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Huijboom L, Rashtchi P, Tempelaars M, Boeren S, van der Linden E, Habibi M, Abee T. Phenotypic and proteomic differences in biofilm formation of two Lactiplantibacillus plantarum strains in static and dynamic flow environments. Biofilm 2024; 7:100197. [PMID: 38706985 PMCID: PMC11066574 DOI: 10.1016/j.bioflm.2024.100197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024] Open
Abstract
Lactiplantibacillus plantarum is a Gram-positive non-motile bacterium capable of producing biofilms that contribute to the colonization of surfaces in a range of different environments. In this study, we compared two strains, WCFS1 and CIP104448, in their ability to produce biofilms in static and dynamic (flow) environments using an in-house designed flow setup. This flow setup enables us to impose a non-uniform flow velocity profile across the well. Biofilm formation occurred at the bottom of the well for both strains, under static and flow conditions, where in the latter condition, CIP104448 also showed increased biofilm formation at the walls of the well in line with the higher hydrophobicity of the cells and the increased initial attachment efficacy compared to WCFS1. Fluorescence and scanning electron microscopy showed open 3D structured biofilms formed under flow conditions, containing live cells and ∼30 % damaged/dead cells for CIP104448, whereas the WCFS1 biofilm showed live cells closely packed together. Comparative proteome analysis revealed minimal changes between planktonic and static biofilm cells of the respective strains suggesting that biofilm formation within 24 h is merely a passive process. Notably, observed proteome changes in WCFS1 and CIP104448 flow biofilm cells indicated similar and unique responses including changes in metabolic activity, redox/electron transfer and cell division proteins for both strains, and myo-inositol production for WCFS1 and oxidative stress response and DNA damage repair for CIP104448 uniquely. Exposure to DNase and protease treatments as well as lethal concentrations of peracetic acid showed highest resistance of flow biofilms. For the latter, CIP104448 flow biofilm even maintained its high disinfectant resistance after dispersal from the bottom and from the walls of the well. Combining all results highlights that L. plantarum biofilm structure and matrix, and physiological state and stress resistance of cells is strain dependent and strongly affected under flow conditions. It is concluded that consideration of effects of flow on biofilm formation is essential to better understand biofilm formation in different settings, including food processing environments.
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Affiliation(s)
- Linda Huijboom
- Food Microbiology, Wageningen University, Wageningen, 6708WG, the Netherlands
| | - Parisa Rashtchi
- Physics and Physical Chemistry of Foods, Wageningen University, Wageningen, 6708WG, the Netherlands
| | - Marcel Tempelaars
- Food Microbiology, Wageningen University, Wageningen, 6708WG, the Netherlands
| | - Sjef Boeren
- Biochemistry, Wageningen University, Wageningen, 6708WG, the Netherlands
| | - Erik van der Linden
- Physics and Physical Chemistry of Foods, Wageningen University, Wageningen, 6708WG, the Netherlands
| | - Mehdi Habibi
- Physics and Physical Chemistry of Foods, Wageningen University, Wageningen, 6708WG, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University, Wageningen, 6708WG, the Netherlands
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2
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Parmentier T, Molero-Baltanás R, Valdivia C, Gaju-Ricart M, Boeckx P, Łukasik P, Wybouw N. Co-habiting ants and silverfish display a converging feeding ecology. BMC Biol 2024; 22:123. [PMID: 38807209 PMCID: PMC11134936 DOI: 10.1186/s12915-024-01914-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 05/10/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Various animal taxa have specialized to living with social hosts. Depending on their level of specialization, these symbiotic animals are characterized by distinct behavioural, chemical, and morphological traits that enable close heterospecific interactions. Despite its functional importance, our understanding of the feeding ecology of animals living with social hosts remains limited. We examined how host specialization of silverfish co-habiting with ants affects several components of their feeding ecology. We combined stable isotope profiling, feeding assays, phylogenetic reconstruction, and microbial community characterization of the Neoasterolepisma silverfish genus and a wider nicoletiid and lepismatid silverfish panel where divergent myrmecophilous lifestyles are observed. RESULTS Stable isotope profiling (δ13C and δ15N) showed that the isotopic niches of granivorous Messor ants and Messor-specialized Neoasterolepisma exhibit a remarkable overlap within an ant nest. Trophic experiments and gut dissections further supported that these specialized Neoasterolepisma silverfish transitioned to a diet that includes plant seeds. In contrast, the isotopic niches of generalist Neoasterolepisma silverfish and generalist nicoletiid silverfish were clearly different from their ant hosts within the shared nest environment. The impact of the myrmecophilous lifestyle on feeding ecology was also evident in the internal silverfish microbiome. Compared to generalists, Messor-specialists exhibited a higher bacterial density and a higher proportion of heterofermentative lactic acid bacteria. Moreover, the nest environment explained the infection profile (or the 16S rRNA genotypes) of Weissella bacteria in Messor-specialized silverfish and the ant hosts. CONCLUSIONS Together, we show that social hosts are important determinants for the feeding ecology of symbiotic animals and can induce diet convergence.
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Affiliation(s)
- Thomas Parmentier
- Department of Biology, Faculty of Sciences, Ghent University, Ghent, Belgium.
| | | | - Catalina Valdivia
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Miquel Gaju-Ricart
- Depto. de Biología Animal (Zoología), University of Córdoba, Córdoba, Spain
| | - Pascal Boeckx
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Nicky Wybouw
- Department of Biology, Faculty of Sciences, Ghent University, Ghent, Belgium.
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Wiull K, Hagen LH, Rončević J, Westereng B, Boysen P, Eijsink VGH, Mathiesen G. Antigen surface display in two novel whole genome sequenced food grade strains, Lactiplantibacillus pentosus KW1 and KW2. Microb Cell Fact 2024; 23:19. [PMID: 38212746 PMCID: PMC10782763 DOI: 10.1186/s12934-024-02296-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Utilization of commensal bacteria for delivery of medicinal proteins, such as vaccine antigens, is an emerging strategy. Here, we describe two novel food-grade strains of lactic acid bacteria, Lactiplantibacillus pentosus KW1 and KW2, as well as newly developed tools for using this relatively unexplored but promising bacterial species for production and surface-display of heterologous proteins. RESULTS Whole genome sequencing was performed to investigate genomic features of both strains and to identify native proteins enabling surface display of heterologous proteins. Basic characterization of the strains revealed the optimum growth temperatures for both strains to be 35-37 °C, with peak heterologous protein production at 33 °C (KW1) and 37 °C (KW2). Negative staining revealed that only KW1 produces closely bound exopolysaccharides. Production of heterologous proteins with the inducible pSIP-expression system enabled high expression in both strains. Exposure to KW1 and KW2 skewed macrophages toward the antigen presenting state, indicating potential adjuvant properties. To develop these strains as delivery vehicles, expression of the mycobacterial H56 antigen was fused to four different strain-specific surface-anchoring sequences. CONCLUSION All experiments that enabled comparison of heterologous protein production revealed KW1 to be the better recombinant protein production host. Use of the pSIP expression system enabled successful construction of L. pentosus strains for production and surface display of an antigen, underpinning the potential of these strains as novel delivery vehicles.
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Affiliation(s)
- Kamilla Wiull
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Jelena Rončević
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Preben Boysen
- Faculty of Veterinary Medicine, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Geir Mathiesen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
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Xiao L, Zhang C, Zhang X, Zhao X, Chaeipeima Mahsa G, Ma K, Ji F, Azarpazhooh E, Ajami M, Rui X, Li W. Effects of Lacticaseibacillus paracasei SNB-derived postbiotic components on intestinal barrier dysfunction and composition of gut microbiota. Food Res Int 2024; 175:113773. [PMID: 38129062 DOI: 10.1016/j.foodres.2023.113773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 11/09/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
The bacterial surface components are considered as effector molecules and show the potential to support intestinal health, but the detailed mechanism of how the gut microbiota changes after the intervention of surface molecules is still unknown. In the present study, capsular polysaccharide (B-CPS) and surface layer protein (B-SLP) were extracted from Lacticaseibacillus paracasei S-NB. The protective effect of direct administration of B-CPS (100 μg/mL) and B-SLP (100 μg/mL) on intestinal epithelial barrier dysfunction was verified based on the LPS-induced Caco-2 cell model. Additionally, the B-CPS and B-SLP could be utilized as carbon source and nitrogen source for the growth of several Lactobacillus strains, respectively. The postbiotic potential of B-CPS and B-SLP was further evaluated by in vitro fermentation with fecal cultures. The B-CPS and a combination of B-CPS and B-SLP regulated the composition of gut microbiota by increasing the relative abundances of Bacteroides, Bifidobacterium, Phascolarctobacterium, Parabacteroides, Subdoligranulum and Collinsella and decreasing the abundance of pathogenic bacteria like Escherichia-Shigella, Blautia, Citrobacter and Fusobacterium. Meanwhile, the total short-chain fatty acid production markedly increased after fermentation with either B-CPS individually or in combination with B-SLP. These results provided an important basis for the application of B-CPS and B-SLP as postbiotics to improve human intestinal health.
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Affiliation(s)
- Luyao Xiao
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Changliang Zhang
- Jiangsu New-Bio Biotechnology Co., Ltd, Jiangyin, Jiangsu 214400, PR China; Jiangsu Biodep Biotechnology Co., Ltd, Jiangyin, Jiangsu 214400, PR China
| | - Xueliang Zhang
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xiaogan Zhao
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Ghahvechi Chaeipeima Mahsa
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Kai Ma
- Jiangsu New-Bio Biotechnology Co., Ltd, Jiangyin, Jiangsu 214400, PR China; Jiangsu Biodep Biotechnology Co., Ltd, Jiangyin, Jiangsu 214400, PR China
| | - Feng Ji
- Jiangsu New-Bio Biotechnology Co., Ltd, Jiangyin, Jiangsu 214400, PR China; Jiangsu Biodep Biotechnology Co., Ltd, Jiangyin, Jiangsu 214400, PR China
| | - Elham Azarpazhooh
- Khorasan Razavi Agricultural and Natural Resources Research and Education Center, AREEO, Iran
| | - Marjan Ajami
- National Nutrition and Food Technology Research Institute, School of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Xin Rui
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Wei Li
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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Hassan MU, Chaudhuri RR, Williamson MP. DUF916 and DUF3324 in the WxL protein cluster bind to WxL and link bacterial and host surfaces. Protein Sci 2023; 32:e4806. [PMID: 37833244 PMCID: PMC10599100 DOI: 10.1002/pro.4806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/15/2023]
Abstract
Bacterial WxL proteins contain peptidoglycan-binding WxL domains, which have a dual Trp-x-Leu motif and are involved in virulence. It was recently shown that WxL proteins occur in gene clusters, containing typically a small WxL protein (which in the mature protein consists only of a WxL domain), a large WxL protein (which contains a C-terminal WxL domain with N-terminal host-binding domains), and a conserved protein annotated as a Domain of Unknown Function (DUF). Here we analyze this DUF and show that it contains two tandem domains-DUF916 and DUF3324-which both have an IgG-like fold and together form a single functional unit, connected to a C-terminal transmembrane helix. DUF3324 is a stable domain, while DUF916 is less stable and is likely to require a stabilizing interaction with WxL. The protein is suggested to have an important role to bind and stabilize WxL on the peptidoglycan surface, via the DUF916 domain, and to bind to host cells via the DUF3324 domain. AlphaFold2 predicts that a β-hairpin strand from DUF916 inserts into WxL adjacent to its N-terminus. We therefore propose to rename the DUF916-DUF3324 pair as WxL Interacting Protein (WxLIP), with DUF916, DUF3324 and the transmembrane helix forming the first, second and third domains of WxLIP, which we characterize as peptidoglycan binding domain (PGBD), host binding domain (HBD), and transmembrane helix (TMH) respectively.
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Affiliation(s)
- Mahreen U. Hassan
- School of BiosciencesUniversity of SheffieldSheffieldUK
- Present address:
Department of MicrobiologyShaheed Benazir Bhutto Women UniversityPeshawarPakistan
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Pal R, Athamneh AI, Deshpande R, Ramirez JAR, Adu KT, Muthuirulan P, Pawar S, Biazzo M, Apidianakis Y, Sundekilde UK, de la Fuente-Nunez C, Martens MG, Tegos GP, Seleem MN. Probiotics: insights and new opportunities for Clostridioides difficile intervention. Crit Rev Microbiol 2023; 49:414-434. [PMID: 35574602 PMCID: PMC9743071 DOI: 10.1080/1040841x.2022.2072705] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/17/2022] [Accepted: 04/28/2022] [Indexed: 02/08/2023]
Abstract
Clostridioides difficile infection (CDI) is a life-threatening disease caused by the Gram-positive, opportunistic intestinal pathogen C. difficile. Despite the availability of antimicrobial drugs to treat CDI, such as vancomycin, metronidazole, and fidaxomicin, recurrence of infection remains a significant clinical challenge. The use of live commensal microorganisms, or probiotics, is one of the most investigated non-antibiotic therapeutic options to balance gastrointestinal (GI) microbiota and subsequently tackle dysbiosis. In this review, we will discuss major commensal probiotic strains that have the potential to prevent and/or treat CDI and its recurrence, reassess the efficacy of probiotics supplementation as a CDI intervention, delve into lessons learned from probiotic modulation of the immune system, explore avenues like genome-scale metabolic network reconstructions, genome sequencing, and multi-omics to identify novel strains and understand their functionality, and discuss the current regulatory framework, challenges, and future directions.
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Affiliation(s)
- Rusha Pal
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Ahmad I.M. Athamneh
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
| | | | - Jose A. R Ramirez
- ProbioWorld Consulting Group, James Cook University, 4811, Queensland, Australia
| | - Kayode T. Adu
- ProbioWorld Consulting Group, James Cook University, 4811, Queensland, Australia
- Cann Group, Walter and Eliza Hall Institute, La Trobe University, Victoria 3083, Australia
| | | | - Shrikant Pawar
- The Anlyan Center Yale Center for Genomic Analysis, Yale School of Medicine, New Haven CT USA
| | - Manuele Biazzo
- The Bioarte Ltd Laboratories at Life Science Park, San Gwann, Malta
| | | | | | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mark G. Martens
- Reading Hospital, Tower Health, West Reading, PA 19611, USA
- Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - George P. Tegos
- Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Mohamed N. Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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Hassan MU, Williamson MP. Bioinformatic analysis of WxL domain proteins. Saudi J Biol Sci 2023; 30:103526. [PMID: 36568411 PMCID: PMC9772566 DOI: 10.1016/j.sjbs.2022.103526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/06/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The WxL domain is found on the cell surface of many bacteria, most of which are commensal gut bacteria. Its functions are generally identified as being related to virulence and/or peptidoglycan attachment, but there is so far no clear function or structure for this domain. Here, a range of bioinformatics tools were used to clarify the structure and function. These indicate that WxL domains occur in cell surface-associated gene clusters that always contain a small WxL, large WxL and DUF916 domain; and that the small and large WxL proteins have distinct structure despite sharing two conserved WxL motifs. The two WxL motifs form a hydrophobic surface buried inside the protein. The likely function of the WxL domain is to attach to bacterial peptidoglycan, forming a platform to allow associated domains in the cluster to interact with host proteins.
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Affiliation(s)
- Mahreen U. Hassan
- School of Biosciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK,Dept of Microbiology, Shaheed Benazir Bhutto Women University, Peshawar 2500, Pakistan1
| | - Mike P. Williamson
- School of Biosciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK,Corresponding author.
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Sechovcová H, Rudl Kulhavá L, Fliegerová K, Killer J, Kopečný J. Advantages of label free method in comparison with 2DE proteomic analysis of Butyrivibrio fibrisolvens 3071 grown on different carbon sources. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2129477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Hana Sechovcová
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | | | - Kateřina Fliegerová
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
| | - Jiří Killer
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - Jan Kopečný
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
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Variability of Genetic Characters Associated with Probiotic Functions in Lacticaseibacillus Species. Microorganisms 2022; 10:microorganisms10051023. [PMID: 35630465 PMCID: PMC9145642 DOI: 10.3390/microorganisms10051023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022] Open
Abstract
This study aims to explore the intra-species distribution of genetic characteristics that favor the persistence in the gastrointestinal tract (GIT) and host interaction of bacteria belonging to species of the Lacticaseibacillus genus. These bacterial species comprise commercial probiotics with the widest use among consumers and strains naturally occurring in GIT and in fermented food. Since little is known about the distribution of genetic traits for adhesion capacity, polysaccharide production, biofilm formation, and utilization of substrates critically important for survival in GIT, which influence probiotic characteristics, a list of genetic determinants possibly involved in such functions was created by a search for specific genes involved in the above aspects in the genome of the extensively characterized probiotic L. rhamnosus GG. Eighty-two gene loci were retrieved and their presence and variability in other Lacticaseibacillus spp. genomes were assessed by alignment with the publicly available fully annotated genome sequences of L. casei, L. paracasei, L. rhamnosus, and L. zeae. Forty-nine of these genes were found to be absent in some strains or species. The remaining genes were conserved and covered almost all the functions considered, indicating that all strains of the genus may exert some probiotic effects. Among the variable loci, a taurine utilization operon and a α-L-fucosidase were examined for the presence/absence in 26 strains isolated from infant feces by PCR-based tests. Results were variable among the isolates, though their common origin indicated the capacity to survive in the intestinal niche. This study indicated that the capacity to exert probiotic actions of Lacticaseibacillus spp. depends on a conserved set of genes but variable genetic factors, whose role is only in part elucidated, are more numerous and can explain the enhanced probiotic characteristics for some strains. The selection of the most promising probiotic candidates to be used in food is feasible by analyzing the presence/absence of a set of variable traits.
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Qiao W, Liu F, Wan X, Qiao Y, Li R, Wu Z, Saris PEJ, Xu H, Qiao M. Genomic Features and Construction of Streamlined Genome Chassis of Nisin Z Producer Lactococcus lactis N8. Microorganisms 2021; 10:microorganisms10010047. [PMID: 35056496 PMCID: PMC8779420 DOI: 10.3390/microorganisms10010047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/03/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022] Open
Abstract
Lactococcus lactis is a commonly used fermenting bacteria in cheese, beverages and meat products. Due to the lack of simplified chassis strains, it has not been widely used in the fields of synthetic biology. Thus, the construction of lactic acid bacteria chassis strains becomes more and more important. In this study, we performed whole genome sequencing, annotation and analysis of L. lactis N8. Based on the genome analysis, we found that L. lactis N8 contains two large plasmids, and the function prediction of the plasmids shows that some regions are related to carbohydrate transport/metabolism, multi-stress resistance and amino acid uptake. L. lactis N8 contains a total of seven prophage-related fragments and twelve genomic islands. A gene cluster encoding a hybrid NRPS–PKS system that was found in L. lactis N8 reveals that the strain has the potential to synthesize novel secondary metabolites. Furthermore, we have constructed a simplified genome chassis of L. lactis N8 and achieved the largest amount of deletion of L. lactis so far. Taken together, the present study offers further insights into the function and potential role of L. lactis N8 as a model strain of lactic acid bacteria and lays the foundation for its application in the field of synthetic biology.
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Affiliation(s)
- Wanjin Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (W.Q.); (F.L.); (Y.Q.)
| | - Fulu Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (W.Q.); (F.L.); (Y.Q.)
| | - Xing Wan
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland; (X.W.); (R.L.); (P.E.J.S.)
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Yu Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (W.Q.); (F.L.); (Y.Q.)
| | - Ran Li
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland; (X.W.); (R.L.); (P.E.J.S.)
| | - Zhenzhou Wu
- State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Protein Sciences, College of Life Sciences, Nankai University, Tianjin 300071, China;
| | - Per Erik Joakim Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland; (X.W.); (R.L.); (P.E.J.S.)
| | - Haijin Xu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (W.Q.); (F.L.); (Y.Q.)
- Correspondence: (H.X.); (M.Q.)
| | - Mingqiang Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (W.Q.); (F.L.); (Y.Q.)
- School of Life Sciences, Shanxi University, Taiyuan 030006, China
- Correspondence: (H.X.); (M.Q.)
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Dell’Anno M, Giromini C, Reggi S, Cavalleri M, Moscatelli A, Onelli E, Rebucci R, Sundaram TS, Coranelli S, Spalletta A, Baldi A, Rossi L. Evaluation of Adhesive Characteristics of L. plantarum and L. reuteri Isolated from Weaned Piglets. Microorganisms 2021; 9:1587. [PMID: 34442665 PMCID: PMC8400209 DOI: 10.3390/microorganisms9081587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/08/2021] [Accepted: 07/22/2021] [Indexed: 11/24/2022] Open
Abstract
Limosilactobacillus reuteri and Lactiplantibacillus plantarum strains, previously isolated from weaned piglets, were considered for the evaluation of their adhesive characteristics. Lactobacilli were treated with LiCl in order to remove the surface protein layer, and probiotic activity was compared with those of untreated strains. The autoaggregation, co-aggregation to E. coli F18+, and adhesive abilities of LiCl-treated Limosilactobacillus reuteri and Lactiplantibacillus plantarum were significantly inhibited (p < 0.05) compared with the respective untreated strain. The hydrophobic and basic phenotypes were observed due to the strong affinity to chloroform and low adherence to ethyl acetate. In particular, L. plantarum showed higher hydrophobicity compared to L. reuteri, which may reflect their different colonizing ability. After treatment with LiCl to remove surface proteins, the adherence capabilities of L. reuteri and L. casei on IPEC-J2 cells decreased significantly (p < 0.001) and L. reuteri adhered more frequently. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) showed that both L. reuteri and L. plantarum had several bands ranging from 20 to 100 kDa. Two-dimensional gel electrophoresis showed an acidic profile of the surface-layer polypeptides for both bacterial strains, and more studies are needed to characterize their profile and functions. The results confirm the pivotal role of surface proteins in the probiotic potential of L. reuteri and L. plantarum.
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Affiliation(s)
- Matteo Dell’Anno
- Department of Health, Animal Science and Food Safety “Carlo Cantoni” (VESPA), Università Degli Studi di Milano, 26900 Lodi, Italy; (M.D.); (S.R.); (M.C.); (R.R.); (T.S.S.); (A.B.); (L.R.)
| | - Carlotta Giromini
- Department of Health, Animal Science and Food Safety “Carlo Cantoni” (VESPA), Università Degli Studi di Milano, 26900 Lodi, Italy; (M.D.); (S.R.); (M.C.); (R.R.); (T.S.S.); (A.B.); (L.R.)
| | - Serena Reggi
- Department of Health, Animal Science and Food Safety “Carlo Cantoni” (VESPA), Università Degli Studi di Milano, 26900 Lodi, Italy; (M.D.); (S.R.); (M.C.); (R.R.); (T.S.S.); (A.B.); (L.R.)
| | - Mariagrazia Cavalleri
- Department of Health, Animal Science and Food Safety “Carlo Cantoni” (VESPA), Università Degli Studi di Milano, 26900 Lodi, Italy; (M.D.); (S.R.); (M.C.); (R.R.); (T.S.S.); (A.B.); (L.R.)
| | - Alessandra Moscatelli
- Department of Biosciences, Università Degli Studi di Milano, 20133 Milan, Italy; (A.M.); (E.O.)
| | - Elisabetta Onelli
- Department of Biosciences, Università Degli Studi di Milano, 20133 Milan, Italy; (A.M.); (E.O.)
| | - Raffaella Rebucci
- Department of Health, Animal Science and Food Safety “Carlo Cantoni” (VESPA), Università Degli Studi di Milano, 26900 Lodi, Italy; (M.D.); (S.R.); (M.C.); (R.R.); (T.S.S.); (A.B.); (L.R.)
| | - Tamil Selvi Sundaram
- Department of Health, Animal Science and Food Safety “Carlo Cantoni” (VESPA), Università Degli Studi di Milano, 26900 Lodi, Italy; (M.D.); (S.R.); (M.C.); (R.R.); (T.S.S.); (A.B.); (L.R.)
| | - Simona Coranelli
- Biotecnologie B.T. Srl, Todi, 06059 Perugia, Italy; (S.C.); (A.S.)
| | - Ambra Spalletta
- Biotecnologie B.T. Srl, Todi, 06059 Perugia, Italy; (S.C.); (A.S.)
| | - Antonella Baldi
- Department of Health, Animal Science and Food Safety “Carlo Cantoni” (VESPA), Università Degli Studi di Milano, 26900 Lodi, Italy; (M.D.); (S.R.); (M.C.); (R.R.); (T.S.S.); (A.B.); (L.R.)
| | - Luciana Rossi
- Department of Health, Animal Science and Food Safety “Carlo Cantoni” (VESPA), Università Degli Studi di Milano, 26900 Lodi, Italy; (M.D.); (S.R.); (M.C.); (R.R.); (T.S.S.); (A.B.); (L.R.)
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12
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Rodríguez-Daza MC, Pulido-Mateos EC, Lupien-Meilleur J, Guyonnet D, Desjardins Y, Roy D. Polyphenol-Mediated Gut Microbiota Modulation: Toward Prebiotics and Further. Front Nutr 2021; 8:689456. [PMID: 34268328 PMCID: PMC8276758 DOI: 10.3389/fnut.2021.689456] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
The genome of gut microbes encodes a collection of enzymes whose metabolic functions contribute to the bioavailability and bioactivity of unabsorbed (poly)phenols. Datasets from high throughput sequencing, metabolome measurements, and other omics have expanded the understanding of the different modes of actions by which (poly)phenols modulate the microbiome conferring health benefits to the host. Progress have been made to identify direct prebiotic effects of (poly)phenols; albeit up to date, these compounds are not recognized as prebiotics sensu stricto. Interestingly, certain probiotics strains have an enzymatic repertoire, such as tannase, α-L-rhamnosidase, and phenolic acid reductase, involved in the transformation of different (poly)phenols into bioactive phenolic metabolites. In vivo studies have demonstrated that these (poly)phenol-transforming bacteria thrive when provided with phenolic substrates. However, other taxonomically distinct gut symbionts of which a phenolic-metabolizing activity has not been demonstrated are still significantly promoted by (poly)phenols. This is the case of Akkermansia muciniphila, a so-called antiobesity bacterium, which responds positively to (poly)phenols and may be partially responsible for the health benefits formerly attributed to these molecules. We surmise that (poly)phenols broad antimicrobial action free ecological niches occupied by competing bacteria, thereby allowing the bloom of beneficial gut bacteria. This review explores the capacity of (poly)phenols to promote beneficial gut bacteria through their direct and collaborative bacterial utilization and their inhibitory action on potential pathogenic species. We propose the term duplibiotic, to describe an unabsorbed substrate modulating the gut microbiota by both antimicrobial and prebiotic modes of action. (Poly)phenol duplibiotic effect could participate in blunting metabolic disturbance and gut dysbiosis, positioning these compounds as dietary strategies with therapeutic potential.
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Affiliation(s)
- Maria Carolina Rodríguez-Daza
- Faculty of Agriculture and Food Sciences, Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, Canada.,Department of Food Science, Faculty of Agriculture and Food Sciences, Laval University, Québec, QC, Canada
| | - Elena C Pulido-Mateos
- Faculty of Agriculture and Food Sciences, Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, Canada.,Department of Food Science, Faculty of Agriculture and Food Sciences, Laval University, Québec, QC, Canada
| | - Joseph Lupien-Meilleur
- Faculty of Agriculture and Food Sciences, Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, Canada.,Department of Food Science, Faculty of Agriculture and Food Sciences, Laval University, Québec, QC, Canada
| | - Denis Guyonnet
- Diana Nova, Symrise Nutrition, Clichy-la-Garenne, France
| | - Yves Desjardins
- Faculty of Agriculture and Food Sciences, Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, Canada.,Department of Plant Science, Faculty of Agriculture and Food Sciences, Laval University, Québec, QC, Canada
| | - Denis Roy
- Faculty of Agriculture and Food Sciences, Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, Canada.,Department of Food Science, Faculty of Agriculture and Food Sciences, Laval University, Québec, QC, Canada
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13
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Dong H, Zhang W, Zhou S, Huang J, Wang P. Engineering bioscaffolds for enzyme assembly. Biotechnol Adv 2021; 53:107721. [PMID: 33631185 DOI: 10.1016/j.biotechadv.2021.107721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/04/2021] [Accepted: 02/14/2021] [Indexed: 12/27/2022]
Abstract
With the demand for green, safe, and continuous biocatalysis, bioscaffolds, compared with synthetic scaffolds, have become a desirable candidate for constructing enzyme assemblages because of their biocompatibility and regenerability. Biocompatibility makes bioscaffolds more suitable for safe and green production, especially in food processing, production of bioactive agents, and diagnosis. The regenerability can enable the engineered biocatalysts regenerate through simple self-proliferation without complex re-modification, which is attractive for continuous biocatalytic processes. In view of the unique biocompatibility and regenerability of bioscaffolds, they can be classified into non-living (polysaccharide, nucleic acid, and protein) and living (virus, bacteria, fungi, spore, and biofilm) bioscaffolds, which can fully satisfy these two unique properties, respectively. Enzymes assembled onto non-living bioscaffolds are based on single or complex components, while enzymes assembled onto living bioscaffolds are based on living bodies. In terms of their unique biocompatibility and regenerability, this review mainly covers the current advances in the research and application of non-living and living bioscaffolds with focus on engineering strategies for enzyme assembly. Finally, the future development of bioscaffolds for enzyme assembly is also discussed. Hopefully, this review will attract the interest of researchers in various fields and empower the development of biocatalysis, biomedicine, environmental remediation, therapy, and diagnosis.
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Affiliation(s)
- Hao Dong
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Wenxue Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaofang Huang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
| | - Ping Wang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, MN 55108, USA.
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14
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Butanol Tolerance of Lactiplantibacillus plantarum: A Transcriptome Study. Genes (Basel) 2021; 12:genes12020181. [PMID: 33514005 PMCID: PMC7911632 DOI: 10.3390/genes12020181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/17/2021] [Accepted: 01/26/2021] [Indexed: 12/26/2022] Open
Abstract
Biobutanol is a promising alternative fuel with impaired microbial production thanks to its toxicity. Lactiplantibacillus plantarum (L. plantarum) is among the few bacterial species that can naturally tolerate 3% (v/v) butanol. This study aims to identify the genetic factors involved in the butanol stress response of L. plantarum by comparing the differential gene expression in two strains with very different butanol tolerance: the highly resistant Ym1, and the relatively sensitive 8-1. During butanol stress, a total of 319 differentially expressed genes (DEGs) were found in Ym1, and 516 in 8-1. Fifty genes were upregulated and 54 were downregulated in both strains, revealing the common species-specific effects of butanol stress: upregulation of multidrug efflux transporters (SMR, MSF), toxin-antitoxin system, transcriptional regulators (TetR/AcrR, Crp/Fnr, and DeoR/GlpR), Hsp20, and genes involved in polysaccharide biosynthesis. Strong inhibition of the pyrimidine biosynthesis occurred in both strains. However, the strains differed greatly in DEGs responsible for the membrane transport, tryptophan synthesis, glycerol metabolism, tRNAs, and some important transcriptional regulators (Spx, LacI). Uniquely upregulated in the butanol-resistant strain Ym1 were the genes encoding GntR, GroEL, GroES, and foldase PrsA. The phosphoenolpyruvate flux and the phosphotransferase system (PTS) also appear to be major factors in butanol tolerance.
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15
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Role of Lactic Acid Bacteria Phospho-β-Glucosidases during the Fermentation of Cereal by-Products. Foods 2021; 10:foods10010097. [PMID: 33466465 PMCID: PMC7830935 DOI: 10.3390/foods10010097] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
Bioprocessing using lactic acid bacteria (LAB) is a powerful means to exploit plant-derived by-products as a food ingredient. LAB have the capability to metabolize a large variety of carbohydrates, but such metabolism only relies on few metabolic routes, conferring on them a high fermentation potential. One example of these pathways is that involving phospho-β-glucosidase genes, which are present in high redundancy within LAB genomes. This enzymatic activity undertakes an ambivalent role during fermentation of plant-based foods related to the release of a wide range of phenolic compounds, from their β-D-glycosylated precursors and the degradation of β-glucopyranosyl derived carbohydrates. We proposed a novel phenomic approach to characterize the metabolism drift of Lactiplantibacillus plantarum and Leuconostoc pseudomesenteroides caused by a lignocellulosic by-product, such as the brewers’ spent grain (BSG), in contrast to Rich De Man, Rogosa and Sharpe (MRS) broth. We observed an increased metabolic activity for gentiobiose, cellobiose and β-glucoside conjugates of phenolic compounds during BSG fermentation. Gene expression analysis confirmed the importance of cellobiose metabolism while a release of lignin-derived aglycones was found during BSG fermentation. We provided a comprehensive view of the important role exerted by LAB 6-phospho-β-glucosidases as well the major metabolic routes undertaken during plant-based fermentations. Further challenges will consider a controlled characterization of pbg gene expression correlated to the metabolism of β-glucosides with different aglycone moieties.
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16
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Qiao W, Qiao Y, Liu F, Zhang Y, Li R, Wu Z, Xu H, Saris PEJ, Qiao M. Engineering Lactococcus lactis as a multi-stress tolerant biosynthetic chassis by deleting the prophage-related fragment. Microb Cell Fact 2020; 19:225. [PMID: 33298073 PMCID: PMC7727215 DOI: 10.1186/s12934-020-01487-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/28/2020] [Indexed: 01/02/2023] Open
Abstract
Background In bioengineering, growth of microorganisms is limited because of environmental and industrial stresses during fermentation. This study aimed to construct a nisin-producing chassis Lactococcus lactis strain with genome-streamlined, low metabolic burden, and multi-stress tolerance characteristics. Results The Cre-loxP recombination system was applied to reduce the genome and obtain the target chassis strain. A prophage-related fragment (PRF; 19,739 bp) in the L. lactis N8 genome was deleted, and the mutant strain L. lactis N8-1 was chosen for multi-stress tolerance studies. Nisin immunity of L. lactis N8-1 was increased to 6500 IU/mL, which was 44.44% higher than that of the wild-type L. lactis N8 (4500 IU/mL). The survival rates of L. lactis N8-1 treated with lysozyme for 2 h and lactic acid for 1 h were 1000- and 10,000-fold higher than that of the wild-type strain, respectively. At 39 ℃, the L. lactis N8-1 could still maintain its growth, whereas the growth of the wild-type strain dramatically dropped. Scanning electron microscopy showed that the cell wall integrity of L. lactis N8-1 was well maintained after lysozyme treatment. Tandem mass tags labeled quantitative proteomics revealed that 33 and 9 proteins were significantly upregulated and downregulated, respectively, in L. lactis N8-1. These differential proteins were involved in carbohydrate and energy transport/metabolism, biosynthesis of cell wall and cell surface proteins. Conclusions PRF deletion was proven to be an efficient strategy to achieve multi-stress tolerance and nisin immunity in L. lactis, thereby providing a new perspective for industrially obtaining engineered strains with multi-stress tolerance and expanding the application of lactic acid bacteria in biotechnology and synthetic biology. Besides, the importance of PRF, which can confer vital phenotypes to bacteria, was established.
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Affiliation(s)
- Wanjin Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China.,Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Yu Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Fulu Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Yating Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Ran Li
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Zhenzhou Wu
- State Key Laboratory of Medicinal Chemical Biology & Tianjin Key Laboratory of Protein Sciences, College of Life Sciences, Nankai University, Tianjin, China
| | - Haijin Xu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China.
| | - Per Erik Joakim Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Mingqiang Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China.
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17
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Aggregation, adhesion and efficacy studies of probiotic candidate Pediococcus acidilactici NCDC 252: a strain of dairy origin. World J Microbiol Biotechnol 2019; 36:10. [DOI: 10.1007/s11274-019-2785-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/13/2019] [Indexed: 11/26/2022]
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18
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Chen C, Wang L, Lu Y, Yu H, Tian H. Comparative Transcriptional Analysis of Lactobacillus plantarum and Its ccpA-Knockout Mutant Under Galactooligosaccharides and Glucose Conditions. Front Microbiol 2019; 10:1584. [PMID: 31338086 PMCID: PMC6629832 DOI: 10.3389/fmicb.2019.01584] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/25/2019] [Indexed: 01/02/2023] Open
Abstract
Galactooligosaccharides (GOS) are documented prebiotic compounds, but knowledge of the metabolic and regulatory mechanisms of GOS utilization by lactic acid bacteria is still limited. Here we used transcriptome and physiological analyses to investigate the differences in the logarithmic growth phase of Lactobacillus plantarum and L. plantarum ΔccpA metabolizing GOS or glucose as the sole source of carbohydrate. In total, 489 genes (16%) were differentially transcribed in the wild-type L. plantarum grown on glucose and GOS and the value is decreased to 7% due to the loss of ccpA. Only 6% genes were differentially expressed when the wild-type and the ccpA mutant were compared on GOS. Transcriptome data revealed that the carbon sources significantly affected the expression of several genes, and some of the genes were mediated by CcpA. In particular, lac and gal gene clusters resembled the corresponding clusters in L. acidophilus NCFM that are involved in GOS metabolism, indicating that these clusters may be participating in GOS utilization. Moreover, reverse transcription-PCR analysis showed that GOS-related gene clusters were organized in five independent polycistronic units. In addition, many commonalities were found between fructooligosaccharides and GOS metabolism in L. plantarum, including differentially expressed genes involved in oligosaccharide metabolism, conversion of metabolites, and changes in fatty acid biosynthesis. Overall, our findings provide new information on gene transcription and the metabolic mechanism associated with GOS utilization, and confirm that CcpA plays an important role in carbon metabolism regulation in L. plantarum.
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Affiliation(s)
- Chen Chen
- Department of Food Science and Technology, Shanghai Institute of Technology, Shanghai, China
| | - Linlin Wang
- Department of Food Science and Technology, Shanghai Institute of Technology, Shanghai, China
| | - Yanqing Lu
- Department of Food Science and Technology, Shanghai Institute of Technology, Shanghai, China
| | - Haiyan Yu
- Department of Food Science and Technology, Shanghai Institute of Technology, Shanghai, China
| | - Huanxiang Tian
- Department of Food Science and Technology, Shanghai Institute of Technology, Shanghai, China
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19
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Qin L, Wang J, Lu J, Yang H, Zheng R, Liu Z, Huang X, Feng Y, Hu Z, Ge B. A deletion in the RD105 region confers resistance to multiple drugs in Mycobacterium tuberculosis. BMC Biol 2019; 17:7. [PMID: 30683096 PMCID: PMC6347829 DOI: 10.1186/s12915-019-0628-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/10/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), especially those that are multidrug resistant poses a serious threat to global tuberculosis control. However, the mechanism underlying the occurrence of drug resistance against more than one drug is poorly understood. Given that the Beijing/W strains are associated with outbreaks and multidrug resistance, they may harbor a genetic advantage and provide useful insight into the disease. One marker found in all Beijing/W Mtb strains is a deletion of RD105 region that results in a gene fusion, Rv0071/74, with a variable number (3-9 m) of VDP (V: Val, D: Asp; P: Pro) repeats (coded by gtggacccg repeat sequences) at the N-terminal. Here, we report that this variable number of VDP repeats in Rv0071/74 regulates the development of multidrug resistance. RESULTS We collected and analyzed 1255 Beijing/W clinical strains. The results showed that the number of VDP repeats in Rv0071/74 was related to the development of multidrug resistance, and the deletion of Rv0071/74-9 m from Beijing/W clinical strain restored drug susceptibility. Rv0071/74-9 m also increased resistance to multiple drugs when transferred to different mycobacterial strains. Cell-free assays indicate that the domain carrying 4-9 VDP repeats (4-9 m) showed a variable binding affinity with peptidoglycan and Rv0071/74 cleaves peptidoglycan. Furthermore, Rv0071/74-9 m increased cell wall thickness and reduced the intracellular concentration of antibiotics. CONCLUSIONS These findings not only identify Rv0071/74 with VDP repeats as a newly identified multidrug resistance gene but also provide a new model for the development of multiple drug resistance.
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Affiliation(s)
- Lianhua Qin
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Jie Wang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Junmei Lu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Hua Yang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Zhonghua Liu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Xiaochen Huang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Yonghong Feng
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Zhongyi Hu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.
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20
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Terán LC, Coeuret G, Raya R, Zagorec M, Champomier-Vergès MC, Chaillou S. Phylogenomic Analysis of Lactobacillus curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates. Genome Biol Evol 2018; 10:1516-1525. [PMID: 29850855 PMCID: PMC6007345 DOI: 10.1093/gbe/evy106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.
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Affiliation(s)
- Lucrecia C Terán
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Gwendoline Coeuret
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Raúl Raya
- CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina
| | - Monique Zagorec
- SECALIM, INRA, Oniris, Université Bretagne Loire, Nantes, France
| | | | - Stéphane Chaillou
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
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21
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Desvaux M, Candela T, Serror P. Surfaceome and Proteosurfaceome in Parietal Monoderm Bacteria: Focus on Protein Cell-Surface Display. Front Microbiol 2018; 9:100. [PMID: 29491848 PMCID: PMC5817068 DOI: 10.3389/fmicb.2018.00100] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/16/2018] [Indexed: 12/12/2022] Open
Abstract
The cell envelope of parietal monoderm bacteria (archetypal Gram-positive bacteria) is formed of a cytoplasmic membrane (CM) and a cell wall (CW). While the CM is composed of phospholipids, the CW is composed at least of peptidoglycan (PG) covalently linked to other biopolymers, such as teichoic acids, polysaccharides, and/or polyglutamate. Considering the CW is a porous structure with low selective permeability contrary to the CM, the bacterial cell surface hugs the molecular figure of the CW components as a well of the external side of the CM. While the surfaceome corresponds to the totality of the molecules found at the bacterial cell surface, the proteinaceous complement of the surfaceome is the proteosurfaceome. Once translocated across the CM, secreted proteins can either be released in the extracellular milieu or exposed at the cell surface by associating to the CM or the CW. Following the gene ontology (GO) for cellular components, cell-surface proteins at the CM can either be integral (GO: 0031226), i.e., the integral membrane proteins, or anchored to the membrane (GO: 0046658), i.e., the lipoproteins. At the CW (GO: 0009275), cell-surface proteins can be covalently bound, i.e., the LPXTG-proteins, or bound through weak interactions to the PG or wall polysaccharides, i.e., the cell wall binding proteins. Besides monopolypeptides, some proteins can associate to each other to form supramolecular protein structures of high molecular weight, namely the S-layer, pili, flagella, and cellulosomes. After reviewing the cell envelope components and the different molecular mechanisms involved in protein attachment to the cell envelope, perspectives in investigating the proteosurfaceome in parietal monoderm bacteria are further discussed.
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Affiliation(s)
- Mickaël Desvaux
- Université Clermont Auvergne, INRA, UMR454 MEDiS, Clermont-Ferrand, France
| | - Thomas Candela
- EA4043 Unité Bactéries Pathogènes et Santé, Châtenay-Malabry, France
| | - Pascale Serror
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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22
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Castro R, Reguera-Brito M, López-Campos GH, Blanco MM, Aguado-Urda M, Fernández-Garayzábal JF, Gibello A. How does temperature influences the development of lactococcosis? Transcriptomic and immunoproteomic in vitro approaches. JOURNAL OF FISH DISEASES 2017; 40:1285-1297. [PMID: 28093775 DOI: 10.1111/jfd.12601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 06/06/2023]
Abstract
Lactococcus garvieae is the aetiological agent of lactococcosis, a haemorrhagic septicaemia that affects marine and freshwater fish, with special incidence and economic relevance in farmed rainbow trout. Water temperature is one of the most important predisposing factors in the development of lactococcosis outbreaks. Lactococcosis in trout usually occur when water temperatures rise to about 18 °C, while fish carriers remain asymptomatic at temperatures below 13 °C. The aim of this work was to analyse the differences in the complete transcriptome response of L. garvieae grown at 18 °C and at 13 °C and to identify the immunogenic proteins expressed by this bacterium at 18 °C. Our results show that water temperature influences the expression of L. garvieae genes involved in the lysis of part of the bacterial cell population and in the cold response bacterial adaptation. Moreover, the surface immunogenic protein profile at 18 °C suggests an important role of the lysozyme-like enzyme, WxL surface proteins and some putative moonlighting proteins (proteins with more than one function, usually associated with different cellular locations) as virulence factors in L. garvieae. The results of this study could provide insights into the understanding of the virulence mechanisms of L. garvieae in fish.
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Affiliation(s)
- R Castro
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - M Reguera-Brito
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - G H López-Campos
- Health and Biomedical Informatics Research Unit, Medical School, University of Melbourne, Melbourne, VIC, Australia
| | - M M Blanco
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - M Aguado-Urda
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - J F Fernández-Garayzábal
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
- Animal Health Surveillance Center (VISAVET), Complutense University, Madrid, Spain
| | - A Gibello
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
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23
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Draft Genome Sequence of Lactobacillus curvatus FLEC03, a Meat-Borne Isolate from Beef Carpaccio Packaged in a Modified Atmosphere. GENOME ANNOUNCEMENTS 2017; 5:5/26/e00584-17. [PMID: 28663298 PMCID: PMC5638282 DOI: 10.1128/genomea.00584-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this study, we present the draft genome sequence for Lactobacillus curvatus FLEC03. This strain was isolated from beef carpaccio packaged in a modified atmosphere. The draft genome will contribute to understanding the role of L. curvatus strains in food products (fermentation, biopreservation, or spoilage) through comparative genomics with other strains.
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24
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Acurcio LB, Bastos RW, Sandes SHDC, Guimarães ACDC, Alves CG, Reis DCD, Wuyts S, Nunes ÁC, Cassali GD, Lebeer S, Souza MRD, Nicoli JR. Protective effects of milk fermented by Lactobacillus plantarum B7 from Brazilian artisanal cheese on a Salmonella enterica serovar Typhimurium infection in BALB/c mice. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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25
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Iskandar CF, Borges F, Taminiau B, Daube G, Zagorec M, Remenant B, Leisner JJ, Hansen MA, Sørensen SJ, Mangavel C, Cailliez-Grimal C, Revol-Junelles AM. Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium. Front Microbiol 2017; 8:357. [PMID: 28337181 PMCID: PMC5341603 DOI: 10.3389/fmicb.2017.00357] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/21/2017] [Indexed: 02/01/2023] Open
Abstract
Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study, Carnobacterium was used as a model genus to elucidate the genetic basis of these colonization differences. Analyses of 16S rRNA gene meta-barcoding data showed that C. maltaromaticum followed by C. divergens are the most prevalent species in foods derived from animals (meat, fish, dairy products), and in the gut. According to phylogenetic analyses, these two animal-adapted species belong to one of two deeply branched lineages. The second lineage contains species isolated from habitats where contact with animal is rare. Genome analyses revealed that members of the animal-adapted lineage harbor a larger secretome than members of the other lineage. The predicted cell-surface proteome is highly diversified in C. maltaromaticum and C. divergens with genes involved in adaptation to the animal milieu such as those encoding biopolymer hydrolytic enzymes, a heme uptake system, and biopolymer-binding adhesins. These species also exhibit genes for gut adaptation and respiration. In contrast, Carnobacterium species belonging to the second lineage encode a poorly diversified cell-surface proteome, lack genes for gut adaptation and are unable to respire. These results shed light on the important genomics traits required for adaptation to animal-linked habitats in generalist Carnobacterium.
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Affiliation(s)
- Christelle F. Iskandar
- Laboratoire d’Ingénierie des Biomolécules, École Nationale Supérieure d’Agronomie et des Industries Alimentaires – Université de LorraineVandoeuvre-lès-Nancy, France
| | - Frédéric Borges
- Laboratoire d’Ingénierie des Biomolécules, École Nationale Supérieure d’Agronomie et des Industries Alimentaires – Université de LorraineVandoeuvre-lès-Nancy, France
| | - Bernard Taminiau
- Laboratory of Food Microbiology, Department of Food Science, Fundamental and Applied Research for Animal and Health, University of LiègeLiège, Belgium
| | - Georges Daube
- Laboratory of Food Microbiology, Department of Food Science, Fundamental and Applied Research for Animal and Health, University of LiègeLiège, Belgium
| | | | | | - Jørgen J. Leisner
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of CopenhagenFrederiksberg, Denmark
| | - Martin A. Hansen
- Molecular Microbial Ecology Group, University of CopenhagenCopenhagen, Denmark
| | - Søren J. Sørensen
- Molecular Microbial Ecology Group, University of CopenhagenCopenhagen, Denmark
| | - Cécile Mangavel
- Laboratoire d’Ingénierie des Biomolécules, École Nationale Supérieure d’Agronomie et des Industries Alimentaires – Université de LorraineVandoeuvre-lès-Nancy, France
| | - Catherine Cailliez-Grimal
- Laboratoire d’Ingénierie des Biomolécules, École Nationale Supérieure d’Agronomie et des Industries Alimentaires – Université de LorraineVandoeuvre-lès-Nancy, France
| | - Anne-Marie Revol-Junelles
- Laboratoire d’Ingénierie des Biomolécules, École Nationale Supérieure d’Agronomie et des Industries Alimentaires – Université de LorraineVandoeuvre-lès-Nancy, France
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26
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Petrova MI, Lievens E, Verhoeven TLA, Macklaim JM, Gloor G, Schols D, Vanderleyden J, Reid G, Lebeer S. The lectin-like protein 1 in Lactobacillus rhamnosus GR-1 mediates tissue-specific adherence to vaginal epithelium and inhibits urogenital pathogens. Sci Rep 2016; 6:37437. [PMID: 27869151 PMCID: PMC5116675 DOI: 10.1038/srep37437] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/28/2016] [Indexed: 12/02/2022] Open
Abstract
The probiotic Lactobacillus rhamnosus GR-1 has been documented to survive implantation onto the vaginal epithelium and interfere with urogenital pathogens. However, the molecular mechanisms involved are largely unknown. Here, we report for the first time the construction of dedicated knock-out mutants in L. rhamnosus GR-1 to enable the study of gene functions. In a search for genes responsible for the adherence capacity of L. rhamnosus GR-1, a genomic region encoding a protein with homology to lectin-like proteins was identified. Phenotypic analyses of the knock-out mutant of L. rhamnosus GR-1 revealed a two-fold decreased adhesion to the vaginal and ectocervical epithelial cell lines compared to wild-type. In contrast, the adhesion to gastro-intestinal epithelial (Caco2) and endocervical cell lines (Hela and End1/E6E7) was not drastically affected by the mutation, suggesting that the LGR-1_Llp1 lectins mediates tissue tropism. The purified LGR-1_Llp1 protein also inhibited biofilm formation and adhesion of uropathogenic Escherichia coli. For the first time, an important role for a novel lectin-like protein in the adhesion capacity and host cell-specific interaction of a vaginal probiotic Lactobacillus strain has been discovered, with an additional role in pathogen inhibition.
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Affiliation(s)
- Mariya I Petrova
- KU Leuven, Centre of Microbial and Plant Genetics, Leuven, Belgium.,University of Antwerp, Department of Bioscience Engineering, Antwerp, Belgium
| | - Elke Lievens
- KU Leuven, Centre of Microbial and Plant Genetics, Leuven, Belgium.,University of Antwerp, Department of Bioscience Engineering, Antwerp, Belgium
| | | | - Jean M Macklaim
- The Lawson Health Research Institute London, Canada Research and Development Centre for Probiotics, London, ON, Canada.,University of Western Ontario, London, ON, Canada
| | | | | | - Jos Vanderleyden
- KU Leuven, Centre of Microbial and Plant Genetics, Leuven, Belgium
| | - Gregor Reid
- The Lawson Health Research Institute London, Canada Research and Development Centre for Probiotics, London, ON, Canada.,University of Western Ontario, London, ON, Canada
| | - Sarah Lebeer
- KU Leuven, Centre of Microbial and Plant Genetics, Leuven, Belgium.,University of Antwerp, Department of Bioscience Engineering, Antwerp, Belgium
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27
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Surface display on lactic acid bacteria without genetic modification: strategies and applications. Appl Microbiol Biotechnol 2016; 100:9407-9421. [DOI: 10.1007/s00253-016-7842-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/31/2016] [Accepted: 09/03/2016] [Indexed: 12/21/2022]
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28
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Petrova MI, Imholz NCE, Verhoeven TLA, Balzarini J, Van Damme EJM, Schols D, Vanderleyden J, Lebeer S. Lectin-Like Molecules of Lactobacillus rhamnosus GG Inhibit Pathogenic Escherichia coli and Salmonella Biofilm Formation. PLoS One 2016; 11:e0161337. [PMID: 27537843 PMCID: PMC4990349 DOI: 10.1371/journal.pone.0161337] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 08/03/2016] [Indexed: 01/01/2023] Open
Abstract
Objectives Increased antibiotic resistance has catalyzed the research on new antibacterial molecules and alternative strategies, such as the application of beneficial bacteria. Since lectin molecules have unique sugar-recognizing capacities, and pathogens are often decorated with sugars that affect their survival and infectivity, we explored whether lectins from the probiotic strain Lactobacillus rhamnosus GG have antipathogenic properties. Methods The genome sequence of L. rhamnosus GG was screened for the presence of lectin-like proteins. Two genes, LGG_RS02780 and LGG_RS02750, encoding for polypeptides with an N-terminal conserved L-type lectin domain were detected and designated Llp1 (lectin-like protein 1) and Llp2. The capacity of Llp1 and Llp2 to inhibit biofilm formation of various pathogens was investigated. Sugar specificity was determined by Sepharose beads assays and glycan array screening. Results The isolated lectin domains of Llp1 and Llp2 possess pronounced inhibitory activity against biofilm formation by various pathogens, including clinical Salmonella species and uropathogenic E. coli, with Llp2 being more active than Llp1. In addition, sugar binding assays with Llp1 and Llp2 indicate specificity for complex glycans. Both proteins are also involved in the adhesion capacity of L. rhamnosus GG to gastrointestinal and vaginal epithelial cells. Conclusions Lectins isolated from or expressed by beneficial lactobacilli could be considered promising bio-active ingredients for improved prophylaxis of urogenital and gastrointestinal infections.
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Affiliation(s)
- Mariya I. Petrova
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, box 2460, B-3001, Leuven, Belgium
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, B-2020, Antwerp, Belgium
- * E-mail: (SL); (MIP)
| | - Nicole C. E. Imholz
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, box 2460, B-3001, Leuven, Belgium
| | - Tine L. A. Verhoeven
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, box 2460, B-3001, Leuven, Belgium
| | - Jan Balzarini
- KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000, Leuven, Belgium
| | - Els J. M. Van Damme
- Ghent University, Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Coupure Links 653, B-9000, Ghent, Belgium
| | - Dominique Schols
- KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000, Leuven, Belgium
| | - Jos Vanderleyden
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, box 2460, B-3001, Leuven, Belgium
| | - Sarah Lebeer
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, box 2460, B-3001, Leuven, Belgium
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, B-2020, Antwerp, Belgium
- * E-mail: (SL); (MIP)
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29
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Transcriptional reprogramming and phenotypic switching associated with the adaptation of Lactobacillus plantarum C2 to plant niches. Sci Rep 2016; 6:27392. [PMID: 27273017 PMCID: PMC4895336 DOI: 10.1038/srep27392] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 05/17/2016] [Indexed: 01/08/2023] Open
Abstract
Lactobacillus plantarum has been isolated from a large variety of ecological niches, thus highlighting its remarkable environmental adaptability as a generalist. Plant fermentation conditions markedly affect the functional features of L. plantarum strains. We investigated the plant niche-specific traits of L. plantarum through whole-transcriptome and phenotypic microarray profiles. Carrot (CJ) and pineapple (PJ) juices were chosen as model systems, and MRS broth was used as a control. A set of 3,122 genes was expressed, and 21 to 31% of genes were differentially expressed depending on the plant niche and cell physiological state. L. plantarum C2 seemed to specifically respond to plant media conditions. When L. plantarum was cultured in CJ, useful pathways were activated, which were aimed to sense the environment, save energy and adopt alternative routes for NAD+ regeneration. In PJ the acidic environment caused a transcriptional switching, which was network-linked to an acid tolerance response involving carbohydrate flow, amino acid and protein metabolism, pH homeostasis and membrane fluidity. The most prominent phenotypic dissimilarities observed in cells grown in CJ and PJ were related to carbon and nitrogen metabolism, respectively. Summarising, a snapshot of a carrot and pineapple sensing and adaptive regulation model for L. plantarum C2 was proposed.
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30
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Combinations of cereal β-glucans and probiotics can enhance the anti-inflammatory activity on host cells by a synergistic effect. J Funct Foods 2016. [DOI: 10.1016/j.jff.2016.02.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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31
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Liu CJ, Wang R, Gong FM, Liu XF, Zheng HJ, Luo YY, Li XR. Complete genome sequences and comparative genome analysis of Lactobacillus plantarum strain 5-2 isolated from fermented soybean. Genomics 2015; 106:404-11. [PMID: 26212213 DOI: 10.1016/j.ygeno.2015.07.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 07/16/2015] [Accepted: 07/17/2015] [Indexed: 01/08/2023]
Abstract
Lactobacillus plantarum is an important probiotic and is mostly isolated from fermented foods. We sequenced the genome of L. plantarum strain 5-2, which was derived from fermented soybean isolated from Yunnan province, China. The strain was determined to contain 3114 genes. Fourteen complete insertion sequence (IS) elements were found in 5-2 chromosome. There were 24 DNA replication proteins and 76 DNA repair proteins in the 5-2 genome. Consistent with the classification of L. plantarum as a facultative heterofermentative lactobacillus, the 5-2 genome encodes key enzymes required for the EMP (Embden-Meyerhof-Parnas) and phosphoketolase (PK) pathways. Several components of the secretion machinery are found in the 5-2 genome, which was compared with L. plantarum ST-III, JDM1 and WCFS1. Most of the specific proteins in the four genomes appeared to be related to their prophage elements.
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Affiliation(s)
- Chen-Jian Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Rui Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Fu-Ming Gong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Xiao-Feng Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Yi-Yong Luo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Xiao-Ran Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
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32
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Alkema W, Boekhorst J, Wels M, van Hijum SAFT. Microbial bioinformatics for food safety and production. Brief Bioinform 2015; 17:283-92. [PMID: 26082168 PMCID: PMC4793891 DOI: 10.1093/bib/bbv034] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Indexed: 12/14/2022] Open
Abstract
In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput 'omics' technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety.
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33
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Cortes-Perez NG, Dumoulin R, Gaubert S, Lacoux C, Bugli F, Martin R, Chat S, Piquand K, Meylheuc T, Langella P, Sanguinetti M, Posteraro B, Rigottier-Gois L, Serror P. Overexpression of Enterococcus faecalis elr operon protects from phagocytosis. BMC Microbiol 2015; 15:112. [PMID: 26003173 PMCID: PMC4522977 DOI: 10.1186/s12866-015-0448-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 05/14/2015] [Indexed: 11/17/2022] Open
Abstract
Background Mechanisms underlying the transition from commensalism to virulence in Enterococcus faecalis are not fully understood. We previously identified the enterococcal leucine-rich protein A (ElrA) as a virulence factor of E. faecalis. The elrA gene is part of an operon that comprises four other ORFs encoding putative surface proteins of unknown function. Results In this work, we compared the susceptibility to phagocytosis of three E. faecalis strains, including a wild-type (WT), a ΔelrA strain, and a strain overexpressing the whole elr operon in order to understand the role of this operon in E. faecalis virulence. While both WT and ΔelrA strains were efficiently phagocytized by RAW 264.7 mouse macrophages, the elr operon-overexpressing strain showed a decreased capability to be internalized by the phagocytic cells. Consistently, the strain overexpressing elr operon was less adherent to macrophages than the WT strain, suggesting that overexpression of the elr operon could confer E. faecalis with additional anti-adhesion properties. In addition, increased virulence of the elr operon-overexpressing strain was shown in a mouse peritonitis model. Conclusions Altogether, our results indicate that overexpression of the elr operon facilitates the E. faecalis escape from host immune defenses. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0448-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Naima G Cortes-Perez
- INRA, UMR1319 Micalis, Jouy-en-Josas, France. .,AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France. .,Current address: INRA, Unité d'Immuno-Allergie Alimentaire, iBiTecS/SPI, Gif-sur-Yvette, France.
| | - Romain Dumoulin
- INRA, UMR1319 Micalis, Jouy-en-Josas, France. .,AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France.
| | - Stéphane Gaubert
- INRA, UMR1319 Micalis, Jouy-en-Josas, France. .,AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France.
| | - Caroline Lacoux
- INRA, UMR1319 Micalis, Jouy-en-Josas, France. .,AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France.
| | - Francesca Bugli
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Rebeca Martin
- INRA, UMR1319 Micalis, Jouy-en-Josas, France. .,AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France.
| | - Sophie Chat
- INRA, UMR1319 Micalis, Jouy-en-Josas, France. .,AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France.
| | - Kevin Piquand
- INRA, UMR1319 Micalis, Jouy-en-Josas, France. .,AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France.
| | - Thierry Meylheuc
- INRA, UMR1319 Micalis, Jouy-en-Josas, France. .,AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France.
| | - Philippe Langella
- INRA, UMR1319 Micalis, Jouy-en-Josas, France. .,AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France.
| | | | - Brunella Posteraro
- Institute of Public Health (Section of Hygiene), Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Lionel Rigottier-Gois
- INRA, UMR1319 Micalis, Jouy-en-Josas, France. .,AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France.
| | - Pascale Serror
- INRA, UMR1319 Micalis, Jouy-en-Josas, France. .,AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France.
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34
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Metselaar KI, Saá Ibusquiza P, Ortiz Camargo AR, Krieg M, Zwietering MH, den Besten HMW, Abee T. Performance of stress resistant variants of Listeria monocytogenes in mixed species biofilms with Lactobacillus plantarum. Int J Food Microbiol 2015; 213:24-30. [PMID: 25935090 DOI: 10.1016/j.ijfoodmicro.2015.04.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/13/2015] [Accepted: 04/15/2015] [Indexed: 11/25/2022]
Abstract
Population diversity and the ability to adapt to changing environments allow Listeria monocytogenes to grow and survive under a wide range of environmental conditions. In this study, we aimed to evaluate the performance of a set of acid resistant L. monocytogenes variants in mixed-species biofilms with Lactobacillus plantarum as well as their benzalkonium chloride (BAC) resistance in these biofilms. L. monocytogenes LO28 wild type and acid resistant variants were capable of forming mixed biofilms with L. plantarum at 20°C and 30°C in BHI supplemented with manganese and glucose. Homolactic fermentation of glucose by L. plantarum created an acidic environment with pH values below the growth boundary of L. monocytogenes. Some of the variants were able to withstand the low pH in the mixed biofilms for a longer time than the WT and there were clear differences in survival between the variants which could not be correlated to (lactic) acid resistance alone. Adaptation to mild pH of liquid cultures during growth to stationary phase increased the acid resistance of some variants to a greater extent than of others, indicating differences in adaptive behaviour between the variants. Two variants that showed a high level of acid adaptation when grown in liquid cultures, showed also better performance in mixed species biofilms. There were no clear differences in BAC resistance between the wild type and variants in mixed biofilms. It can be concluded that acid resistant variants of L. monocytogenes show diversity in their adaptation to acidic conditions and their capacity to survive in mixed cultures and biofilms with L. plantarum.
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Affiliation(s)
- Karin I Metselaar
- Top Institute Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Paula Saá Ibusquiza
- Top Institute Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Angela R Ortiz Camargo
- Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Myriam Krieg
- Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Marcel H Zwietering
- Top Institute Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Heidy M W den Besten
- Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Tjakko Abee
- Top Institute Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands.
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Ellegaard KM, Tamarit D, Javelind E, Olofsson TC, Andersson SGE, Vásquez A. Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut. BMC Genomics 2015; 16:284. [PMID: 25880915 PMCID: PMC4449606 DOI: 10.1186/s12864-015-1476-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 03/23/2015] [Indexed: 01/09/2023] Open
Abstract
Background In the honeybee Apis mellifera, the bacterial gut community is consistently colonized by eight distinct phylotypes of bacteria. Managed bee colonies are of considerable economic interest and it is therefore important to elucidate the diversity and role of this microbiota in the honeybee. In this study, we have sequenced the genomes of eleven strains of lactobacilli and bifidobacteria isolated from the honey crop of the honeybee A. mellifera. Results Single gene phylogenies confirmed that the isolated strains represent the diversity of lactobacilli and bifidobacteria in the gut, as previously identified by 16S rRNA gene sequencing. Core genome phylogenies of the lactobacilli and bifidobacteria further indicated extensive divergence between strains classified as the same phylotype. Phylotype-specific protein families included unique surface proteins. Within phylotypes, we found a remarkably high level of gene content diversity. Carbohydrate metabolism and transport functions contributed up to 45% of the accessory genes, with some genomes having a higher content of genes encoding phosphotransferase systems for the uptake of carbohydrates than any previously sequenced genome. These genes were often located in highly variable genomic segments that also contained genes for enzymes involved in the degradation and modification of sugar residues. Strain-specific gene clusters for the biosynthesis of exopolysaccharides were identified in two phylotypes. The dynamics of these segments contrasted with low recombination frequencies and conserved gene order structures for the core genes. Hits for CRISPR spacers were almost exclusively found within phylotypes, suggesting that the phylotypes are associated with distinct phage populations. Conclusions The honeybee gut microbiota has been described as consisting of a modest number of phylotypes; however, the genomes sequenced in the current study demonstrated a very high level of gene content diversity within all three described phylotypes of lactobacilli and bifidobacteria, particularly in terms of metabolic functions and surface structures, where many features were strain-specific. Together, these results indicate niche differentiation within phylotypes, suggesting that the honeybee gut microbiota is more complex than previously thought. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1476-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kirsten M Ellegaard
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Daniel Tamarit
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Emelie Javelind
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Tobias C Olofsson
- Department of Laboratory Medicine, Medical Microbiology, Lund University, Medicon Village, Scheelevägen 2, SE-223 62, Lund, Sweden.
| | - Siv G E Andersson
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Alejandra Vásquez
- Department of Laboratory Medicine, Medical Microbiology, Lund University, Medicon Village, Scheelevägen 2, SE-223 62, Lund, Sweden.
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Galloway-Peña JR, Liang X, Singh KV, Yadav P, Chang C, La Rosa SL, Shelburne S, Ton-That H, Höök M, Murray BE. The identification and functional characterization of WxL proteins from Enterococcus faecium reveal surface proteins involved in extracellular matrix interactions. J Bacteriol 2015; 197:882-92. [PMID: 25512313 PMCID: PMC4325096 DOI: 10.1128/jb.02288-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/10/2014] [Indexed: 11/20/2022] Open
Abstract
The WxL domain recently has been identified as a novel cell wall binding domain found in numerous predicted proteins within multiple Gram-positive bacterial species. However, little is known about the function of proteins containing this novel domain. Here, we identify and characterize 6 Enterococcus faecium proteins containing the WxL domain which, by reverse transcription-PCR (RT-PCR) and genomic analyses, are located in three similarly organized operons, deemed WxL loci A, B, and C. Western blotting, electron microscopy, and enzyme-linked immunosorbent assays (ELISAs) determined that genes of WxL loci A and C encode antigenic, cell surface proteins exposed at higher levels in clinical isolates than in commensal isolates. Secondary structural analyses of locus A recombinant WxL domain-containing proteins found they are rich in β-sheet structure and disordered segments. Using Biacore analyses, we discovered that recombinant WxL proteins from locus A bind human extracellular matrix proteins, specifically type I collagen and fibronectin. Proteins encoded by locus A also were found to bind to each other, suggesting a novel cell surface complex. Furthermore, bile salt survival assays and animal models using a mutant from which all three WxL loci were deleted revealed the involvement of WxL operons in bile salt stress and endocarditis pathogenesis. In summary, these studies extend our understanding of proteins containing the WxL domain and their potential impact on colonization and virulence in E. faecium and possibly other Gram-positive bacterial species.
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Affiliation(s)
- Jessica R Galloway-Peña
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas, USA Center for the Study of Emerging and Re-emerging Pathogens, University of Texas Health Science Center, Houston, Texas, USA
| | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases, Institute for Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
| | - Kavindra V Singh
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas, USA Center for the Study of Emerging and Re-emerging Pathogens, University of Texas Health Science Center, Houston, Texas, USA
| | - Puja Yadav
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas, USA Center for the Study of Emerging and Re-emerging Pathogens, University of Texas Health Science Center, Houston, Texas, USA
| | - Chungyu Chang
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA
| | - Sabina Leanti La Rosa
- Department of Chemistry, Biotechnology and Food Science, Laboratory of Microbial Gene Technology and Food Microbiology, The Norwegian University of Life Sciences, Aas, Norway
| | - Samuel Shelburne
- Department of Infectious Diseases, Infection Control and Employee Health, M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Hung Ton-That
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA
| | - Magnus Höök
- Center for Infectious and Inflammatory Diseases, Institute for Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
| | - Barbara E Murray
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, Texas, USA Center for the Study of Emerging and Re-emerging Pathogens, University of Texas Health Science Center, Houston, Texas, USA
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Lactococcus lactis metabolism and gene expression during growth on plant tissues. J Bacteriol 2014; 197:371-81. [PMID: 25384484 DOI: 10.1128/jb.02193-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactic acid bacteria have been isolated from living, harvested, and fermented plant materials; however, the adaptations these bacteria possess for growth on plant tissues are largely unknown. In this study, we investigated plant habitat-specific traits of Lactococcus lactis during growth in an Arabidopsis thaliana leaf tissue lysate (ATL). L. lactis KF147, a strain originally isolated from plants, exhibited a higher growth rate and reached 7.9-fold-greater cell densities during growth in ATL than the dairy-associated strain L. lactis IL1403. Transcriptome profiling (RNA-seq) of KF147 identified 853 induced and 264 repressed genes during growth in ATL compared to that in GM17 laboratory culture medium. Genes induced in ATL included those involved in the arginine deiminase pathway and a total of 140 carbohydrate transport and metabolism genes, many of which are involved in xylose, arabinose, cellobiose, and hemicellulose metabolism. The induction of those genes corresponded with L. lactis KF147 nutrient consumption and production of metabolic end products in ATL as measured by gas chromatography-time of flight mass spectrometry (GC-TOF/MS) untargeted metabolomic profiling. To assess the importance of specific plant-inducible genes for L. lactis growth in ATL, xylose metabolism was targeted for gene knockout mutagenesis. Wild-type L. lactis strain KF147 but not an xylA deletion mutant was able to grow using xylose as the sole carbon source. However, both strains grew to similarly high levels in ATL, indicating redundancy in L. lactis carbohydrate metabolism on plant tissues. These findings show that certain strains of L. lactis are well adapted for growth on plants and possess specific traits relevant for plant-based food, fuel, and feed fermentations.
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Abstract
The cell wall of Gram-positive bacteria is a complex assemblage of glycopolymers and proteins. It consists of a thick peptidoglycan sacculus that surrounds the cytoplasmic membrane and that is decorated with teichoic acids, polysaccharides, and proteins. It plays a major role in bacterial physiology since it maintains cell shape and integrity during growth and division; in addition, it acts as the interface between the bacterium and its environment. Lactic acid bacteria (LAB) are traditionally and widely used to ferment food, and they are also the subject of more and more research because of their potential health-related benefits. It is now recognized that understanding the composition, structure, and properties of LAB cell walls is a crucial part of developing technological and health applications using these bacteria. In this review, we examine the different components of the Gram-positive cell wall: peptidoglycan, teichoic acids, polysaccharides, and proteins. We present recent findings regarding the structure and function of these complex compounds, results that have emerged thanks to the tandem development of structural analysis and whole genome sequencing. Although general structures and biosynthesis pathways are conserved among Gram-positive bacteria, studies have revealed that LAB cell walls demonstrate unique properties; these studies have yielded some notable, fundamental, and novel findings. Given the potential of this research to contribute to future applied strategies, in our discussion of the role played by cell wall components in LAB physiology, we pay special attention to the mechanisms controlling bacterial autolysis, bacterial sensitivity to bacteriophages and the mechanisms underlying interactions between probiotic bacteria and their hosts.
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Ainsworth S, Stockdale S, Bottacini F, Mahony J, van Sinderen D. The Lactococcus lactis plasmidome: much learnt, yet still lots to discover. FEMS Microbiol Rev 2014; 38:1066-88. [PMID: 24861818 DOI: 10.1111/1574-6976.12074] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/17/2014] [Accepted: 05/07/2014] [Indexed: 01/20/2023] Open
Abstract
Lactococcus lactis is used extensively worldwide for the production of a variety of fermented dairy products. The ability of L. lactis to successfully grow and acidify milk has long been known to be reliant on a number of plasmid-encoded traits. The recent availability of low-cost, high-quality genome sequencing, and the quest for novel, technologically desirable characteristics, such as novel flavour development and increased stress tolerance, has led to a steady increase in the number of available lactococcal plasmid sequences. We will review both well-known and very recent discoveries regarding plasmid-encoded traits of biotechnological significance. The acquired lactococcal plasmid sequence information has in recent years progressed our understanding of the origin of lactococcal dairy starter cultures. Salient points on the acquisition and evolution of lactococcal plasmids will be discussed in this review, as well as prospects of finding novel plasmid-encoded functions.
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Affiliation(s)
- Stuart Ainsworth
- Department of Microbiology, University College Cork, Cork, Ireland
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40
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Hendrickx APA, van Schaik W, Willems RJL. The cell wall architecture of Enterococcus faecium: from resistance to pathogenesis. Future Microbiol 2014; 8:993-1010. [PMID: 23902146 DOI: 10.2217/fmb.13.66] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The cell wall of Gram-positive bacteria functions as a surface organelle that continuously interacts with its environment through a plethora of cell wall-associated molecules. Enterococcus faecium is a normal inhabitant of the GI tract of mammals, but has recently become an important etiological agent of hospital-acquired infections in debilitated patients. Insights into the assembly and function of enterococcal cell wall components and their interactions with the host during colonization and infection are essential to explain the worldwide emergence of E. faecium as an important multiantibiotic-resistant nosocomial pathogen. Understanding the biochemistry of cell wall biogenesis and principles of antibiotic resistance at the molecular level may open up new frontiers in research on enterococci, particularly for the development of novel antimicrobial strategies. In this article, we outline the current knowledge on the most important antimicrobial resistance mechanisms that involve peptidoglycan synthesis and the role of cell wall constituents, including lipoteichoic acid, wall teichoic acid, capsular polysaccharides, LPxTG cell wall-anchored surface proteins, WxL-type surface proteins and pili, in the pathogenesis of E. faecium.
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Affiliation(s)
- Antoni P A Hendrickx
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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41
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Vastano V, Salzillo M, Siciliano RA, Muscariello L, Sacco M, Marasco R. The E1 beta-subunit of pyruvate dehydrogenase is surface-expressed in Lactobacillus plantarum and binds fibronectin. Microbiol Res 2014; 169:121-7. [DOI: 10.1016/j.micres.2013.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 07/08/2013] [Accepted: 07/18/2013] [Indexed: 11/16/2022]
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Turroni F, Ventura M, Buttó LF, Duranti S, O’Toole PW, Motherway MO, van Sinderen D. Molecular dialogue between the human gut microbiota and the host: a Lactobacillus and Bifidobacterium perspective. Cell Mol Life Sci 2014; 71:183-203. [PMID: 23516017 PMCID: PMC11113728 DOI: 10.1007/s00018-013-1318-0] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/13/2013] [Accepted: 03/04/2013] [Indexed: 02/06/2023]
Abstract
The human gut represents a highly complex ecosystem, which is densely colonized by a myriad of microorganisms that influence the physiology, immune function and health status of the host. Among the many members of the human gut microbiota, there are microorganisms that have co-evolved with their host and that are believed to exert health-promoting or probiotic effects. Probiotic bacteria isolated from the gut and other environments are commercially exploited, and although there is a growing list of health benefits provided by the consumption of such probiotics, their precise mechanisms of action have essentially remained elusive. Genomics approaches have provided exciting new opportunities for the identification of probiotic effector molecules that elicit specific responses to influence the physiology and immune function of their human host. In this review, we describe the current understanding of the intriguing relationships that exist between the human gut and key members of the gut microbiota such as bifidobacteria and lactobacilli, discussed here as prototypical groups of probiotic microorganisms.
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Affiliation(s)
- Francesca Turroni
- Alimentary Pharmabiotic Centre, Department of Microbiology Biosciences Institute, University College Cork, National University of Ireland, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy
| | - Ludovica F. Buttó
- Alimentary Pharmabiotic Centre, Department of Microbiology Biosciences Institute, University College Cork, National University of Ireland, Western Road, Cork, Ireland
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy
| | - Paul W. O’Toole
- Alimentary Pharmabiotic Centre, Department of Microbiology Biosciences Institute, University College Cork, National University of Ireland, Western Road, Cork, Ireland
| | - Mary O’Connell Motherway
- Alimentary Pharmabiotic Centre, Department of Microbiology Biosciences Institute, University College Cork, National University of Ireland, Western Road, Cork, Ireland
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre, Department of Microbiology Biosciences Institute, University College Cork, National University of Ireland, Western Road, Cork, Ireland
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Toh H, Oshima K, Nakano A, Takahata M, Murakami M, Takaki T, Nishiyama H, Igimi S, Hattori M, Morita H. Genomic adaptation of the Lactobacillus casei group. PLoS One 2013; 8:e75073. [PMID: 24116025 PMCID: PMC3792948 DOI: 10.1371/journal.pone.0075073] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 08/10/2013] [Indexed: 11/23/2022] Open
Abstract
Lactobacillus casei, L. paracasei, and L. rhamnosus form a closely related taxonomic group (Lactobacillus casei group) within the facultatively heterofermentative lactobacilli. Here, we report the complete genome sequences of L. paracasei JCM 8130 and L. casei ATCC 393, and the draft genome sequence of L. paracasei COM0101, all of which were isolated from daily products. Furthermore, we re-annotated the genome of L. rhamnosus ATCC 53103 (also known as L. rhamnosus GG), which we have previously reported. We confirmed that ATCC 393 is distinct from other strains previously described as L. paracasei. The core genome of 10 completely sequenced strains of the L. casei group comprised 1,682 protein-coding genes. Although extensive genome-wide synteny was found among the L. casei group, the genomes of ATCC 53103, JCM 8130, and ATCC 393 contained genomic islands compared with L. paracasei ATCC 334. Several genomic islands, including carbohydrate utilization gene clusters, were found at the same loci in the chromosomes of the L. casei group. The spaCBA pilus gene cluster, which was first identified in GG, was also found in other strains of the L. casei group, but several L. paracasei strains including COM0101 contained truncated spaC gene. ATCC 53103 encoded a higher number of proteins involved in carbohydrate utilization compared with intestinal lactobacilli, and extracellular adhesion proteins, several of which are absent in other strains of the L. casei group. In addition to previously fully sequenced L. rhamnosus and L. paracasei strains, the complete genome sequences of L. casei will provide valuable insights into the evolution of the L. casei group.
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Affiliation(s)
- Hidehiro Toh
- Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Kenshiro Oshima
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Akiyo Nakano
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Muneaki Takahata
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Masaru Murakami
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | | | | | - Shizunobu Igimi
- Division of Biomedical Food Research, National Institute of Health Sciences, Kamiyoga, Setagaya, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hidetoshi Morita
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
- * E-mail:
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Smokvina T, Wels M, Polka J, Chervaux C, Brisse S, Boekhorst J, van Hylckama Vlieg JET, Siezen RJ. Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity. PLoS One 2013; 8:e68731. [PMID: 23894338 PMCID: PMC3716772 DOI: 10.1371/journal.pone.0068731] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 05/31/2013] [Indexed: 12/11/2022] Open
Abstract
Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon) are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis, in order to link the distribution pattern of a specific phenotype to the presence/absence of specific sets of genes.
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Enterococcal Rgg-like regulator ElrR activates expression of the elrA operon. J Bacteriol 2013; 195:3073-83. [PMID: 23645602 DOI: 10.1128/jb.00121-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Enterococcus faecalis leucine-rich protein ElrA promotes virulence by stimulating bacterial persistence in macrophages and production of the interleukin-6 (IL-6) cytokine. The ElrA protein is encoded within an operon that is poorly expressed under laboratory conditions but induced in vivo. In this study, we identify ef2687 (renamed elrR), which encodes a member of the Rgg (regulator gene for glucosyltransferase) family of putative regulatory proteins. Using quantitative reverse transcription-PCR, translational lacZ fusions, and electrophoretic mobility shift assays, we demonstrate that ElrR positively regulates expression of elrA. These results correlate with the attenuated virulence of the ΔelrR strain in a mouse peritonitis model. Virulence of simple and double elrR and elrA deletion mutants also suggests a remaining ElrR-independent expression of elrA in vivo and additional virulence-related genes controlled by ElrR.
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Fukao M, Oshima K, Morita H, Toh H, Suda W, Kim SW, Suzuki S, Yakabe T, Hattori M, Yajima N. Genomic analysis by deep sequencing of the probiotic Lactobacillus brevis KB290 harboring nine plasmids reveals genomic stability. PLoS One 2013; 8:e60521. [PMID: 23544154 PMCID: PMC3609814 DOI: 10.1371/journal.pone.0060521] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 02/28/2013] [Indexed: 11/18/2022] Open
Abstract
We determined the complete genome sequence of Lactobacillus brevis KB290, a probiotic lactic acid bacterium isolated from a traditional Japanese fermented vegetable. The genome contained a 2,395,134-bp chromosome that housed 2,391 protein-coding genes and nine plasmids that together accounted for 191 protein-coding genes. KB290 contained no virulence factor genes, and several genes related to presumptive cell wall-associated polysaccharide biosynthesis and the stress response were present in L. brevis KB290 but not in the closely related L. brevis ATCC 367. Plasmid-curing experiments revealed that the presence of plasmid pKB290-1 was essential for the strain's gastrointestinal tract tolerance and tendency to aggregate. Using next-generation deep sequencing of current and 18-year-old stock strains to detect low frequency variants, we evaluated genome stability. Deep sequencing of four periodic KB290 culture stocks with more than 1,000-fold coverage revealed 3 mutation sites and 37 minority variation sites, indicating long-term stability and providing a useful method for assessing the stability of industrial bacteria at the nucleotide level.
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Affiliation(s)
- Masanori Fukao
- Research Institute, KAGOME Co., Ltd., Nasushiobara, Tochigi, Japan.
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A specific mutation in the promoter region of the silent cel cluster accounts for the appearance of lactose-utilizing Lactococcus lactis MG1363. Appl Environ Microbiol 2012; 78:5612-21. [PMID: 22660716 DOI: 10.1128/aem.00455-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Lactococcus lactis laboratory strain MG1363 has been described to be unable to utilize lactose. However, in a rich medium supplemented with lactose as the sole carbon source, it starts to grow after prolonged incubation periods. Transcriptome analyses showed that L. lactis MG1363 Lac(+) cells expressed celB, encoding a putative cellobiose-specific phosphotransferase system (PTS) IIC component, which is normally silent in MG1363 Lac(-) cells. Nucleotide sequence analysis of the cel cluster of a Lac(+) isolate revealed a change from one of the guanines to adenine in the promoter region. We showed here that one particular mutation, taking place at increased frequency, accounts for the lactose-utilizing phenotype occurring in MG1363 cultures. The G-to-A transition creates a -10 element at an optimal distance from the -35 element. Thus, a fully active promoter is created, allowing transcription of the otherwise cryptic cluster. Nuclear magnetic resonance (NMR) spectroscopy results show that MG1363 Lac(+) uses a novel pathway of lactose utilization.
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Muscariello L, Marino C, Capri U, Vastano V, Marasco R, Sacco M. CcpA and three newly identified proteins are involved in biofilm development in Lactobacillus plantarum. J Basic Microbiol 2012; 53:62-71. [PMID: 22585750 DOI: 10.1002/jobm.201100456] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 11/24/2011] [Indexed: 12/17/2022]
Abstract
The aim of this study was to identify genes involved in biofilm development in the probiotic lactic acid bacterium Lactobacillus plantarum. The ability of L. plantarum LM3 and of some derivative mutant strains to form biofilm has been investigated. Biofilm microtitre plate assays showed that L. plantarum LM3-2, carrying a null mutation in the ccpA gene, coding the CcpA master regulator, was partially impaired in biofilm production compared to wild type (LM3). Moreover, we found three genes in the L. plantarum genome, hereby named flmA, flmB, and flmC, whose deduced amino acid sequences show significant identity with the Streptococcus mutans BrpA (biofilm regulatory protein A). We investigated the role of FlmA, FlmB, and FlmC in biofilm formation by isolating strains carrying null mutations in the corresponding genes. Our results suggest involvement of the Flm proteins in biofilm development. Moreover, transcriptional studies show that expression of flmA, flmB, and flmC is under the control of CcpA. These results, together with the reduced ability of LM3-2 (ccpA1) to form biofilm, strongly suggest a positive role of the master regulator CcpA in biofilm development.
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Affiliation(s)
- Lidia Muscariello
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Italy
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Ventura M, Turroni F, van Sinderen D. Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut. Bioeng Bugs 2012; 3:73-9. [PMID: 22095053 DOI: 10.4161/bbug.18540] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bifidobacteria and lactobacilli are widely exploited as health-promoting bacteria in many functional foods. However, the molecular mechanisms as to how these bacteria positively impact on host health are far from completely understood. For this reason these microorganisms represent a growing area of interest with respect to their genomics, molecular biology and genetics. Recent genome sequencing of a large number of strains of bifidobacteria and lactobacilli has allowed access to the complete genetic makeup of representative members of these bacteria. Here, we will discuss how the analysis of genomic data has helped us to understand the mechanisms by which these bacteria adapt to the specific environment of the gastrointestinal tract, while also revealing genetic functions that mediate specific host-microbe interactions.
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Affiliation(s)
- Marco Ventura
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy.
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Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. J Bacteriol 2012; 194:195-6. [PMID: 22156394 DOI: 10.1128/jb.06275-11] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
There is growing interest in the beneficial effects of Lactobacillus plantarum on human health. The genome of L. plantarum WCFS1, first sequenced in 2001, was resequenced using Solexa technology. We identified 116 nucleotide corrections and improved function prediction for nearly 1,200 proteins, with a focus on metabolic functions and cell surface-associated proteins.
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