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Elcheninov AG, Zayulina KS, Klyukina AA, Kremneva MK, Kublanov IV, Kochetkova TV. Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia. Microorganisms 2023; 12:16. [PMID: 38276185 PMCID: PMC10819033 DOI: 10.3390/microorganisms12010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.
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Affiliation(s)
- Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Kseniya S. Zayulina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Mariia K. Kremneva
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia;
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Tatiana V. Kochetkova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
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2
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Shiver AL, Sun J, Culver R, Violette A, Wynter C, Nieckarz M, Mattiello SP, Sekhon PK, Friess L, Carlson HK, Wong D, Higginbottom S, Weglarz M, Wang W, Knapp BD, Guiberson E, Sanchez J, Huang PH, Garcia PA, Buie CR, Good B, DeFelice B, Cava F, Scaria J, Sonnenburg J, Sinderen DV, Deutschbauer AM, Huang KC. A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555234. [PMID: 37693407 PMCID: PMC10491234 DOI: 10.1101/2023.08.29.555234] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Bifidobacteria commonly represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest as a probiotic therapy, predicting the nutritional requirements and health-promoting effects of Bifidobacteria is challenging due to major knowledge gaps. To overcome these deficiencies, we used large-scale genetics to create a compendium of mutant fitness in Bifidobacterium breve (Bb). We generated a high density, randomly barcoded transposon insertion pool in Bb, and used this pool to determine Bb fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of in vitro perturbations. To enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1462 genes. We leveraged these tools to improve models of metabolic pathways, reveal unexpected host- and diet-specific requirements for colonization, and connect the production of immunomodulatory molecules to growth benefits. These resources will greatly reduce the barrier to future investigations of this important beneficial microbe.
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Affiliation(s)
- Anthony L. Shiver
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Rebecca Culver
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Arvie Violette
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Charles Wynter
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Marta Nieckarz
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Samara Paula Mattiello
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- College of Mathematics and Science, The University of Tennessee Southern, Pulaski TN 38478, USA
| | - Prabhjot Kaur Sekhon
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, 74074, USA
| | - Lisa Friess
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Hans K. Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel Wong
- Department of Applied Physics, Stanford University, Stanford CA 94305, USA
| | - Steven Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Meredith Weglarz
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, California, USA
| | - Weigao Wang
- Department of Chemical Engineering, Stanford University, Stanford CA 94305, USA
| | | | - Emma Guiberson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Po-Hsun Huang
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Paulo A. Garcia
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Cullen R. Buie
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Benjamin Good
- Department of Applied Physics, Stanford University, Stanford CA 94305, USA
| | | | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, 74074, USA
| | - Justin Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Douwe Van Sinderen
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158
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3
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Sheridan PO, Odat MA, Scott KP. Establishing genetic manipulation for novel strains of human gut bacteria. MICROBIOME RESEARCH REPORTS 2023; 2:1. [PMID: 38059211 PMCID: PMC10696588 DOI: 10.20517/mrr.2022.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/29/2022] [Accepted: 12/12/2022] [Indexed: 12/08/2023]
Abstract
Recent years have seen the development of high-accuracy and high-throughput genetic manipulation techniques, which have greatly improved our understanding of genetically tractable microbes. However, challenges remain in establishing genetic manipulation techniques in novel organisms, owing largely to exogenous DNA defence mechanisms, lack of selectable markers, lack of efficient methods to introduce exogenous DNA and an inability of genetic vectors to replicate in their new host. In this review, we describe some of the techniques that are available for genetic manipulation of novel microorganisms. While many reviews exist that focus on the final step in genetic manipulation, the editing of recipient DNA, we particularly focus on the first step in this process, the transfer of exogenous DNA into a strain of interest. Examples illustrating the use of these techniques are provided for a selection of human gut bacteria in which genetic tractability has been established, such as Bifidobacterium, Bacteroides and Roseburia. Ultimately, this review aims to provide an information source for researchers interested in developing genetic manipulation techniques for novel bacterial strains, particularly those of the human gut microbiota.
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Affiliation(s)
- Paul O. Sheridan
- School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Ma’en Al Odat
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD, UK
| | - Karen P. Scott
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD, UK
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Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium. Proc Natl Acad Sci U S A 2022; 119:e2205068119. [PMID: 35857876 PMCID: PMC9335239 DOI: 10.1073/pnas.2205068119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Bifidobacterium is a commensal bacterial genus ubiquitous in the human gastrointestinal tract, which is associated with a range of health benefits. The advent of CRISPR-based genome editing technologies provides opportunities to investigate the genetics of important bacteria and transcend the lack of genetic tools in bifidobacteria to study the basis for their health-promoting attributes. Here, we repurpose the endogenous type I-G CRISPR-Cas system and adopt an exogenous CRISPR base editor for genome engineering in B. animalis subsp. lactis, demonstrating that both genomic and epigenetic contexts drive editing outcomes across strains. We reprogrammed the endogenous type I-G system to screen for naturally occurring large deletions up to 27 kb and to generate a 500-bp deletion in tetW to abolish tetracycline resistance. A CRISPR-cytosine base editor was optimized to install C•G-to-T•A amber mutations to resensitize multiple B. lactis strains to tetracycline. Remarkably, we uncovered epigenetic patterns that are distributed unevenly among B. lactis strains, despite their genomic homogeneity, that may contribute to editing efficiency variability. Insights were also expanded to Bifidobacterium longum subsp. infantis to emphasize the broad relevance of these findings. This study highlights the need to develop individualized CRISPR-based genome engineering approaches for distinct bacterial strains and opens avenues for engineering of next generation probiotics.
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Singh RP, Shadan A, Ma Y. Biotechnological Applications of Probiotics: A Multifarious Weapon to Disease and Metabolic Abnormality. Probiotics Antimicrob Proteins 2022; 14:1184-1210. [PMID: 36121610 PMCID: PMC9483357 DOI: 10.1007/s12602-022-09992-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2022] [Indexed: 12/25/2022]
Abstract
Consumption of live microorganisms "Probiotics" for health benefits and well-being is increasing worldwide. Their use as a therapeutic approach to confer health benefits has fascinated humans for centuries; however, its conceptuality gradually evolved with methodological advancement, thereby improving our understanding of probiotics-host interaction. However, the emerging concern regarding safety aspects of live microbial is enhancing the interest in non-viable or microbial cell extracts, as they could reduce the risks of microbial translocation and infection. Due to technical limitations in the production and formulation of traditionally used probiotics, the scientific community has been focusing on discovering new microbes to be used as probiotics. In many scientific studies, probiotics have been shown as potential tools to treat metabolic disorders such as obesity, type-2 diabetes, non-alcoholic fatty liver disease, digestive disorders (e.g., acute and antibiotic-associated diarrhea), and allergic disorders (e.g., eczema) in infants. However, the mechanistic insight of strain-specific probiotic action is still unknown. In the present review, we analyzed the scientific state-of-the-art regarding the mechanisms of probiotic action, its physiological and immuno-modulation on the host, and new direction regarding the development of next-generation probiotics. We discuss the use of recently discovered genetic tools and their applications for engineering the probiotic bacteria for various applications including food, biomedical applications, and other health benefits. Finally, the review addresses the future development of biological techniques in combination with clinical and preclinical studies to explain the molecular mechanism of action, and discover an ideal multifunctional probiotic bacterium.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand India
| | - Afreen Shadan
- Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand India
| | - Ying Ma
- College of Resource and Environment, Southwest University, Chongqing, China
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Morales-Contreras JA, Rodríguez-Pérez JE, Álvarez-González CA, Martínez-López MC, Juárez-Rojop IE, Ávila-Fernández Á. Potential applications of recombinant bifidobacterial proteins in the food industry, biomedicine, process innovation and glycobiology. Food Sci Biotechnol 2021; 30:1277-1291. [PMID: 34721924 DOI: 10.1007/s10068-021-00957-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 07/13/2021] [Accepted: 07/26/2021] [Indexed: 12/27/2022] Open
Abstract
Bifidobacterial proteins have been widely studied to elucidate the metabolic mechanisms of diet adaptation and survival of Bifidobacteria, among others. The use of heterologous expression systems to obtain proteins in sufficient quantities to be characterized has been essential in these studies. L. lactis and the same Bifidobacterium as expression systems highlight ways to corroborate some of the functions attributed to these proteins. The most studied proteins are enzymes related to carbohydrate metabolism, particularly glycosidases, due to their potential application in the synthesis of neoglycoconjugates, prebiotic neooligosaccharides, and active metabolites as well as their high specificity and efficiency in processing glycoconjugates. In this review, we classified the recombinant bifidobacterial proteins reported to date whose characterization has demonstrated their usefulness or their ability to produce a product of commercial interest for the food industry, biomedicine, process innovation and glycobiology. Future directions for their study are also discussed. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-021-00957-1.
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Affiliation(s)
- José A Morales-Contreras
- Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez no. 2838-A. Col. Tamulté, 86150 Villahermosa, Centro, Tabasco Mexico
| | - Jessica E Rodríguez-Pérez
- Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez no. 2838-A. Col. Tamulté, 86150 Villahermosa, Centro, Tabasco Mexico
| | - Carlos A Álvarez-González
- Laboratorio de Acuacultura, DACBiol-UJAT, Carr. Villahermosa-Cárdenas Km 0.5, 86139 Villahermosa, Tabasco Mexico
| | - Mirian C Martínez-López
- Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez no. 2838-A. Col. Tamulté, 86150 Villahermosa, Centro, Tabasco Mexico
| | - Isela E Juárez-Rojop
- Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez no. 2838-A. Col. Tamulté, 86150 Villahermosa, Centro, Tabasco Mexico.,Laboratorio de Acuacultura, DACBiol-UJAT, Carr. Villahermosa-Cárdenas Km 0.5, 86139 Villahermosa, Tabasco Mexico
| | - Ángela Ávila-Fernández
- Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez no. 2838-A. Col. Tamulté, 86150 Villahermosa, Centro, Tabasco Mexico
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7
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Engineer probiotic bifidobacteria for food and biomedical applications - Current status and future prospective. Biotechnol Adv 2020; 45:107654. [DOI: 10.1016/j.biotechadv.2020.107654] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/14/2020] [Accepted: 11/01/2020] [Indexed: 12/15/2022]
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Zuo F, Zeng Z, Hammarström L, Marcotte H. Inducible Plasmid Self-Destruction (IPSD) Assisted Genome Engineering in Lactobacilli and Bifidobacteria. ACS Synth Biol 2019; 8:1723-1729. [PMID: 31277549 DOI: 10.1021/acssynbio.9b00114] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Genome engineering is essential for application of synthetic biology in probiotics including lactobacilli and bifidobacteria. Several homologous recombination system-based mutagenesis tools have been developed for these bacteria, but still have many limitations in different species or strains. Here we developed a genome engineering method based on an inducible self-destruction plasmid delivering homologous DNA into bacteria. Excision of the replicon by induced recombinase facilitates selection of homologous recombination events. This new genome editing tool called inducible plasmid self-destruction (IPSD) was successfully used to perform gene knockout and knock-in in lactobacilli and bifidobacteria. Due to its simplicity and universality, the IPSD strategy may provide a general approach for genetic engineering of various bacterial species.
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Affiliation(s)
- Fanglei Zuo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden
| | - Zhu Zeng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden
| | - Lennart Hammarström
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden
| | - Harold Marcotte
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden
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Abstract
Genetic engineering is a powerful approach for discovering fundamental aspects of bacterial physiology, metabolism, and pathogenesis as well as for harnessing the capabilities of bacteria for human use. However, the full power of genetic engineering can only be applied to a few model organisms. Biological diversity and strain-level variation in restriction-modification systems are critical barriers keeping most bacteria beyond the full potential of genetics. We have designed a systematic approach to effectively evade restriction-modification systems and successfully applied this approach to a clinically relevant USA300 strain of the human pathogen Staphylococcus aureus. Our results demonstrate the simplicity and effectiveness of this stealth-by-engineering approach, which could enable microbial genetic system design not restrained by innate restriction-modification defense mechanisms. Bacteria that are recalcitrant to genetic manipulation using modern in vitro techniques are termed genetically intractable. Genetic intractability is a fundamental barrier to progress that hinders basic, synthetic, and translational microbiology research and development beyond a few model organisms. The most common underlying causes of genetic intractability are restriction-modification (RM) systems, ubiquitous defense mechanisms against xenogeneic DNA that hinder the use of genetic approaches in the vast majority of bacteria and exhibit strain-level variation. Here, we describe a systematic approach to overcome RM systems. Our approach was inspired by a simple hypothesis: if a synthetic piece of DNA lacks the highly specific target recognition motifs for a host’s RM systems, then it is invisible to these systems and will not be degraded during artificial transformation. Accordingly, in this process, we determine the genome and methylome of an individual bacterial strain and use this information to define the bacterium’s RM target motifs. We then synonymously eliminate RM targets from the nucleotide sequence of a genetic tool in silico, synthesize an RM-silent “SyngenicDNA” tool, and propagate the tool as minicircle plasmids, termed SyMPL (SyngenicDNA Minicircle Plasmid) tools, before transformation. In a proof-of-principle of our approach, we demonstrate a profound improvement (five orders of magnitude) in the transformation of a clinically relevant USA300 strain of Staphylococcus aureus. This stealth-by-engineering SyngenicDNA approach is effective, flexible, and we expect in future applications could enable microbial genetics free of the restraints of restriction-modification barriers.
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Sun Z, Yue Z, Yang X, Hao X, Song M, Li L, Chen C, Chu C, Li C. Efficient Phytase Secretion and Phytate Degradation by Recombinant Bifidobacterium longum JCM 1217. Front Microbiol 2019; 10:796. [PMID: 31040837 PMCID: PMC6476914 DOI: 10.3389/fmicb.2019.00796] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/28/2019] [Indexed: 12/18/2022] Open
Abstract
Genetic engineering of probiotics, like bifidobacteria, may improve their microbial cell factory economy. This work designed a novel shuttle plasmid pBPES, which bears exogenous appA and is stable within Bifidobacterium longum JCM 1217. Cloning of three predicted promoters into pBPES proved that all of them drive appA expression in B. longum JCM 1217. Transformation of plasmids pBPES-tu and pBPES-groEL into B. longum JCM1217 resulted in much more phytase secretion suggests P tu and P groEL are strong promoters. Further in vitro and in vivo experiments suggested B. longum JCM 1217/pBPES-tu degrades phytate efficiently. In conclusion, the study screened two stronger promoters and constructed a recombinant live probiotic strain for effectively phytase secretion and phytate degradation in gut. The strategy used in the study provided a novel technique for improving the bioaccessibility of phytate and decreasing phosphorus excretion.
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Affiliation(s)
- Zhongke Sun
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou, China.,College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, China
| | - Zonghao Yue
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Xingdong Yang
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Xinqi Hao
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, China
| | - Maoping Song
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, China
| | - Lili Li
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou, China.,Key Laboratory of Plant Molecular Breeding and Bioreactor, Zhoukou, China
| | - Can Chen
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Cuiwei Chu
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Chengwei Li
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou, China.,Key Laboratory of Plant Molecular Breeding and Bioreactor, Zhoukou, China
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11
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Thinbanmai T, Lulitanond V, Mayo B, Lulitanond A, Panya M. Cloning and expression of enterovirus 71 capsid protein 1 in a probiotic Bifidobacterium pseudocatenulatum. Lett Appl Microbiol 2018; 68:9-16. [PMID: 30357884 DOI: 10.1111/lam.13089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/03/2018] [Accepted: 10/03/2018] [Indexed: 12/19/2022]
Abstract
This study investigated cloning and expression of enterovirus 71 viral capsid protein 1 (EV71-VP1) in Bifidobacterium pseudocatenulatum (B. pseudocatenulatum) M115. To achieve this, a codon-optimized gene coding for EV71-VP1 was analysed, designed, synthesized and cloned into a plasmid vector flanked by a transcriptional promoter and terminator sequences. The promoter was based on that of P919, a constitutive promoter of the gene encoding the large ribosomal protein of B. bifidum BGN4, while the terminator was based on that of the peptidase N gene of Lactococcus lactis. The construct was amplified in Escherichia coli XL1-blue and then transferred into B. pseudocatenulatum M115 by electrotransformation. Western blot analysis revealed that the EV71-VP1 was intracellularly expressed in B. pseudocatenulatum M115 under the control of the selected heterologous promoter. In addition, plasmid stability analysis showed the construct was maintained stably for more than 160 generations, enough for most future applications. The results derived from this study open the possibility to utilize the bacterium carrying a specific expression plasmid as cell factory for the production of proteins with high commercial and health-promoting value. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrated the first successful expression of a codon-optimized gene coding for enterovirus 71 viral capsid protein 1 (EV71-VP1) in Bifidobacterium pseudocatenulatum M115, a novel probiotic strain isolated from human intestines. The EV71-VP1 was constitutively expressed under the control of P919 promoter derived from B. bifidum BGN4 in the cytoplasm of bacterial cells supporting the use of heterologous promoter and terminator sequences for viral gene expression in Bifidobacterium species.
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Affiliation(s)
- T Thinbanmai
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - V Lulitanond
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - B Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Spain
| | - A Lulitanond
- Department of Clinical Microbiology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - M Panya
- College of Medicine and Public Health, Ubon Ratchathani University, Ubon Ratchathani, Thailand
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Li J, Shen Y, Jiang Y, He L, Sun Z. Bioinformatic Survey of S-Layer Proteins in Bifidobacteria. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/cmb.2018.82003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Ruiz L, Bottacini F, Boinett CJ, Cain AK, O'Connell-Motherway M, Lawley TD, van Sinderen D. The essential genomic landscape of the commensal Bifidobacterium breve UCC2003. Sci Rep 2017; 7:5648. [PMID: 28717159 PMCID: PMC5514069 DOI: 10.1038/s41598-017-05795-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/02/2017] [Indexed: 01/15/2023] Open
Abstract
Bifidobacteria are common gut commensals with purported health-promoting effects. This has encouraged scientific research into bifidobacteria, though recalcitrance to genetic manipulation and scarcity of molecular tools has hampered our knowledge on the precise molecular determinants of their health-promoting attributes and gut adaptation. To overcome this problem and facilitate functional genomic analyses in bifidobacteria, we created a large Tn5 transposon mutant library of the commensal Bifidobacterium breve UCC2003 that was further characterized by means of a Transposon Directed Insertion Sequencing (TraDIS) approach. Statistical analysis of transposon insertion distribution revealed a set of 453 genes that are essential for or markedly contribute to growth of this strain under laboratory conditions. These essential genes encode functions involved in the so-called bifid-shunt, most enzymes related to nucleotide biosynthesis and a range of housekeeping functions. Comparison to the Bifidobacterium and B. breve core genomes highlights a high degree of conservation of essential genes at the species and genus level, while comparison to essential gene datasets from other gut bacteria identified essential genes that appear specific to bifidobacteria. This work establishes a useful molecular tool for scientific discovery of bifidobacteria and identifies targets for further studies aimed at characterizing essential functions not previously examined in bifidobacteria.
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Affiliation(s)
- Lorena Ruiz
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland.,Department of Nutrition, Bromatology and Food Technology, Complutense University, Avda Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Francesca Bottacini
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland
| | | | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Mary O'Connell-Motherway
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland
| | | | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland.
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14
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Ruiz L, Hidalgo C, Blanco-Míguez A, Lourenço A, Sánchez B, Margolles A. Tackling probiotic and gut microbiota functionality through proteomics. J Proteomics 2016; 147:28-39. [DOI: 10.1016/j.jprot.2016.03.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/19/2016] [Accepted: 03/10/2016] [Indexed: 12/24/2022]
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15
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O'Callaghan A, van Sinderen D. Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Front Microbiol 2016; 7:925. [PMID: 27379055 PMCID: PMC4908950 DOI: 10.3389/fmicb.2016.00925] [Citation(s) in RCA: 502] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/31/2016] [Indexed: 12/11/2022] Open
Abstract
Members of the genus Bifidobacterium are among the first microbes to colonize the human gastrointestinal tract and are believed to exert positive health benefits on their host. Due to their purported health-promoting properties, bifidobacteria have been incorporated into many functional foods as active ingredients. Bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract, such as the human oral cavity, the insect gut and sewage. To be able to survive in these particular ecological niches, bifidobacteria must possess specific adaptations to be competitive. Determination of genome sequences has revealed genetic attributes that may explain bifidobacterial ecological fitness, such as metabolic abilities, evasion of the host adaptive immune system and colonization of the host through specific appendages. However, genetic modification is crucial toward fully elucidating the mechanisms by which bifidobacteria exert their adaptive abilities and beneficial properties. In this review we provide an up to date summary of the general features of bifidobacteria, whilst paying particular attention to the metabolic abilities of this species. We also describe methods that have allowed successful genetic manipulation of bifidobacteria.
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Affiliation(s)
- Amy O'Callaghan
- Alimentary Pharmabiotic Centre and School of Microbiology, University College Cork Cork, Ireland
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and School of Microbiology, University College Cork Cork, Ireland
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16
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Landete JM, Medina M, Arqués JL. Fluorescent reporter systems for tracking probiotic lactic acid bacteria and bifidobacteria. World J Microbiol Biotechnol 2016; 32:119. [PMID: 27263014 DOI: 10.1007/s11274-016-2077-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 04/27/2016] [Indexed: 12/19/2022]
Abstract
In the last two decades, there has been increasing evidence supporting the role of the intestinal microbiota in health and disease, as well as the use of probiotics to modulate its activity and composition. Probiotic bacteria selected for commercial use in foods, mostly lactic acid bacteria and bifidobacteria, must survive in sufficient numbers during the manufacturing process, storage, and passage through the gastro-intestinal tract. They have several modes of action and it is crucial to unravel the mechanisms underlying their postulated beneficial effects. To track their survival and persistence, and to analyse their interaction with the gastro-intestinal epithelia it is essential to discriminate probiotic strains from endogenous microbiota. Fluorescent reporter proteins are relevant tools that can be exploited as a non-invasive marker system for in vivo real-time imaging in complex ecosystems as well as in vitro fluorescence labelling. Oxygen is required for many of these reporter proteins to fluoresce, which is a major drawback in anoxic environments. However, some new fluorescent proteins are able to overcome the potential problems caused by oxygen limitations. The current available approaches and the benefits/disadvantages of using reporter vectors containing fluorescent proteins for labelling of bacterial probiotic species commonly used in food are addressed.
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Affiliation(s)
- José M Landete
- Dpto. de Tecnología de Alimentos, INIA, Carretera de La Coruña Km 7, 28040, Madrid, Spain
| | - Margarita Medina
- Dpto. de Tecnología de Alimentos, INIA, Carretera de La Coruña Km 7, 28040, Madrid, Spain
| | - Juan L Arqués
- Dpto. de Tecnología de Alimentos, INIA, Carretera de La Coruña Km 7, 28040, Madrid, Spain.
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17
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Montenegro-Rodríguez C, Peirotén A, Sanchez-Jimenez A, Arqués JL, Landete JM. Analysis of gene expression of bifidobacteria using as the reporter an anaerobic fluorescent protein. Biotechnol Lett 2015; 37:1405-13. [DOI: 10.1007/s10529-015-1802-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/26/2015] [Indexed: 01/16/2023]
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18
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Functional analysis of bifidobacterial promoters in Bifidobacterium longum and Escherichia coli using the α-galactosidase gene as a reporter. J Biosci Bioeng 2014; 118:489-95. [DOI: 10.1016/j.jbiosc.2014.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/27/2014] [Accepted: 05/01/2014] [Indexed: 01/15/2023]
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19
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Sun Z, Westermann C, Yuan J, Riedel CU. Experimental determination and characterization of the gap promoter of Bifidobacterium bifidum S17. Bioengineered 2014; 5:371-7. [PMID: 25482086 DOI: 10.4161/bioe.34423] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The DNA sequence upstream of the glyceraldehyde 3-phosphate dehydrogenase gene (gap) of various strains of bifidobacteria is used in a number of vector systems for homologous and heterologous expression in this group of bacteria. To date none of the bifidobacterial gap promoters (Pgap) have been verified experimentally. Here, we probe a range of putative bifidobacterial promoters hypothesized to show high constitutive transcriptional activity using a β-glucuronidase reporter system. In silico analysis revealed a predicted bacterial promoter upstream of the gap gene of Bifidobacterium bifidum S17. The corresponding DNA sequences was cloned into the promoter probe vector pMDY23 and yielded highest reporter activities among the promoter sequences tested confirming previous studies. Using rapid amplification of cDNA ends (5'-RACE), we identified the transcription start site (TSS) of Pgap of B. bifidum S17. The experimentally determined TSS and the associated -10 and -35 regions do not match with the promoter predicted in silico. Moreover, a potential ribosome-binding site (RBS) was identified upstream of the ATG start codon of the gap gene, which is complementary to the 3'-end of the 16S rRNA with only 1 mismatch suggesting efficient initiation of translation. Alignment of the Pgap sequences of a number of representative bifidobacteria showed a high level of conservation and the presence of -35 and -10 regions, which are similar but not identical to the consensus promoter sequences of house-keeping genes of Escherichia coli and Bacillus subtilis. Collectively, these results confirm the suitability of Pgap for high level, constitutive expression in bifidobacteria.
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Affiliation(s)
- Zhongke Sun
- a Institute of Microbiology and Biotechnology ; University of Ulm ; Ulm , Germany
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20
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Zuo F, Yu R, Feng X, Khaskheli GB, Chen L, Ma H, Chen S. Combination of heterogeneous catalase and superoxide dismutase protects Bifidobacterium longum strain NCC2705 from oxidative stress. Appl Microbiol Biotechnol 2014; 98:7523-34. [PMID: 24903816 DOI: 10.1007/s00253-014-5851-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 01/27/2023]
Abstract
Bifidobacteria are generally sensitive to oxidative stress caused by reactive oxygen species (ROS). To improve oxidative-stress tolerance, the superoxide dismutase (SOD) gene from Streptococcus thermophilus (StSodA) and the heme-dependent catalase (KAT) gene from Lactobacillus plantarum (LpKatL) were heterologously expressed in Bifidobacterium longum strain NCC2705. Three types of strain NCC2705 transformants were obtained: with transgenic SOD expression, with transgenic KAT expression, and with coexpression of the two genes. Intracellular expression of the genes and their functional role in oxidative-stress resistance were evaluated. In response to oxidative stress, B. longum NCC2705/pDP401-LpKatL (expressing LpKatL) and NCC2705/pDP-Kat-Sod (coexpressing LpKatL and StSodA) rapidly degraded exogenous H2O2 and the peroxides generated as a byproduct of aerobic cultivation, preventing oxidative damage to DNA and RNA. Individual expression of StSodA or LpKatL both improved B. longum NCC2705 cell viability. Survival rate of strain NCC2705 was further improved by combining SOD and KAT expression. The two enzymes played complementary roles in ROS-scavenging pathways, and coexpression led to a synergistic beneficial effect under conditions of intensified oxidative stress. Our results illustrate that heterogeneous expression of heme-dependent KAT and Mn(2+)-dependent SOD is functional in the B. longum oxidative-stress response, and synergistic protection is achieved when their expressions are combined.
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Affiliation(s)
- Fanglei Zuo
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qinghua East Road, Haidian District, Beijing, 100083, China
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21
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O′Connell Motherway M, Watson D, Bottacini F, Clark TA, Roberts RJ, Korlach J, Garault P, Chervaux C, van Hylckama Vlieg JET, Smokvina T, van Sinderen D. Identification of restriction-modification systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT sequencing and associated methylome analysis. PLoS One 2014; 9:e94875. [PMID: 24743599 PMCID: PMC3990576 DOI: 10.1371/journal.pone.0094875] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/20/2014] [Indexed: 01/25/2023] Open
Abstract
Bifidobacterium animalis subsp. lactis CNCM I-2494 is a component of a commercialized fermented dairy product for which beneficial effects on health has been studied by clinical and preclinical trials. To date little is known about the molecular mechanisms that could explain the beneficial effects that bifidobacteria impart to the host. Restriction-modification (R-M) systems have been identified as key obstacles in the genetic accessibility of bifidobacteria, and circumventing these is a prerequisite to attaining a fundamental understanding of bifidobacterial attributes, including the genes that are responsible for health-promoting properties of this clinically and industrially important group of bacteria. The complete genome sequence of B. animalis subsp. lactis CNCM I-2494 is predicted to harbour the genetic determinants for two type II R-M systems, designated BanLI and BanLII. In order to investigate the functionality and specificity of these two putative R-M systems in B. animalis subsp. lactis CNCM I-2494, we employed PacBio SMRT sequencing with associated methylome analysis. In addition, the contribution of the identified R-M systems to the genetic accessibility of this strain was assessed.
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Affiliation(s)
- Mary O′Connell Motherway
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Debbie Watson
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Francesca Bottacini
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Tyson A. Clark
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | | | | | | | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland
- * E-mail:
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Landete JM, Peirotén Á, Rodríguez E, Margolles A, Medina M, Arqués JL. Anaerobic green fluorescent protein as a marker of Bifidobacterium strains. Int J Food Microbiol 2014; 175:6-13. [DOI: 10.1016/j.ijfoodmicro.2014.01.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/11/2014] [Indexed: 12/20/2022]
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23
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Expression of fluorescent proteins in bifidobacteria for analysis of host-microbe interactions. Appl Environ Microbiol 2014; 80:2842-50. [PMID: 24584243 DOI: 10.1128/aem.04261-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Bifidobacteria are an important component of the human gastrointestinal microbiota and are frequently used as probiotics. The genetic inaccessibility and lack of molecular tools commonly used in other bacteria have hampered a detailed analysis of the genetic determinants of bifidobacteria involved in their adaptation to, colonization of, and interaction with the host. In the present study, a range of molecular tools were developed that will allow the closing of some of the gaps in functional analysis of bifidobacteria. A number of promoters were tested for transcriptional activity in Bifidobacterium bifidum S17 using pMDY23, a previously published promoter probe vector. The promoter of the gap gene (Pgap) of B. bifidum S17 yielded the highest promoter activity among the promoters tested. Thus, this promoter and the pMDY23 backbone were used to construct a range of vectors for expression of different fluorescent proteins (FPs). Successful expression of cyan fluorescent protein (CFP), green fluorescent protein (GFP), yellow fluorescent protein (YFP), and mCherry could be shown for three strains representing three different Bifidobacterium spp. The red fluorescent B. bifidum S17/pVG-mCherry was further used to demonstrate application of fluorescent bifidobacteria for adhesion assays and detection in primary human macrophages cultured in vitro. Furthermore, pMGC-mCherry was cloned by combining a chloramphenicol resistance marker and expression of the FP mCherry under the control of Pgap. The chloramphenicol resistance marker of pMGC-mCherry was successfully used to determine gastrointestinal transit time of B. bifidum S17. Moreover, B. bifidum S17/pMGC-mCherry could be detected in fecal samples of mice after oral administration.
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Ruiz L, Motherway MO, Lanigan N, van Sinderen D. Transposon mutagenesis in Bifidobacterium breve: construction and characterization of a Tn5 transposon mutant library for Bifidobacterium breve UCC2003. PLoS One 2013; 8:e64699. [PMID: 23737995 PMCID: PMC3667832 DOI: 10.1371/journal.pone.0064699] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/17/2013] [Indexed: 01/20/2023] Open
Abstract
Bifidobacteria are claimed to contribute positively to human health through a range of beneficial or probiotic activities, including amelioration of gastrointestinal and metabolic disorders, and therefore this particular group of gastrointestinal commensals has enjoyed increasing industrial and scientific attention in recent years. However, the molecular mechanisms underlying these probiotic mechanisms are still largely unknown, mainly due to the fact that molecular tools for bifidobacteria are rather poorly developed, with many strains lacking genetic accessibility. In this work, we describe the generation of transposon insertion mutants in two bifidobacterial strains, B. breve UCC2003 and B. breve NCFB2258. We also report the creation of the first transposon mutant library in a bifidobacterial strain, employing B. breve UCC2003 and a Tn5-based transposome strategy. The library was found to be composed of clones containing single transposon insertions which appear to be randomly distributed along the genome. The usefulness of the library to perform phenotypic screenings was confirmed through identification and analysis of mutants defective in D-galactose, D-lactose or pullulan utilization abilities.
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Affiliation(s)
- Lorena Ruiz
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
| | - Mary O’Connell Motherway
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
| | - Noreen Lanigan
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
| | - Douwe van Sinderen
- Department of Microbiology and Alimentary Pharmabiotic Centre, National University of Ireland, Cork, Ireland
- * E-mail:
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Brancaccio VF, Zhurina DS, Riedel CU. Tough nuts to crack: site-directed mutagenesis of bifidobacteria remains a challenge. Bioengineered 2013; 4:197-202. [PMID: 23314785 DOI: 10.4161/bioe.23381] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Most members of the genus Bifidobacterium are commensals of the human gastrointestinal tract and some strains were shown to exert beneficial effects on their host. Based on these effects and due to their status as GRAS (generally recognized as safe) microorganisms, specific strains of bifidobacteria are marketed as probiotics. Despite their important role in food and dairy industries, the mechanisms responsible for the probiotic effects of bifidobacteria are mostly unknown. Over the last decade, the genomes of a large number of bifidobacteria have been sequenced and analyzed. This has yielded a number of genes and their products that are speculated to contribute to the probiotic effects of bifidobacteria. The gold standard to demonstrate a role for specific genes is the analysis of mutants. At present, only a small number of mutants of bifidobacteria have been generated by targeted mutagenesis. This is owed to the genetic inaccessibility of most strains and a lack of appropriate molecular tools. Successful generation of mutants of bifidobacteria was achieved by various methods including classical suicide vector strategies, increase of transformation efficiencies by methylation of plasmids and the use of temperature-sensitive vectors. In this commentary, we will describe the methods successfully used for mutagenesis of bifidobacteria and discuss their advantages and limitations.
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