Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters

Marsh, Alan J.

Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters

dc.check.embargoformat	Not applicable	en
dc.check.info	No embargo required	en
dc.check.opt-out	No	en
dc.check.reason	No embargo required	en
dc.check.type	No Embargo Required
dc.contributor.advisor	Cotter, Paul D.	en
dc.contributor.advisor	Ross, R. Paul	en
dc.contributor.advisor	Hill, Colin	en
dc.contributor.author	Marsh, Alan J.
dc.contributor.funder	Science Foundation Ireland	en
dc.contributor.funder	Teagasc
dc.date.accessioned	2014-04-30T15:39:01Z
dc.date.available	2014-04-30T15:39:01Z
dc.date.issued	2013
dc.date.submitted	2013
dc.description.abstract	To screen for novel ribosomally synthesised antimicrobials, in-silico genome mining was performed on all publically available fully sequenced bacterial genomes. 49 novel type 1 lantibiotic clusters were identified from a number of species, genera and phyla not usually associated with lantibiotic production, and indicates high prevalence. A crucial step towards the commercialisation of fermented beverages is the characterisation of the microbial content. To achieve this goal, we applied next-generation sequencing techniques to analyse the bacterial and yeast populations of the organic, symbiotically-fermented beverages kefir, water kefir and kombucha. A number of minor components were revealed, many of which had not previously been associated with these beverages. The dominant microorganism in each of the water kefir grains and fermentates was Zymomonas, an ethanol-producing bacterium that had not previously been detected on such a scale. These studies represent the most accurate description of these populations to date, and should aid in future starter design and in determining which species are responsible for specific attributes of the beverages. Finally, high-throughput robotics was applied to screen for the presence of antimicrobial producers associated with these beverages. This revealed a low frequency of bacteriocin production amongst the bacterial isolates, with only lactococcins A, B and LcnN of lactococcin M being identified. However, a proteinaceous antimicrobial produced by the yeast Dekkera bruxellensis, isolated from kombucha, was found to be active against Lactobacillus bulgaricus. This peptide was patially purified.	en
dc.description.sponsorship	Science Foundation Ireland (SFI CSET 2 Grant APC 07/CE/B1368)	en
dc.description.status	Not peer reviewed	en
dc.description.version	Accepted Version
dc.format.mimetype	application/pdf	en
dc.identifier.citation	Marsh, A. J. 2013. Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters. PhD Thesis, University College Cork.	en
dc.identifier.endpage	328
dc.identifier.uri	https://hdl.handle.net/10468/1547
dc.language.iso	en	en
dc.publisher	University College Cork	en
dc.rights	© 2013, Alan J. Marsh	en
dc.rights.uri	http://creativecommons.org/licenses/by-nc-nd/3.0/	en
dc.subject	Kombucha	en
dc.subject	Kefir	en
dc.subject	Water kefir	en
dc.subject	Bacteriocin	en
dc.subject	High-throughput screening	en
dc.thesis.opt-out	false
dc.title	Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters	en
dc.type	Doctoral thesis	en
dc.type.qualificationlevel	PhD	en
dc.type.qualificationname	PhD (Science)	en
ucc.workflow.supervisor	c.hill@ucc.ie