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Dineen RL, Bottacini F, O'Connell‐Motherway M, van Sinderen D. Transcriptional landscape of the pMP7017 megaplasmid and its impact on the Bifidobacterium breve UCC2003 transcriptome. Microb Biotechnol 2024; 17:e14405. [PMID: 38206097 PMCID: PMC10832533 DOI: 10.1111/1751-7915.14405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/02/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
The 190 kb megaplasmid pMP7017 of Bifidobacterium breve JCM7017 represents the first conjugative and largest plasmid characterised within this genus to date. In the current study, we adopted an integrated approach combining transcriptomics, whole genome comparative analysis and metagenomic data mining to understand the biology of pMP7017 and related megaplasmids, and to assess the impact of plasmid-carriage on the host strain. The data generated revealed variations within basic features of promoter elements which correlate with a high level of transcription on the plasmid and highlight the transcriptional activity of genes encoding both offensive and defensive adaptations, including a Type IIL restriction-modification system, an anti-restriction system and four Type II toxin-antitoxin systems. Furthermore, a highly transcribed tmRNA, which likely provides translational support to the host strain, was identified, making pMP7017 the first plasmid of the Bifidobacterium genus and the smallest plasmid known to express a tmRNA. Analyses of synteny and variability among pMP7017 and related plasmids indicate substantial diversity in gene organisation and accessory gene cargo highlighting diverse (co-)evolution and potential host-specific rearrangements and adaptations. Systematic analysis of the codon usage profile of transcriptionally active pMP7017-encoded genes suggests that pMP7017 originated from (sub)species of Bifidobacterium longum. Furthermore, mining of metagenomic data suggests the presence of pMP7017-homologues in ~10% of microbiome samples, mostly infants and/or mothers from various geographical locations. Comparative transcriptome analysis of the B. breve UCC2003 chromosome in the presence or absence of pMP7017 revealed differential expression of genes representing 8% of the total gene pool. Genes involved in genetic information processing were exclusively upregulated, while altered expression of genes involved in biofilm production and polysaccharide biosynthesis was also observed.
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Affiliation(s)
- Rebecca L. Dineen
- APC Microbiome IrelandUniversity College CorkCorkIreland
- School of MicrobiologyUniversity College CorkCorkIreland
| | - Francesca Bottacini
- School of MicrobiologyUniversity College CorkCorkIreland
- Department of Biological SciencesMunster Technological UniversityCorkIreland
| | | | - Douwe van Sinderen
- APC Microbiome IrelandUniversity College CorkCorkIreland
- School of MicrobiologyUniversity College CorkCorkIreland
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Li X, Zhai Z, Hao Y, Zhang M, Hou C, He J, Shi S, Zhao Z, Sang Y, Ren F, Wang R. The plasmid-encoded lactose operon plays a vital role in the acid production rate of Lacticaseibacillus casei during milk beverage fermentation. Front Microbiol 2022; 13:1016904. [PMID: 36386630 PMCID: PMC9647812 DOI: 10.3389/fmicb.2022.1016904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Lacticaseibacillus casei is used extensively in the fermented milk-beverage industry as a starter culture. Acid production capacity during fermentation is the main criterion for evaluating starters although it is strain-dependent. In this study, the acid production rates of 114 L. casei strains were determined and then classified into high acid (HC), medium acid (MC), and low acid (LC) groups. Comparative genomics analysis found that the lac operon genes encoding the phosphoenolpyruvate-lactose phosphotransferase system (PTSLac) were located on plasmids in the HC strains; however, it is notable that the corresponding operons were located on the chromosome in LC strains. Real-time PCR analysis showed that the copy numbers of lac operon genes in HC strains were between 3.1 and 9.3. To investigate the relationship between copy number and acid production rate, the lac operon cluster of the HC group was constitutively expressed in LC strains. The resulting copy numbers of lac operon genes were between 15.8 and 18.1; phospho-β-galactosidase activity increased by 1.68–1.99-fold; and the acid production rates increased by 1.24–1.40-fold, which enhanced the utilization rate of lactose from 17.5 to 42.6% in the recombinant strains. The markedly increased expression of lac operon genes increased lactose catabolism and thereby increased the acid production rate of L. casei.
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Affiliation(s)
- Xiaoxia Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zhengyuan Zhai
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yanling Hao
- Department of Nutrition and Health, Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Government, China Agricultural University, Beijing, China
| | - Ming Zhang
- School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Caiyun Hou
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jingjing He
- Department of Nutrition and Health, Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Government, China Agricultural University, Beijing, China
| | - Shaoqi Shi
- Department of Nutrition and Health, Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Government, China Agricultural University, Beijing, China
| | - Zhi Zhao
- Department of Nutrition and Health, Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Government, China Agricultural University, Beijing, China
| | - Yue Sang
- Department of Nutrition and Health, Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Government, China Agricultural University, Beijing, China
| | - Fazheng Ren
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Department of Nutrition and Health, Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Government, China Agricultural University, Beijing, China
- *Correspondence: Fazheng Ren, Ran Wang,
| | - Ran Wang
- Department of Nutrition and Health, Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Government, China Agricultural University, Beijing, China
- *Correspondence: Fazheng Ren, Ran Wang,
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Mariat D, Robert V, Langella P, Chatel JM. Plasmid transfer efficiency using Lactoccocus lactis strains depends on invasiveness status but also on plasmid copy number. FEMS Microbiol Lett 2018; 364:3827360. [PMID: 28505315 DOI: 10.1093/femsle/fnx100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/12/2017] [Indexed: 12/19/2022] Open
Abstract
Lactic acid bacteria as Lactococcus lactis are used as vector for protein but also DNA delivery into intestinal cells in vitro and in vivo. For the plasmid delivery strategy, the plasmid copy number per bacteria (PCN) is thus of great importance. The aim of this paper is to determine the physiological conditions when PCN is the highest in the bacteria. PCN was characterized by qPCR in five different recombinant Lactococcus lactis strains, containing one (mono-) or two different plasmids (biplasmidic), at exponential or stationary phase. We showed that in all cases but one, PCN is higher at exponential than stationary phase. PCN seems to depend on (i) monoplasmidic or biplasmidic strain; (ii) origin of replication of the plasmid; and (iii) the DNA load of the bacteria. Then we studied plasmid transfer in vitro from recombinant L. lactis to eukaryotic COS-7 cells using culture at exponential or stationary phase. We showed that plasmid transfer can be improved in vitro by using bacteria at exponential phase.
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Affiliation(s)
- Denis Mariat
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Véronique Robert
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Philippe Langella
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jean-Marc Chatel
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Cui Y, Hu T, Qu X, Zhang L, Ding Z, Dong A. Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments. Int J Mol Sci 2015; 16:13172-202. [PMID: 26068451 PMCID: PMC4490491 DOI: 10.3390/ijms160613172] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/09/2015] [Accepted: 05/22/2015] [Indexed: 12/24/2022] Open
Abstract
Plasmids are widely distributed in different sources of lactic acid bacteria (LAB) as self-replicating extrachromosomal genetic materials, and have received considerable attention due to their close relationship with many important functions as well as some industrially relevant characteristics of the LAB species. They are interesting with regard to the development of food-grade cloning vectors. This review summarizes new developments in the area of lactic acid bacteria plasmids and aims to provide up to date information that can be used in related future research.
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Affiliation(s)
- Yanhua Cui
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Tong Hu
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin 150010, China.
| | - Lanwei Zhang
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Zhongqing Ding
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Aijun Dong
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
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Ma Y, Xie TT, Hu Q, Qiu Z, Song F. Sequencing analysis and characterization of the plasmid pBIF10 isolated from Bifidobacterium longum. Can J Microbiol 2015; 61:124-30. [DOI: 10.1139/cjm-2014-0581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A resident plasmid, pBIF10, was isolated from Bifidobacterium longum B200304, and the full-length sequence of pBIF10 was analyzed. In this sequence, we identified at least 17 major open reading frames longer than 200 bp. A tetracycline resistance gene, tetQ, was identified and verified to confer antibiotic resistance to tetracycline. The plasmid replicon with replication protein B gene (repB) and a typical iteron was identified in pBIF10. An artificial clone vector was constructed with the replicon of pBIF10; the results showed that repB controlled plasmid replication in other bifidobacteria host cells at low transformation frequency. Taken together, the analysis and characterization of pBIF10 provided necessary information for the understanding of antibiotic resistance mediated by a plasmid in a Bifidobacterium strain. GC% and repB sequence analyses indicated that pBIF10 was a molecular hybrid of at least 2 other bacterial genera plasmids.
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Affiliation(s)
- Yongping Ma
- Key Laboratory of Biochemistry and Molecular Biology, Molecular Medical and Cancer Research Center, Chongqing Medical University, Yuzhong District, Yi XueYuan Road, No. 1, Chongqing 400016, People’s Republic of China
| | - Ting-ting Xie
- Key Laboratory of Biochemistry and Molecular Biology, Molecular Medical and Cancer Research Center, Chongqing Medical University, Yuzhong District, Yi XueYuan Road, No. 1, Chongqing 400016, People’s Republic of China
| | - Qiongwen Hu
- Key Laboratory of Biochemistry and Molecular Biology, Molecular Medical and Cancer Research Center, Chongqing Medical University, Yuzhong District, Yi XueYuan Road, No. 1, Chongqing 400016, People’s Republic of China
| | - Zongyin Qiu
- Key Laboratory of Biochemistry and Molecular Biology, Molecular Medical and Cancer Research Center, Chongqing Medical University, Yuzhong District, Yi XueYuan Road, No. 1, Chongqing 400016, People’s Republic of China
| | - Fangzhou Song
- Key Laboratory of Biochemistry and Molecular Biology, Molecular Medical and Cancer Research Center, Chongqing Medical University, Yuzhong District, Yi XueYuan Road, No. 1, Chongqing 400016, People’s Republic of China
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Alvarez-Martín P, Zycka-Krzesińska J, Bardowski J, Mayo B. Sequence analysis of plasmid pSP02 from Bifidobacterium longum M62 and construction of pSP02-derived cloning vectors. Plasmid 2012; 69:119-26. [PMID: 23228478 DOI: 10.1016/j.plasmid.2012.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 10/22/2012] [Accepted: 11/16/2012] [Indexed: 11/18/2022]
Abstract
Replicons from bifidobacteria species are required for the construction of general- and special-purpose vectors that would allow the undertaking of molecular studies of these bacteria. In this work, pSP02, a cryptic plasmid from Bifidobacterium longum M62, was cloned, sequenced and characterized. pSP02 was found to consist of 4896bp with four ORFs coding for proteins over 50 amino acids long. Among the deduced protein sequences only a replicase (RepA) and a mobilization-like protein (MobA) showed known functional domains. Similar to previously described bifidobacterial plasmids, the organization of the putative ori region of pSP02 resembles that of the theta-replicating plasmids of Gram-positives. In spite of this, hybridization experiments detected single stranded (ss)-DNA as an intermediate product in the pSP02 replication, demonstrating it follows the rolling-circle (RC) replication mode. The ori region of pSP02 was used to construct a series of first generation cloning vectors able to replicate in many bifidobacterial species. Real time quantitative PCR established the copy number of pSP02 and its derived vectors to be around 12 copies per chromosome equivalent. pSP02-derivatives showed full segregational and structural stability even in the absence of antibiotic selection.
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Affiliation(s)
- Pablo Alvarez-Martín
- Departamento de Microbiología y Bioquímica de Productos Lácteos, Instituto de Productos Lácteos de Asturias-IPLA-CSIC, Paseo Río Linares, s/n, 33300 Villaviciosa, Asturias, Spain
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Ogilvie LA, Firouzmand S, Jones BV. Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome. Bioeng Bugs 2012; 3:13-31. [PMID: 22126801 PMCID: PMC3329251 DOI: 10.4161/bbug.3.1.17883] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed.
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Affiliation(s)
- Lesley A Ogilvie
- Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK
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Cronin M, Ventura M, Fitzgerald GF, van Sinderen D. Progress in genomics, metabolism and biotechnology of bifidobacteria. Int J Food Microbiol 2011; 149:4-18. [PMID: 21320731 DOI: 10.1016/j.ijfoodmicro.2011.01.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 01/06/2011] [Accepted: 01/10/2011] [Indexed: 12/16/2022]
Abstract
Members of the genus Bifidobacterium were first described over a century ago and were quickly associated with a healthy intestinal tract due to their numerical dominance in breast-fed babies as compared to bottle-fed infants. Health benefits elicited by bifidobacteria to its host, as supported by clinical trials, have led to their wide application as probiotic components of health-promoting foods, especially in fermented dairy products. However, the relative paucity of genetic tools available for bifidobacteria has impeded development of a comprehensive molecular understanding of this genus. In this review we present a summary of current knowledge on bifidobacterial metabolism, classification, physiology and genetics and outline the currently available methods for genetically accessing and manipulating the genus.
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Affiliation(s)
- Michelle Cronin
- Cork Cancer Research Centre, Mercy University Hospital and Leslie C. Quick Jnr. Laboratory, University College Cork, Cork, Ireland
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Zhang H, Hao Y, Zhang D, Luo Y. Characterization of the cryptic plasmid pTXW from Lactobacillus paracasei TXW. Plasmid 2011; 65:1-7. [DOI: 10.1016/j.plasmid.2010.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 08/07/2010] [Accepted: 08/09/2010] [Indexed: 10/19/2022]
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Bottacini F, Medini D, Pavesi A, Turroni F, Foroni E, Riley D, Giubellini V, Tettelin H, van Sinderen D, Ventura M. Comparative genomics of the genus Bifidobacterium. MICROBIOLOGY-SGM 2010; 156:3243-3254. [PMID: 20634238 DOI: 10.1099/mic.0.039545-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Whole-genome sequencing efforts have revolutionized the study of bifidobacterial genetics and physiology. Unfortunately, the sequence of a single genome does not provide information on bifidobacterial genetic diversity and on how genetic variability supports improved adaptation of these bacteria to the environment of the human gastrointestinal tract (GIT). Analysis of nine genomes from bifidobacterial species showed that such genomes display an open pan-genome structure. Mathematical extrapolation of the data indicates that the genome reservoir available to the bifidobacterial pan-genome consists of more than 5000 genes, many of which are uncharacterized, but which are probably important to provide adaptive abilities pertinent to the human GIT. We also define a core bifidobacterial gene set which will undoubtedly provide a new baseline from which one can examine the evolution of bifidobacteria. Phylogenetic investigation performed on a total of 506 orthologues that are common to nine complete bifidobacterial genomes allowed the construction of a Bifidobacterium supertree which is largely concordant with the phylogenetic tree obtained using 16S rRNA genes. Moreover, this supertree provided a more robust phylogenetic resolution than the 16S rRNA gene-based analysis. This comparative study of the genus Bifidobacterium thus presents a foundation for future functional analyses of this important group of GIT bacteria.
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Affiliation(s)
- Francesca Bottacini
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland.,Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy
| | | | - Angelo Pavesi
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy
| | - Elena Foroni
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy
| | - David Riley
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Vanessa Giubellini
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy
| | - Hervé Tettelin
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, 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, Italy
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Hao Y, Li D, Piao X, Piao X. Forsythia suspensa extract alleviates hypersensitivity induced by soybean beta-conglycinin in weaned piglets. JOURNAL OF ETHNOPHARMACOLOGY 2010; 128:412-8. [PMID: 20083183 DOI: 10.1016/j.jep.2010.01.035] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 01/04/2010] [Accepted: 01/11/2010] [Indexed: 05/28/2023]
Abstract
AIM OF THE STUDY Soybeans are known to stimulate food allergies; however, current therapies are lacking in alleviating hypersensitivity. The present study investigated whether Forsythia suspensa extract could attenuate purified soybean beta-conglycinin-induced anaphylactic reactions in weaned piglets. MATERIALS AND METHODS Eighteen 14-day-old piglets were sensitized and boosted by oral administration of purified beta-conglycinin. Forsythia suspensa extract was supplemented in the diet after the initial sensitization and continued for the remainder of the experiment. Piglets were challenged on day 28, and anaphylactic symptoms, passive cutaneous anaphylaxis, plasma histamine and intestinal microbial flora were analyzed. T-cell proliferative responses and cytokine production were also determined. RESULTS Forsythia suspensa extract alleviated beta-conglycinin-induced anaphylactic symptoms by markedly reducing anaphylactic antibodies, mast cell degranulation, and histamine release while improving intestinal microbial flora. Furthermore, Forsythia suspensa extract significantly suppressed beta-conglycinin-induced T lymphocyte proliferation and IL-4 synthesis. CONCLUSION Forsythia suspensa extract protected beta-conglycinin-sensitized piglets from anaphylactic reactions. Forsythia suspensa extract may provide a novel effective therapy for soybean allergy.
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Affiliation(s)
- Yue Hao
- State Key Laboratory of Animal Nutrition, China Agricultural University, No 2 Yuanmingyuan West Road, Beijing 100193, China
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Yazdankhah S, Midtvedt T, Narvhus J, Berstad A, Lassen J, Halvorsen R. The use of probiotics for critically ill patients in hospitals. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2009. [DOI: 10.3109/08910600903495046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Siamak Yazdankhah
- Norwegian Scientific Committee for Food Safety, Norwegian Institute of Public Health
| | | | - Judith Narvhus
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Arnold Berstad
- Institute of Medicine, University of Bergen, Haukeland University Hospital, Bergen, Norway
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Cronin M, Sleator RD, Hill C, Fitzgerald GF, van Sinderen D. Development of a luciferase-based reporter system to monitor Bifidobacterium breve UCC2003 persistence in mice. BMC Microbiol 2008; 8:161. [PMID: 18816375 PMCID: PMC2564955 DOI: 10.1186/1471-2180-8-161] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 09/24/2008] [Indexed: 12/12/2022] Open
Abstract
Background Probiotics such as bifidobacteria have been shown to maintain a healthy intestinal microbial balance and help protect against infections. However, despite these benefits, bifidobacteria still remain poorly understood at the biochemical, physiological and especially the genetic level. Herein we describe, for the first time, the development of a non-invasive luciferase-based reporter system for real-time tracking of Bifidobacterium species in vivo. Results The reporter vector pLuxMC1 is based on the recently described theta-type plasmid pBC1 from B. catenatulatum [1] and the luxABCDE operon from pPL2lux [2]. Derivatives of pLuxMC1, harbouring a bifidobacterial promoter (pLuxMC2) as well as a synthetically derived promoter (pLuxMC3) [3] placed upstream of luxABCDE, were constructed and found to stably replicate in B. breve UCC2003. The subsequent analysis of these strains allowed us to assess the functionality of pLuxMC1 both in vitro and in vivo. Conclusion Our results demonstrate the potential of pLuxMC1 as a real-time, non-invasive reporter system for Bifidobacterium. It has also allowed us, for the first time, to track the colonisation potential and persistence of this probiotic species in real time. An interesting and significant outcome of the study is the identification of the caecum as a niche environment for B. breve UCC2003 within the mouse gastrointestinal tract (GI) tract.
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Affiliation(s)
- Michelle Cronin
- Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland.
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Shkoporov AN, Efimov BA, Khokhlova EV, Steele JL, Kafarskaia LI, Smeianov VV. Characterization of plasmids from human infant Bifidobacterium strains: sequence analysis and construction of E. coli-Bifidobacterium shuttle vectors. Plasmid 2008; 60:136-48. [PMID: 18652842 DOI: 10.1016/j.plasmid.2008.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 06/26/2008] [Accepted: 06/27/2008] [Indexed: 11/29/2022]
Abstract
A survey of infant fecal Bifidobacterium isolates for plasmid DNA revealed that a significant portion of the strains, 17.6%, carry small plasmids. The majority of plasmid-harboring strains belonged to the Bifidobacterium longum/infantis group. Most of the plasmids could be assigned into two groups based on their sizes and the restriction profiles. Three plasmids, pB44 (3.6 kb) from B. longum, pB80 (4.9 kb) from Bifidobacterium bifidum, and pB21a (5.2kb) from Bifidobacterium breve were sequenced. While the former two plasmids were found to be highly similar to previously characterized rolling-circle replicating pKJ36 and pKJ56, respectively, the third plasmid, pB21a, does not share significant nucleotide homology with known plasmids. However, it might be placed into the pCIBb1-like group of bifidobacterial rolling-plasmids based on the homology of its Rep protein and the overall molecular organization. Two sets of Escherichia coli-Bifidobacterium shuttle vectors constructed based on pB44 and pB80 replicons were capable of transforming B. bifidum and B. breve strains with efficiency up to 3x10(4)cfu/microg DNA. Additionally, an attempt was made to employ a broad host range conjugation element, RP4, in developing of E. coli-Bifidobacterium gene transfer system.
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Affiliation(s)
- Andrei N Shkoporov
- Department of Microbiology, Russia State Medical University, Moscow, Russia
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15
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Improved cloning vectors for bifidobacteria, based on the Bifidobacterium catenulatum pBC1 replicon. Appl Environ Microbiol 2008; 74:4656-65. [PMID: 18539807 DOI: 10.1128/aem.00074-08] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study reports the development of several cloning vectors for bifidobacteria based on the replicon of pBC1, a cryptic plasmid from Bifidobacterium catenulatum L48 thought to replicate via the theta mode. These vectors, in which antibiotic resistance genes encoding either erythromycin or tetracycline resistance acted as selection markers, were able to replicate in a series of eight Bifidobacterium species at frequencies ranging from 4.0 x 10(1) to 1.0 x 10(5) transformants microg(-1) but not in Lactococcus lactis or Lactobacillus casei. They showed a relative copy number of around 30 molecules per chromosome equivalent and a good segregational stability, with more than 95% of the cells retaining the vectors after 80 to 100 generations in the absence of selection. Vectors contain multiple cloning sites of different lengths, and the lacZalpha peptide gene was introduced into one of the molecules, thus allowing the easy selection of colonies harboring recombinant plasmids in Escherichia coli. The functionality of the vectors for engineering Bifidobacterium strains was assessed by cloning and examining the expression of an alpha-l-arabinofuranosidase gene belonging to Bifidobacterium longum. E. coli and Bifidobacterium pseudocatenulatum recombinant clones were stable and showed an increase in alpha-arabinofuranosidase activity of over 100-fold compared to that of the untransformed hosts.
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Abstract
The 2.1-kb cryptic plasmid pCIBAO89 from Bifidobacterium asteroides harbors a 1.4-kb segment which is sufficient for its autonomous replication. The segment is divided into two parts, the presumed replication origin, ori89, and the rep gene encoding the putative 41-kDa Rep89 replication initiation protein. This minimal replication region of pCIBAO89 was functionally dissected by transcriptional analyses as well as by DNA-binding studies, and the information obtained was exploited to create a number of Escherichia coli-Bifidobacterium shuttle vectors capable of transforming various bifidobacteria with an efficiency of up to 10(6) transformants/mug DNA.
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Alvarez-Martín P, O'Connell-Motherway M, van Sinderen D, Mayo B. Functional analysis of the pBC1 replicon from Bifidobacterium catenulatum L48. Appl Microbiol Biotechnol 2007; 76:1395-402. [PMID: 17704917 DOI: 10.1007/s00253-007-1115-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Revised: 07/06/2007] [Accepted: 07/07/2007] [Indexed: 10/22/2022]
Abstract
To determine the minimal replicon of pBC1 (a 2.5-kb cryptic plasmid of Bifidobacterium catenulatum L48) and to check the functionality of its identified open reading frames (ORFs) and surrounding sequences, different segments of pBC1 were amplified by polymerase chain reaction (PCR) and cloned into pBif, a replication probe vector for bifidobacteria. The largest fragment tested in this manner encompassed most of the pBC1 sequence, while the shortest just included the repB gene and its immediate upstream sequences. Derivatives were all shown to allow replication in bifidobacteria. Surprisingly, both the transformation frequency and segregational stability in the absence of antibiotic selection decreased with reducing plasmid length. The relative copy number of the constructs (ranging from around 3 to 23 copies per chromosome equivalent, as compared to 30 copies for the original pBC1) was shown to be strain dependent and to decrease with reducing plasmid length. These results suggest that, although not essential, the copG-like and orfX-like genes of pBC1 play important roles in pBC1 replication. Interruption of repB produced a construct incapable of replicating in bifidobacteria. The analysis of pBC1 will allow its use in the construction of general and specific cloning vectors.
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Affiliation(s)
- Pablo Alvarez-Martín
- Departamento de Microbiología y Bioquímica de Productos Lácteos, Instituto de Productos Lácteos de Asturias (CSIC), Carretera de Infiesto s/n, 33300 Villaviciosa, Asturias, Spain
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