018) to investigate trends in species distribution and antifungal resistance. The isolates were identified by rDNA ITS region sequencing, and antifungal susceptibility tests were performed against fluconazole, voriconazole, anidulafungin, and amphotericin B using the CLSI microbroth method. M. guilliermondii sensu stricto (s.s.; n = 116) was the most prevalent species, followed by Meyerozyma caribbica (n = 12) and Meyerozyma carpophila (n = 2). Based on rDNA ITS identification, three clades within M. guilliermondii sensu stricto were characterized (clade 1 n = 94; clade 2 n = 19; and clade 3 n = 3). In the second period of study, we found a substantial increment in the isolation of M. caribbica (3.4% versus 13.8%; P = 0.06) and clade 2 M. guilliermondii s.s. exhibiting lower susceptibility to one or more triazoles. IMPORTANCE Yeast-invasive infections play a relevant role in human health, and there is a concern with the emergence of non-Candida pathogens causing disease worldwide. There is a lack of studies addressing the prevalence and antifungal susceptibility of different species within the M. guilliermondii complex that cause invasive infections. We evaluated 130 episodes of M. guilliermondii species complex candidemia documented in eight medical centers over 18 years. We detected the emergence of less common species within the Meyerozyma complex causing candidemia and described a new clade of M. guilliermondii with limited susceptibility to triazoles. These results support the relevance of continued global surveillance efforts to early detect, characterize, and report emergent fungal pathogens exhibiting limited susceptibility to antifungals.
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Affiliation(s)
- Elaine Cristina Francisco
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Felipe de Camargo Ribeiro
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - João Nobrega Almeida Junior
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Diego Betto Pedoni
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Daniel Archimedes da Matta
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maribel Dolande
- Department of Mycology, Instituto Nacional de Higiene Rafael Rangel, Caracas, Venezuela
| | - Analy Salles de Azevedo Melo
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ricardo Ferreira Lima
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Dora E Corzo-León
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Jeannete Zurita
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
- Facultad de Medicina, Pontificia Universidad Catolica del Ecuador, Quito, Ecuador
| | - Jorge Alberto Cortes
- Facultad de Medicina, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
| | - Marcio Nucci
- Departamento de Clínica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Arnaldo Lopes Colombo
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
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Wu N, Wu Y, Chu Y, Ren Z, Li H, Rong C, Yang M, Jiang N, Jiang Y, Chen J, Zhang J, Tian S. The first rare case of Candida palmioleophila infection reported in China and its genomic evolution in a human host environment. Front Microbiol 2023; 14:1165721. [PMID: 37664129 PMCID: PMC10469324 DOI: 10.3389/fmicb.2023.1165721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/13/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Candida palmioleophila is a rare human pathogenic fungus, which has been poorly characterized at the genome level. In this study, we reported the first fatal case of C. palmioleophila infection in China and investigate the microevolution of C. palmioleophila in the human host environment. Methods A series of C. palmioleophila stains were collected from the patient at different time points for routine microbial and drug sensitivity testing. The first C. palmioleophila isolate 07202534 was identified by de novo whole genome sequencing. The in vitro and in vivo genetic evolutionary characteristics of C. palmioleophila were discussed based on the analysis of bioinformatics data. Results The six C. palmioleophila isolates displayed dose-dependent sensitivity to fluconazole. The C. palmioleophila genome contained homologous genes such as CDR1 and MDR1, which were recognized to be related to azole resistance. In addition, amino acid variation was detected at F105L and other important sites of ERG11. In addition, the mean divergence time between C. palmioleophila and Scheffersomyces stipites CBS 6054 was 406.04 million years, indicating that C. palmioleophila originated earlier than its closest relative. In addition, the six strains of C. palmioleophila isolated form the patient had higher homology and fewer mutation sites, which indicated the stability in C. palmioleophila genome. We also found that C. palmioleophila had a wide natural niche and may evolve slowly. Discussion We believe that this study will contribute to improve our understanding of the genetic evolution, pathogenicity, and drug resistance of C. palmioleophila and will aid in the prevention and control of its spread.
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Affiliation(s)
- Na Wu
- Department of Infectious Diseases, The First Hospital of China Medical University, Shenyang, China
| | - Yusheng Wu
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Yunzhuo Chu
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Zhihui Ren
- Department of Intensive Care Unit, Shenyang Fourth People’s Hospital of China Medical University, Shenyang, China
| | - Hailong Li
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Chen Rong
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Min Yang
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Ning Jiang
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Yanyan Jiang
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Jingjing Chen
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Jingping Zhang
- Department of Infectious Diseases, The First Hospital of China Medical University, Shenyang, China
| | - Sufei Tian
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
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5
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Larcombe DE, Bohovych IM, Pradhan A, Ma Q, Hickey E, Leaves I, Cameron G, Avelar GM, de Assis LJ, Childers DS, Bain JM, Lagree K, Mitchell AP, Netea MG, Erwig LP, Gow NAR, Brown AJP. Glucose-enhanced oxidative stress resistance-A protective anticipatory response that enhances the fitness of Candida albicans during systemic infection. PLoS Pathog 2023; 19:e1011505. [PMID: 37428810 PMCID: PMC10358912 DOI: 10.1371/journal.ppat.1011505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 07/20/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023] Open
Abstract
Most microbes have developed responses that protect them against stresses relevant to their niches. Some that inhabit reasonably predictable environments have evolved anticipatory responses that protect against impending stresses that are likely to be encountered in their niches-termed "adaptive prediction". Unlike yeasts such as Saccharomyces cerevisiae, Kluyveromyces lactis and Yarrowia lipolytica and other pathogenic Candida species we examined, the major fungal pathogen of humans, Candida albicans, activates an oxidative stress response following exposure to physiological glucose levels before an oxidative stress is even encountered. Why? Using competition assays with isogenic barcoded strains, we show that "glucose-enhanced oxidative stress resistance" phenotype enhances the fitness of C. albicans during neutrophil attack and during systemic infection in mice. This anticipatory response is dependent on glucose signalling rather than glucose metabolism. Our analysis of C. albicans signalling mutants reveals that the phenotype is not dependent on the sugar receptor repressor pathway, but is modulated by the glucose repression pathway and down-regulated by the cyclic AMP-protein kinase A pathway. Changes in catalase or glutathione levels do not correlate with the phenotype, but resistance to hydrogen peroxide is dependent on glucose-enhanced trehalose accumulation. The data suggest that the evolution of this anticipatory response has involved the recruitment of conserved signalling pathways and downstream cellular responses, and that this phenotype protects C. albicans from innate immune killing, thereby promoting the fitness of C. albicans in host niches.
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Affiliation(s)
- Daniel E. Larcombe
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
- Medical Research Council Centre for Medical Mycology, University of Exeter, School of Biosciences, Geoffrey Pope Building, Exeter, United Kingdom
| | - Iryna M. Bohovych
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Arnab Pradhan
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
- Medical Research Council Centre for Medical Mycology, University of Exeter, School of Biosciences, Geoffrey Pope Building, Exeter, United Kingdom
| | - Qinxi Ma
- Medical Research Council Centre for Medical Mycology, University of Exeter, School of Biosciences, Geoffrey Pope Building, Exeter, United Kingdom
| | - Emer Hickey
- Medical Research Council Centre for Medical Mycology, University of Exeter, School of Biosciences, Geoffrey Pope Building, Exeter, United Kingdom
| | - Ian Leaves
- Medical Research Council Centre for Medical Mycology, University of Exeter, School of Biosciences, Geoffrey Pope Building, Exeter, United Kingdom
| | - Gary Cameron
- Rowett Institute, School of Medicine Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Gabriela M. Avelar
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Leandro J. de Assis
- Medical Research Council Centre for Medical Mycology, University of Exeter, School of Biosciences, Geoffrey Pope Building, Exeter, United Kingdom
| | - Delma S. Childers
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Judith M. Bain
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Katherine Lagree
- Department of Microbiology, Biosciences Building, University of Georgia, Athens, Georgia, United States of America
| | - Aaron P. Mitchell
- Department of Microbiology, Biosciences Building, University of Georgia, Athens, Georgia, United States of America
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Department for Immunology & Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Lars P. Erwig
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
- Johnson-Johnson Innovation, EMEA Innovation Centre, One Chapel Place, London, United Kingdom
| | - Neil A. R. Gow
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
- Medical Research Council Centre for Medical Mycology, University of Exeter, School of Biosciences, Geoffrey Pope Building, Exeter, United Kingdom
| | - Alistair J. P. Brown
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
- Medical Research Council Centre for Medical Mycology, University of Exeter, School of Biosciences, Geoffrey Pope Building, Exeter, United Kingdom
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Félix CR, Nascimento BEDS, Valente P, Landell MF. Different plant compartments, different yeasts: the example of the bromeliad phyllosphere. Yeast 2022; 39:363-400. [PMID: 35715939 DOI: 10.1002/yea.3804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/14/2022] [Accepted: 06/14/2022] [Indexed: 11/09/2022] Open
Abstract
The plant phyllosphere is one of the largest sources of microorganisms, including yeasts. In bromeliads, the knowledge of yeasts is dispersed and still incipient. To understand the extent of our knowledge on the subject, this review proposes to compile and synthesize existing knowledge, elucidating possible patterns, biotechnological and taxonomic potentials, bringing to light new knowledge, and identifying information gaps. For such, we systematically review scientific production on yeasts in bromeliads using various databases. The results indicated that the plant compartments flowers, fruits, leaves, and water tank (phytotelma) have been studied when focusing on the yeast community in the bromeliad phyllosphere. More than 180 species of yeasts and yeast-like fungi were recorded from the phyllosphere, 70% were exclusively found in one of these four compartments and only 2% were shared among all. In addition, most of the community had a low frequency of occurrence, and approximately half of the species had a single record. Variables such as bromeliad subfamilies and functional types, as well as plant compartments, were statistically significant, though inconclusive and with low explanatory power. At least 50 yeast species with some biotechnological potentials have been isolated from bromeliads. More than 90% of these species were able to produce extracellular enzymes. In addition, other biotechnological applications have also been recorded. Moreover, new species have been described, though yeasts were only exploited in approximately 1% of the existing bromeliads species, which highlights that there is still much to be explored. Nevertheless, it appears that we are still far from recovering the completeness of the diversity of yeasts in this host. Furthermore, bromeliads proved to be a good ecological model for prospecting new yeasts and for studies on the interaction between plants and yeasts. In addition, the yeast community diverged among plant compartments, establishing bromeliads as a microbiologically complex and heterogeneous mosaic. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ciro Ramon Félix
- Universidade Federal de Alagoas, Instituto de Ciências Biológicas e da Saúde, Maceió, AL, Brazil.,Programa de Pós-graduação em Diversidade Biológica e Conservação nos Trópicos, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | | | - Patrícia Valente
- Universidade Federal do Rio Grande do Sul, Departamento de Microbiologia, Imunologia e Parasitologia, Porto Alegre, RS, Brazil
| | - Melissa Fontes Landell
- Universidade Federal de Alagoas, Instituto de Ciências Biológicas e da Saúde, Maceió, AL, Brazil
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Chisanga M, Muhamadali H, McDougall D, Xu Y, Lockyer N, Goodacre R. Metabolism in action: stable isotope probing using vibrational spectroscopy and SIMS reveals kinetic and metabolic flux of key substrates. Analyst 2021; 146:1734-1746. [PMID: 33465215 DOI: 10.1039/d0an02319a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Microbial communities play essential functions which drive various ecosystems supporting animal and aquatic life. However, linking bacteria with specific metabolic functions is difficult, since microbial communities consist of numerous and phylogenetically diverse microbes. Stable isotope probing (SIP) combined with single-cell tools has emerged as a novel culture-independent strategy for unravelling microbial metabolic roles and intertwined interactions in complex communities. In this study, we applied Raman and Fourier-transform infrared (FT-IR) spectroscopies, secondary ion mass spectrometry (SIMS) with SIP to probe the rate of 13C incorporation in Escherichia coli at 37 and 25 °C. Our results indicate quantitative enrichment and flow of 13C into E. coli at various time points. Multivariate and univariate analyses of Raman and FT-IR data demonstrated distinctive 13C concentration-dependent trends that were due to vibrational bands shifting to lower frequencies and these shifts were a result of incubation time and metabolic rate. SIMS results were in complete agreement with the spectroscopy findings, and confirmed the detected levels of 13C incorporation into microbial biomass at the investigated conditions. Having established that FT-IR and Raman spectroscopy with SIP can measure metabolism kinetics in this simple system, we have applied the kinetics concept to study the metabolism of phenol by Pseudomonas putida and metabolic interactions within a two-species consortia with E. coli that could not degrade phenol. Raman spectroscopy combined with SIP identified quantitative shifts in P. putida due to temporal assimilation of phenol. Although E. coli was unable to grow on phenol, in co-culture with P. putida, general metabolic probing using deuterated water for SIP revealed that E. coli displayed increasing metabolic activity, presumably due to cross feeding from metabolites generated by P. putida. This study clearly demonstrates that Raman and FT-IR combined with SIP provide rapid and sensitive detection of carbon incorporation rates and microbial interactions. These novel findings may guide the identification of primary substrate consumers in complex microbial communities in situ, which is a key step towards the characterisation of novel genes, enzymes and metabolic flux analysis in microbial consortia.
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Affiliation(s)
- Malama Chisanga
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
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8
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Preliminary Studies on Fungal Contamination of Two Rupestrian Churches from Matera (Southern Italy). SUSTAINABILITY 2020. [DOI: 10.3390/su12176988] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Sassi, a UNESCO World Heritage Site and its rupestrian churches, are richly decorated and visited by thousands of visitors every year. It is important to preserve this heritage which shows signs of deterioration due to abiotic and/or biotic factors. Aiming to carry out in the future an environmental-friendly restoration, a screening of the fungi present on walls and frescoes of two rupestrian churches “Santa Lucia alle Malve” and “La Madonna dei derelitti” located, respectively, in the “Sasso Caveoso” and in the “Sasso Barisano” was performed. Isolation and characterization of fungal species from investigated sites was carried out. Total genomic DNA (gDNA) was extracted from pure fungal cultures and subsequently utilized in PCRs using primers that amplify a portion of the ribosomal DNA (ITS5/ITS4) or the β-tubulin gene (Bt2a/Bt2b). The amplicons were directly sequenced. Obtained nucleotide sequences were compared to those present in the GenBank (NCBI) showing a very high similarity (99–100%) with the following species: Parengyodontium album, Alternaria alternata, Cladosporium cladosporioides, Lecanicillium psalliotae, Meyerozyma guilliermondii and Botryotrichum atrogriseum. All sequences from this study were deposited in the EMBL database. Detailed knowledge about fungi isolated from stone is indispensable not only to counter/reduce the structural and aesthetic damage but also to protect the health of both guardians and visitors who may develop different pathologies due to the spores diffused in the environment.
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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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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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11
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Ramírez-Castrillón M, Usman LM, Silva-Bedoya LM, Osorio-Cadavid E. Dominant yeasts associated to mango (Mangifera indica) and rose apple (Syzygium malaccense) fruit pulps investigated by culture-based methods. AN ACAD BRAS CIENC 2019; 91:e20190052. [PMID: 31800704 DOI: 10.1590/0001-3765201920190052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/02/2019] [Indexed: 05/30/2023] Open
Abstract
The biotechnological potential of yeasts associated to different habitats in Colombia has been poorly studied, especially the yeasts associated with different plant structures. Fruit pulps are interesting substrates mainly for the growth of yeast species, that can positively affect the productivity and quality of some bioeconomic species. Therefore, the objective of this study was to identify the dominant yeast species associated with mango and rose apple fruit pulps in Cali, Colombia. A total of 90 isolates were obtained, which were grouped considering their colony morphology. The D1/D2 domain of the large ribosomal RNA gene (LSU rRNA gene) or internal transcribed spacer (ITS) 1, ribosomal gene 5.8S and ITS 2 (ITS) regions of one to several representative isolates from each group was sequenced and compared with type strains for identification. The species Hanseniaspora thailandica, H. opuntiae and Clavispora lusitaniae were reported as shared by both fruits, specific for rose apple (H. uvarum, Pichia terricola, Rhodosporidiobolus ruineniae and Candida albicans), or for Mango (Meyerozyma caribbica, M. guilliermondii, C. natalensis, Aureobasidium pullulans, Pichia sp., Saturnispora diversa and C. jaroonii). Two morphotypes were not identified at the taxonomic level of species and were reported as candidates for new species, belonging to the genera Wickerhamomyces and Pichia.
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Affiliation(s)
| | - Luisa M Usman
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Calle 13, 100-00 Cali, Valle del Cauca, Colombia
| | - Lina M Silva-Bedoya
- Maestría en Ciencias Biotecnología, Universidad Nacional de Colombia, sede Medellín, Carrera 65, 59A-110 Medellín, Antioquia, Colombia
| | - Esteban Osorio-Cadavid
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Calle 13, 100-00 Cali, Valle del Cauca, Colombia
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12
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Xylitol Production: Identification and Comparison of New Producing Yeasts. Microorganisms 2019; 7:microorganisms7110484. [PMID: 31652879 PMCID: PMC6920771 DOI: 10.3390/microorganisms7110484] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/14/2019] [Indexed: 01/31/2023] Open
Abstract
Xylitol is a sugar alcohol with five carbons that can be used in the pharmaceutical and food industries. It is industrially produced by chemical route; however, a more economical and environmentally friendly production process is of interest. In this context, this study aimed to select wild yeasts able to produce xylitol and compare their performance in sugarcane bagasse hydrolysate. For this, 960 yeast strains, isolated from soil, wood, and insects have been prospected and selected for the ability to grow on defined medium containing xylose as the sole carbon source. A total of 42 yeasts was selected and their profile of sugar consumption and metabolite production were analyzed in microscale fermentation. The six best xylose-consuming strains were molecularly identified as Meyerozyma spp. The fermentative kinetics comparisons on defined medium and on sugarcane bagasse hydrolysate showed physiological differences among these strains. Production yields vary from YP/S = 0.25 g/g to YP/S = 0.34 g/g in defined medium and from YP/S = 0.41 g/g to YP/S = 0.60 g/g in the hydrolysate. Then, the xylitol production performance of the best xylose-consuming strain obtained in the screening, which was named M. guilliermondii B12, was compared with the previously reported xylitol producing yeasts M. guilliermondii A3, Spathaspora sp. JA1, and Wickerhamomyces anomalus 740 in sugarcane bagasse hydrolysate under oxygen-limited conditions. All the yeasts were able to metabolize xylose, but W. anomalus 740 showed the highest xylitol production yield, reaching a maximum of 0.83 g xylitol/g of xylose in hydrolysate. The screening strategy allowed identification of a new M. guilliermondii strain that efficiently grows in xylose even in hydrolysate with a high content of acetic acid (~6 g/L). In addition, this study reports, for the first time, a high-efficient xylitol producing strain of W. anomalus, which achieved, to the best of our knowledge, one of the highest xylitol production yields in hydrolysate reported in the literature.
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13
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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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14
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Trichez D, Steindorff AS, Soares CEVF, Formighieri EF, Almeida JRM. Physiological and comparative genomic analysis of new isolated yeasts Spathaspora sp. JA1 and Meyerozyma caribbica JA9 reveal insights into xylitol production. FEMS Yeast Res 2019; 19:5480466. [DOI: 10.1093/femsyr/foz034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 04/25/2019] [Indexed: 12/30/2022] Open
Abstract
ABSTRACT
Xylitol is a five-carbon polyol of economic interest that can be produced by microbial xylose reduction from renewable resources. The current study sought to investigate the potential of two yeast strains, isolated from Brazilian Cerrado biome, in the production of xylitol as well as the genomic characteristics that may impact this process. Xylose conversion capacity by the new isolates Spathaspora sp. JA1 and Meyerozyma caribbica JA9 was evaluated and compared with control strains on xylose and sugarcane biomass hydrolysate. Among the evaluated strains, Spathaspora sp. JA1 was the strongest xylitol producer, reaching product yield and productivity as high as 0.74 g/g and 0.20 g/(L.h) on xylose, and 0.58 g/g and 0.44 g/(L.h) on non-detoxified hydrolysate. Genome sequences of Spathaspora sp. JA1 and M. caribbica JA9 were obtained and annotated. Comparative genomic analysis revealed that the predicted xylose metabolic pathway is conserved among the xylitol-producing yeasts Spathaspora sp. JA1, M. caribbica JA9 and Meyerozyma guilliermondii, but not in Spathaspora passalidarum, an efficient ethanol-producing yeast. Xylitol-producing yeasts showed strictly NADPH-dependent xylose reductase and NAD+-dependent xylitol-dehydrogenase activities. This imbalance of cofactors favors the high xylitol yield shown by Spathaspora sp. JA1, which is similar to the most efficient xylitol producers described so far.
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Affiliation(s)
- Débora Trichez
- Embrapa Agroenergia. Parque Estação Biológica, PqEB – W3 Norte Final, Postal code 70.770–901, Brasília-DF, Brazil
| | - Andrei S Steindorff
- Embrapa Agroenergia. Parque Estação Biológica, PqEB – W3 Norte Final, Postal code 70.770–901, Brasília-DF, Brazil
| | - Carlos E V F Soares
- Embrapa Agroenergia. Parque Estação Biológica, PqEB – W3 Norte Final, Postal code 70.770–901, Brasília-DF, Brazil
- Graduate Program in Chemical and Biological Technologies, Institute of Chemistry, University of Brasília, Campus Darcy Ribeiro, Postal code 70.910-900, Brasília-DF, Brazil
| | - Eduardo F Formighieri
- Embrapa Agroenergia. Parque Estação Biológica, PqEB – W3 Norte Final, Postal code 70.770–901, Brasília-DF, Brazil
| | - João R M Almeida
- Embrapa Agroenergia. Parque Estação Biológica, PqEB – W3 Norte Final, Postal code 70.770–901, Brasília-DF, Brazil
- Graduate Program in Chemical and Biological Technologies, Institute of Chemistry, University of Brasília, Campus Darcy Ribeiro, Postal code 70.910-900, Brasília-DF, Brazil
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15
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Feliciano RJ, Estilo EEC, Nakano H, Gabriel AA. Ultraviolet-C resistance of selected spoilage yeasts in orange juice. Food Microbiol 2019; 78:73-81. [DOI: 10.1016/j.fm.2018.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/17/2018] [Accepted: 10/07/2018] [Indexed: 01/29/2023]
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16
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Corte L, Casagrande Pierantoni D, Tascini C, Roscini L, Cardinali G. Biofilm Specific Activity: A Measure to Quantify Microbial Biofilm. Microorganisms 2019; 7:microorganisms7030073. [PMID: 30866438 PMCID: PMC6463164 DOI: 10.3390/microorganisms7030073] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/23/2019] [Accepted: 03/04/2019] [Indexed: 12/21/2022] Open
Abstract
Microbes growing onto solid surfaces form complex 3-D biofilm structures characterized by the production of extracellular polymeric compounds and an increased resistance to drugs. The quantification of biofilm relays currently on a number of different approaches and techniques, often leading to different evaluations of the ability to form biofilms of the studied microbial strains. Measures of biofilm biomass were carried out with crystal violet (CV) and a direct reading at 405 nm, whereas the activity was assessed with the XTT ((2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide) method. The strains of four pathogenic species of the genus Candida (C. albicans, C. glabrata, C. parapsilosis and C. tropicalis) and of Staphylococcus aureus were employed to determine the effective relatedness among techniques and the specific activity of the biofilm, as a ratio between the XTT and the CV outcomes. Since the ability to form biomass and to be metabolically active are not highly related, their simultaneous use allowed for a categorization of the strains. This classification is putatively amenable of further study by comparing the biofilm type and the medical behavior of the strains.
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Affiliation(s)
- Laura Corte
- Department of Pharmaceutical Sciences⁻Microbiology, University of Perugia, 06123 Perugia, Italy.
| | | | - Carlo Tascini
- First Division of Infectious Diseases, Cotugno Hospital, 80181 Naples, Italy.
| | - Luca Roscini
- CEMIN-Excellence Research Center, University of Perugia, 06123 Perugia, Italy.
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences⁻Microbiology, University of Perugia, 06123 Perugia, Italy.
- CEMIN-Excellence Research Center, University of Perugia, 06123 Perugia, Italy.
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17
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Feliciano RJ, Estilo EEC, Nakano H, Gabriel AA. Decimal reduction energies of UV-C-irradiated spoilage yeasts in coconut liquid endosperm. Int J Food Microbiol 2019; 290:170-179. [PMID: 30340115 DOI: 10.1016/j.ijfoodmicro.2018.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/20/2018] [Accepted: 10/10/2018] [Indexed: 11/19/2022]
Abstract
The ultraviolet-C (UV-C) decimal reduction energy (DUV-C) values of 17 spoilage yeasts and their composited inoculum were determined in coconut liquid endosperm (pH 5.26, 5.8 °Brix, 0.04% malic acid, 0.17% w/v insoluble solids). Growth kinetic parameters of all the test yeast strains were first established to standardize the growth stage of the cells prior to inactivation studies. Approximately 4.0 to 5.0 log CFU/mL cells in the mid-stationary growth phase (30.3 to 39.9 h, 25 °C) were suspended in 4 mL turbulent flowing juice and subjected to UV-C irradiation at a surface irradiance range of 3.42 to 4.99 mW/cm2. Survivor populations after exposure to predetermined UV-C energy were enumerated, and were used to derive the DUV-C values using the linear regression and Baranyi and Roberts (1994) model fitting. Results show that the yeast strains exhibited either log-linear or biphasic inactivation behavior with inactivation lag. The most UV-C resistant spoilage yeast was found to be Cryptococcus albidus (LJY1) with DUV-C values of 122.72 and 214.89 mJ/cm2 determined from linear regression and model-fitting, respectively. The least UV-C resistant was Torulaspora delbrueckii (LYJ5) with a DUV-C of 17.34 (linear regression) and 17.35 mJ/cm2 (model-fitting). The DUV-C values determined from the model fitting were generally greater than those calculated from linear regression, although only those determined for C. albidus were significantly different. To the investigators' knowledge, this is the first report of the UV-C inactivation kinetic parameters of Kluyveromyces marxianus, Trichosporon cutaneum, Pichia anomala, and Meyerozyma guilliermondii and C. albidus in coconut liquid endosperm. The results of this study can be used in the establishment and validation of UV-C process schedules for coconut liquid endosperm and other similar commodities.
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Affiliation(s)
- Rodney J Feliciano
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Nutrition, College of Home Economics, Alonso Hall, A. Ma. Regidor Street, University of the Philippines Diliman, 1101 Quezon City, Philippines
| | - Emil Emmanuel C Estilo
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Nutrition, College of Home Economics, Alonso Hall, A. Ma. Regidor Street, University of the Philippines Diliman, 1101 Quezon City, Philippines
| | - Hiroyuki Nakano
- Laboratory of Food Microbiology and Hygiene, Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, 1-4-4, Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Alonzo A Gabriel
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Nutrition, College of Home Economics, Alonso Hall, A. Ma. Regidor Street, University of the Philippines Diliman, 1101 Quezon City, Philippines.
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18
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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: 63] [Impact Index Per Article: 10.5] [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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19
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Romero J, Joo Y, Park J, Tiezzi F, Gutierrez-Rodriguez E, Castillo M. Bacterial and fungal communities, fermentation, and aerobic stability of conventional hybrids and brown midrib hybrids ensiled at low moisture with or without a homo- and heterofermentative inoculant. J Dairy Sci 2018; 101:3057-3076. [DOI: 10.3168/jds.2017-13754] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/28/2017] [Indexed: 11/19/2022]
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20
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Yeast Biofilm as a Bridge Between Medical and Environmental Microbiology Across Different Detection Techniques. Infect Dis Ther 2018; 7:27-34. [PMID: 29549654 PMCID: PMC5856731 DOI: 10.1007/s40121-018-0191-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Indexed: 10/25/2022] Open
Abstract
Medical and environmental microbiology have two distinct, although very short, histories stemming, the first from the pioneering works of Sommelweiss, Pasteur, Lister and Koch, the second mainly from the studies of Bejerink and Winogradsky. These two branches of microbiology evolved and specialized separately producing distinct communities and evolving rather different approaches and techniques. The evidence accumulated in recent decades indicate that indeed most of the medically relevant microorganisms have a short circulation within the nosocomial environment and a larger one involving the external, i.e. non-nosocomial, and the hospital environments. This evidence suggests that the differences between approaches should yield to a convergent approach aimed at solving the increasing problem represented by infectious diseases for the increasingly less resistant human communities. Microbial biofilm is one of the major systems used by these microbes to resist the harsh conditions of the natural and anthropic environment, and the even worse ones related to medical settings. This paper presents a brief outline of the converging interest of both environmental and medical microbiology toward a better understanding of microbial biofilm and of the various innovative techniques that can be employed to characterize, in a timely and quantitative manner, these complex structures. Among these, micro-Raman along with micro-Brillouin offer high hopes of describing biofilms both at the subcellular and supercellular level, with the possibility of characterizing the various landscapes of the different biofilms. The possibility of adding a taxonomic identification of the cells comprising the biofilm is a complex aspect presenting several technical issues that will require further studies in the years to come.
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21
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Morales‐Cruz A, Allenbeck G, Figueroa‐Balderas R, Ashworth VE, Lawrence DP, Travadon R, Smith RJ, Baumgartner K, Rolshausen PE, Cantu D. Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk disease complex. MOLECULAR PLANT PATHOLOGY 2018; 19:490-503. [PMID: 28218463 PMCID: PMC6638111 DOI: 10.1111/mpp.12544] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/13/2017] [Indexed: 05/20/2023]
Abstract
Grapevines, like other perennial crops, are affected by so-called 'trunk diseases', which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development, especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i.e. metatranscriptomics) approach that could monitor simultaneously the virulence activities of multiple GTPs in planta. The availability of annotated genomes for the most relevant co-infecting GTPs in diseased grapevine wood provided the unprecedented opportunity to generate a multi-species reference for the mapping and quantification of DNA and RNA sequencing reads. We first evaluated popular sequence read mappers using permutations of multiple simulated datasets. Alignment parameters of the selected mapper were optimized to increase the specificity and sensitivity for its application to metagenomics and metatranscriptomics analyses. Initial testing on grapevine wood experimentally inoculated with individual GTPs confirmed the validity of the method. Using naturally infected field samples expressing a variety of trunk disease symptoms, we show that our approach provides quantitative assessments of species composition, as well as genome-wide transcriptional profiling of potential virulence factors, namely cell wall degradation, secondary metabolism and nutrient uptake for all co-infecting GTPs.
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Affiliation(s)
- Abraham Morales‐Cruz
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | - Gabrielle Allenbeck
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | | | - Vanessa E. Ashworth
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCA92521USA
| | - Daniel P. Lawrence
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Renaud Travadon
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Rhonda J. Smith
- University of California Cooperative Extension, Sonoma CountySanta RosaCA95403USA
| | - Kendra Baumgartner
- United States Department of Agriculture ‐ Agricultural Research ServiceCrops Pathology and Genetics Research UnitDavisCA95616USA
| | - Philippe E. Rolshausen
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCA92521USA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
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Cardinali F, Taccari M, Milanović V, Osimani A, Polverigiani S, Garofalo C, Foligni R, Mozzon M, Zitti S, Raffaelli N, Clementi F, Aquilanti L. Yeast and mould dynamics in Caciofiore della Sibilla cheese coagulated with an aqueous extract ofCarlina acanthifoliaAll. Yeast 2016; 33:403-14. [DOI: 10.1002/yea.3168] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/23/2016] [Indexed: 12/17/2022] Open
Affiliation(s)
- Federica Cardinali
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
| | - Manuela Taccari
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
| | - Vesna Milanović
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
| | - Andrea Osimani
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
| | - Serena Polverigiani
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
| | - Cristiana Garofalo
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
| | - Roberta Foligni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
| | - Massimo Mozzon
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
| | - Silvia Zitti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
| | - Nadia Raffaelli
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
| | - Francesca Clementi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
| | - Lucia Aquilanti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A); Università Politecnica delle Marche; Ancona Italy
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23
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Exploring ecological modelling to investigate factors governing the colonization success in nosocomial environment of Candida albicans and other pathogenic yeasts. Sci Rep 2016; 6:26860. [PMID: 27246511 PMCID: PMC4887984 DOI: 10.1038/srep26860] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/04/2016] [Indexed: 01/23/2023] Open
Abstract
Two hundred seventy seven strains from eleven opportunistic species of the genus Candida, isolated from two Italian hospitals, were identified and analyzed for their ability to form biofilm in laboratory conditions. The majority of Candida albicans strains formed biofilm while among the NCAC species there were different level of biofilm forming ability, in accordance with the current literature. The relation between the variables considered, i.e. the departments and the hospitals or the species and their ability to form biofilm, was tested with the assessment of the probability associated to each combination. Species and biofilm forming ability appeared to be distributed almost randomly, although some combinations suggest a potential preference of some species or of biofilm forming strains for specific wards. On the contrary, the relation between biofilm formation and species isolation frequency was highly significant (R2 around 0.98). Interestingly, the regression analyses carried out on the data of the two hospitals separately were rather different and the analysis on the data merged together gave a much lower correlation. These findings suggest that, harsh environments shape the composition of microbial species significantly and that each environment should be considered per se to avoid less significant statistical treatments.
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24
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O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 2015; 44:D733-45. [PMID: 26553804 PMCID: PMC4702849 DOI: 10.1093/nar/gkv1189] [Citation(s) in RCA: 3414] [Impact Index Per Article: 379.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/24/2015] [Indexed: 12/12/2022] Open
Abstract
The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
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Affiliation(s)
- Nuala A O'Leary
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Mathew W Wright
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Stacy Ciufo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Rich McVeigh
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Bhanu Rajput
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Brian Smith-White
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Danso Ako-Adjei
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Alexander Astashyn
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Azat Badretdin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Yiming Bao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Olga Blinkova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Vyacheslav Brover
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Vyacheslav Chetvernin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jinna Choi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Eric Cox
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Olga Ermolaeva
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Catherine M Farrell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Tamara Goldfarb
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Tripti Gupta
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Daniel Haft
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Eneida Hatcher
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Wratko Hlavina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Vinita S Joardar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Vamsi K Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Wenjun Li
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Donna Maglott
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kelly M McGarvey
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Michael R Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kathleen O'Neill
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Sanjida H Rangwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Daniel Rausch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Lillian D Riddick
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Conrad Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Andrei Shkeda
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Susan S Storz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Hanzhen Sun
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Igor Tolstoy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Raymond E Tully
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Anjana R Vatsan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Craig Wallin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - David Webb
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Wendy Wu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Melissa J Landrum
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Avi Kimchi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Tatiana Tatusova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Michael DiCuccio
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Paul Kitts
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
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25
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Zhang G, Sadiq FA, Zhu L, Liu T, Yang H, Wang X, He G. Investigation of Microbial Communities of Chinese Sourdoughs Using Culture-Dependent and DGGE Approaches. J Food Sci 2015; 80:M2535-42. [DOI: 10.1111/1750-3841.13093] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/24/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Guohua Zhang
- College of Biosystems Engineering and Food Science; Zhejiang Univ; Hangzhou 310058 China
- Zhejiang Provincial Key Laboratory of Food Microbiology; Zhejiang Univ; Hangzhou 310058 China
| | - Faizan A. Sadiq
- College of Biosystems Engineering and Food Science; Zhejiang Univ; Hangzhou 310058 China
- Zhejiang Provincial Key Laboratory of Food Microbiology; Zhejiang Univ; Hangzhou 310058 China
| | - Liying Zhu
- College of Biosystems Engineering and Food Science; Zhejiang Univ; Hangzhou 310058 China
- Zhejiang Provincial Key Laboratory of Food Microbiology; Zhejiang Univ; Hangzhou 310058 China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Inst. of Plant Protection and Microbiology; Zhejiang Academy of Agricultural Sciences; Hangzhou 310021 China
| | - Tongjie Liu
- College of Biosystems Engineering and Food Science; Zhejiang Univ; Hangzhou 310058 China
- Zhejiang Provincial Key Laboratory of Food Microbiology; Zhejiang Univ; Hangzhou 310058 China
| | - Huanyi Yang
- College of Biosystems Engineering and Food Science; Zhejiang Univ; Hangzhou 310058 China
- Zhejiang Provincial Key Laboratory of Food Microbiology; Zhejiang Univ; Hangzhou 310058 China
| | - Xin Wang
- Zhejiang Provincial Key Laboratory of Food Microbiology; Zhejiang Univ; Hangzhou 310058 China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Inst. of Plant Protection and Microbiology; Zhejiang Academy of Agricultural Sciences; Hangzhou 310021 China
| | - Guoqing He
- College of Biosystems Engineering and Food Science; Zhejiang Univ; Hangzhou 310058 China
- Zhejiang Provincial Key Laboratory of Food Microbiology; Zhejiang Univ; Hangzhou 310058 China
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26
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Wrent P, Rivas EM, Peinado JM, de Silóniz MI. Development of an affordable typing method for Meyerozyma guilliermondii using microsatellite markers. Int J Food Microbiol 2015; 217:1-6. [PMID: 26476570 DOI: 10.1016/j.ijfoodmicro.2015.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 09/16/2015] [Accepted: 10/06/2015] [Indexed: 11/25/2022]
Abstract
Despite previously published methods, there is still a lack of rapid and affordable methods for genotyping the Meyerozyma guilliermondii yeast species. The development of microsatellite markers is a useful genotyping method in several yeast species. Using the Tandem Repeat Finder Software, a total of 19 microsatellite motifs (di-, tri-, and tetra- repetition) were found in silico in seven of the nine scaffolds published so far. Primer pairs were designed for all of them, although only four were used in this work. All microsatellite amplifications showed size polymorphism, and the results were identical when repeated. The combination of three microsatellite markers (sc15F/R, sc32 F/R and sc72 F/R) produced a different pattern for each of the Type Culture Collection strains of M. guilliermondii used to optimize the method. The three primer pairs can be used in the same PCR reaction, which reduces costs, in tandem with the fluorescent labeling of only the forward primer in each primer pair. Microsatellite typing was applied on 40 more M. guilliermondii strains. The results showed that no pattern is repeated between the different environmental niches. Four M. guilliermondii strains were only amplified with primer pair sc32 F/R, and subsequently identified as Meyerozyma caribbica by Taq I-RFLP of the 5.8S ITS rDNA. Most out-group species gave negative results even for physiologically similarly species such as Debaryomyces hansenii. The microsatellite markers used in this work were stable over time, which enables their use as a traceability tool.
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Affiliation(s)
- Petra Wrent
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain
| | - Eva-María Rivas
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain
| | - José M Peinado
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain
| | - María-Isabel de Silóniz
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain.
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27
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Wrent P, Rivas EM, de Prado EG, Peinado JM, de Silóniz MI. Assessment of the Factors Contributing to the Growth or Spoilage of Meyerozyma guilliermondii in Organic Yogurt: Comparison of Methods for Strain Differentiation. Microorganisms 2015; 3:428-40. [PMID: 27682098 PMCID: PMC5023252 DOI: 10.3390/microorganisms3030428] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 07/30/2015] [Accepted: 08/07/2015] [Indexed: 11/16/2022] Open
Abstract
In this work we analyze the spoiling potential of Meyerozyma guilliermondii in yogurt. The analysis was based on contaminated samples sent to us by an industrial laboratory over two years. All the plain and fruit yogurt packages were heavily contaminated by yeasts, but only the last ones, containing fermentable sugars besides lactose, were spoiled by gas swelling. These strains were unable to grow and ferment lactose (as the type strain); they did grow on lactate plus galactose, fermented glucose and sucrose, and galactose (weakly), but did not compete with lactic acid bacteria for lactose. This enables them to grow in any yogurt, although only those with added jam were spoiled due to the fermentation of the fruit sugars. Fermentation, but not growth, was strongly inhibited at 8 °C. In consequence, in plain yogurt as well as in any yogurt maintained at low temperature, yeast contamination would not be detected by the consumer. The risk could be enhanced because the species has been proposed for biological control of fungal infections in organic agriculture. The combination of the IGS PCR-RFLP (amplification of the intergenic spacer region of rDNA followed by restriction fragment length polymorphism analysis) method and mitochondrial DNA-RFLP makes a good tool to trace and control the contamination by M. guilliermondii.
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Affiliation(s)
- Petra Wrent
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/José Antonio Novais, 12, 28040 Madrid, Spain.
| | - Eva-María Rivas
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/José Antonio Novais, 12, 28040 Madrid, Spain.
- Campus of International Excellence (CEI) Campus Moncloa, Universidad Complutense de Madrid, Universidad Politécnica de Madrid (UCM-UPM), 28040 Madrid, Spain.
| | - Elena Gil de Prado
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/José Antonio Novais, 12, 28040 Madrid, Spain.
| | - José M Peinado
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/José Antonio Novais, 12, 28040 Madrid, Spain.
- Campus of International Excellence (CEI) Campus Moncloa, Universidad Complutense de Madrid, Universidad Politécnica de Madrid (UCM-UPM), 28040 Madrid, Spain.
| | - María-Isabel de Silóniz
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/José Antonio Novais, 12, 28040 Madrid, Spain.
- Campus of International Excellence (CEI) Campus Moncloa, Universidad Complutense de Madrid, Universidad Politécnica de Madrid (UCM-UPM), 28040 Madrid, Spain.
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