Taxonomy changes in the genus Lactobacillus finally published
The publication of the extensive taxonomical changes in the genus Lactobacillus has now been published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). In October 2018 we organised an Expert Workshop on this topic in Verona. The changes in the genus and its consequences for industry were extensively discussed and the outcome of this workshop was published in Trends in Food Science and Technology November 2019. Find herewith a blog by Bruno Pot with a link to the publication in IJSEM and a tool that allows you to check the conversion from the old to the new name or vice versa. Also the publication on the outcome of the workshop is enclosed. We thank Bruno Pot and all scientists involved for all the work done.
Supporting two Stakeholder documents initiated by the International Chamber of Commerce (ICC)
Following the discussions at the LABIP Expert Workshop on the human microbiota and the Nagoya protocol and the publication of the outcome of the workshop in Microbial Cell Factories, LABIP has been asked to contribute to and co-sign two documents, initiated by the ICC knowingly:
- Implications of EU regulation 511/2014 on research on the human microbiome
- Promoting sustainable use and conservation of biodiversity through open exchange of Digital Sequence Information (DSI)
The first document supports the view that the human microbiome, being a specific part of a human being, belongs to the individual and therefore should not be subject to any obligations under the EU regulation 511/2014, related to the Convention on Biological Diversity (CBD) and the Nagoya Protocol. Accordingly, States cannot assert sovereign rights over the microbiomes of their citizens.
The second document expresses the concern on the proposal to let the Digital Sequence Information fall under the regulations of the CBD and the Nagoya Protocol. It states that barriers to sharing and use of DSI would discourage innovation and scientific research and consequently the advancement of science. Regulatory authorities are therefore asked to recognize the continued and ready access of DSI for advancing R&D.
LABIP has signed both documents, in line with the discussions at the above mentioned workshop.
LABIP Expert Workshop
“Major changes in the taxonomy of Bifidobacterium and Lactobacillus; consequences for industry”
In June this year, Salvettia and coworkers (*) published the result of a whole genome sequence analysis of 269 species, primarily belonging to the 25 families of the Lactobacillaceae and the Leuconostocaceae. Not surprisingly, the results showed a tree in which phylogeny and taxonomy were in serious disagreement. In order to solve this confusing situation, a considerable renaming at genus level might be necessary. The current genus Lactobacillus (containing over 200 species) is therefore in risk of being renamed and split into at least 10 new genera.
While very defendable from a scientific point of view, practical implications are far reaching, given the fact that many lactobacilli are involved in food fermentations and therefore have a legal status in relation to their use, functionality and safety (labelling, ingredient status, QPS status, GRAS notification, etc…). Name changes could also have consequences for the medical community, as new names may only slowly penetrate into medical laboratories.
In order to make an inventory of the possible consequences and discuss the different options to deal with this extensive renaming, LABIP has composed an impressive international panel of experts, representing Academia and Industry. October 4 and 5 these stakeholders have discussed the pros, cons and possible consequences and make some recommendations for a smooth ‘taxonomic transition’. The workshop was attended by 35 participants, 14 experts and 21 LABIP representatives.
While taxonomic renaming’s have been quite frequent in the past, the scale at which this is going to happen for microorganisms with such a great importance in food and health, is unprecedented.
A link to the hand-out, comprising the program, the abstracts and the names of all participants will be find hereunder.
Mary-Ellen Sanders from ISAPP, one of the participants, has published a blog which can be followed through the following link: Forthcoming Changes in Lactobacillus Taxonomy
The official result of the workshop will be made available on our website as a formal publication. The full presentations will be available at our Intranet.
* Elisa Salvetti, Hugh M. B. Harris, Giovanna E. Felis, Paul W. O’Toole. 2018. Comparative genomics reveals robust phylogroups in the genus Lactobacillus as the basis for reclassification. Appl. Environ. Microbiol. doi:10.1128/AEM.00993-18
LABIP Contribution to the first Assessment and Review of the Nagoya Protocol
As an extra outcome of the LABIP Expert Workshop “Future access and improvement of industrial LAB cultures”, LABIP did send in a contribution to the first Assessment and Review of the Effectiveness of the Nagoya Protocol, asked for by the Secretariat of the Convention on Biological Diversity (CBD) which is part of the United Nations Environmental Programme. Find here the Notification for a contribution: Notification contribution Nagoya Protocol
Based on the discussions at the workshop and the publication of the outcome, the following contribution has been send on behalve of LABIP: LABIP contribution assessment Nagoya Protocol
LABIP Activities at LAB12
At the LAB Symposium 12, held from August 27 till 31 at Egmond aan Zee, The Netherlands, for the fifth time the LABIP awards for the Mid Career Senior Scientist and for the best 3 posters have been presented by the LABIP Chairman Esben Laulund. Also for the third time LABIP has organized a thematic session at the LAB Symposium.
The LABIP Awards
The prize of 2500 € for the Mid Career Senior Scientist has been given to Prof. Sarah Lebeer from University of Antwerp, Belgium for the research she has don one Bacteria-host interaction for beneficial microbes and probiotics, specifically Lactobacillus rhamnosus GG. The LABIP Steering Group considers her research to be completely in line with the criteria of “Outstanding Excellence in Lactic Acid Bacteria Research with an Industrial Relevance”. In her research she has used the full spectrum of modern molecular approaches, while she also has also worked together with a top chef developing cooking techniques to bring in new bacteria into foods.
Using the same criteria also 3 posters have been selected out of the 350 posters, that were presented at the Symposium, for the poster prizes of 500 € each. The poster prizes were given to:
Tesfemarian Berhe, School of Animal & Range Sciences, Harmaya University,Ethiopia, poster A013: Metagenomic Analysis of the Bacterial Community in Dhanaan: Traditional Ethiopian Fermented Camel Milk
Fergal J. Ryan, APC Microbiome Institute, Phageonomics lab. Cork, Ireland, poster A019 : The Human Gut Virome at the Extremes of Life
Florence Vande Capelle, Biochemistry, Biophysics & Genetics of Microorganisms, Life Sciences Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium, poster B044 : Two-component systems in Streptococcus salivarius: signal transduction controlling natural competence
LABIP Thematic Session
This year the session was entitled “Future access and improvement of industrial LAB cultures” based on the LABIP Expert Workshop held in May this year. The thematic session was chaired by Esben Laulund and consisted of 2 keynote speakers:
Martin Brink, University of Wageningen, The Netherlands: The Nagoya Protocol and the consequences for users of genetic resources
Eric Johansen, Chr. Hansen A/S, Horsholm, Denmark: Is the development of new starter cultures caught between a rock and a hard place?
Also 3 poster presenters were asked to give a short presentation:
Simon van der Els, NIZO, Ede, The Netherlands: PTarget a genome editing vector for implementation of CRISPR-Cas9 technology in LAB
Pierre Renault, INRA, Jouy en Josas, France: Lactococcus rafinolactis, an underestimated dairy Lactococcus revealed by genomic and metagenomic analysis
Johann Mignolet, Université Catholique de Louvain, Louvain-la-Neuve, Belgium: Ubiquitous rewiring of transcriptional control in streptococci: lesson from competence and predation coupling in Streptococcus salivarius
The presentations during the Thematic Session were well appreciated by the more than 450 participants of the LAB12 Symposium.
LABIP Expert Workshop
“Future access and improvement of industrial LAB cultures”
May 10 and 11 2017 an expert workshop has been organised aiming at the implementation of new natural and genetic selection methods for industrial starter cultures and the influence of legislation which is being implemented as a consequence of the Nagoya Protocol. This protocol from 2014 is now ratified by almost 100 countries, including the EU and establishes the compliance to Access and Benefit-Sharing (ABS) rules of the countries. These rules have been implemented after the Convention of Biological Diversity of 1993.
In the workshop, the potential of the new genetic approaches for LAB was depicted, including examples of what has been achieved during the latest years. On the other hand it was made clear that the legislation, following the Nagoya protocol and which is still under debate, will have an enormous influence on academic and industrial research.
The outcome of the workshop will be in the form of a position paper, which will be written in the coming months and published. The Hand-out, containing program of the workshop, the list of participants and the abstracts of the presentations, as well as the complete presentations of all expert speakers can be found in the Members Only section of the website.
The position paper has now been published in the Open Access Journal “Microbial Cell Factories” on December 14 2018. It can be accessed by the following link: http://rdcu.be/CZxF
LABIP Awards at LAB11
At the LAB Symposium 11, held from August 31st till September 4th 2014 at Egmond aan Zee, The Netherlands, for the fourth time the LABIP awards for the Mid Career Senior Scientist and for the best 3 posters have been presented by the LABIP Chairman Esben Laulund.
The prize of 2000 € for the Mid Career Senior Scientist has been given to Prof. Bas Teusink for the way he is moving the field by the application of bioinformatics and systems biology, needed to handle big data in the field of metabolomics and analysis of complex microbial communities. These approaches will also become more and more relevant for industrial application of these fields.
Three poster prizes of 500 € each, for which criteria are based on “Outstanding Excellence in Lactic Acid Bacteria Research with an Industrial Relevance” where chosen out of ~350 posters. The poster prizes were given to:
B.R. Johnson, North Carolina State University, Department of Microbiology, poster A26: Proteomic analysis of secreted surface proteins in S-layer forming species of the Lactobacillus acidophilus complex
F. Hugenholtz, Wageningen University, Department of Laboratory of Microbiology, poster D034: Unravelling the fate of dietary fibers in the murine cecum
W. Kot, University of Copenhagen, Department of Biology, poster F013: Development of a method for tracking industrial important strains of Lactococcus lactis
LABIP awards at the Final Cross-Talk Symposium
The ITN Cross-Talk has organized its final Symposium in Paris on September 3-4 2012 entitled “The Disruption of the War Metaphor of Human-Microbe Interactions in the Gastrointestinal Tract”. With this meeting a highly interesting EU financed project has ended, in which LABIP was an associated partner. LABIP has played a key role in the training programme of the ITN. By our contribution we have ensured that the requirements for career development in industry and the possibilities for research in industry have been covered. Our activities have given the 17 research fellows an insight in the opportunities for a (research) career in industry, while the LABIP members had the possibility to interact with a group of high quality young scientists in the area of the human gut – microbiota interactions, as well to follow the latest results in this fascinating area of research, so relevant for the food industry.
At this final Symposium, Aat Ledeboer has given, on behalf of LABIP, the last 2 prizes of 300 € each for the best oral presentation and best poster. The poster award was given to Frank Duca, a PhD student from INRA, Joy-en-Josas, entitled “Replication of obesity and associated signalling pathways through gut microbiota transfer”. The price was given for the very convincing way it was presented as well as for the intriguing research results. The award for the best oral presentation was given to the Cross-Talk fellow Agata Korecka, who is doing her PhD at the Karolinski Univeristy in Sweden.
The EU is discussing the new framework programme for research funding until 2020. The programme is called Horizon 2020. A link to the website of the programme can be found under “Links “as well as Websites of other organisations of interest for LABIP. Find herewith also the links to 3 documents of interest:
The Green Paper
Presentation Horizon 2020
Programme Horizon 2020
Cross-Talk Summer School in Wageningen
From 12 to 16 September 2011 the third Network Meeting of the ITN Cross-Talk has been held in Wageningen, The Netherlands. The first 2 days consisted of scientific presentations on the interaction of the gut microbiota and the host with among others short presentations of all fellows on their research and chaired by one of the other fellows. This formula led to a highly interactive meeting with a lot of scientific debate among the fellows and their supervisors. During the last 3 days the third and final Summerschool was held, organized by LABIP. At the first day the group of 16 fellows visited the Dutch Dairy Institute, NIZO in Ede, where they listened to peresentations of young NIZO scientists and where 3 of the fellows presented on their research in Cross-Talk. After a short tour through the building and the pilot plant and a lunch, the group went to the Yakult factory in Almere. The fellows clearly were impressed by the high quality standards of the factory and also by the scientific presentations. Back in Wageningen they were given a traditional Dutch pancake meal. The second day of Summerschool a Career Perspectives Workshop was given by professional trainers. Also LABIP members were involved during the job interviews. The fellows considered this to be very valuable for their career development especially since most of them now are at the end of their PhD period. The last day of Summerschool focused on health claims, the role of EFSA was discussed.
LABIP Awards at LAB10 Symposium
During the Tenth Symposium on Lactic Acid Bacteria, held from August 28 till September 1 2011 in Egmond aan Zee, The Netherlands, LABIP has offered for the third time an award of 2000 € for the Mid-Career Senior Scientist and 3 awards of 500 € for the best posters. The awards were presented by the LABIP Chairman Esben Laulund and all are based on outstanding excellence in LAB research with industrial relevance.
The award for the Mid-Career Senior Scientist was given to Sylvain Moineau, University of Laval, Canada, on his longstanding research on LAB bacteriophages and specifically for his recent outstanding and innovative research, together with researchers from Danisco, on the CRISPR/Cas bacterial immune system against bacteriophages. Sylvain joins herewith the winners from 2005 and 2008, Michiel Kleerebezem and Joel Doré.
The best poster awards were given to:
Herwich Bachman, VU University Amsterdam, The Netherlands entitled “Opening up the full potential of genome-scale modeling through a novel selection method”
Rebecca Wall, TEAGASC, Moorepark, Ireland entitled “Contrasting effects of B. breve DPC6330 and B. breve NCIMB702258 on fatty acid metabolism and gut microbiota composition”
Damien Dandoy, UCL, Louvain la Neuve, Belgium entitled “Conversion from slow to fast milk acidification through natural transfer of the cell-envelope proteinase prtS gene in S. thermophilus strains”.
LABIP Prizes at Cross-Talk workshop in Milan
LABIP has given 2 prizes of 300 € each for the best oral presentation and best poster at the Cross-Talk workshop “Lessons from Host-Pathogens Interactions” held in Milan, Italy April 28-29, 2011. The poster prize was given to the Cross-Talk fellow Krzysztof Regulski on “The influence of peptidoglycan metabolism in L. casei on its immunomodulatory properties”. The prize was given as well for the quality of the poster, its content and on the excellent, convincing way it was presented. The oral presentation prize was given to Mariangela Cavarelli, a young postdoc from the San Raffaele Scientific Institute in Milan who was invited to present on “Dendritic cells mediate the selective transmission of R5 human immunodeficiency virus (HIV)-1 through the intestinal mucosa”. This prize was given for the excellent way it was presented, its contents and the excellent slides.