Consolidating a genomic framework for exploiting lactobacilli

Project Information

GENOLACT

Grant agreement ID: 659801

DOI

10.3030/659801

Project closed

EC signature date 30 March 2015

Start date 1 June 2015

End date 31 May 2017

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 187 866,00

EU contribution

€ 187 866,00

Coordinated by

UNIVERSITY COLLEGE CORK - NATIONAL UNIVERSITY OF IRELAND, CORK
Ireland

Periodic Reporting for period 1 - GENOLACT (Consolidating a genomic framework for exploiting lactobacilli)

Reporting period: 2015-06-01 to 2017-05-31

Summary of the context and overall objectives of the project

GENOLACT was about the comparative genomic analysis of 238 species belonging to Lactobacillus genus and associated genera in order to i) understand the genomic relatedness and radiative evolution of lactobacilli; ii) establish a complete inventory of genes and pathways involved in health promoting effects and their interaction with the host; iii) investigate the molecular basis of the antibiotic resistance in lactobacilli.
Data obtained supported the development of a more consistent taxonomic scheme for genus Lactobacillus which is expected to be helpful for regulatory applications and scientific communication related to lactobacilli as well as for the selection of new beneficial or technological strains.
Mining the genomes of lactobacilli, we unravelled for the first time the potential of lactobacilli to produce probiotic-related metabolites; concurrently, the genetic sequences of antibiotic resistance genes were also identified, allowing the description of the Lactobacillus resistome make-up, previously unknown.
During the secondment In Chr. Hansen A/S (Denmark), basic comparative genomics and taxonomic data obtained in the first part of GENOLACT were used to successfully develop a new multilocus sequence typing scheme and for the genome-based safety assessment of a panel of potential probiotic lactobacilli to add them on the European Market in compliance with the requirements by EFSA (the European Food Safety Agency).
The knowledge and the results acquired within GENOLACT regarding the evolutionary history of lactobacilli as well as their potential of coding probiotic traits, on one side, and antibiotic resistance traits, on the other, irrefutably contribute to ensure the flow of evidence-based, non-misleading, clearly understandable information about lactobacilli and their application in the food industry and as probiotics.
Within GENOLACT, high-level research was performed with leading scientists at UCC and successfully transferred to Chr. Hansen A/S in form of novel industrial solutions, thus giving evidence that in the framework of GENOLACT public and private sectors worked together, through innovative partnerships, increasing manufacturers’ interest in selecting and placing new Lactobacillus-based beneficial products on the EU market and meeting the consumer’s ambitions on probiotics and functional foods as form of preventive medicine.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The combination of distance-based and sequence-based methods applied to 238 genomes showed that the Lactobacillus genus was polyphyletic, intermixed with other genera and characterized by a complex evolutionary history, confirming also previous findings on limited sets of data. The data irrefutably indicate that the extraordinarily diverse genus Lactobacillus should be sub-divided into more homogeneous genera whose members share similar evolutionary events, characterised by uniform patterns of presence/absence of specific sets of genes.
The full analysis of the mechanisms of action are required by EFSA for the approval of probiotic claims and clinical use of probiotics. We investigated the presence of the gene coding for an immunomodulatory protein the soluble p40 protein in all lactobacilli and we found out that 24 Lactobacillus genomes harbour the gene of interest and seven of them are able to produce the protein and release it in the supernatants.
Besides health-promoting traits, we also improved the knowledge about the antibiotic resistance (AR) genes in the Lactobacillus genus, by determining the antibiotic susceptibility patterns of 196 strains from the phenotypic and genotypic point of view. As for the phenotypic analysis, lactobacilli MIC of 16 antibiotics have been determined with vet-MIC plates; on the second hand, the comparative genomics analysis mainly consisted in BLAST searches against CARD database and the investigation of the genetic organization of the putative AR genes and their associated resistance mechanisms. This study, carried out in collaboration with Teagasc Food Research Centre (Fermoy, Ireland) and University of Verona, is expected to be used as a new guideline for the use of lactobacilli as starter cultures, food preservatives or probiotic bacteria by food and probiotic stakeholders and legislative bodies.
During the secondment in Chr. Hansen A/S, data obtained within the first part of GENOLACT contributed to the whole genome sequence strain typing process in the Strain Supply Chain and to develope a new Multilocus Sequence Typing Scheme. Further, activities in Chr. Hansen included thorough safety assessment of a potential Lactobacillus probiotic strain through MIC determination as requested by EFSA along with a comparative genomic study of 30 closely related strains of three different Lactobacillus species.
In the whole, I published 2 peer-reviewed papers and 6 posters, I participated to 5 conferences, I gave 4 oral presentations, I contributed as a volunteer to 7 activities related to public engagement, and I attended 9 sessions organised by UCC regarding research management and complementary skills development. Furthermore, I participated to other 3 training courses (in Sweden, Germany and UK) on technology transfer, intellectual property management and regulatory affairs in Europe.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

data obtained within GENOLACT directly related to the objectives of Horizon 2020 Societal Challenges 1 & 2 Work Programme. The knowledge and the results acquired in GENOLACT, in fact, contribute to ensure the flow of evidence-based, non-misleading, clearly understandable information about probiotics. A more consistent taxonomic scheme for genus Lactobacillus will be helpful for regulatory applications and scientific communication related to lactobacilli, thus preventing mis-identification issues which are still the major cause of mislabelling of probiotic and food products reported worldwide (as we highlighted also in the paper “When regulation challenges innovation: the case of genus Lactobacillus”). We also focused on the safety of the consumer by expanding the knowledge of the resistome of lactobacilli which can be used as a new guideline for the use of lactobacilli as starter cultures, food preservatives or probiotic bacteria by food and probiotic stakeholders as well as legislative bodies. Finally the secondment in Chr. Hansen A/S gave new insights about how innovation partnerships can be fruitful both for the public and the private sector. In fact, basic data obtained in the first part of GENOLACT were successfully transferred to Chr. Hansen A/S and used to improve the genome sequence strain typing process in the Strain Supply Chain and co-developed a new Multilocus Sequence Typing Scheme for strain tracking and characterization. Further, an other internal project regarding the safety assessment of a panel of Chr. Hansen A/S strains was realized aimed to add a new probiotic Lactobacillus strain on the European Market in compliancy with Eu regulatory bodies.

Volunteering Activity at the Over 50s Show in Cork City Hall

Presentation of GENOLACT at the APC Microbiome Institute Launch Symposium