NCYC - Yeast Research at NCYC

NCYC Research

Research associated with the Collection aims to improve techniques to identify and classify yeasts, particularly those associated with brewing and food spoilage. This research has shed new light on yeast evolution and genetic interrelationship, including mechanisms of speciation (Fischer et al 2000, Delneri et al 2003) and has developed a number of novel molecular approaches to identifying and characterising yeast biodiversity (e.g. Naumov et al 2000, Wesselink et al 2002). NCYC research is pre-eminent in areas such as phylogenetic analysis of yeasts using ribosomal RNA gene sequences (e.g. Steels et al 2002) and sub-species discrimination using molecular fingerprinting (e.g. Olver et al 2002).

Yeast has long been acknowledged as the most important organism in biotechnology. Our research has demonstrated that there is considerable value contained in the biodiversity of the yeasts that the collection comprises. Such diversity can be of considerable value to a variety of industry sectors including food, pharmaceuticals, fine chemicals, and others. The diversity that has been collected in the NCYC and the know-how and skills of NCYC researchers in understanding and working with the collection is available for contract research. Precision characterisation at the most detailed molecular level makes the collection a most attractive source for commercial partners, particularly when linked to other technologies for physical measurement available within IFR e.g. the metabolomics suite.

NCYC Research Projects:

Below is a list of current and recent research projects which the NCYC personnel are involved in.

UK INDUSTRIAL “Confidential vector development” (2006-2007).
BBSRC BEPII “ComparaGrid – enabling GRID technologies for comparative genomics” (2005–200).
DEFRA LINK "Spoilage Index for Yeasts and Moulds" (2003-2006).
USA INDUSTRIAL “Confidential metabolic screening” (2002-2003).
Wellcome Trust "Intelligent Catalogue for Single Gene Deletant Mutants arising from research in Functional Genomics" (2001-2004).
JAPAN INDUSTRIAL “Confidential molecular typing” (2000-2002).
BBSRC GDB "Comparative genomics of Saccharomyces" (1999-2002).
BBSRC Bioinformatics "Datamining for Emerging Microbial Threats" (1999-2002).
EU EUROFAN "Functional analysis of genes identified by genome sequencing" (1996-1999).
EU AIR "Phylogenetic analysis of food spoilage yeasts" (1994-1997).
EU Yeast Genome Sequencing Project (1992-1996).

Recent NCYC Publications:

Below is a list of recent publications made by the NCYC personnel.

MPP: A Microarray-To-Phylogeny Pipeline for Analysis of Gene and Marker Content Datasets
Davey RP, Savva G, Dicks J and Roberts IN
Bioinformatics 23 (8): 1023-1025 (2007).
Metabolic footprinting as a tool for discriminating between brewing yeasts
Pope GA, MacKenzie DA, Defernez M, Aroso MA, Fuller LJ, Mellon FA, Dunn WB, Brown M, Goodacre R, Kel
Yeast. 2007 Aug;24(8):667-79. (2007).
Molecular evidence for the existence of natural hybrids in the genus Zygosaccharomyces
James SA, Bond CJ, Stratford M and Roberts IN
FEMS Yeast Research 5, 747-755 (2005).
Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric associated sequences in the Saccharomyces sensu stricto complex
Liti G, Peruffo A, James SA, Roberts IN and Louis EJ
Yeast 22, 177-192 (2005).
Recombination Analysis Tool (RAT): A program for the highthroughput detection of recombination
Etherington GJ, Dicks JL and Roberts IN
Bioinformatics 21, 278-281 Epub Aug 27 (2004).
Spoilage yeasts with emphasis on the genus Zygosaccharomyces.
    James, S.A. and Stratford, M.
    Behrs Verlag: In Yeasts in Foods: Beneficial and Detrimental Aspects, pp. 171-191. (2003).
    Edited by T. Boekhout and V. Robert.
Non-alcoholic beverages and yeasts
    Stratford, M. and James, S.A.
    Behrs Verlag: In Yeasts in Foods: Beneficial and Detrimental Aspects, pp. 309-345. (2003).
    Edited by T. Boekhout and V. Robert.
Engineering evolution to study speciation in yeasts
Delneri D, Colson I, Grammenoudi S, Roberts IN, Louis EJ and Oliver SG
Nature 422, 68–72 (2003).
Nosocomial transmission of Saccharomyces cerevisiae in bone marrow transplant patients.
Olver, W.J., James, S.A., Lennard, A., Galloway, A., Roberts, I.N., Boswell, T.C. and Russell, N.H.
of Hospital Infection 52, 268-272. (2002).
Determining a unique defining DNA sequence for yeast species using hashing techniques.
Wesselink, J-J., de la Iglesia, B., James, S.A., Dicks, J.L., Roberts, I.N. and Rayward-Smith, V.J.
Bioinformatics 18, 1004-1010. (2002).
Zygosaccharomyces kombuchaensis: the physiology of a new species related to the spoilage yeasts Zygosaccharomyces lentus and Zygosaccharomyces bailii.
Steels, S., James, S.A., Bond, C.J., Roberts, I.N. and Stratford, M.
FEMS Yeast Research 2, 113-121. (2002).
Identification and distribution of a novel Malassezia species yeast on normal equine skin.
Nell, A., James, S.A., Bond, C.J., Hunt, B. and Herrtage, M.E.
Veterinary Record 150, 395-398. (2002).
Candida davenportii sp. nov., a potential soft-drinks spoilage yeast isolated from a wasp.
Stratford, M., Bond, C.J., James, S.A., Roberts, I.N. and Steels, H.
International Journal of Systematic and Evolutionary Microbiology 52, 1369-1375. (2002).
Genetic analysis of food spoilage yeasts.
    James, S.A., Collins, M.D. and Roberts, I.N.
    Humana Press.: In Methods in Biotechnology, Volume 14: Food Microbiology Protocols, pp. 37-51. (2001).
    Edited by J.F.T. Spencer and A.L. Ragout de Spencer.
Phylogenetic analysis of the psychrophobic yeast Arxiozyma telluris and the reinstatement of Candida pintolopesii (van Uden) Meyer et Yarrow and Candida slooffii van Uden et do Carmo Sousa.
James, S.A., Collins, M.D. and Roberts, I.N.
International Journal of Systematic and Evolutionary Microbiology 51, 1917-1925. (2001).
Candida sorbosivorans sp. nov., a new member of the genus Candida Berkhout.
James, S.A., Bond, C.J. and Roberts, I.N.
International Journal of Systematic and Evolutionary Microbiology 51, 1215-1219. (2001).
Chromosomal evolution in Saccharomyces.
Fischer, G., James, S.A., Roberts, I.N., Oliver, S.G. and Louis, E.J.
Nature 405, 451-454. (2000).
Three new species in the Saccharomyces sensu stricto complex: Saccharomyces cariocanus, Saccharomyces kudriavzevii and Saccharomyces mikatae.
Naumov, G.I., James, S.A., Naumova, E.S., Louis, E.J. and Roberts, I.N.
International Journal of Systematic and Evolutionary Microbiology 50, 1931-1942. (2000).
Zygosaccharomyces lentus: a significant new osmophilic, preservative-resistant spoilage yeast, capable of growth at low temperature.
Steels, H., James, S.A., Roberts, I.N. and Stratford, M.
Journal of Applied Microbiology 87, 520-527. (1999).
Zygosaccharomyces lentus sp. nov., a new member of the yeast genus Zygosaccharomyces Barker.
Steels, H., Bond, C.J., Collins, M.D., Roberts, I.N., Stratford, M. and James, S.A.
International Journal of Systematic Bacteriology 49, 319-327. (1999).
Molecular Systematics of Ascomycetous Yeasts.
James, S.A.
PhD Thesis. (1998).
A phylogenetic analysis of the genus Williopsis based on 18S rRNA gene sequences.
James, S.A., Roberts, I.N. and Collins, M.D.
International Journal of Systematic Bacteriology 48, 591-596. (1998).
A phylogenetic analysis of the genus Saccharomyces based on 18S rRNA gene sequences: description of Saccharomyces kunashirensis sp. nov. and Saccharomyces martiniae sp. nov.
James, S.A., Cai, J., Roberts, I.N. and Collins, M.D.
International Journal of Systematic Bacteriology 47, 453-460. (1997).
Use of an rRNA internal transcribed spacer region to distinguish phylogenetically closely related species of the genera Zygosaccharomyces and Torulaspora.
James, S.A., Collins, M.D. and Roberts, I.N.
International Journal of Systematic Bacteriology 46, 189-194. (1996).
Differentiation of the spoilage yeast Zygosaccharomyces bailii from other Zygosaccharomyces species using 18S rDNA as target for a non-radioactive ligase detection reaction.
Stubbs, S., James, S. and Collins, M.D.
Letters in Applied Microbiology 19, 268-272. (1994).
Genetic interrelationship among species of the genus Zygosaccharomyces as revealed by small-subunit rRNA gene sequences.
James, S.A., Collins, M.D. and Roberts, I.N.
Yeast 10, 871-881. (1994).
The genetic relationship of Lodderomyces elongisporus to other ascomycete yeast species as revealed by small-subunit rRNA gene sequences.
James, S.A., Collins, M.D., and Roberts, I.N.
Letters in Applied Microbiology 19, 308-311. (1994).