This special thematic issue of FEMS Microbiology Reviews is truly special, because it contains contributions to a meeting that is yet to happen! As many others, the thirteenth Interna- tional Symposium on Lactic Acid Bacteria (LAB13) was a victim of the COVID-19 pandemic and has been postponed to next year. The conference is held every 3 years in The Netherlands, and is attended by researchers from academia and industry from all over the world, reflecting the importance of these microorgan- isms in food, health and basic science. As a tradition, the invited speakers are asked to contribute not only by a talk, but also by a thorough review on the topic of their presentation. These papers were already under review by the time it became clear that the coronavirus would not be contained and that we had to post- pone the meeting. However, we decided to move on and publish the reviews now, when still timely, and we are eagerly awaiting updated presentations next summer

Kuipers, Oscar P

Moineau, Sylvain

Teusink, Bas

English

Proceedings - University of Groningen

   University of GroningenSymposium on Lactic Acid Bacteria-reading while waiting for a meetingTeusink, Bas; Kuipers, Oscar P; Moineau, SylvainPublished in:FEMS Microbiology ReviewsDOI:10.1093/femsre/fuaa049IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2021Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Teusink, B., Kuipers, O. P., & Moineau, S. (2021). Symposium on Lactic Acid Bacteria-reading whilewaiting for a meeting. FEMS Microbiology Reviews, 45(2), [fuaa049].https://doi.org/10.1093/femsre/fuaa049CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 04-06-2022FEMS Microbiology Reviews, fuaa049, 45, 2020, 1–2doi: 10.1093/femsre/fuaa049EditorialSymposium on Lactic Acid Bacteria—reading while waiting for ameetingThis special thematic issue of FEMS Microbiology Reviews istruly special, because it contains contributions to a meetingthat is yet to happen! As many others, the thirteenth Interna-tional Symposium on Lactic Acid Bacteria (LAB13) was a victimof the COVID-19 pandemic and has been postponed to next year.The conference is held every 3 years in The Netherlands, and isattended by researchers from academia and industry from allover the world, reflecting the importance of these microorgan-isms in food, health and basic science. As a tradition, the invitedspeakers are asked to contribute not only by a talk, but also by athorough review on the topic of their presentation. These paperswere already under review by the time it became clear that thecoronavirus would not be contained and that we had to post-pone the meeting. However, we decided to move on and publishthe reviews now, when still timely, and we are eagerly awaitingupdated presentations next summer.Lactic acid bacteria, or LAB for friends, are a group of phyloge-netically diverse, but metabolically rather similar, bacteria. Theyplay important roles in food and feed fermentations, where theycontribute to safe, healthy and tasty food. Some strains haveprobiotic properties and they are even potential delivery vehi-cles for (oral) vaccines. They are selected from spontaneouslyfermented products or through evolution experiments in thelaboratory. They are screened for desired flavor-producing prop-erties, or for antimicrobials that they produce to defend theiroften nutrient-rich niches. They need to defend against (bacte-rial) viruses, which are a significant risk for industrial food fer-mentations. They are studied for their metabolism and phys-iology, in isolation or increasingly in the context of microbialconsortia such as the human microbiome or complex fermentedfoods. These broad topics are discussed at the LAB Symposiumseries, and this issue reflects the current state of the art of theexciting and diverse field of LAB research.Research into viruses—bacteriophages in the case of bac-terial viruses—has never been more pressing than in currentpandemic times, but has been a focal area in LAB research fordecades. It is not only a threat to industrial production pro-cesses, but fundamental studies on the clustered regularly inter-spaced short palindromic repeats (CRISPR)-CRISPR-associated(Cas) systems in Streptococcus thermophilus led to the discoveryof the molecular mechanisms of this adaptive immune system.We have come a long way since then. Roberts and Barrangou dis-cuss the history, the different systems and their mode of actionand highlights the applications of the CRISPR-Cas system in thecontext of LAB.While CRISPR-Cas systems may limit horizontal geneexchange in some LAB species, bacteria have still numerousways to exchange genes as mobile genetic elements are driversof microbial evolution. Various mechanisms of horizontal genetransfer can also occur in microbial communities. However,monitoring DNA transfers and their effects in these communi-ties has been challenging. Christina Saak and colleagues exploreexisting and emerging technologies for tracking mobile ele-ments and assigning them to microbes in order to generatecomprehensive community-level information. They also makethe case that LAB-driven fermented foods are, among others,ideal models to apply these techniques and address outstand-ing questions in the field of horizontal gene transfer in microbialcommunities.Dennis Romero and colleagues address phage–host interac-tions in Lactococcus lactis and Streptococcus thermophilus. They pro-vide a timely overview of the diversity of these phages and theirbiology, as well as the defence mechanisms operating in theseLAB. This knowledge has led to improved industrial starter cul-tures, e.g. specifically designed and adapted to prevent fermen-tation delays and low-quality fermented products. The authorsalso describe the oldest and still highly dynamic arms racebetween prey and predator and its relevance for developingrobust dairy fermentation processes.While phages are arguably the master regulators of LAB com-munities, they also likely play a role in other ecosystems, includ-ing the human gut. The function and composition of our gutmicrobiome are clearly linked to human health. Consequently,the promise of being able to precisely modulate this microbialcommunity has become an area of intense research worldwide.Torben Rasmussen and colleagues discuss the promises andlimitations of fecal microbiota transplantation, which offers anattractive therapeutic strategy for patients suffering from gutdysbiosis and bacterial infections. Growing evidence also sug-gests that cascading effects are initiated when phage commu-nities are also transferred to the gut, which leads to changes inits microbial composition and the host metabolome as well asimproving health.As the role of microorganisms in intestinal health hasbecome clearer with every LAB symposium due to advancedtools and new databases, we have invited a number of contribu-tions related to this topic. Shaopu Wang and colleagues reviewReceived: 16 September 2020; Accepted: 28 September 2020C© The Author(s) 2020. Published by Oxford University Press on behalf of FEMS. This is an Open Access article distributed under the terms of theCreative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, andreproduction in any medium, provided the original work is properly cited.1Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 20212 FEMS Microbiology Reviews, 2021, Vol. 45, No. 2the impact of early-life exposures on the microbiota develop-ment during childhood, and how this affects health at a laterage. They identify ‘golden’ perinatal factors and risk factors thatimpact on physiology, immunity and even cognitive develop-ment. They also describe possible interventions and their poten-tial.One of the first colonizers of the human gut are bifidobacte-ria, which are strictly speaking not LAB, but whose LAB-assistedapplications, metabolism and impact on gut health warrant aplace in this thematic issue. Chyn Wong and colleagues describethe biology and physiology of the Human Residential Bifidobac-teria, and what factors contribute to their ecological fitness.These factors may be used for the selection of ‘bifido’ strainswith desired properties and health benefits. Strain selection isalso essential for the production of healthy fermented foods.Francesca De Filippis and colleagues discuss the role of fer-mented foods as a source of potentially probiotic LAB, and howto mine the wealth of genomics and metagenomics data withbioinformatics and data analysis tools. While more researchis still needed to better understand the health benefits of fer-mented foods and their associated LAB, the field keeps progress-ing between each LAB Symposium.De Vuyst and Leroy looked at fermentation processes anddescribe in particular how yeasts, acetic acid bacteria and LABcollaborate during the fermentation of cocoa beans, a necessarystep to obtain the chocolate flavors we love so much. The com-plexity of food fermentations is in full display, yet it also showsthe great progress made in our understanding of the interactionsand the physiology of these microorganisms through a combi-nation of (functional) genomics, controlled fermentations andmodeling. Michiel Kleerebezem and colleagues review the latestinsights into the physiology of Lactococcus lactis, one of the keyspecies in starter cultures for a.o. cheesemaking, and an impor-tant model for LAB research. They describe both the functionalgenomics and bacterial physiology approaches to understandthe adaptation of L. lactis to different environmental conditions,including zero growth conditions that are relevant for cheeseripening. L. lactis was also the first LAB for which a genome-scale metabolic model was developed. Frank Bruggeman andcolleagues take us on a journey into the theory of bacterial phys-iology and growth that forms the rationale for all constraint-based modeling approaches. They show from first principleshow the strategy of growth rate (fitness) maximization underbiochemical constraints can explain a surprisingly large part ofmicrobial behavior, from L. lactis to Escherichia coli to yeast. Thisincludes stress resistance, overflow metabolism and cataboliterepression.Finally, as LAB take up many nutrients from the environ-ment, one of the key constraints is the cell wall and membrane.The cell wall is also important for stress-resistant properties andadherence to other cells and surfaces. Martinez and colleaguesdescribe the biochemistry of cell walls in LAB, and discuss thechallenges, insults and defenses that LAB have evolved to copewith in the nutrient-rich environments as well as in stressfulones. They show the crucial interplay between cell wall biosyn-thesis and global cellular metabolism, guiding the plasticity ofthe wall. Moreover, the important role of the bacterial cell wallin phage adsorption and bacteriocin activity is discussed, show-ing both a receptor and a defensive role of the cell wall. Over-all, this underscores the importance of understanding cell wallstructure and function to develop novel applications of LAB inhealth and biotechnology.We hope that this thematic issue will be of interest to manyresearchers inside and outside of the LAB field, and that it willinspire many to attend the thirteenth International Symposiumon Lactic Acid bacteria in 2021.REFERENCESBruggeman F, Planqué R, Teusink B. Predicting microbial phys-iology from biochemical and evolutionary principles. FEMSMicrobiol Rev 2020;44:821–44.De Filippis F, Pasolli E, Ercolini D. Food-gut axis, lactic acid bac-teria and their link, role and relevance for gut microbiomehealth and functions. FEMS Microbiol Rev 2020;44:454–89.De Vuyst L, Leroy F. Functional role of lactic acid bacte-ria in cocoa fermentation processes. FEMS Microbiol Rev2020;44:432–53.Kleerebezem M, Bachmann H, van Pelt-KleinJan E et al. Growthrate and physiology of Lactococcus lactis. FEMS Microbiol Rev2020;44:804–20.Martı́nez B, Rodrı́guez A, Kulakauskas S et al. Cell wall home-ostasis in LAB: insults and defenses. FEMS Microbiol Rev2020;44:538–64.Rasmussen TS, Koefoed AK, Jakobsen RR et al. Bacteriophagesand antimicrobials in gut and vaginal tracks. FEMS MicrobiolRev 2020;44:507–21.Roberts A, Barrangou R. Functions and applications of CRISPR-Cas systems in lactic acid bacteria. FEMS Microbiol Rev2020;44:523–37.Romero D, Magill D, Millen A et al. Dairy lactococcal and strepto-coccal phage-host interactions: industrial perspective in anevolving phage landscape. FEMS Microbiol Rev 2020;44:909–32.Saak CC, Dinh CB, Dutton RJ. Horizontal gene transfer withinmicrobial communities. FEMS Microbiol Rev 2020;44:606–30.Wang S, Egan M, Ryan CA et al. A good start in life is important-perinatal factors dictate early microbiota development andlonger term maturation. FEMS Microbiol Rev 2020;44:763–81.Wong CB, Odamaki T, Xiao J-Z. The physiology of bifidobacteria.FEMS Microbiol Rev 2020;44:369–85.Bas TeusinkAmsterdam Institute of Molecular and Life Sciences (AIMMS), VrijeUniversiteit Amsterdam, O2 building, location code 2E51, DeBoelelaan 1085, NL-1081HV Amsterdam, The NetherlandsOscar P. KuipersMolecular Genetics, University of Groningen, Nijenborgh 7(Linnaeusborg, building 5172, room 6.50), 9747AG Groningen theNetherlands, The NetherlandsSylvain MoineauDépartement de biochimie, de microbiologie, et de bio-informatique,Faculté des sciences et de génie1045, avenue de la MédecineUniversitéLaval, Québec, Canada, G1V 0A6Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 2021

Symposium on Lactic Acid Bacteria-reading while waiting for a meeting

Dissertations of the University of Groningen

   University of GroningenSymposium on Lactic Acid Bacteria-reading while waiting for a meetingTeusink, Bas; Kuipers, Oscar P; Moineau, SylvainPublished in:FEMS Microbiology ReviewsDOI:10.1093/femsre/fuaa049IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2021Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Teusink, B., Kuipers, O. P., & Moineau, S. (2021). Symposium on Lactic Acid Bacteria-reading whilewaiting for a meeting. FEMS Microbiology Reviews, 45(2), Article fuaa049. Advance online publication.https://doi.org/10.1093/femsre/fuaa049CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 31-10-2023FEMS Microbiology Reviews, fuaa049, 45, 2020, 1–2doi: 10.1093/femsre/fuaa049EditorialSymposium on Lactic Acid Bacteria—reading while waiting for ameetingThis special thematic issue of FEMS Microbiology Reviews istruly special, because it contains contributions to a meetingthat is yet to happen! As many others, the thirteenth Interna-tional Symposium on Lactic Acid Bacteria (LAB13) was a victimof the COVID-19 pandemic and has been postponed to next year.The conference is held every 3 years in The Netherlands, and isattended by researchers from academia and industry from allover the world, reflecting the importance of these microorgan-isms in food, health and basic science. As a tradition, the invitedspeakers are asked to contribute not only by a talk, but also by athorough review on the topic of their presentation. These paperswere already under review by the time it became clear that thecoronavirus would not be contained and that we had to post-pone the meeting. However, we decided to move on and publishthe reviews now, when still timely, and we are eagerly awaitingupdated presentations next summer.Lactic acid bacteria, or LAB for friends, are a group of phyloge-netically diverse, but metabolically rather similar, bacteria. Theyplay important roles in food and feed fermentations, where theycontribute to safe, healthy and tasty food. Some strains haveprobiotic properties and they are even potential delivery vehi-cles for (oral) vaccines. They are selected from spontaneouslyfermented products or through evolution experiments in thelaboratory. They are screened for desired flavor-producing prop-erties, or for antimicrobials that they produce to defend theiroften nutrient-rich niches. They need to defend against (bacte-rial) viruses, which are a significant risk for industrial food fer-mentations. They are studied for their metabolism and phys-iology, in isolation or increasingly in the context of microbialconsortia such as the human microbiome or complex fermentedfoods. These broad topics are discussed at the LAB Symposiumseries, and this issue reflects the current state of the art of theexciting and diverse field of LAB research.Research into viruses—bacteriophages in the case of bac-terial viruses—has never been more pressing than in currentpandemic times, but has been a focal area in LAB research fordecades. It is not only a threat to industrial production pro-cesses, but fundamental studies on the clustered regularly inter-spaced short palindromic repeats (CRISPR)-CRISPR-associated(Cas) systems in Streptococcus thermophilus led to the discoveryof the molecular mechanisms of this adaptive immune system.We have come a long way since then. Roberts and Barrangou dis-cuss the history, the different systems and their mode of actionand highlights the applications of the CRISPR-Cas system in thecontext of LAB.While CRISPR-Cas systems may limit horizontal geneexchange in some LAB species, bacteria have still numerousways to exchange genes as mobile genetic elements are driversof microbial evolution. Various mechanisms of horizontal genetransfer can also occur in microbial communities. However,monitoring DNA transfers and their effects in these communi-ties has been challenging. Christina Saak and colleagues exploreexisting and emerging technologies for tracking mobile ele-ments and assigning them to microbes in order to generatecomprehensive community-level information. They also makethe case that LAB-driven fermented foods are, among others,ideal models to apply these techniques and address outstand-ing questions in the field of horizontal gene transfer in microbialcommunities.Dennis Romero and colleagues address phage–host interac-tions in Lactococcus lactis and Streptococcus thermophilus. They pro-vide a timely overview of the diversity of these phages and theirbiology, as well as the defence mechanisms operating in theseLAB. This knowledge has led to improved industrial starter cul-tures, e.g. specifically designed and adapted to prevent fermen-tation delays and low-quality fermented products. The authorsalso describe the oldest and still highly dynamic arms racebetween prey and predator and its relevance for developingrobust dairy fermentation processes.While phages are arguably the master regulators of LAB com-munities, they also likely play a role in other ecosystems, includ-ing the human gut. The function and composition of our gutmicrobiome are clearly linked to human health. Consequently,the promise of being able to precisely modulate this microbialcommunity has become an area of intense research worldwide.Torben Rasmussen and colleagues discuss the promises andlimitations of fecal microbiota transplantation, which offers anattractive therapeutic strategy for patients suffering from gutdysbiosis and bacterial infections. Growing evidence also sug-gests that cascading effects are initiated when phage commu-nities are also transferred to the gut, which leads to changes inits microbial composition and the host metabolome as well asimproving health.As the role of microorganisms in intestinal health hasbecome clearer with every LAB symposium due to advancedtools and new databases, we have invited a number of contribu-tions related to this topic. Shaopu Wang and colleagues reviewReceived: 16 September 2020; Accepted: 28 September 2020C© The Author(s) 2020. Published by Oxford University Press on behalf of FEMS. This is an Open Access article distributed under the terms of theCreative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, andreproduction in any medium, provided the original work is properly cited.1Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 20212 FEMS Microbiology Reviews, 2021, Vol. 45, No. 2the impact of early-life exposures on the microbiota develop-ment during childhood, and how this affects health at a laterage. They identify ‘golden’ perinatal factors and risk factors thatimpact on physiology, immunity and even cognitive develop-ment. They also describe possible interventions and their poten-tial.One of the first colonizers of the human gut are bifidobacte-ria, which are strictly speaking not LAB, but whose LAB-assistedapplications, metabolism and impact on gut health warrant aplace in this thematic issue. Chyn Wong and colleagues describethe biology and physiology of the Human Residential Bifidobac-teria, and what factors contribute to their ecological fitness.These factors may be used for the selection of ‘bifido’ strainswith desired properties and health benefits. Strain selection isalso essential for the production of healthy fermented foods.Francesca De Filippis and colleagues discuss the role of fer-mented foods as a source of potentially probiotic LAB, and howto mine the wealth of genomics and metagenomics data withbioinformatics and data analysis tools. While more researchis still needed to better understand the health benefits of fer-mented foods and their associated LAB, the field keeps progress-ing between each LAB Symposium.De Vuyst and Leroy looked at fermentation processes anddescribe in particular how yeasts, acetic acid bacteria and LABcollaborate during the fermentation of cocoa beans, a necessarystep to obtain the chocolate flavors we love so much. The com-plexity of food fermentations is in full display, yet it also showsthe great progress made in our understanding of the interactionsand the physiology of these microorganisms through a combi-nation of (functional) genomics, controlled fermentations andmodeling. Michiel Kleerebezem and colleagues review the latestinsights into the physiology of Lactococcus lactis, one of the keyspecies in starter cultures for a.o. cheesemaking, and an impor-tant model for LAB research. They describe both the functionalgenomics and bacterial physiology approaches to understandthe adaptation of L. lactis to different environmental conditions,including zero growth conditions that are relevant for cheeseripening. L. lactis was also the first LAB for which a genome-scale metabolic model was developed. Frank Bruggeman andcolleagues take us on a journey into the theory of bacterial phys-iology and growth that forms the rationale for all constraint-based modeling approaches. They show from first principleshow the strategy of growth rate (fitness) maximization underbiochemical constraints can explain a surprisingly large part ofmicrobial behavior, from L. lactis to Escherichia coli to yeast. Thisincludes stress resistance, overflow metabolism and cataboliterepression.Finally, as LAB take up many nutrients from the environ-ment, one of the key constraints is the cell wall and membrane.The cell wall is also important for stress-resistant properties andadherence to other cells and surfaces. Martinez and colleaguesdescribe the biochemistry of cell walls in LAB, and discuss thechallenges, insults and defenses that LAB have evolved to copewith in the nutrient-rich environments as well as in stressfulones. They show the crucial interplay between cell wall biosyn-thesis and global cellular metabolism, guiding the plasticity ofthe wall. Moreover, the important role of the bacterial cell wallin phage adsorption and bacteriocin activity is discussed, show-ing both a receptor and a defensive role of the cell wall. Over-all, this underscores the importance of understanding cell wallstructure and function to develop novel applications of LAB inhealth and biotechnology.We hope that this thematic issue will be of interest to manyresearchers inside and outside of the LAB field, and that it willinspire many to attend the thirteenth International Symposiumon Lactic Acid bacteria in 2021.REFERENCESBruggeman F, Planqué R, Teusink B. Predicting microbial phys-iology from biochemical and evolutionary principles. FEMSMicrobiol Rev 2020;44:821–44.De Filippis F, Pasolli E, Ercolini D. Food-gut axis, lactic acid bac-teria and their link, role and relevance for gut microbiomehealth and functions. FEMS Microbiol Rev 2020;44:454–89.De Vuyst L, Leroy F. Functional role of lactic acid bacte-ria in cocoa fermentation processes. FEMS Microbiol Rev2020;44:432–53.Kleerebezem M, Bachmann H, van Pelt-KleinJan E et al. Growthrate and physiology of Lactococcus lactis. FEMS Microbiol Rev2020;44:804–20.Martı́nez B, Rodrı́guez A, Kulakauskas S et al. Cell wall home-ostasis in LAB: insults and defenses. FEMS Microbiol Rev2020;44:538–64.Rasmussen TS, Koefoed AK, Jakobsen RR et al. Bacteriophagesand antimicrobials in gut and vaginal tracks. FEMS MicrobiolRev 2020;44:507–21.Roberts A, Barrangou R. Functions and applications of CRISPR-Cas systems in lactic acid bacteria. FEMS Microbiol Rev2020;44:523–37.Romero D, Magill D, Millen A et al. Dairy lactococcal and strepto-coccal phage-host interactions: industrial perspective in anevolving phage landscape. FEMS Microbiol Rev 2020;44:909–32.Saak CC, Dinh CB, Dutton RJ. Horizontal gene transfer withinmicrobial communities. FEMS Microbiol Rev 2020;44:606–30.Wang S, Egan M, Ryan CA et al. A good start in life is important-perinatal factors dictate early microbiota development andlonger term maturation. FEMS Microbiol Rev 2020;44:763–81.Wong CB, Odamaki T, Xiao J-Z. The physiology of bifidobacteria.FEMS Microbiol Rev 2020;44:369–85.Bas TeusinkAmsterdam Institute of Molecular and Life Sciences (AIMMS), VrijeUniversiteit Amsterdam, O2 building, location code 2E51, DeBoelelaan 1085, NL-1081HV Amsterdam, The NetherlandsOscar P. KuipersMolecular Genetics, University of Groningen, Nijenborgh 7(Linnaeusborg, building 5172, room 6.50), 9747AG Groningen theNetherlands, The NetherlandsSylvain MoineauDépartement de biochimie, de microbiologie, et de bio-informatique,Faculté des sciences et de génie1045, avenue de la MédecineUniversitéLaval, Québec, Canada, G1V 0A6Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 2021

University of Groningen

   University of GroningenSymposium on Lactic Acid Bacteria-reading while waiting for a meetingTeusink, Bas; Kuipers, Oscar P; Moineau, SylvainPublished in:FEMS Microbiology ReviewsDOI:10.1093/femsre/fuaa049IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2021Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Teusink, B., Kuipers, O. P., & Moineau, S. (2021). Symposium on Lactic Acid Bacteria-reading whilewaiting for a meeting. FEMS Microbiology Reviews, 45(2), [fuaa049].https://doi.org/10.1093/femsre/fuaa049CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 19-11-2022FEMS Microbiology Reviews, fuaa049, 45, 2020, 1–2doi: 10.1093/femsre/fuaa049EditorialSymposium on Lactic Acid Bacteria—reading while waiting for ameetingThis special thematic issue of FEMS Microbiology Reviews istruly special, because it contains contributions to a meetingthat is yet to happen! As many others, the thirteenth Interna-tional Symposium on Lactic Acid Bacteria (LAB13) was a victimof the COVID-19 pandemic and has been postponed to next year.The conference is held every 3 years in The Netherlands, and isattended by researchers from academia and industry from allover the world, reflecting the importance of these microorgan-isms in food, health and basic science. As a tradition, the invitedspeakers are asked to contribute not only by a talk, but also by athorough review on the topic of their presentation. These paperswere already under review by the time it became clear that thecoronavirus would not be contained and that we had to post-pone the meeting. However, we decided to move on and publishthe reviews now, when still timely, and we are eagerly awaitingupdated presentations next summer.Lactic acid bacteria, or LAB for friends, are a group of phyloge-netically diverse, but metabolically rather similar, bacteria. Theyplay important roles in food and feed fermentations, where theycontribute to safe, healthy and tasty food. Some strains haveprobiotic properties and they are even potential delivery vehi-cles for (oral) vaccines. They are selected from spontaneouslyfermented products or through evolution experiments in thelaboratory. They are screened for desired flavor-producing prop-erties, or for antimicrobials that they produce to defend theiroften nutrient-rich niches. They need to defend against (bacte-rial) viruses, which are a significant risk for industrial food fer-mentations. They are studied for their metabolism and phys-iology, in isolation or increasingly in the context of microbialconsortia such as the human microbiome or complex fermentedfoods. These broad topics are discussed at the LAB Symposiumseries, and this issue reflects the current state of the art of theexciting and diverse field of LAB research.Research into viruses—bacteriophages in the case of bac-terial viruses—has never been more pressing than in currentpandemic times, but has been a focal area in LAB research fordecades. It is not only a threat to industrial production pro-cesses, but fundamental studies on the clustered regularly inter-spaced short palindromic repeats (CRISPR)-CRISPR-associated(Cas) systems in Streptococcus thermophilus led to the discoveryof the molecular mechanisms of this adaptive immune system.We have come a long way since then. Roberts and Barrangou dis-cuss the history, the different systems and their mode of actionand highlights the applications of the CRISPR-Cas system in thecontext of LAB.While CRISPR-Cas systems may limit horizontal geneexchange in some LAB species, bacteria have still numerousways to exchange genes as mobile genetic elements are driversof microbial evolution. Various mechanisms of horizontal genetransfer can also occur in microbial communities. However,monitoring DNA transfers and their effects in these communi-ties has been challenging. Christina Saak and colleagues exploreexisting and emerging technologies for tracking mobile ele-ments and assigning them to microbes in order to generatecomprehensive community-level information. They also makethe case that LAB-driven fermented foods are, among others,ideal models to apply these techniques and address outstand-ing questions in the field of horizontal gene transfer in microbialcommunities.Dennis Romero and colleagues address phage–host interac-tions in Lactococcus lactis and Streptococcus thermophilus. They pro-vide a timely overview of the diversity of these phages and theirbiology, as well as the defence mechanisms operating in theseLAB. This knowledge has led to improved industrial starter cul-tures, e.g. specifically designed and adapted to prevent fermen-tation delays and low-quality fermented products. The authorsalso describe the oldest and still highly dynamic arms racebetween prey and predator and its relevance for developingrobust dairy fermentation processes.While phages are arguably the master regulators of LAB com-munities, they also likely play a role in other ecosystems, includ-ing the human gut. The function and composition of our gutmicrobiome are clearly linked to human health. Consequently,the promise of being able to precisely modulate this microbialcommunity has become an area of intense research worldwide.Torben Rasmussen and colleagues discuss the promises andlimitations of fecal microbiota transplantation, which offers anattractive therapeutic strategy for patients suffering from gutdysbiosis and bacterial infections. Growing evidence also sug-gests that cascading effects are initiated when phage commu-nities are also transferred to the gut, which leads to changes inits microbial composition and the host metabolome as well asimproving health.As the role of microorganisms in intestinal health hasbecome clearer with every LAB symposium due to advancedtools and new databases, we have invited a number of contribu-tions related to this topic. Shaopu Wang and colleagues reviewReceived: 16 September 2020; Accepted: 28 September 2020C© The Author(s) 2020. Published by Oxford University Press on behalf of FEMS. This is an Open Access article distributed under the terms of theCreative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, andreproduction in any medium, provided the original work is properly cited.1Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 20212 FEMS Microbiology Reviews, 2021, Vol. 45, No. 2the impact of early-life exposures on the microbiota develop-ment during childhood, and how this affects health at a laterage. They identify ‘golden’ perinatal factors and risk factors thatimpact on physiology, immunity and even cognitive develop-ment. They also describe possible interventions and their poten-tial.One of the first colonizers of the human gut are bifidobacte-ria, which are strictly speaking not LAB, but whose LAB-assistedapplications, metabolism and impact on gut health warrant aplace in this thematic issue. Chyn Wong and colleagues describethe biology and physiology of the Human Residential Bifidobac-teria, and what factors contribute to their ecological fitness.These factors may be used for the selection of ‘bifido’ strainswith desired properties and health benefits. Strain selection isalso essential for the production of healthy fermented foods.Francesca De Filippis and colleagues discuss the role of fer-mented foods as a source of potentially probiotic LAB, and howto mine the wealth of genomics and metagenomics data withbioinformatics and data analysis tools. While more researchis still needed to better understand the health benefits of fer-mented foods and their associated LAB, the field keeps progress-ing between each LAB Symposium.De Vuyst and Leroy looked at fermentation processes anddescribe in particular how yeasts, acetic acid bacteria and LABcollaborate during the fermentation of cocoa beans, a necessarystep to obtain the chocolate flavors we love so much. The com-plexity of food fermentations is in full display, yet it also showsthe great progress made in our understanding of the interactionsand the physiology of these microorganisms through a combi-nation of (functional) genomics, controlled fermentations andmodeling. Michiel Kleerebezem and colleagues review the latestinsights into the physiology of Lactococcus lactis, one of the keyspecies in starter cultures for a.o. cheesemaking, and an impor-tant model for LAB research. They describe both the functionalgenomics and bacterial physiology approaches to understandthe adaptation of L. lactis to different environmental conditions,including zero growth conditions that are relevant for cheeseripening. L. lactis was also the first LAB for which a genome-scale metabolic model was developed. Frank Bruggeman andcolleagues take us on a journey into the theory of bacterial phys-iology and growth that forms the rationale for all constraint-based modeling approaches. They show from first principleshow the strategy of growth rate (fitness) maximization underbiochemical constraints can explain a surprisingly large part ofmicrobial behavior, from L. lactis to Escherichia coli to yeast. Thisincludes stress resistance, overflow metabolism and cataboliterepression.Finally, as LAB take up many nutrients from the environ-ment, one of the key constraints is the cell wall and membrane.The cell wall is also important for stress-resistant properties andadherence to other cells and surfaces. Martinez and colleaguesdescribe the biochemistry of cell walls in LAB, and discuss thechallenges, insults and defenses that LAB have evolved to copewith in the nutrient-rich environments as well as in stressfulones. They show the crucial interplay between cell wall biosyn-thesis and global cellular metabolism, guiding the plasticity ofthe wall. Moreover, the important role of the bacterial cell wallin phage adsorption and bacteriocin activity is discussed, show-ing both a receptor and a defensive role of the cell wall. Over-all, this underscores the importance of understanding cell wallstructure and function to develop novel applications of LAB inhealth and biotechnology.We hope that this thematic issue will be of interest to manyresearchers inside and outside of the LAB field, and that it willinspire many to attend the thirteenth International Symposiumon Lactic Acid bacteria in 2021.REFERENCESBruggeman F, Planqué R, Teusink B. Predicting microbial phys-iology from biochemical and evolutionary principles. FEMSMicrobiol Rev 2020;44:821–44.De Filippis F, Pasolli E, Ercolini D. Food-gut axis, lactic acid bac-teria and their link, role and relevance for gut microbiomehealth and functions. FEMS Microbiol Rev 2020;44:454–89.De Vuyst L, Leroy F. Functional role of lactic acid bacte-ria in cocoa fermentation processes. FEMS Microbiol Rev2020;44:432–53.Kleerebezem M, Bachmann H, van Pelt-KleinJan E et al. Growthrate and physiology of Lactococcus lactis. FEMS Microbiol Rev2020;44:804–20.Martı́nez B, Rodrı́guez A, Kulakauskas S et al. Cell wall home-ostasis in LAB: insults and defenses. FEMS Microbiol Rev2020;44:538–64.Rasmussen TS, Koefoed AK, Jakobsen RR et al. Bacteriophagesand antimicrobials in gut and vaginal tracks. FEMS MicrobiolRev 2020;44:507–21.Roberts A, Barrangou R. Functions and applications of CRISPR-Cas systems in lactic acid bacteria. FEMS Microbiol Rev2020;44:523–37.Romero D, Magill D, Millen A et al. Dairy lactococcal and strepto-coccal phage-host interactions: industrial perspective in anevolving phage landscape. FEMS Microbiol Rev 2020;44:909–32.Saak CC, Dinh CB, Dutton RJ. Horizontal gene transfer withinmicrobial communities. FEMS Microbiol Rev 2020;44:606–30.Wang S, Egan M, Ryan CA et al. A good start in life is important-perinatal factors dictate early microbiota development andlonger term maturation. FEMS Microbiol Rev 2020;44:763–81.Wong CB, Odamaki T, Xiao J-Z. The physiology of bifidobacteria.FEMS Microbiol Rev 2020;44:369–85.Bas TeusinkAmsterdam Institute of Molecular and Life Sciences (AIMMS), VrijeUniversiteit Amsterdam, O2 building, location code 2E51, DeBoelelaan 1085, NL-1081HV Amsterdam, The NetherlandsOscar P. KuipersMolecular Genetics, University of Groningen, Nijenborgh 7(Linnaeusborg, building 5172, room 6.50), 9747AG Groningen theNetherlands, The NetherlandsSylvain MoineauDépartement de biochimie, de microbiologie, et de bio-informatique,Faculté des sciences et de génie1045, avenue de la MédecineUniversitéLaval, Québec, Canada, G1V 0A6Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 2021

   University of GroningenSymposium on Lactic Acid Bacteria-reading while waiting for a meetingTeusink, Bas; Kuipers, Oscar P; Moineau, SylvainPublished in:FEMS Microbiology ReviewsDOI:10.1093/femsre/fuaa049IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2021Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Teusink, B., Kuipers, O. P., & Moineau, S. (2021). Symposium on Lactic Acid Bacteria-reading whilewaiting for a meeting. FEMS Microbiology Reviews, 45(2), [fuaa049].https://doi.org/10.1093/femsre/fuaa049CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 29-04-2023FEMS Microbiology Reviews, fuaa049, 45, 2020, 1–2doi: 10.1093/femsre/fuaa049EditorialSymposium on Lactic Acid Bacteria—reading while waiting for ameetingThis special thematic issue of FEMS Microbiology Reviews istruly special, because it contains contributions to a meetingthat is yet to happen! As many others, the thirteenth Interna-tional Symposium on Lactic Acid Bacteria (LAB13) was a victimof the COVID-19 pandemic and has been postponed to next year.The conference is held every 3 years in The Netherlands, and isattended by researchers from academia and industry from allover the world, reflecting the importance of these microorgan-isms in food, health and basic science. As a tradition, the invitedspeakers are asked to contribute not only by a talk, but also by athorough review on the topic of their presentation. These paperswere already under review by the time it became clear that thecoronavirus would not be contained and that we had to post-pone the meeting. However, we decided to move on and publishthe reviews now, when still timely, and we are eagerly awaitingupdated presentations next summer.Lactic acid bacteria, or LAB for friends, are a group of phyloge-netically diverse, but metabolically rather similar, bacteria. Theyplay important roles in food and feed fermentations, where theycontribute to safe, healthy and tasty food. Some strains haveprobiotic properties and they are even potential delivery vehi-cles for (oral) vaccines. They are selected from spontaneouslyfermented products or through evolution experiments in thelaboratory. They are screened for desired flavor-producing prop-erties, or for antimicrobials that they produce to defend theiroften nutrient-rich niches. They need to defend against (bacte-rial) viruses, which are a significant risk for industrial food fer-mentations. They are studied for their metabolism and phys-iology, in isolation or increasingly in the context of microbialconsortia such as the human microbiome or complex fermentedfoods. These broad topics are discussed at the LAB Symposiumseries, and this issue reflects the current state of the art of theexciting and diverse field of LAB research.Research into viruses—bacteriophages in the case of bac-terial viruses—has never been more pressing than in currentpandemic times, but has been a focal area in LAB research fordecades. It is not only a threat to industrial production pro-cesses, but fundamental studies on the clustered regularly inter-spaced short palindromic repeats (CRISPR)-CRISPR-associated(Cas) systems in Streptococcus thermophilus led to the discoveryof the molecular mechanisms of this adaptive immune system.We have come a long way since then. Roberts and Barrangou dis-cuss the history, the different systems and their mode of actionand highlights the applications of the CRISPR-Cas system in thecontext of LAB.While CRISPR-Cas systems may limit horizontal geneexchange in some LAB species, bacteria have still numerousways to exchange genes as mobile genetic elements are driversof microbial evolution. Various mechanisms of horizontal genetransfer can also occur in microbial communities. However,monitoring DNA transfers and their effects in these communi-ties has been challenging. Christina Saak and colleagues exploreexisting and emerging technologies for tracking mobile ele-ments and assigning them to microbes in order to generatecomprehensive community-level information. They also makethe case that LAB-driven fermented foods are, among others,ideal models to apply these techniques and address outstand-ing questions in the field of horizontal gene transfer in microbialcommunities.Dennis Romero and colleagues address phage–host interac-tions in Lactococcus lactis and Streptococcus thermophilus. They pro-vide a timely overview of the diversity of these phages and theirbiology, as well as the defence mechanisms operating in theseLAB. This knowledge has led to improved industrial starter cul-tures, e.g. specifically designed and adapted to prevent fermen-tation delays and low-quality fermented products. The authorsalso describe the oldest and still highly dynamic arms racebetween prey and predator and its relevance for developingrobust dairy fermentation processes.While phages are arguably the master regulators of LAB com-munities, they also likely play a role in other ecosystems, includ-ing the human gut. The function and composition of our gutmicrobiome are clearly linked to human health. Consequently,the promise of being able to precisely modulate this microbialcommunity has become an area of intense research worldwide.Torben Rasmussen and colleagues discuss the promises andlimitations of fecal microbiota transplantation, which offers anattractive therapeutic strategy for patients suffering from gutdysbiosis and bacterial infections. Growing evidence also sug-gests that cascading effects are initiated when phage commu-nities are also transferred to the gut, which leads to changes inits microbial composition and the host metabolome as well asimproving health.As the role of microorganisms in intestinal health hasbecome clearer with every LAB symposium due to advancedtools and new databases, we have invited a number of contribu-tions related to this topic. Shaopu Wang and colleagues reviewReceived: 16 September 2020; Accepted: 28 September 2020C© The Author(s) 2020. Published by Oxford University Press on behalf of FEMS. This is an Open Access article distributed under the terms of theCreative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, andreproduction in any medium, provided the original work is properly cited.1Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 20212 FEMS Microbiology Reviews, 2021, Vol. 45, No. 2the impact of early-life exposures on the microbiota develop-ment during childhood, and how this affects health at a laterage. They identify ‘golden’ perinatal factors and risk factors thatimpact on physiology, immunity and even cognitive develop-ment. They also describe possible interventions and their poten-tial.One of the first colonizers of the human gut are bifidobacte-ria, which are strictly speaking not LAB, but whose LAB-assistedapplications, metabolism and impact on gut health warrant aplace in this thematic issue. Chyn Wong and colleagues describethe biology and physiology of the Human Residential Bifidobac-teria, and what factors contribute to their ecological fitness.These factors may be used for the selection of ‘bifido’ strainswith desired properties and health benefits. Strain selection isalso essential for the production of healthy fermented foods.Francesca De Filippis and colleagues discuss the role of fer-mented foods as a source of potentially probiotic LAB, and howto mine the wealth of genomics and metagenomics data withbioinformatics and data analysis tools. While more researchis still needed to better understand the health benefits of fer-mented foods and their associated LAB, the field keeps progress-ing between each LAB Symposium.De Vuyst and Leroy looked at fermentation processes anddescribe in particular how yeasts, acetic acid bacteria and LABcollaborate during the fermentation of cocoa beans, a necessarystep to obtain the chocolate flavors we love so much. The com-plexity of food fermentations is in full display, yet it also showsthe great progress made in our understanding of the interactionsand the physiology of these microorganisms through a combi-nation of (functional) genomics, controlled fermentations andmodeling. Michiel Kleerebezem and colleagues review the latestinsights into the physiology of Lactococcus lactis, one of the keyspecies in starter cultures for a.o. cheesemaking, and an impor-tant model for LAB research. They describe both the functionalgenomics and bacterial physiology approaches to understandthe adaptation of L. lactis to different environmental conditions,including zero growth conditions that are relevant for cheeseripening. L. lactis was also the first LAB for which a genome-scale metabolic model was developed. Frank Bruggeman andcolleagues take us on a journey into the theory of bacterial phys-iology and growth that forms the rationale for all constraint-based modeling approaches. They show from first principleshow the strategy of growth rate (fitness) maximization underbiochemical constraints can explain a surprisingly large part ofmicrobial behavior, from L. lactis to Escherichia coli to yeast. Thisincludes stress resistance, overflow metabolism and cataboliterepression.Finally, as LAB take up many nutrients from the environ-ment, one of the key constraints is the cell wall and membrane.The cell wall is also important for stress-resistant properties andadherence to other cells and surfaces. Martinez and colleaguesdescribe the biochemistry of cell walls in LAB, and discuss thechallenges, insults and defenses that LAB have evolved to copewith in the nutrient-rich environments as well as in stressfulones. They show the crucial interplay between cell wall biosyn-thesis and global cellular metabolism, guiding the plasticity ofthe wall. Moreover, the important role of the bacterial cell wallin phage adsorption and bacteriocin activity is discussed, show-ing both a receptor and a defensive role of the cell wall. Over-all, this underscores the importance of understanding cell wallstructure and function to develop novel applications of LAB inhealth and biotechnology.We hope that this thematic issue will be of interest to manyresearchers inside and outside of the LAB field, and that it willinspire many to attend the thirteenth International Symposiumon Lactic Acid bacteria in 2021.REFERENCESBruggeman F, Planqué R, Teusink B. Predicting microbial phys-iology from biochemical and evolutionary principles. FEMSMicrobiol Rev 2020;44:821–44.De Filippis F, Pasolli E, Ercolini D. Food-gut axis, lactic acid bac-teria and their link, role and relevance for gut microbiomehealth and functions. FEMS Microbiol Rev 2020;44:454–89.De Vuyst L, Leroy F. Functional role of lactic acid bacte-ria in cocoa fermentation processes. FEMS Microbiol Rev2020;44:432–53.Kleerebezem M, Bachmann H, van Pelt-KleinJan E et al. Growthrate and physiology of Lactococcus lactis. FEMS Microbiol Rev2020;44:804–20.Martı́nez B, Rodrı́guez A, Kulakauskas S et al. Cell wall home-ostasis in LAB: insults and defenses. FEMS Microbiol Rev2020;44:538–64.Rasmussen TS, Koefoed AK, Jakobsen RR et al. Bacteriophagesand antimicrobials in gut and vaginal tracks. FEMS MicrobiolRev 2020;44:507–21.Roberts A, Barrangou R. Functions and applications of CRISPR-Cas systems in lactic acid bacteria. FEMS Microbiol Rev2020;44:523–37.Romero D, Magill D, Millen A et al. Dairy lactococcal and strepto-coccal phage-host interactions: industrial perspective in anevolving phage landscape. FEMS Microbiol Rev 2020;44:909–32.Saak CC, Dinh CB, Dutton RJ. Horizontal gene transfer withinmicrobial communities. FEMS Microbiol Rev 2020;44:606–30.Wang S, Egan M, Ryan CA et al. A good start in life is important-perinatal factors dictate early microbiota development andlonger term maturation. FEMS Microbiol Rev 2020;44:763–81.Wong CB, Odamaki T, Xiao J-Z. The physiology of bifidobacteria.FEMS Microbiol Rev 2020;44:369–85.Bas TeusinkAmsterdam Institute of Molecular and Life Sciences (AIMMS), VrijeUniversiteit Amsterdam, O2 building, location code 2E51, DeBoelelaan 1085, NL-1081HV Amsterdam, The NetherlandsOscar P. KuipersMolecular Genetics, University of Groningen, Nijenborgh 7(Linnaeusborg, building 5172, room 6.50), 9747AG Groningen theNetherlands, The NetherlandsSylvain MoineauDépartement de biochimie, de microbiologie, et de bio-informatique,Faculté des sciences et de génie1045, avenue de la MédecineUniversitéLaval, Québec, Canada, G1V 0A6Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 2021

Kuipers, Oscar P.

NARCIS 

ARTS repository - University of Groningen

   University of GroningenSymposium on Lactic Acid Bacteria-reading while waiting for a meetingTeusink, Bas; Kuipers, Oscar P; Moineau, SylvainPublished in:FEMS Microbiology ReviewsDOI:10.1093/femsre/fuaa049IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2021Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Teusink, B., Kuipers, O. P., & Moineau, S. (2021). Symposium on Lactic Acid Bacteria-reading whilewaiting for a meeting. FEMS Microbiology Reviews, 45(2), Article fuaa049. Advance online publication.https://doi.org/10.1093/femsre/fuaa049CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 10-09-2023FEMS Microbiology Reviews, fuaa049, 45, 2020, 1–2doi: 10.1093/femsre/fuaa049EditorialSymposium on Lactic Acid Bacteria—reading while waiting for ameetingThis special thematic issue of FEMS Microbiology Reviews istruly special, because it contains contributions to a meetingthat is yet to happen! As many others, the thirteenth Interna-tional Symposium on Lactic Acid Bacteria (LAB13) was a victimof the COVID-19 pandemic and has been postponed to next year.The conference is held every 3 years in The Netherlands, and isattended by researchers from academia and industry from allover the world, reflecting the importance of these microorgan-isms in food, health and basic science. As a tradition, the invitedspeakers are asked to contribute not only by a talk, but also by athorough review on the topic of their presentation. These paperswere already under review by the time it became clear that thecoronavirus would not be contained and that we had to post-pone the meeting. However, we decided to move on and publishthe reviews now, when still timely, and we are eagerly awaitingupdated presentations next summer.Lactic acid bacteria, or LAB for friends, are a group of phyloge-netically diverse, but metabolically rather similar, bacteria. Theyplay important roles in food and feed fermentations, where theycontribute to safe, healthy and tasty food. Some strains haveprobiotic properties and they are even potential delivery vehi-cles for (oral) vaccines. They are selected from spontaneouslyfermented products or through evolution experiments in thelaboratory. They are screened for desired flavor-producing prop-erties, or for antimicrobials that they produce to defend theiroften nutrient-rich niches. They need to defend against (bacte-rial) viruses, which are a significant risk for industrial food fer-mentations. They are studied for their metabolism and phys-iology, in isolation or increasingly in the context of microbialconsortia such as the human microbiome or complex fermentedfoods. These broad topics are discussed at the LAB Symposiumseries, and this issue reflects the current state of the art of theexciting and diverse field of LAB research.Research into viruses—bacteriophages in the case of bac-terial viruses—has never been more pressing than in currentpandemic times, but has been a focal area in LAB research fordecades. It is not only a threat to industrial production pro-cesses, but fundamental studies on the clustered regularly inter-spaced short palindromic repeats (CRISPR)-CRISPR-associated(Cas) systems in Streptococcus thermophilus led to the discoveryof the molecular mechanisms of this adaptive immune system.We have come a long way since then. Roberts and Barrangou dis-cuss the history, the different systems and their mode of actionand highlights the applications of the CRISPR-Cas system in thecontext of LAB.While CRISPR-Cas systems may limit horizontal geneexchange in some LAB species, bacteria have still numerousways to exchange genes as mobile genetic elements are driversof microbial evolution. Various mechanisms of horizontal genetransfer can also occur in microbial communities. However,monitoring DNA transfers and their effects in these communi-ties has been challenging. Christina Saak and colleagues exploreexisting and emerging technologies for tracking mobile ele-ments and assigning them to microbes in order to generatecomprehensive community-level information. They also makethe case that LAB-driven fermented foods are, among others,ideal models to apply these techniques and address outstand-ing questions in the field of horizontal gene transfer in microbialcommunities.Dennis Romero and colleagues address phage–host interac-tions in Lactococcus lactis and Streptococcus thermophilus. They pro-vide a timely overview of the diversity of these phages and theirbiology, as well as the defence mechanisms operating in theseLAB. This knowledge has led to improved industrial starter cul-tures, e.g. specifically designed and adapted to prevent fermen-tation delays and low-quality fermented products. The authorsalso describe the oldest and still highly dynamic arms racebetween prey and predator and its relevance for developingrobust dairy fermentation processes.While phages are arguably the master regulators of LAB com-munities, they also likely play a role in other ecosystems, includ-ing the human gut. The function and composition of our gutmicrobiome are clearly linked to human health. Consequently,the promise of being able to precisely modulate this microbialcommunity has become an area of intense research worldwide.Torben Rasmussen and colleagues discuss the promises andlimitations of fecal microbiota transplantation, which offers anattractive therapeutic strategy for patients suffering from gutdysbiosis and bacterial infections. Growing evidence also sug-gests that cascading effects are initiated when phage commu-nities are also transferred to the gut, which leads to changes inits microbial composition and the host metabolome as well asimproving health.As the role of microorganisms in intestinal health hasbecome clearer with every LAB symposium due to advancedtools and new databases, we have invited a number of contribu-tions related to this topic. Shaopu Wang and colleagues reviewReceived: 16 September 2020; Accepted: 28 September 2020C© The Author(s) 2020. Published by Oxford University Press on behalf of FEMS. This is an Open Access article distributed under the terms of theCreative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, andreproduction in any medium, provided the original work is properly cited.1Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 20212 FEMS Microbiology Reviews, 2021, Vol. 45, No. 2the impact of early-life exposures on the microbiota develop-ment during childhood, and how this affects health at a laterage. They identify ‘golden’ perinatal factors and risk factors thatimpact on physiology, immunity and even cognitive develop-ment. They also describe possible interventions and their poten-tial.One of the first colonizers of the human gut are bifidobacte-ria, which are strictly speaking not LAB, but whose LAB-assistedapplications, metabolism and impact on gut health warrant aplace in this thematic issue. Chyn Wong and colleagues describethe biology and physiology of the Human Residential Bifidobac-teria, and what factors contribute to their ecological fitness.These factors may be used for the selection of ‘bifido’ strainswith desired properties and health benefits. Strain selection isalso essential for the production of healthy fermented foods.Francesca De Filippis and colleagues discuss the role of fer-mented foods as a source of potentially probiotic LAB, and howto mine the wealth of genomics and metagenomics data withbioinformatics and data analysis tools. While more researchis still needed to better understand the health benefits of fer-mented foods and their associated LAB, the field keeps progress-ing between each LAB Symposium.De Vuyst and Leroy looked at fermentation processes anddescribe in particular how yeasts, acetic acid bacteria and LABcollaborate during the fermentation of cocoa beans, a necessarystep to obtain the chocolate flavors we love so much. The com-plexity of food fermentations is in full display, yet it also showsthe great progress made in our understanding of the interactionsand the physiology of these microorganisms through a combi-nation of (functional) genomics, controlled fermentations andmodeling. Michiel Kleerebezem and colleagues review the latestinsights into the physiology of Lactococcus lactis, one of the keyspecies in starter cultures for a.o. cheesemaking, and an impor-tant model for LAB research. They describe both the functionalgenomics and bacterial physiology approaches to understandthe adaptation of L. lactis to different environmental conditions,including zero growth conditions that are relevant for cheeseripening. L. lactis was also the first LAB for which a genome-scale metabolic model was developed. Frank Bruggeman andcolleagues take us on a journey into the theory of bacterial phys-iology and growth that forms the rationale for all constraint-based modeling approaches. They show from first principleshow the strategy of growth rate (fitness) maximization underbiochemical constraints can explain a surprisingly large part ofmicrobial behavior, from L. lactis to Escherichia coli to yeast. Thisincludes stress resistance, overflow metabolism and cataboliterepression.Finally, as LAB take up many nutrients from the environ-ment, one of the key constraints is the cell wall and membrane.The cell wall is also important for stress-resistant properties andadherence to other cells and surfaces. Martinez and colleaguesdescribe the biochemistry of cell walls in LAB, and discuss thechallenges, insults and defenses that LAB have evolved to copewith in the nutrient-rich environments as well as in stressfulones. They show the crucial interplay between cell wall biosyn-thesis and global cellular metabolism, guiding the plasticity ofthe wall. Moreover, the important role of the bacterial cell wallin phage adsorption and bacteriocin activity is discussed, show-ing both a receptor and a defensive role of the cell wall. Over-all, this underscores the importance of understanding cell wallstructure and function to develop novel applications of LAB inhealth and biotechnology.We hope that this thematic issue will be of interest to manyresearchers inside and outside of the LAB field, and that it willinspire many to attend the thirteenth International Symposiumon Lactic Acid bacteria in 2021.REFERENCESBruggeman F, Planqué R, Teusink B. Predicting microbial phys-iology from biochemical and evolutionary principles. FEMSMicrobiol Rev 2020;44:821–44.De Filippis F, Pasolli E, Ercolini D. Food-gut axis, lactic acid bac-teria and their link, role and relevance for gut microbiomehealth and functions. FEMS Microbiol Rev 2020;44:454–89.De Vuyst L, Leroy F. Functional role of lactic acid bacte-ria in cocoa fermentation processes. FEMS Microbiol Rev2020;44:432–53.Kleerebezem M, Bachmann H, van Pelt-KleinJan E et al. Growthrate and physiology of Lactococcus lactis. FEMS Microbiol Rev2020;44:804–20.Martı́nez B, Rodrı́guez A, Kulakauskas S et al. Cell wall home-ostasis in LAB: insults and defenses. FEMS Microbiol Rev2020;44:538–64.Rasmussen TS, Koefoed AK, Jakobsen RR et al. Bacteriophagesand antimicrobials in gut and vaginal tracks. FEMS MicrobiolRev 2020;44:507–21.Roberts A, Barrangou R. Functions and applications of CRISPR-Cas systems in lactic acid bacteria. FEMS Microbiol Rev2020;44:523–37.Romero D, Magill D, Millen A et al. Dairy lactococcal and strepto-coccal phage-host interactions: industrial perspective in anevolving phage landscape. FEMS Microbiol Rev 2020;44:909–32.Saak CC, Dinh CB, Dutton RJ. Horizontal gene transfer withinmicrobial communities. FEMS Microbiol Rev 2020;44:606–30.Wang S, Egan M, Ryan CA et al. A good start in life is important-perinatal factors dictate early microbiota development andlonger term maturation. FEMS Microbiol Rev 2020;44:763–81.Wong CB, Odamaki T, Xiao J-Z. The physiology of bifidobacteria.FEMS Microbiol Rev 2020;44:369–85.Bas TeusinkAmsterdam Institute of Molecular and Life Sciences (AIMMS), VrijeUniversiteit Amsterdam, O2 building, location code 2E51, DeBoelelaan 1085, NL-1081HV Amsterdam, The NetherlandsOscar P. KuipersMolecular Genetics, University of Groningen, Nijenborgh 7(Linnaeusborg, building 5172, room 6.50), 9747AG Groningen theNetherlands, The NetherlandsSylvain MoineauDépartement de biochimie, de microbiologie, et de bio-informatique,Faculté des sciences et de génie1045, avenue de la MédecineUniversitéLaval, Québec, Canada, G1V 0A6Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 2021

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   University of GroningenSymposium on Lactic Acid Bacteria-reading while waiting for a meetingTeusink, Bas; Kuipers, Oscar P; Moineau, SylvainPublished in:FEMS Microbiology ReviewsDOI:10.1093/femsre/fuaa049IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2021Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Teusink, B., Kuipers, O. P., & Moineau, S. (2021). Symposium on Lactic Acid Bacteria-reading whilewaiting for a meeting. FEMS Microbiology Reviews, 45(2), Article fuaa049. Advance online publication.https://doi.org/10.1093/femsre/fuaa049CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 11-09-2023FEMS Microbiology Reviews, fuaa049, 45, 2020, 1–2doi: 10.1093/femsre/fuaa049EditorialSymposium on Lactic Acid Bacteria—reading while waiting for ameetingThis special thematic issue of FEMS Microbiology Reviews istruly special, because it contains contributions to a meetingthat is yet to happen! As many others, the thirteenth Interna-tional Symposium on Lactic Acid Bacteria (LAB13) was a victimof the COVID-19 pandemic and has been postponed to next year.The conference is held every 3 years in The Netherlands, and isattended by researchers from academia and industry from allover the world, reflecting the importance of these microorgan-isms in food, health and basic science. As a tradition, the invitedspeakers are asked to contribute not only by a talk, but also by athorough review on the topic of their presentation. These paperswere already under review by the time it became clear that thecoronavirus would not be contained and that we had to post-pone the meeting. However, we decided to move on and publishthe reviews now, when still timely, and we are eagerly awaitingupdated presentations next summer.Lactic acid bacteria, or LAB for friends, are a group of phyloge-netically diverse, but metabolically rather similar, bacteria. Theyplay important roles in food and feed fermentations, where theycontribute to safe, healthy and tasty food. Some strains haveprobiotic properties and they are even potential delivery vehi-cles for (oral) vaccines. They are selected from spontaneouslyfermented products or through evolution experiments in thelaboratory. They are screened for desired flavor-producing prop-erties, or for antimicrobials that they produce to defend theiroften nutrient-rich niches. They need to defend against (bacte-rial) viruses, which are a significant risk for industrial food fer-mentations. They are studied for their metabolism and phys-iology, in isolation or increasingly in the context of microbialconsortia such as the human microbiome or complex fermentedfoods. These broad topics are discussed at the LAB Symposiumseries, and this issue reflects the current state of the art of theexciting and diverse field of LAB research.Research into viruses—bacteriophages in the case of bac-terial viruses—has never been more pressing than in currentpandemic times, but has been a focal area in LAB research fordecades. It is not only a threat to industrial production pro-cesses, but fundamental studies on the clustered regularly inter-spaced short palindromic repeats (CRISPR)-CRISPR-associated(Cas) systems in Streptococcus thermophilus led to the discoveryof the molecular mechanisms of this adaptive immune system.We have come a long way since then. Roberts and Barrangou dis-cuss the history, the different systems and their mode of actionand highlights the applications of the CRISPR-Cas system in thecontext of LAB.While CRISPR-Cas systems may limit horizontal geneexchange in some LAB species, bacteria have still numerousways to exchange genes as mobile genetic elements are driversof microbial evolution. Various mechanisms of horizontal genetransfer can also occur in microbial communities. However,monitoring DNA transfers and their effects in these communi-ties has been challenging. Christina Saak and colleagues exploreexisting and emerging technologies for tracking mobile ele-ments and assigning them to microbes in order to generatecomprehensive community-level information. They also makethe case that LAB-driven fermented foods are, among others,ideal models to apply these techniques and address outstand-ing questions in the field of horizontal gene transfer in microbialcommunities.Dennis Romero and colleagues address phage–host interac-tions in Lactococcus lactis and Streptococcus thermophilus. They pro-vide a timely overview of the diversity of these phages and theirbiology, as well as the defence mechanisms operating in theseLAB. This knowledge has led to improved industrial starter cul-tures, e.g. specifically designed and adapted to prevent fermen-tation delays and low-quality fermented products. The authorsalso describe the oldest and still highly dynamic arms racebetween prey and predator and its relevance for developingrobust dairy fermentation processes.While phages are arguably the master regulators of LAB com-munities, they also likely play a role in other ecosystems, includ-ing the human gut. The function and composition of our gutmicrobiome are clearly linked to human health. Consequently,the promise of being able to precisely modulate this microbialcommunity has become an area of intense research worldwide.Torben Rasmussen and colleagues discuss the promises andlimitations of fecal microbiota transplantation, which offers anattractive therapeutic strategy for patients suffering from gutdysbiosis and bacterial infections. Growing evidence also sug-gests that cascading effects are initiated when phage commu-nities are also transferred to the gut, which leads to changes inits microbial composition and the host metabolome as well asimproving health.As the role of microorganisms in intestinal health hasbecome clearer with every LAB symposium due to advancedtools and new databases, we have invited a number of contribu-tions related to this topic. Shaopu Wang and colleagues reviewReceived: 16 September 2020; Accepted: 28 September 2020C© The Author(s) 2020. Published by Oxford University Press on behalf of FEMS. This is an Open Access article distributed under the terms of theCreative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, andreproduction in any medium, provided the original work is properly cited.1Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 20212 FEMS Microbiology Reviews, 2021, Vol. 45, No. 2the impact of early-life exposures on the microbiota develop-ment during childhood, and how this affects health at a laterage. They identify ‘golden’ perinatal factors and risk factors thatimpact on physiology, immunity and even cognitive develop-ment. They also describe possible interventions and their poten-tial.One of the first colonizers of the human gut are bifidobacte-ria, which are strictly speaking not LAB, but whose LAB-assistedapplications, metabolism and impact on gut health warrant aplace in this thematic issue. Chyn Wong and colleagues describethe biology and physiology of the Human Residential Bifidobac-teria, and what factors contribute to their ecological fitness.These factors may be used for the selection of ‘bifido’ strainswith desired properties and health benefits. Strain selection isalso essential for the production of healthy fermented foods.Francesca De Filippis and colleagues discuss the role of fer-mented foods as a source of potentially probiotic LAB, and howto mine the wealth of genomics and metagenomics data withbioinformatics and data analysis tools. While more researchis still needed to better understand the health benefits of fer-mented foods and their associated LAB, the field keeps progress-ing between each LAB Symposium.De Vuyst and Leroy looked at fermentation processes anddescribe in particular how yeasts, acetic acid bacteria and LABcollaborate during the fermentation of cocoa beans, a necessarystep to obtain the chocolate flavors we love so much. The com-plexity of food fermentations is in full display, yet it also showsthe great progress made in our understanding of the interactionsand the physiology of these microorganisms through a combi-nation of (functional) genomics, controlled fermentations andmodeling. Michiel Kleerebezem and colleagues review the latestinsights into the physiology of Lactococcus lactis, one of the keyspecies in starter cultures for a.o. cheesemaking, and an impor-tant model for LAB research. They describe both the functionalgenomics and bacterial physiology approaches to understandthe adaptation of L. lactis to different environmental conditions,including zero growth conditions that are relevant for cheeseripening. L. lactis was also the first LAB for which a genome-scale metabolic model was developed. Frank Bruggeman andcolleagues take us on a journey into the theory of bacterial phys-iology and growth that forms the rationale for all constraint-based modeling approaches. They show from first principleshow the strategy of growth rate (fitness) maximization underbiochemical constraints can explain a surprisingly large part ofmicrobial behavior, from L. lactis to Escherichia coli to yeast. Thisincludes stress resistance, overflow metabolism and cataboliterepression.Finally, as LAB take up many nutrients from the environ-ment, one of the key constraints is the cell wall and membrane.The cell wall is also important for stress-resistant properties andadherence to other cells and surfaces. Martinez and colleaguesdescribe the biochemistry of cell walls in LAB, and discuss thechallenges, insults and defenses that LAB have evolved to copewith in the nutrient-rich environments as well as in stressfulones. They show the crucial interplay between cell wall biosyn-thesis and global cellular metabolism, guiding the plasticity ofthe wall. Moreover, the important role of the bacterial cell wallin phage adsorption and bacteriocin activity is discussed, show-ing both a receptor and a defensive role of the cell wall. Over-all, this underscores the importance of understanding cell wallstructure and function to develop novel applications of LAB inhealth and biotechnology.We hope that this thematic issue will be of interest to manyresearchers inside and outside of the LAB field, and that it willinspire many to attend the thirteenth International Symposiumon Lactic Acid bacteria in 2021.REFERENCESBruggeman F, Planqué R, Teusink B. Predicting microbial phys-iology from biochemical and evolutionary principles. FEMSMicrobiol Rev 2020;44:821–44.De Filippis F, Pasolli E, Ercolini D. Food-gut axis, lactic acid bac-teria and their link, role and relevance for gut microbiomehealth and functions. FEMS Microbiol Rev 2020;44:454–89.De Vuyst L, Leroy F. Functional role of lactic acid bacte-ria in cocoa fermentation processes. FEMS Microbiol Rev2020;44:432–53.Kleerebezem M, Bachmann H, van Pelt-KleinJan E et al. Growthrate and physiology of Lactococcus lactis. FEMS Microbiol Rev2020;44:804–20.Martı́nez B, Rodrı́guez A, Kulakauskas S et al. Cell wall home-ostasis in LAB: insults and defenses. FEMS Microbiol Rev2020;44:538–64.Rasmussen TS, Koefoed AK, Jakobsen RR et al. Bacteriophagesand antimicrobials in gut and vaginal tracks. FEMS MicrobiolRev 2020;44:507–21.Roberts A, Barrangou R. Functions and applications of CRISPR-Cas systems in lactic acid bacteria. FEMS Microbiol Rev2020;44:523–37.Romero D, Magill D, Millen A et al. Dairy lactococcal and strepto-coccal phage-host interactions: industrial perspective in anevolving phage landscape. FEMS Microbiol Rev 2020;44:909–32.Saak CC, Dinh CB, Dutton RJ. Horizontal gene transfer withinmicrobial communities. FEMS Microbiol Rev 2020;44:606–30.Wang S, Egan M, Ryan CA et al. A good start in life is important-perinatal factors dictate early microbiota development andlonger term maturation. FEMS Microbiol Rev 2020;44:763–81.Wong CB, Odamaki T, Xiao J-Z. The physiology of bifidobacteria.FEMS Microbiol Rev 2020;44:369–85.Bas TeusinkAmsterdam Institute of Molecular and Life Sciences (AIMMS), VrijeUniversiteit Amsterdam, O2 building, location code 2E51, DeBoelelaan 1085, NL-1081HV Amsterdam, The NetherlandsOscar P. KuipersMolecular Genetics, University of Groningen, Nijenborgh 7(Linnaeusborg, building 5172, room 6.50), 9747AG Groningen theNetherlands, The NetherlandsSylvain MoineauDépartement de biochimie, de microbiologie, et de bio-informatique,Faculté des sciences et de génie1045, avenue de la MédecineUniversitéLaval, Québec, Canada, G1V 0A6Downloaded from https://academic.oup.com/femsre/article/45/2/fuaa049/5983770 by guest on 10 June 2021

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