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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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Duboux S, Muller JA, De Franceschi F, Mercenier A, Kleerebezem M. Using fluorescent promoter-reporters to study sugar utilization control in Bifidobacterium longum NCC 2705. Sci Rep 2022; 12:10477. [PMID: 35729224 PMCID: PMC9213400 DOI: 10.1038/s41598-022-14638-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023] Open
Abstract
Bifidobacteria are amongst the first bacteria to colonize the human gastro-intestinal system and have been proposed to play a crucial role in the development of the infant gut since their absence is correlated to the development of diseases later in life. Bifidobacteria have the capacity to metabolize a diverse range of (complex) carbohydrates, reflecting their adaptation to the lower gastro-intestinal tract. Detailed understanding of carbohydrate metabolism regulation in this genus is of prime importance and availability of additional genetic tools easing such studies would be beneficial. To develop a fluorescent protein-based reporter system that can be used in B. longum NCC 2705, we first selected the most promising fluorescent protein out of the seven we tested (i.e., mCherry). This reporter protein was then used to study the carbohydrate mediated activation of PBl1518 and PBl1694, two promoters respectively predicted to be controlled by the transcriptional factors AraQ and AraU, previously suggested to regulate arabinose utilization and proposed to also act as global transcriptional regulators in bifidobacteria. We confirmed that in B. longum NCC 2705 the AraQ controlled promoter (PBl1518) is induced strongly by arabinose and established that the AraU controlled promoter (PBl1694) was mostly induced by the hexoses galactose and fructose. Combining the mCherry reporter system with flow cytometry, we established that NCC 2705 is able to co-metabolize arabinose and glucose while galactose was only consumed after glucose exhaustion, thus illustrating the complexity of different carbohydrate consumption patterns and their specific regulation in this strain.
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Affiliation(s)
- S Duboux
- Nestlé Research, Lausanne, Switzerland. .,Host-Microbe Interactomics Group, Wageningen University and Research, De Elst 1, 6708WD, Wageningen, The Netherlands.
| | | | | | - A Mercenier
- Host-Microbe Interactomics Group, Wageningen University and Research, De Elst 1, 6708WD, Wageningen, The Netherlands
| | - M Kleerebezem
- Host-Microbe Interactomics Group, Wageningen University and Research, De Elst 1, 6708WD, Wageningen, The Netherlands.
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Jeong J, Mun S, Oh Y, Cho CS, Yun K, Ahn Y, Chung WH, Lim MY, Lee KE, Hwang TS, Han K. A qRT-PCR Method Capable of Quantifying Specific Microorganisms Compared to NGS-Based Metagenome Profiling Data. Microorganisms 2022; 10:microorganisms10020324. [PMID: 35208779 PMCID: PMC8875016 DOI: 10.3390/microorganisms10020324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 01/25/2023] Open
Abstract
Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been actively conducted, and there is a growing interest in the quantitative and diagnostic technology for specific microorganisms. According to recent trends, quantitative real-time PCR (qRT-PCR) is still a considerable technique in detecting and quantifying bacteria associated with the human oral and nasal cavities, due to the analytical cost and time burden of NGS technology. Here, based on NGS metagenome profiling data produced by utilizing 100 gut microbiota samples, we conducted a comparative analysis for the identification and quantification of five bacterial genera (Akkermansia, Bacteroides, Bifidobacterium, Phascolarctobacterium, and Roseburia) within same metagenomic DNA samples through qRT-PCR assay in parallel. Genus-specific primers, targeting the particular gene of each genus for qRT-PCR assay, allowed a statistically consistent quantification pattern with the metagenome profiling data. Furthermore, results of bacterial identification through Sanger validation demonstrated the high genus-specificity of each primer set. Therefore, our study suggests that an approach to quantifying specific microorganisms by applying the qRT-PCR method can compensate for the concerns (potential issues) of NGS while also providing efficient benefits to various microbial industries.
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Affiliation(s)
- Jinuk Jeong
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea; (J.J.); (Y.O.)
| | - Seyoung Mun
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Korea;
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
| | - Yunseok Oh
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea; (J.J.); (Y.O.)
| | - Chun-Sung Cho
- Department of Neurosurgery, College of Medicine, Dankook University, Cheonan 31116, Korea;
| | - Kyeongeui Yun
- HuNBiome Co., Ltd., Seoul 08507, Korea; (K.Y.); (Y.A.)
| | - Yongju Ahn
- HuNBiome Co., Ltd., Seoul 08507, Korea; (K.Y.); (Y.A.)
| | - Won-Hyong Chung
- Research Group of Healthcare, Korea Food Research Institute, Wanju 55365, Korea; (W.-H.C.); (M.Y.L.)
| | - Mi Young Lim
- Research Group of Healthcare, Korea Food Research Institute, Wanju 55365, Korea; (W.-H.C.); (M.Y.L.)
| | - Kyung Eun Lee
- Department of Oral Medicine, School of Dentistry, Jeonbuk National University, Jeonju 54896, Korea;
| | | | - Kyudong Han
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea; (J.J.); (Y.O.)
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Correspondence: ; Tel.: +82-550-1240
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Huang H, Liu Z, Qiu Y, Wang X, Wang H, Xiao H, Lu Z. Efficient electrotransformation of Rhodococcus ruber YYL with abundant extracellular polymeric substances via a cell wall-weakening strategy. FEMS Microbiol Lett 2021; 368:6273628. [PMID: 33974050 DOI: 10.1093/femsle/fnab049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/08/2021] [Indexed: 11/14/2022] Open
Abstract
Rhodococcus spp. have broad potential applications related to the degradation of organic contaminants and the transformation or synthesis of useful compounds. However, some Gram-positive bacteria are difficult to manipulate genetically due to low transformation efficiency. In this study, we investigated the effects of chemicals including glycine, isonicotinic acid hydrazide (INH), Tween 80 and penicillin G, as well as cell growth status, competent cell concentration, electroporation field strength, electroporation time and heat shock time, on the electrotransformation efficiency of the tetrahydrofuran-degrading bacterium Rhodococcus ruber YYL with low transformation efficiency. The highest electrotransformation efficiency was 1.60 × 106 CFU/µg DNA after parameter optimization. GmhD (D-glycero-D-manno-heptose 1-phosphate guanosyltransferase) gene, which is important in the biosynthesis of lipopolysaccharide, was deleted via the optimized electrotransformation method. Compared with wild-type strain, YYL ΔgmhD showed extremely high electrotransformation efficiency because the surface of it had no mushroom-like extracellular polymeric substances (EPS). In addition, the results showed that cell wall-weakening reagents might cause some translucent substances like EPS, to detach from the cells, increasing the electrotransformation efficiency of strain YYL. We propose that these results could provide a new strategy for unique bacteria that are rich in EPS, for which genetic manipulation systems are difficult to establish.
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Affiliation(s)
- Hui Huang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zubi Liu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yiyang Qiu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xuejun Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Haixia Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hailong Xiao
- Hangzhou Institute for Food and Drug Control, Hangzhou, Zhejiang 310018, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Bifidobacterium Transformation. Methods Mol Biol 2021. [PMID: 33649944 DOI: 10.1007/978-1-0716-1274-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The protocol presented in this chapter describes a generic method for electrotransformation of Bifidobacterium spp., outlining a technique that is ideal for conferring selective properties onto strains as well as allowing the user to introduce or knock out/in selected genes for phenotypic characterization purposes. We have generalized on the plasmid chosen for transformation and antibiotic selection marker, but the protocol is versatile in this respect and we are able to achieve transformation efficiencies up to 107 transformants/μg of DNA.
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Welker DL, Crowley BL, Evans JB, Welker MH, Broadbent JR, Roberts RF, Mills DA. Transformation of Lactiplantibacillus plantarum and Apilactobacillus kunkeei is influenced by recipient cell growth temperature, vector replicon, and DNA methylation. J Microbiol Methods 2020; 175:105967. [DOI: 10.1016/j.mimet.2020.105967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 01/24/2023]
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Park MJ, Park MS, Ji GE. Improvement of electroporation-mediated transformation efficiency for a Bifidobacterium strain to a reproducibly high level. J Microbiol Methods 2018; 159:112-119. [PMID: 30529116 DOI: 10.1016/j.mimet.2018.11.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 02/07/2023]
Abstract
Bifidobacteria are representative probiotics which are defined as live microorganisms that confer a health benefit on the host. Because of their safety and healthfulness when applied to humans, bifidobacteria are suitable as genetically engineered bacteria for applications to benefit human physiology and pathology. However, molecular biological studies of bifidobacteria have been limited due to insufficient genetic tools including effective transformation methods. The aim of this study is to improve the electroporation-mediated transformation efficiency of bifidobacteria to a reproducibly high level. The crucial factors that determine electroporation efficiency are the restriction-modification system, together with the cell wall and cell membrane structure of the bacteria. We optimized the bifidobacterial electroporation conditions by focusing on these factors as well as the amount of plasmid DNA used, the electrical parameters and the bacterial growth phase. As a result, the electroporation efficiency of B. bifidum BGN4 drastically and consistently increased from 103 to 105 CFU / μg DNA. The most significant factor for increasing the electroporation efficiency was the cell wall weakening mediated by NaCl, which improved the electroporation frequency by 20 times. Because the optimized electrotransformation conditions reported here should be widely applicable to other Bifidobacterium species, these could promote the extensive genetic manipulation of the various Bifidobacterium species in future studies.
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Affiliation(s)
- Min Ju Park
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Myeong Soo Park
- Research Center, BIFIDO Co., Ltd, Hongcheon 205-804, Republic of Korea; Department of Hotel Culinary Arts, Yeonsung University, Anyang 430-749, Republic of Korea.
| | - Geun Eog Ji
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 151-742, Republic of Korea; Research Center, BIFIDO Co., Ltd, Hongcheon 205-804, Republic of Korea.
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A Transposon Mutagenesis System for Bifidobacterium longum subsp. longum Based on an IS 3 Family Insertion Sequence, IS Blo11. Appl Environ Microbiol 2018; 84:AEM.00824-18. [PMID: 29934330 DOI: 10.1128/aem.00824-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 06/16/2018] [Indexed: 12/29/2022] Open
Abstract
Bifidobacteria are a major component of the intestinal microbiota in humans, particularly breast-fed infants. Therefore, elucidation of the mechanisms by which these bacteria colonize the intestine is desired. One approach is transposon mutagenesis, a technique currently attracting much attention because, in combination with next-generation sequencing, it enables exhaustive identification of genes that contribute to microbial fitness. We now describe a transposon mutagenesis system for Bifidobacterium longum subsp. longum 105-A (JCM 31944) based on ISBlo11, a native IS3 family insertion sequence. To build this system, xylose-inducible or constitutive bifidobacterial promoters were tested to drive the expression of full-length or a truncated form at the N terminus of the ISBlo11 transposase. An artificial transposon plasmid, pBFS12, in which ISBlo11 terminal inverted repeats are separated by a 3-bp spacer, was also constructed to mimic the transposition intermediate of IS3 elements. The introduction of this plasmid into a strain expressing transposase resulted in the insertion of the plasmid with an efficiency of >103 CFU/μg DNA. The plasmid targets random 3- to 4-bp sequences, but with a preference for noncoding regions. This mutagenesis system also worked at least in B. longum NCC2705. Characterization of a transposon insertion mutant revealed that a putative α-glucosidase mediates palatinose and trehalose assimilation, demonstrating the suitability of transposon mutagenesis for loss-of-function analysis. We anticipate that this approach will accelerate functional genomic studies of B. longum subsp. longumIMPORTANCE Several hundred species of bacteria colonize the mammalian intestine. However, the genes that enable such bacteria to colonize and thrive in the intestine remain largely unexplored. Transposon mutagenesis, combined with next-generation sequencing, is a promising tool to comprehensively identify these genes but has so far been applied only to a small number of intestinal bacterial species. In this study, a transposon mutagenesis system was established for Bifidobacterium longum subsp. longum, a representative health-promoting Bifidobacterium species. The system enables the identification of genes that promote colonization and survival in the intestine and should help illuminate the physiology of this species.
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Parker A, Lawson MAE, Vaux L, Pin C. Host-microbe interaction in the gastrointestinal tract. Environ Microbiol 2018; 20:2337-2353. [PMID: 28892253 PMCID: PMC6175405 DOI: 10.1111/1462-2920.13926] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/25/2017] [Accepted: 08/31/2017] [Indexed: 12/13/2022]
Abstract
The gastrointestinal tract is a highly complex organ in which multiple dynamic physiological processes are tightly coordinated while interacting with a dense and extremely diverse microbial population. From establishment in early life, through to host-microbe symbiosis in adulthood, the gut microbiota plays a vital role in our development and health. The effect of the microbiota on gut development and physiology is highlighted by anatomical and functional changes in germ-free mice, affecting the gut epithelium, immune system and enteric nervous system. Microbial colonisation promotes competent innate and acquired mucosal immune systems, epithelial renewal, barrier integrity, and mucosal vascularisation and innervation. Interacting or shared signalling pathways across different physiological systems of the gut could explain how all these changes are coordinated during postnatal colonisation, or after the introduction of microbiota into germ-free models. The application of cell-based in-vitro experimental systems and mathematical modelling can shed light on the molecular and signalling pathways which regulate the development and maintenance of homeostasis in the gut and beyond.
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Affiliation(s)
- Aimée Parker
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
| | | | - Laura Vaux
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
| | - Carmen Pin
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
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Stevens MJ, Venturini A, Lacroix C, Meile L. Enhancing oxidative stress resistance in Bifidobacterium thermophilum using a novel overexpression vector and transformation protocol. Plasmid 2017; 92:43-48. [DOI: 10.1016/j.plasmid.2017.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/09/2017] [Accepted: 06/09/2017] [Indexed: 12/30/2022]
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Mechanistic Study of Utilization of Water-Insoluble Saccharomyces cerevisiae Glucans by Bifidobacterium breve Strain JCM1192. Appl Environ Microbiol 2017; 83:AEM.03442-16. [PMID: 28115383 DOI: 10.1128/aem.03442-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/14/2017] [Indexed: 11/20/2022] Open
Abstract
Bifidobacteria exert beneficial effects on hosts and are extensively used as probiotics. However, due to the genetic inaccessibility of these bacteria, little is known about their mechanisms of carbohydrate utilization and regulation. Bifidobacterium breve strain JCM1192 can grow on water-insoluble yeast (Saccharomyces cerevisiae) cell wall glucans (YCWG), which were recently considered as potential prebiotics. According to the results of 1H nuclear magnetic resonance (NMR) spectrometry, the YCWG were composed of highly branched (1→3,1→6)-β-glucans and (1→4,1→6)-α-glucans. Although the YCWG were composed of 78.3% β-glucans and 21.7% α-glucans, only α-glucans were consumed by the B. breve strain. The ABC transporter (malEFG1) and pullulanase (aapA) genes were transcriptionally upregulated in the metabolism of insoluble yeast glucans, suggesting their potential involvement in the process. A nonsense mutation identified in the gene encoding an ABC transporter ATP-binding protein (MalK) led to growth failure of an ethyl methanesulfonate-generated mutant with yeast glucans. Coculture of the wild-type strain and the mutant showed that this protein was responsible for the import of yeast glucans or their breakdown products, rather than the export of α-glucan-catabolizing enzymes. Further characterization of the carbohydrate utilization of the mutant and three of its revertants indicated that this mutation was pleiotropic: the mutant could not grow with maltose, glycogen, dextrin, raffinose, cellobiose, melibiose, or turanose. We propose that insoluble yeast α-glucans are hydrolyzed by extracellular pullulanase into maltose and/or maltooligosaccharides, which are then transported into the cell by the ABC transport system composed of MalEFG1 and MalK. The mechanism elucidated here will facilitate the development of B. breve and water-insoluble yeast glucans as novel synbiotics.IMPORTANCE In general, Bifidobacterium strains are genetically intractable. Coupling classic forward genetics with next-generation sequencing, here we identified an ABC transporter ATP-binding protein (MalK) responsible for the import of insoluble yeast glucan breakdown products by B. breve JCM1192. We demonstrated the pleiotropic effects of the ABC transporter ATP-binding protein in maltose/maltooligosaccharide, raffinose, cellobiose, melibiose, and turanose transport. With the addition of transcriptional analysis, we propose that insoluble yeast glucans are broken down by extracellular pullulanase into maltose and/or maltooligosaccharides, which are then transported into the cell by the ABC transport system composed of MalEFG1 and MalK. The mechanism elucidated here will facilitate the development of B. breve and water-insoluble yeast glucans as novel synbiotics.
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How to transform a recalcitrant Paenibacillus strain: From culture medium to restriction barrier. J Microbiol Methods 2016; 131:135-143. [PMID: 27780731 DOI: 10.1016/j.mimet.2016.10.012] [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: 09/09/2016] [Revised: 10/11/2016] [Accepted: 10/21/2016] [Indexed: 11/20/2022]
Abstract
Paenibacillus riograndensis SBR5T is a plant growth-promoting bacterium isolated from the wheat rhizosphere. Its recalcitrance to genetic manipulation is a major bottleneck for molecular studies, as has been reported for other Paenibacillus environmental isolates. An efficient electroporation protocol was established by evaluating diverse parameters and optimizing the culture medium, culture growth phase, electroporation solution, recovery medium, DNA input, and electric field strength. Efficiencies of approximately 2.8×104transformantsμg-1 of plasmid DNA were obtained. The optimized protocol was tested with other Paenibacillus species, and the relevance of bypassing the restriction DNA defense system to transform Paenibacillus was highlighted. This protocol is the tool needed to deepen molecular studies with this strain and will aid in the manipulation of other new environmental isolates that also exhibit recalcitrant transformation difficulties.
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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: 506] [Impact Index Per Article: 63.3] [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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Zanotti I, Turroni F, Piemontese A, Mancabelli L, Milani C, Viappiani A, Prevedini G, Sanchez B, Margolles A, Elviri L, Franco B, van Sinderen D, Ventura M. Evidence for cholesterol-lowering activity by Bifidobacterium bifidum PRL2010 through gut microbiota modulation. Appl Microbiol Biotechnol 2015; 99:6813-29. [DOI: 10.1007/s00253-015-6564-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/17/2015] [Accepted: 03/19/2015] [Indexed: 12/22/2022]
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15
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Welker DL, Hughes JE, Steele JL, Broadbent JR. High efficiency electrotransformation of Lactobacillus casei. FEMS Microbiol Lett 2014; 362:1-6. [PMID: 25670703 DOI: 10.1093/femsle/fnu033] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We investigated whether protocols allowing high efficiency electrotransformation of other lactic acid bacteria were applicable to five strains of Lactobacillus casei (12A, 32G, A2-362, ATCC 334 and BL23). Addition of 1% glycine or 0.9 M NaCl during cell growth, limitation of the growth of the cell cultures to OD600 0.6-0.8, pre-electroporation treatment of cells with water or with a lithium acetate (100 mM)/dithiothreitol (10 mM) solution and optimization of electroporation conditions all improved transformation efficiencies. However, the five strains varied in their responses to these treatments. Transformation efficiencies of 10(6) colony forming units μg(-1) pTRKH2 DNA and higher were obtained with three strains which is sufficient for construction of chromosomal gene knock-outs and gene replacements.
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Affiliation(s)
- Dennis L Welker
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
| | - Joanne E Hughes
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
| | - James L Steele
- Department of Food Science, University of Wisconsin, Madison, WI 53706, USA
| | - Jeff R Broadbent
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, Logan, UT 84322-8700, USA
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Rajagopal K, Singh PK, Kumar R, Siddiqui KF. CTAB-mediated, single-step preparation of competent Escherichia coli, Bifidobacterium sp. and Kluyveromyces lactis cells. Meta Gene 2014; 2:807-18. [PMID: 25606463 PMCID: PMC4287956 DOI: 10.1016/j.mgene.2014.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/11/2014] [Accepted: 10/04/2014] [Indexed: 12/02/2022] Open
Abstract
An efficient and reproducible method for transformation depends on the competency of the organism. We have developed a simple method for the preparation of competent Escherichia coli, Kluyveromyces lactis, and Bifidobacterium sp. by using a buffer containing cetyl trimethyl ammonium bromide (CTAB) and permits efficient uptake of plasmid DNA and ligation-reaction products. Cells are harvested, washed, mixed with 1–10 μg/ml CTAB, incubated, and followed by a buffer wash. For long-term storage of competent cells, bacteria may be frozen in 10% glycerol without the addition of other components. The transformation process is very simple; plasmid DNA and the cells are mixed and incubated for 5–60 min at 4 °C; no heat pulse is required, and the duration of incubation at 4 °C is not crucial. We developed a simple and rapid procedure for the preparation of competent E. coli, Bifidobacterium sp., and K. lactis. CTAB permits efficient uptake of plasmid, as well as ligation reaction products. The equal transformation efficiencies were observed with cells harvested at late exponential and stationary phases. CTAB treated cells are used for transformation by heat shock, electroporation, etc.
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Affiliation(s)
- Kammara Rajagopal
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore, India
| | - Praveen Kumar Singh
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore, India ; (CSIR-IMTECH) Institute of Microbial Technology, Sector-39a, Chandigarh, India
| | - Rajesh Kumar
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore, India ; (CSIR-IMTECH) Institute of Microbial Technology, Sector-39a, Chandigarh, India
| | - Kaneez Fatima Siddiqui
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore, India ; (CSIR-IMTECH) Institute of Microbial Technology, Sector-39a, Chandigarh, India
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Murein lytic enzyme TgaA of Bifidobacterium bifidum MIMBb75 modulates dendritic cell maturation through its cysteine- and histidine-dependent amidohydrolase/peptidase (CHAP) amidase domain. Appl Environ Microbiol 2014; 80:5170-7. [PMID: 24814791 DOI: 10.1128/aem.00761-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bifidobacteria are Gram-positive inhabitants of the human gastrointestinal tract that have evolved close interaction with their host and especially with the host's immune system. The molecular mechanisms underlying such interactions, however, are largely unidentified. In this study, we investigated the immunomodulatory potential of Bifidobacterium bifidum MIMBb75, a bacterium of human intestinal origin commercially used as a probiotic. Particularly, we focused our attention on TgaA, a protein expressed on the outer surface of MIMBb75's cells and homologous to other known bacterial immunoactive proteins. TgaA is a peptidoglycan lytic enzyme containing two active domains: lytic murein transglycosylase (LT) and cysteine- and histidine-dependent amidohydrolase/peptidase (CHAP). We ran immunological experiments stimulating dendritic cells (DCs) with the B. bifidum MIMBb75 and TgaA, with the result that both the bacterium and the protein activated DCs and triggered interleukin-2 (IL-2) production. In addition, we observed that the heterologous expression of TgaA in Bifidobacterium longum transferred to the bacterium the ability to induce IL-2. Subsequently, immunological experiments performed using two purified recombinant proteins corresponding to the single domains LT and CHAP demonstrated that the CHAP domain is the immune-reactive region of TgaA. Finally, we also showed that TgaA-dependent activation of DCs requires the protein CD14, marginally involves TRIF, and is independent of Toll-like receptor 4 (TLR4) and MyD88. In conclusion, our study suggests that the bacterial CHAP domain is a novel microbe-associated molecular pattern actively participating in the cross talk mechanisms between bifidobacteria and the host's immune system.
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Bifidobacterium bifidum PRL2010 modulates the host innate immune response. Appl Environ Microbiol 2013; 80:730-40. [PMID: 24242237 DOI: 10.1128/aem.03313-13] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Here, we describe data obtained from transcriptome profiling of human cell lines and intestinal cells of a murine model upon exposure and colonization, respectively, with Bifidobacterium bifidum PRL2010. Significant changes were detected in the transcription of genes that are known to be involved in innate immunity. Furthermore, results from enzyme-linked immunosorbent assays (ELISAs) showed that exposure to B. bifidum PRL2010 causes enhanced production of interleukin 6 (IL-6) and IL-8 cytokines, presumably through NF-κB activation. The obtained global transcription profiles strongly suggest that Bifidobacterium bifidum PRL2010 modulates the innate immune response of the host.
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Guglielmetti S, Mayo B, Álvarez-Martín P. Mobilome and genetic modification of bifidobacteria. Benef Microbes 2013; 4:143-66. [PMID: 23271067 DOI: 10.3920/bm2012.0031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Until recently, proper development of molecular studies in Bifidobacterium species has been hampered by growth difficulties, because of their exigent nutritive requirements, oxygen sensitivity and lack of efficient genetic tools. These studies, however, are critical to uncover the cross-talk between bifidobacteria and their hosts' cells and to prove unequivocally the supposed beneficial effects provided through the endogenous bifidobacterial populations or after ingestion as probiotics. The genome sequencing projects of different bifidobacterial strains have provided a wealth of genetic data that will be of much help in deciphering the molecular basis of the physiological properties of bifidobacteria. To this end, the purposeful development of stable cloning and expression vectors based on robust replicons - either from temperate phages or resident plasmids - is still needed. This review addresses the current knowledge on the mobile genetic elements of bifidobacteria (prophages, plasmids and transposons) and summarises the different types of vectors already available, together with the transformation procedures for introducing DNA into the cells. It also covers recent molecular studies performed with such vectors and incipient results on the genetic modification of these organisms, establishing the basis that would allow the use of bifidobacteria for future biotechnological applications.
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Affiliation(s)
- S Guglielmetti
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Sezione di Microbiologia Industriale, Università degli studi di Milano, Via Celoria 2, 20133 Milan, Italy
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Lam KL, Chi-Keung Cheung P. Non-digestible long chain beta-glucans as novel prebiotics. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.bcdf.2013.09.001] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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