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Yu X, Wu X, Qiu L, Wang D, Gan M, Chen X, Wei H, Xu F. Analysis of the intestinal microbial community structure of healthy and long-living elderly residents in Gaotian Village of Liuyang City. Appl Microbiol Biotechnol 2015; 99:9085-95. [DOI: 10.1007/s00253-015-6888-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/24/2015] [Accepted: 07/28/2015] [Indexed: 11/24/2022]
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Oberg TS, Ward RE, Steele JL, Broadbent JR. Transcriptome analysis of Bifidobacterium longum strains that show a differential response to hydrogen peroxide stress. J Biotechnol 2015; 212:58-64. [PMID: 26299205 DOI: 10.1016/j.jbiotec.2015.06.405] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 06/16/2015] [Accepted: 06/19/2015] [Indexed: 01/02/2023]
Abstract
Consumer and commercial interest in foods containing probiotic bifidobacteria is increasing. However, because bifidobacteria are anaerobic, oxidative stress can diminish cell viability during production and storage of bioactive foods. We previously found Bifidobacterium longum strain NCC2705 had significantly greater intrinsic and inducible resistance to hydrogen peroxide (H2O2) than strain D2957. Here, we explored the basis for these differences by examining the transcriptional responses of both strains to sub-lethal H2O2 exposure for 5- or 60-min. Strain NCC2705 had 288 genes that were differentially expressed after the 5-min treatment and 114 differentially expressed genes after the 60-min treatment. In contrast, strain D2957 had only 21 and 90 differentially expressed genes after the 5- and 60-min treatments, respectively. Both strains showed up-regulation of genes coding enzymes implicated in oxidative stress resistance, such as thioredoxin, thioredoxin reductase, peroxiredoxin, ferredoxin, glutaredoxin, and anaerobic ribonucleotide reductase, but induction levels were typically highest in NCC2705. Compared to D2957, NCC2705 also had more up-regulated genes involved in transcriptional regulation and more down-regulated genes involved in sugar transport and metabolism. These results provide a greater understanding of the molecular basis for oxidative stress resistance in B. longum and the factors that contribute to strain-to-strain variability in survival in bioactive food products.
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Affiliation(s)
- Taylor S Oberg
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, USA.
| | - Robert E Ward
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, USA
| | - James L Steele
- Department of Food Science, University of Wisconsin, 1605 Linden Drive, Madison, WI 53706-1565, USA
| | - Jeff R Broadbent
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, USA
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Yang X, Hang X, Tan J, Yang H. Differences in acid tolerance between Bifidobacterium breve BB8 and its acid-resistant derivative B. breve BB8dpH, revealed by RNA-sequencing and physiological analysis. Anaerobe 2015; 33:76-84. [DOI: 10.1016/j.anaerobe.2015.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/18/2015] [Accepted: 02/25/2015] [Indexed: 01/25/2023]
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Wei YX, Ye L, Liu DB, Zhang ZY, Liu C, Guo XK. Activation of the chromosomally encoded mazEF(Bif) locus of Bifidobacterium longum under acid stress. Int J Food Microbiol 2015; 207:16-22. [PMID: 25950853 DOI: 10.1016/j.ijfoodmicro.2015.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 02/18/2015] [Accepted: 04/19/2015] [Indexed: 01/15/2023]
Abstract
Toxin-antitoxin (TA) systems are distributed within the genomes of almost all free-living bacteria. Although the roles of chromosomally encoded TA systems are still under debate, they are suspected to be involved in various stress responses. Here, we provide the first report of a type II TA system in the probiotic bacterium Bifidobacterium longum. Bioinformatic analysis of the B. longum JDM301 genome identified a pair of linked genes encoding a MazEF-like TA system at the locus BLJ_811-BLJ_812. Our results showed that B. longum mazEF(Bif) genes form a bicistronic operon. The over-expression of MazF(Bif) was toxic to Escherichia coli and could be neutralized by the co-expression of its cognate antitoxin MazE(Bif). We demonstrated that MazEF(Bif) was activated during acid stress, which would most likely be encountered in the gastrointestinal tract. In addition, we found that the protease ClpPX(Bif), in addition to MazEF(Bif), was induced under acid stress. Furthermore, we examined antitoxin levels over time for MazEF(Bif) and observed that the antitoxin MazE(Bif) was degraded by ClpPX(Bif), which suggested that MazEF(Bif) was activated through the hydrolysis of MazE(Bif) by ClpP1X(Bif) and ClpP2X(Bif) under acid stress. Our results suggest that the MazEF(Bif) TA module may play an important role in cell physiology and may represent a cell growth modulator that helps bacteria to cope with acid stress in the gastrointestinal tract and environment.
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Affiliation(s)
- Yan-Xia Wei
- Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity/School of Stomatology, Xuzhou Medical College, Xuzhou, Jiangsu 221004, China; Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lu Ye
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Dian-Bin Liu
- Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity/School of Stomatology, Xuzhou Medical College, Xuzhou, Jiangsu 221004, China
| | - Zhuo-Yang Zhang
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chang Liu
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Xiao-Kui Guo
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Sun E, Zhao L, Ren F, Liu S, Zhang M, Guo H. Complete genome sequence of Bifidobacterium animalis subsp. lactis A6, a probiotic strain with high acid resistance ability. J Biotechnol 2015; 200:8-9. [DOI: 10.1016/j.jbiotec.2015.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 02/12/2015] [Indexed: 01/11/2023]
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Liu S, Ren F, Zhao L, Jiang L, Hao Y, Jin J, Zhang M, Guo H, Lei X, Sun E, Liu H. Starch and starch hydrolysates are favorable carbon sources for bifidobacteria in the human gut. BMC Microbiol 2015; 15:54. [PMID: 25887661 PMCID: PMC4349234 DOI: 10.1186/s12866-015-0362-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 01/23/2015] [Indexed: 12/16/2022] Open
Abstract
Background Bifidobacteria are key commensals in human gut, and their abundance is associated with the health of their hosts. Although they are dominant in infant gut, their number becomes lower in adult gut. The changes of the diet are considered to be main reason for this difference. Large amounts of whole-genomic sequence data of bifidobacteria make it possible to elucidate the genetic interpretation of their adaptation to the nutrient environment. Among the nutrients in human gut, starch is a highly fermentable substrate and can exert beneficial effects by increasing bifidobacteria and/or being fermented to short chain fatty acids. Results In order to determine the potential substrate preference of bifidobacteria, we compared the glycoside hydrolase (GH) profiles of a pooled-bifidobacterial genome (PBG) with a representative microbiome (RM) of the human gut. In bifidobacterial genomes, only 15% of GHs contained signal peptides, suggesting their weakness in utilization of complex carbohydrate, such as plant cell wall polysaccharides. However, compared with other intestinal bacteria, bifidobacteiral genomes encoded more GH genes for degrading starch and starch hydrolysates, indicating that they have genetic advantages in utilizing these substrates. Bifidobacterium longum subsp. longum BBMN68 isolated from centenarian’s faeces was used as a model strain to further investigate the carbohydrate utilization. The pathway for degrading starch and starch hydrolysates was the only complete pathway for complex carbohydrates in human gut. It is noteworthy that all of the GH genes for degrading starch and starch hydrolysates in the BBMN68 genome were conserved in all studied bifidobacterial strains. The in silico analyses of BBMN68 were further confirmed by growth experiments, proteomic and real-time quantitative PCR (RT-PCR) analyses. Conclusions Our results demonstrated that starch and starch hydrolysates were the most universal and favorable carbon sources for bifidobacteria. The low amount of these carbon sources in adult intestine was speculated to contribute to the low relative abundance of bifidobacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0362-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Songling Liu
- Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Fazheng Ren
- Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Liang Zhao
- Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Lu Jiang
- Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China. .,Higher Institution Engineering Research Center of Animal Product, Beijing, 10083, China.
| | - Yanling Hao
- Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Junhua Jin
- Beijing Laboratory for Food Quality and Safety, Beijing, 10083, China.
| | - Ming Zhang
- Higher Institution Engineering Research Center of Animal Product, Beijing, 10083, China.
| | - Huiyuan Guo
- Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China. .,Beijing Laboratory for Food Quality and Safety, Beijing, 10083, China.
| | - Xingen Lei
- Department of Animal Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Erna Sun
- Higher Institution Engineering Research Center of Animal Product, Beijing, 10083, China.
| | - Hongna Liu
- Higher Institution Engineering Research Center of Animal Product, Beijing, 10083, China.
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Effect of Pre-Stressing on the Acid-Stress Response in Bifidobacterium Revealed Using Proteomic and Physiological Approaches. PLoS One 2015; 10:e0117702. [PMID: 25689631 PMCID: PMC4331358 DOI: 10.1371/journal.pone.0117702] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/29/2014] [Indexed: 02/02/2023] Open
Abstract
Weak acid resistance limits the application of Bifidobacteria as a probiotic in food. The acid tolerance response (ATR), caused by pre-stressing cells at a sublethal pH, could improve the acid resistance of Bifidobacteria to subsequent acid stress. In this study, we used Bifidobacterium longum sub. longum BBMN68 to investigate the effect of the ATR on the acid stress response (ASR), and compared the difference between the ATR and the ASR by analyzing the two-dimensional-PAGE protein profiles and performing physiological tests. The results revealed that a greater abundance of proteins involved in carbohydrate metabolism and protein protection was present after the ASR than after the ATR in Bifidobacterium. Pre-stressing cells increased the abundance of proteins involved in energy production, amino acid metabolism, and peptidoglycan synthesis during the ASR of Bifidobacterium. Moreover, after the ASR, the content of ATP, NH3, thiols, and peptidoglycan, the activity of H+-ATPase, and the maintenance of the intracellular pH in the pre-stressed Bifidobacterium cells was significantly higher than in the uninduced cells. These results provide the first explanation as to why the resistance of Bifidobacterium to acid stress improved after pre-stressing.
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Papadimitriou K, Zoumpopoulou G, Foligné B, Alexandraki V, Kazou M, Pot B, Tsakalidou E. Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches. Front Microbiol 2015; 6:58. [PMID: 25741323 PMCID: PMC4330916 DOI: 10.3389/fmicb.2015.00058] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 01/17/2015] [Indexed: 12/13/2022] Open
Abstract
Over the past decades the food industry has been revolutionized toward the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer’s health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut–brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms.
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Affiliation(s)
- Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens Greece
| | - Georgia Zoumpopoulou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens Greece
| | - Benoit Foligné
- Bactéries Lactiques et Immunité des Muqueuses, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Université Lille Nord de France, CNRS UMR8204, Lille France
| | - Voula Alexandraki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens Greece
| | - Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens Greece
| | - Bruno Pot
- Bactéries Lactiques et Immunité des Muqueuses, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Université Lille Nord de France, CNRS UMR8204, Lille France
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens Greece
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Relationship between acid tolerance and cell membrane in Bifidobacterium, revealed by comparative analysis of acid-resistant derivatives and their parental strains grown in medium with and without Tween 80. Appl Microbiol Biotechnol 2015; 99:5227-36. [DOI: 10.1007/s00253-015-6447-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/10/2015] [Accepted: 01/29/2015] [Indexed: 02/06/2023]
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60
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Physiological and proteomic analysis of Lactobacillus casei in response to acid adaptation. ACTA ACUST UNITED AC 2014; 41:1533-40. [DOI: 10.1007/s10295-014-1487-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 07/05/2014] [Indexed: 01/01/2023]
Abstract
Abstract
The aim of this study was to investigate the acid tolerance response (ATR) in Lactobacillus casei by a combined physiological and proteomic analysis. To optimize the ATR induction, cells were acid adapted for 1 h at different pHs, and then acid challenged at pH 3.5. The result showed that acid adaptation improved acid tolerance, and the highest survival was observed in cells adapted at pH 4.5 for 1 h. Analysis of the physiological data showed that the acid-adapted cells exhibited higher intracellular pH (pHi), intracellular NH4+ content, and lower inner permeability compared with the cells without adaptation. Proteomic analysis was performed upon acid adaptation to different pHs (pH 6.5 vs. pH 4.5) using two-dimensional electrophoresis. A total of 24 proteins that exhibited at least 1.5-fold differential expression were identified. Four proteins (Pgk, LacD, Hpr, and Galm) involved in carbohydrate catabolism and five classic stress response proteins (GroEL, GrpE, Dnak, Hspl, and LCAZH_2811) were up-regulated after acid adaptation at pH 4.5 for 1 h. Validation of the proteomic data was performed by quantitative RT-PCR, and transcriptional regulation of all selected genes showed a positive correlation with the proteomic patterns of the identified proteins. Results presented in this study may be useful for further elucidating the acid tolerance mechanisms and may help in formulating new strategies to improve the industrial performance of this species during acid stress.
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The pH-dependent expression of the urease operon in Streptococcus salivarius is mediated by CodY. Appl Environ Microbiol 2014; 80:5386-93. [PMID: 24951785 DOI: 10.1128/aem.00755-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Urease gene expression in Streptococcus salivarius 57.I, a strain of one of the major alkali producers in the mouth, is induced by acidic pH and excess amounts of carbohydrate. Expression is controlled primarily at the transcriptional level from a promoter, pureI. Recent sequencing analysis revealed a CodY box located 2 bases 5' to the -35 element of pureI. Using continuous chemostat culture, transcription from pureI was shown to be repressed by CodY, and at pH 7 the repression was more pronounced than that in cells grown at pH 5.5 under both 20 and 100 mM glucose. The direct binding of CodY to pureI was demonstrated by electrophoretic mobility shift assay and chromatin immunoprecipitation (ChIP)-quantitative real-time PCR (qPCR). The result of ChIP-qPCR also confirmed that the regulation of CodY is indeed modulated by pH and the binding of CodY at neutral pH is further enhanced by a limited supply of glucose (20 mM). In the absence of CodY, the C-terminal domain of the RNA polymerase (RNAP) α subunit interacted with the AT tracks within the CodY box, indicating that CodY and RNAP compete for the same binding region. Such regulation could ensure optimal urease expression when the enzyme is most required, i.e., at an acidic growth pH with an excess amount of carbon nutrients.
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Tan Y, Liu J, Chen X, Zheng H, Li F. RNA-seq-based comparative transcriptome analysis of the syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528 grown autotrophically and heterotrophically. MOLECULAR BIOSYSTEMS 2014; 9:2775-84. [PMID: 24056499 DOI: 10.1039/c3mb70232d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Clostridium ljungdahlii DSM 13528 represents a promising platform organism for production of a whole variety of different biofuels and biochemicals from syngas. Although the publication of its genome gave us the first possibility to understand the molecular mechanism for carbon utilization, reports on the profiling of the transcriptome were unavailable. In this study, RNA-seq-based global transcriptome analysis was performed to compare the transcriptomes of C. ljungdahlii grown on CO-CO2 with those grown on fructose. In total, 1852 differentially expressed genes were identified, which included 366 upregulated genes and 1486 downregulated genes under CO-CO2 conditions. These up- and downregulated genes are predicted to be involved in the Wood-Ljungdahl pathway, CO2 reduction to acetic acid, fructose fermentation, central carbon metabolism and transport, and vitamin B12 synthesis. In addition, 36 small RNAs were identified, 20 of which were novel small RNAs. Quantitative real-time PCR (qRT-PCR) and RT-PCR analysis of the selected functional genes and sRNA genes expression profiles were found to be consistent with the RNA-seq data. The study allowed a deeper understanding of the molecular mechanisms underlying syngas utilization and could help guide the design of rational strategies to increase the efficiency of syngas fixation in the future.
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Affiliation(s)
- Yang Tan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road No. 189, Qingdao 266101, China.
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Lindenstrauss AG, Ehrmann MA, Behr J, Landstorfer R, Haller D, Sartor RB, Vogel RF. Transcriptome analysis of Enterococcus faecalis toward its adaption to surviving in the mouse intestinal tract. Arch Microbiol 2014; 196:423-33. [PMID: 24700373 DOI: 10.1007/s00203-014-0982-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 02/27/2014] [Accepted: 03/24/2014] [Indexed: 12/15/2022]
Abstract
We have performed a transcriptomic in vivo study with Enterococcus faecalis OG1RF in the intestine of living mice to identify novel latent and adaptive fitness determinants within E. faecalis. From 2,658 genes that are present in E. faecalis strain OG1RF, 124 genes were identified as significantly differentially expressed within the intestinal tract of living mice as compared to exponential growth in BHI broth. The groups of significantly up- or down-regulated genes consisted of 94 and 30 genes, respectively, for which 46 and 18 a clear annotation to a functionally described protein was found. These included genes involved in energy metabolism (e.g., dhaK and glpK pathway), transport and binding mechanisms (e.g., phosphoenolpyruvate carbohydrate PTS) as well as fatty acid metabolism (fab genes). The novel putative fitness determinants found in this work may be helpful for future studies of E. faecalis adaptation to the intestinal tract, which is also a prerequisite for infection in a compromised or inflamed host.
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Affiliation(s)
- Angela G Lindenstrauss
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350, Freising, Germany
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