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Dreyer A, Lenz C, Groß U, Bohne W, Zautner AE. Comparative analysis of proteomic adaptations in Enterococcus faecalis and Enterococcus faecium after long term bile acid exposure. BMC Microbiol 2024; 24:110. [PMID: 38570789 PMCID: PMC10988882 DOI: 10.1186/s12866-024-03253-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND All gastrointestinal pathogens, including Enterococcus faecalis and Enterococcus faecium, undergo adaptation processes during colonization and infection. In this study, we investigated by data-independent acquisition mass spectrometry (DIA-MS) two crucial adaptations of these two Enterococcus species at the proteome level. Firstly, we examined the adjustments to cope with bile acid concentrations at 0.05% that the pathogens encounter during a potential gallbladder infection. Therefore, we chose the primary bile acids cholic acid (CA) and chenodeoxycholic acid (CDCA) as well as the secondary bile acid deoxycholic acid (DCA), as these are the most prominent bile acids. Secondly, we investigated the adaptations from an aerobic to a microaerophilic environment, as encountered after oral-fecal infection, in the absence and presence of deoxycholic acid (DCA). RESULTS Our findings showed similarities, but also species-specific variations in the response to the different bile acids. Both Enterococcus species showed an IC50 in the range of 0.01- 0.023% for DCA and CDCA in growth experiments and both species were resistant towards 0.05% CA. DCA and CDCA had a strong effect on down-expression of proteins involved in translation, transcription and replication in E. faecalis (424 down-expressed proteins with DCA, 376 down-expressed proteins with CDCA) and in E. faecium (362 down-expressed proteins with DCA, 391 down-expressed proteins with CDCA). Proteins commonly significantly altered in their expression in all bile acid treated samples were identified for both species and represent a "general bile acid response". Among these, various subunits of a V-type ATPase, different ABC-transporters, multi-drug transporters and proteins related to cell wall biogenesis were up-expressed in both species and thus seem to play an essential role in bile acid resistance. Most of the differentially expressed proteins were also identified when E. faecalis was incubated with low levels of DCA at microaerophilic conditions instead of aerobic conditions, indicating that adaptations to bile acids and to a microaerophilic atmosphere can occur simultaneously. CONCLUSIONS Overall, these findings provide a detailed insight into the proteomic stress response of two Enterococcus species and help to understand the resistance potential and the stress-coping mechanisms of these important gastrointestinal bacteria.
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Affiliation(s)
- Annika Dreyer
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Uwe Groß
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Wolfgang Bohne
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas Erich Zautner
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany.
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University Magdeburg, Magdeburg, Germany.
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2
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Zhang G, He M, Xiao L, Jiao Y, Han J, Li C, Miller MJ, Zhang L. Milk fat globule membrane protects Bifidobacterium longum ssp. infantis ATCC 15697 against bile stress by modifying global transcriptional responses. J Dairy Sci 2024; 107:91-104. [PMID: 37678788 DOI: 10.3168/jds.2023-23591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/17/2023] [Indexed: 09/09/2023]
Abstract
The milk fat globule membrane (MFGM) can protect probiotic bacteria from bile stress. However, its potential mechanism has not been reported. In this study, the viability, morphology and gene transcriptional response of Bifidobacterium longum ssp. infantis ATCC 15697 (BI_15697) stressed by bile salts with or without MFGM were investigated. It was shown that MFGM alleviated the reduction in BI_15697 population induced by 0.2% porcine bile stress and restored the population to the control levels. MFGM ameliorated the shrunken, fragmented appearance and irregular morphology of BI_15697 and maintained cell integrity disrupted by bile stress. RNA-sequencing results showed that MFGM increased transport of glucose and raffinose and decreased that of branched-chain amino acids (BCAA) in the presence of bile salts. MFGM stimulated the expression of genes involved in the synthesis of raffinose in galactose metabolism and the metabolism of BCAA, suggesting that MFGM stimulated the accumulation of raffinose and BCAA in the presence of bile. In addition, MFGM stimulated the expression of 2 bile efflux transporters under bile stress. Together, the multifactorial response helps BI_15697 excrete bile salts and maintain cellular integrity in response to bile stress. This study proposes a mechanism for the protection of BI_15697 against bile salt stress by MFGM, thereby providing a molecular basis for its application in incorporation of probiotics.
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Affiliation(s)
- Gongsheng Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Mingxue He
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Lihong Xiao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yuehua Jiao
- Center of Drug Safety Evaluation, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Jianchun Han
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China; Heilongjiang Green Food Science Research Institute, Harbin 150030, China.
| | - Chun Li
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China; Center of Drug Safety Evaluation, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Michael J Miller
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL 61801
| | - Lili Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China.
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3
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Mörschbächer AP, Berghahn E, Shibuya FY, Cardoso ML, Ulguim GK, de Freitas Michelon N, Torgeski N, Vivian TP, Wissmann D, de Camargo FCDLS, de Andrade GM, Sturza DAF, Dos Santos HF, Dilkin P, Timmers LFSM, Granada CE. Feeding laying hens with lactobacilli improves internal egg quality and animal health. World J Microbiol Biotechnol 2023; 40:5. [PMID: 37925366 DOI: 10.1007/s11274-023-03820-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Feeding animals with lactobacilli strains is a biotechnological strategy to improve production, food quality, and animal health. Thus, this study aimed to select new lactic acid bacteria (LAB) able to improve laying hens health and egg production. Forty Bovans White layers (two days old) were randomly divided into four experimental groups that receive an oral gavage with saline solution (control group) or with one of the three lactobacilli selected (KEG3, TBB10, and KMG127) by their antagonistic activity against the foodborne pathogen Bacillus cereus GGD_EGG01. 16 S rRNA sequencing identified KEG3 as Lentilactobacillus sp., and TBB10 and KMG127 as Lactiplantibacillus sp. The data showed that feeding birds with LAB increased weight uniformity and improved the internal quality of the eggs (high yolk index and Haugh unit) compared with the control group (p < 0.05). Beta-diversity analysis showed that LAB supplementation modifies the cecal microbiota of laying hens. The prokaryotic families Bacteroidaceae, Ruminococcaceae, Rikenellaceae, and Lactobacillaceae were most important to the total dissimilarity of the cecal microbial community (calculated by SIMPER test). At end of in vivo experiments, it was possible to conclude that the feed of laying hens with Lentilactobacillus sp. TBB10 and Lentilactobacillus sp. KEG3 can be an important biotechnological tool for improving food quality and animal health.
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Affiliation(s)
- Ana Paula Mörschbächer
- Graduate Program in Biotechnology, University of Taquari Valley - Univates, Lajeado, Brazil
| | - Emílio Berghahn
- Graduate Program in Biotechnology, University of Taquari Valley - Univates, Lajeado, Brazil
| | - Fabio Yuji Shibuya
- Graduate Program in Veterinary Medicine, Federal University of Santa Maria - UFSM, Santa Maria, Brazil
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Mateus Luis Cardoso
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Gustavo Kutscher Ulguim
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Nathalia de Freitas Michelon
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Natália Torgeski
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Tamiris Prussiano Vivian
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Daiani Wissmann
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
- Uniprofessional Residency Program in Veterinary Medicine, Federal University of Santa Maria, Santa Maria, Brazil
| | - Flávia Constância de Los Santos de Camargo
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
- Uniprofessional Residency Program in Veterinary Medicine, Federal University of Santa Maria, Santa Maria, Brazil
| | - Gabriela Monteiro de Andrade
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
- Uniprofessional Residency Program in Veterinary Medicine, Federal University of Santa Maria, Santa Maria, Brazil
| | | | - Helton Fernandes Dos Santos
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Paulo Dilkin
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
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Marcos-Fernández R, Blanco-Míguez A, Ruiz L, Margolles A, Ruas-Madiedo P, Sánchez B. Towards the isolation of more robust next generation probiotics: The first aerotolerant Bifidobacterium bifidum strain. Food Res Int 2023; 165:112481. [PMID: 36869494 DOI: 10.1016/j.foodres.2023.112481] [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: 03/18/2022] [Revised: 11/20/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
This work reports on the first described aerotolerant Bifidobacterium bifidum strain, Bifidobacterium bifidum IPLA60003, which has the ability to form colonies on the surface of agar plates under aerobic conditions, a weird phenotype that to our knowledge has never been observed in B. bifidum. The strain IPLA60003 was generated after random UV mutagenesis from an intestinal isolate. It incorporates 26 single nucleotide polymorphisms that activate the expression of native oxidative-defense mechanisms such as the alkyl hydroxyperoxide reductase, the glycolytic pathway and several genes coding for enzymes involved in redox reactions. In the present work, we discuss the molecular mechanisms underlying the aerotolerance phenotype of B. bifidum IPLA60003, which will open new strategies for the selection and inclusion of probiotic gut strains and next generation probiotics into functional foods.
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Affiliation(s)
- Raquel Marcos-Fernández
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Aitor Blanco-Míguez
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Lorena Ruiz
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Patricia Ruas-Madiedo
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
| | - Borja Sánchez
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
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5
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Abstract
Bifidobacteria naturally inhabit diverse environments, including the gastrointestinal tracts of humans and animals. Members of the genus are of considerable scientific interest due to their beneficial effects on health and, hence, their potential to be used as probiotics. By definition, probiotic cells need to be viable despite being exposed to several stressors in the course of their production, storage, and administration. Examples of common stressors encountered by probiotic bifidobacteria include oxygen, acid, and bile salts. As bifidobacteria are highly heterogenous in terms of their tolerance to these stressors, poor stability and/or robustness can hamper the industrial-scale production and commercialization of many strains. Therefore, interest in the stress physiology of bifidobacteria has intensified in recent decades, and many studies have been established to obtain insights into the molecular mechanisms underlying their stability and robustness. By complementing traditional methodologies, omics technologies have opened new avenues for enhancing the understanding of the defense mechanisms of bifidobacteria against stress. In this review, we summarize and evaluate the current knowledge on the multilayered responses of bifidobacteria to stressors, including the most recent insights and hypotheses. We address the prevailing stressors that may affect the cell viability during production and use as probiotics. Besides phenotypic effects, molecular mechanisms that have been found to underlie the stress response are described. We further discuss strategies that can be applied to improve the stability of probiotic bifidobacteria and highlight knowledge gaps that should be addressed in future studies.
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Affiliation(s)
- Marie Schöpping
- Systems Biology, Discovery, Chr. Hansen A/S, Hørsholm, Denmark
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ahmad A. Zeidan
- Systems Biology, Discovery, Chr. Hansen A/S, Hørsholm, Denmark
| | - Carl Johan Franzén
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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6
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Liu B, Zhuang S, Tian R, Liu Y, Wang Y, Lei X, Wang C. Chemoproteomic Profiling Reveals the Mechanism of Bile Acid Tolerance in Bacteria. ACS Chem Biol 2022; 17:2461-2470. [PMID: 36049085 DOI: 10.1021/acschembio.2c00286] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Bile acids (BAs) are a class of endogenous metabolites with important functions. As amphipathic molecules, BAs have strong antibacterial effects, preventing overgrowth of the gut microbiota and defending the invasion of pathogens. However, some disease-causing pathogens can survive the BA stress and knowledge is limited about how they develop BA tolerance. In this work, we applied a quantitative chemoproteomic strategy to profile BA-interacting proteins in bacteria, aiming to discover the sensing pathway of BAs. Using a clickable and photo-affinity BA probe with quantitative mass spectrometry, we identified a list of histidine kinases (HKs) of the two-component systems (TCS) in bacteria as the novel binding targets of BA. Genetic screening revealed that knocking out one specific HK, EnvZ, renders bacteria with significant sensitivity to BA. Further biochemical and genetic experiments demonstrated that BA binds to a specific pocket in EnvZ and activates a downstream signaling pathway to help efflux of BA from bacteria, resulting in BA tolerance. Collectively, our data revealed that EnvZ is a novel sensor of BA in bacteria and its associated TCS signaling pathway plays a critical role in mediating bacterial BA tolerance, which opens new opportunities to combat BA-tolerating pathogens.
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Affiliation(s)
- Biwei Liu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shentian Zhuang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Runze Tian
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yanqi Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaoguang Lei
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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7
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Paria P, Chakraborty HJ, Behera BK. Identification of novel salt tolerance-associated proteins from the secretome of Enterococcus faecalis. World J Microbiol Biotechnol 2022; 38:177. [PMID: 35934729 DOI: 10.1007/s11274-022-03354-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022]
Abstract
The ability of bacteria to adapt to the external environment is fundamental for their survival. A halotolerant microorganism Enterococcus faecalis able to grow under high salt stress conditions was isolated in the present study. The SDS-PAGE analysis of the secretome showed a protein band with a molecular weight of 28 kDa, gradually increased with an increase in salt concentration, and the highest intensity was observed at 15% salt stress condition. LC-MS/MS analysis of this particular band identified fourteen different proteins, out of which nine proteins were uncharacterized. Further, the function of uncharacterized proteins was predicted based on structure-function relationship using a reverse template search approach deciphering uncharacterized protein into type III polyketide synthases, stress-induced protein-1, Eed-h3k79me3, ba42 protein, 3-methyladenine DNA glycosylase, Atxa protein, membrane-bound respiratory hydrogenase, type-i restriction-modification system methylation subunit and ManxA. STRING network analysis further a showed strong association among the proteins. The processes predicted involvement of these proteins in signal transduction, ions transport, synthesis of the protective layer, cellular homeostasis and regulation of gene expression and different metabolic pathways. Thus, the fourteen proteins identified in the secretome play an essential role in maintaining cellular homeostasis in E. faecalis under high-salinity stress. This may represent a novel and previously unreported strategy by E. faecalis to maintain their normal growth and physiology under high salinity conditions.
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Affiliation(s)
- Prasenjit Paria
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
| | - Hirak Jyoti Chakraborty
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India.
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8
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Prebiotic Isomaltooligosaccharide Provides an Advantageous Fitness to the Probiotic Bacillus subtilis CU1. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12136404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bacillus subtilis CU1 is a probiotic strain with beneficial effects on immune health in elderly subjects and diarrhea. Commercialized under spore form, new strategies to improve the germination, fitness and beneficial effects of the probiotic once in the gut have to be explored. For this purpose, functional food ingredients, such as isomaltooligosaccharides (IMOSs), could improve the fitness of Bacillus probiotics. IMOSs are composed of α(1 → 6)- and α(1 → 4)-linked oligosaccharides and are partially indigestible. Dietary IMOSs stimulate beneficial members of intestinal microbiota, but the effect of a combination of IMOSs with probiotics, such as B. subtilis CU1, is unknown. In this study, we evaluate the potential effect of IMOSs in B. subtilis CU1 and identify the metabolic pathways involved. The biochemical analysis of the commercial IMOSs highlights a degree of polymerization (DP) comprised between 1 and 29. The metabolism of IMOSs in CU1 was attributed to an α-glucosidase, secreted in the extracellular compartment one hundred times more than with glucose, and which seems to hydrolyze high DP IMOSs into shorter oligosaccharides (DP1, DP2 and DP3) in the culture medium. Proteomic analysis of CU1 after growth on IMOSs showed a reshaping of B. subtilis CU1 metabolism and functions, associated with a decreased production of lactic acid and acetic acid by two times. Moreover, we show for the first time that IMOSs could improve the germination of a Bacillus probiotic in the presence of bile salts in vitro, with an 8 h reduced lag-time when compared to a glucose substrate. Moreover, bacterial concentration (CFU/mL) was increased by about 1 log in IMOS liquid cultures after 48 h when compared to glucose. In conclusion, the use of IMOSs in association with probiotic B. subtilis CU1 in a synbiotic product could improve the fitness and benefits of the probiotic.
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9
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Wang H, An J, Fan C, Zhai Z, Zhang H, Hao Y. Transcriptome analysis revealed growth phase-associated changes of a centenarian-originated probiotic Bifidobacterium animalis subsp. lactis A6. BMC Microbiol 2022; 22:61. [PMID: 35209838 PMCID: PMC8876546 DOI: 10.1186/s12866-022-02474-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/07/2022] [Indexed: 12/14/2022] Open
Abstract
Background The physiology and application characteristics of probiotics are closely associated with the growth phase. Bifidobacterium animalis subsp. lactis A6 is a promising probiotic strain isolated from the feces of a healthy centenarian in China. In this study, RNA-seq was carried out to investigate the metabolic mechanism between the exponential and the stationary phase in B. lactis A6. Results Differential expression analysis showed that a total of 815 genes were significantly changed in the stationary phase compared to the exponential phase, which consisted of 399 up-regulated and 416 down-regulated genes. The results showed that the transport and metabolism of cellobiose, xylooligosaccharides and raffinose were enhanced at the stationary phase, which expanded carbon source utilizing profile to confront with glucose consumption. Meanwhile, genes involved in cysteine-cystathionine-cycle (CCC) pathway, glutamate dehydrogenase, branched-chain amino acids (BCAAs) biosynthesis, and Clp protease were all up-regulated in the stationary phase, which may enhance the acid tolerance of B. lactis A6 during stationary phase. Acid tolerance assay indicated that the survival rate of stationary phase cells was 51.07% after treatment by pH 3.0 for 2h, which was 730-fold higher than that of 0.07% with log phase cells. In addition, peptidoglycan biosynthesis was significantly repressed, which is comparable with the decreased growth rate during the stationary phase. Remarkably, a putative gene cluster encoding Tad pili was up-regulated by 6.5 to 12.1-fold, which is consistent with the significantly increased adhesion rate to mucin from 2.38% to 4.90% during the transition from the exponential phase to the stationary phase. Conclusions This study reported growth phase-associated changes of B. lactis A6 during fermentation, including expanded carbon source utilizing profile, enhanced acid tolerance, and up-regulated Tad pili gene cluster responsible for bacterial adhesion in the stationary phase. These findings provide a novel insight into the growth phase associated characteristics in B. lactis A6 and provide valuable information for further application in the food industry. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02474-5.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China
| | - Jieran An
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China
| | - Chengfei Fan
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China
| | - Zhengyuan Zhai
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Hongxing Zhang
- Department of Food Science, Beijing University of Agriculture, 7 Bei Nong Road, Changping District, Beijing, 102206, China
| | - Yanling Hao
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China. .,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
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10
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Singh RP, Shadan A, Ma Y. Biotechnological Applications of Probiotics: A Multifarious Weapon to Disease and Metabolic Abnormality. Probiotics Antimicrob Proteins 2022; 14:1184-1210. [PMID: 36121610 PMCID: PMC9483357 DOI: 10.1007/s12602-022-09992-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2022] [Indexed: 12/25/2022]
Abstract
Consumption of live microorganisms "Probiotics" for health benefits and well-being is increasing worldwide. Their use as a therapeutic approach to confer health benefits has fascinated humans for centuries; however, its conceptuality gradually evolved with methodological advancement, thereby improving our understanding of probiotics-host interaction. However, the emerging concern regarding safety aspects of live microbial is enhancing the interest in non-viable or microbial cell extracts, as they could reduce the risks of microbial translocation and infection. Due to technical limitations in the production and formulation of traditionally used probiotics, the scientific community has been focusing on discovering new microbes to be used as probiotics. In many scientific studies, probiotics have been shown as potential tools to treat metabolic disorders such as obesity, type-2 diabetes, non-alcoholic fatty liver disease, digestive disorders (e.g., acute and antibiotic-associated diarrhea), and allergic disorders (e.g., eczema) in infants. However, the mechanistic insight of strain-specific probiotic action is still unknown. In the present review, we analyzed the scientific state-of-the-art regarding the mechanisms of probiotic action, its physiological and immuno-modulation on the host, and new direction regarding the development of next-generation probiotics. We discuss the use of recently discovered genetic tools and their applications for engineering the probiotic bacteria for various applications including food, biomedical applications, and other health benefits. Finally, the review addresses the future development of biological techniques in combination with clinical and preclinical studies to explain the molecular mechanism of action, and discover an ideal multifunctional probiotic bacterium.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand India
| | - Afreen Shadan
- Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand India
| | - Ying Ma
- College of Resource and Environment, Southwest University, Chongqing, China
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11
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Gao X, Zhao D, Wang L, Cui Y, Wang S, Lv M, Zang F, Dai R. Proteomic Changes in Sarcoplasmic and Myofibrillar Proteins Associated with Color Stability of Ovine Muscle during Post-Mortem Storage. Foods 2021; 10:foods10122989. [PMID: 34945539 PMCID: PMC8700786 DOI: 10.3390/foods10122989] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 12/23/2022] Open
Abstract
The objective of this study was to investigate the proteomic characteristics for the sarcoplasmic and myofibrillar proteomes of M. longissimus lumborum (LL) and M. psoasmajor (PM) from Small-tailed Han Sheep. During post-mortem storage periods (1, 3, and 5 days), proteome analysis was applied to elucidate sarcoplasmic and myofibrillar protein changes in skeletal muscles with different color stability. Proteomic results revealed that the identified differentially abundant proteins were glycolytic enzymes, energy metabolism enzymes, chaperone proteins, and structural proteins. Through Pearson’s correlation analysis, a few of those identified proteins (Pyruvate kinase, Adenylate kinase isoenzyme 1, Creatine kinase M-type, and Carbonic anhydrase 3) were closely correlated to representative meat color parameters. Besides, bioinformatics analysis of differentially abundant proteins revealed that the proteins mainly participated in glycolysis and energy metabolism pathways. Some of these proteins may have the potential probability to be predictors of meat discoloration during post-mortem storage. Within the insight of proteomics, these results accumulated some basic theoretical understanding of the molecular mechanisms of meat discoloration.
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Affiliation(s)
- Xiaoguang Gao
- College of Food Science and Biology, Hebei University of Science and Technology, No. 26 Yuxiang Street, Yuhua District, Shijiazhuang 050000, China; (X.G.); (D.Z.); (L.W.); (Y.C.); (S.W.); (M.L.); (F.Z.)
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Dandan Zhao
- College of Food Science and Biology, Hebei University of Science and Technology, No. 26 Yuxiang Street, Yuhua District, Shijiazhuang 050000, China; (X.G.); (D.Z.); (L.W.); (Y.C.); (S.W.); (M.L.); (F.Z.)
| | - Lin Wang
- College of Food Science and Biology, Hebei University of Science and Technology, No. 26 Yuxiang Street, Yuhua District, Shijiazhuang 050000, China; (X.G.); (D.Z.); (L.W.); (Y.C.); (S.W.); (M.L.); (F.Z.)
| | - Yue Cui
- College of Food Science and Biology, Hebei University of Science and Technology, No. 26 Yuxiang Street, Yuhua District, Shijiazhuang 050000, China; (X.G.); (D.Z.); (L.W.); (Y.C.); (S.W.); (M.L.); (F.Z.)
| | - Shijie Wang
- College of Food Science and Biology, Hebei University of Science and Technology, No. 26 Yuxiang Street, Yuhua District, Shijiazhuang 050000, China; (X.G.); (D.Z.); (L.W.); (Y.C.); (S.W.); (M.L.); (F.Z.)
| | - Meng Lv
- College of Food Science and Biology, Hebei University of Science and Technology, No. 26 Yuxiang Street, Yuhua District, Shijiazhuang 050000, China; (X.G.); (D.Z.); (L.W.); (Y.C.); (S.W.); (M.L.); (F.Z.)
| | - Fangbo Zang
- College of Food Science and Biology, Hebei University of Science and Technology, No. 26 Yuxiang Street, Yuhua District, Shijiazhuang 050000, China; (X.G.); (D.Z.); (L.W.); (Y.C.); (S.W.); (M.L.); (F.Z.)
| | - Ruitong Dai
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, China
- Correspondence: ; Tel.: +86-010-62737547
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12
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Alonso García E, de la Fuente Ordoñez JJ, Lavilla Lerma L, Estudillo-Martínez MD, Castillo-Gutiérrez S, Benomar N, Knapp CW, Abriouel H. Transcriptomic Profile and Probiotic Properties of Lactiplantibacillus pentosus Pre-adapted to Edible Oils. Front Microbiol 2021; 12:747043. [PMID: 34721347 PMCID: PMC8553220 DOI: 10.3389/fmicb.2021.747043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, we determined whether pre-adapting Lactiplantibacillus pentosus strains, isolated from Aloreña green table olives, to vegetable-based edible oils improved their robustness and functionality; this may have great importance on their stress response during fermentation, storage, and digestion. Pre-adapting the strains to the corresponding oils significantly increased their probiotic functionality (e.g., auto-aggregation, co-aggregation with pathogens, and mucin adhesion), although results depended on the strain and the oil used for pre-adaptation. As such, we selected olive-adapted (TO) L. pentosus AP2-16, which exhibited improved functionality, and subjected it to transcriptomic profiling with the aim to understand the molecular mechanisms involved in the adaptation and the increased functionality. Global transcriptomic analysis of oil-adapted (olive or almond) and non-adapted (control) L. pentosus AP2-16 realized that 3,259 genes were expressed, with 2,779 mapped to the reference database. Comparative transcriptomic analysis showed that 125 genes (olive vs. control) and 108 genes (olive vs. almond) became significantly differentially expressed. TO L. pentosus AP2-16 responded by rerouting its metabolic pathways to balance energy production and storage, cell growth and survivability, host interactions (glycoconjugates), and other physiological features. As such, the pre-adaptation of lactobacilli with olive oil switches their transcriptional network to regulate robustness and functionality, possibly representing a novel approach toward the design and manufacture of probiotic products with improved stability and functionality.
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Affiliation(s)
- Esther Alonso García
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Juan José de la Fuente Ordoñez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Leyre Lavilla Lerma
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - María D Estudillo-Martínez
- Área de Estadística e Investigación Operativa, Departamento de Estadística e Investigación Operativa, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Sonia Castillo-Gutiérrez
- Área de Estadística e Investigación Operativa, Departamento de Estadística e Investigación Operativa, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Charles W Knapp
- Centre for Water, Environment, Sustainability and Public Health, Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, United Kingdom
| | - Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
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13
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Zhang S, Li D, Zhang X, Sun Y, Xu S, Wang X, Zhang N, Wang M, Tian H, Li C. Global transcriptomic analysis of Lactobacillus delbrueckii subsp . bulgaricus ATCC11842 reveals the role of LDB_RS05285 in the post-acidification of yogurt. Food Funct 2021; 12:9077-9086. [PMID: 34387638 DOI: 10.1039/d1fo01357b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
During the storage of yogurt, acid-resistant bacteria continue to produce lactic acid (i.e., post-acidification process), leading to undesirable taste and flavor. Many methods have been proposed to inhibit post-acidification. However, the specific genes involved during this biological process have not yet been systematically studied. Hence, herein, we assessed the culture starter Lactobacillus delbrueckii subsp. bulgaricus ATCC11842 with regards to its transcriptomes under in vitro acid- and cold-culture conditions. Through differential gene expression analysis, we screened out 69 candidate genes that persistently responded to acid with or without cold stress. qPCR was then used to determine the in situ expression levels of these candidate genes at different stages of yogurt fermentation and storage. Genes whose expression levels did not change much from the end of fermentation to the early stage of yogurt storage were more likely to be post-acidification genes, as such stability indicated that they were not affected by cold stress. LDB_RS05285 was determined to be one such gene; the overexpression of this gene showed that the increase of gene expression could reduce the acid production of the strain without affecting normal growth. Therefore, the genetic manipulation techniques that increased the expression level of the LDB_RS05285 gene might have the potential to inhibit the post-acidification of yogurt. Thus, LDB_RS05285 plays an important role in the post-acidification process and would become a new target for regulating yogurt post-acidification.
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Affiliation(s)
- Shuai Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Dongyao Li
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Xin Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Yongsheng Sun
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Sha Xu
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Xinyu Wang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Na Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China. and College of Biochemistry and Environmental Engineering, Baoding University, Baoding, Hebei, 071000, China
| | - Miaoshu Wang
- New Hope Tensun (Hebei) Dairy Co. Ltd, Baoding, Hebei, 071000, China and Hebei Technology Innovation Center of Probiotic Functional Dairy Product, Baoding, Hebei, 071000, China
| | - Hongtao Tian
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China. and National Engineering Research Center for Agriculture in Northern Mountainous Areas, Baoding, Hebei, 071000, China
| | - Chen Li
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China.
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Yin J, Song Y, Hu Y, Wang Y, Zhang B, Wang J, Ji X, Wang S. Dose-Dependent Beneficial Effects of Tryptophan and Its Derived Metabolites on Akkermansia In Vitro: A Preliminary Prospective Study. Microorganisms 2021; 9:microorganisms9071511. [PMID: 34361945 PMCID: PMC8305782 DOI: 10.3390/microorganisms9071511] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 12/14/2022] Open
Abstract
Akkermansia muciniphila, a potential probiotic, has been proven to lessen the effects of several diseases. As established, the relative abundance of Akkermansia is positively correlated with tryptophan metabolism. However, the reciprocal interaction between tryptophan and Akkemansia is still unclear. Herein, for the first time, the possible effects of tryptophan and its derived metabolites on A. muciniphila were preliminarily investigated, including growth, physiological function, and metabolism. Obtained results suggested that 0.4 g/L of tryptophan treatment could significantly promote the growth of A. muciniphila. Notably, when grown in BHI with 0.8 g/L of tryptophan, the hydrophobicity and adhesion of A. muciniphila were significantly improved, potentially due to the increase in the rate of cell division. Furthermore, A. muciniphila metabolized tryptophan to indole, indole-3-acetic acid, indole-3-carboxaldehyde, and indole-3-lactic acid. Indoles produced by gut microbiota could significantly promote the growth of A. muciniphila. These results could provide a valuable reference for future research on the relationship between tryptophan metabolism and A. muciniphila.
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Affiliation(s)
| | | | | | | | | | | | | | - Shuo Wang
- Correspondence: ; Tel.: +86-22-85358445
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15
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Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization. Proc Natl Acad Sci U S A 2021; 118:2017709118. [PMID: 33526676 PMCID: PMC8017965 DOI: 10.1073/pnas.2017709118] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The transformation of bile acids (BAs) by the gut microbiota is increasingly recognized as an important factor shaping host health. The prerequisite step of BA metabolism is carried out by bile salt hydrolases (BSHs), which are encoded by select gut and probiotic bacteria. Despite their prevalence, the utility of harboring a bsh is unclear. Here, we investigate the role of BSHs encoded by Lactobacillus acidophilus and Lactobacillus gasseri. We show that BA type and BSH substrate preferences affect in vitro and in vivo growth of both species. These findings contribute to a mechanistic understanding of bacterial survival in various BA-rich niches and inform future efforts to leverage BSHs as a therapeutic tool for manipulating the gut microbiota. Primary bile acids (BAs) are a collection of host-synthesized metabolites that shape physiology and metabolism. BAs transit the gastrointestinal tract and are subjected to a variety of chemical transformations encoded by indigenous bacteria. The resulting microbiota-derived BA pool is a mediator of host–microbiota interactions. Bacterial bile salt hydrolases (BSHs) cleave the conjugated glycine or taurine from BAs, an essential upstream step for the production of deconjugated and secondary BAs. Probiotic lactobacilli harbor a considerable number and diversity of BSHs; however, their contribution to Lactobacillus fitness and colonization remains poorly understood. Here, we define and compare the functions of multiple BSHs encoded by Lactobacillus acidophilus and Lactobacillus gasseri. Our genetic and biochemical characterization of lactobacilli BSHs lend to a model of Lactobacillus adaptation to the gut. These findings deviate from previous notions that BSHs generally promote colonization and detoxify bile. Rather, we show that BSH enzymatic preferences and the intrinsic chemical features of various BAs determine the toxicity of these molecules during Lactobacillus growth. BSHs were able to alter the Lactobacillus transcriptome in a BA-dependent manner. Finally, BSHs were able to dictate differences in bacterial competition in vitro and in vivo, defining their impact on BSH-encoding bacteria within the greater gastrointestinal tract ecosystem. This work emphasizes the importance of considering the enzymatic preferences of BSHs alongside the conjugated/deconjugated BA–bacterial interaction. These results deepen our understanding of the BA–microbiome axis and provide a framework to engineer lactobacilli with improved bile resistance and use probiotics as BA-altering therapeutics.
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16
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Roh H, Kim DH. Genotypic and Phenotypic Characterization of Highly Alkaline-Resistant Carnobacterium maltaromaticum V-Type ATPase from the Dairy Product Based on Comparative Genomics. Microorganisms 2021; 9:microorganisms9061233. [PMID: 34204143 PMCID: PMC8229585 DOI: 10.3390/microorganisms9061233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
Although Carnobacterium maltaromaticum derived from dairy products has been used as a lactic acid bacterium industrially, several studies have reported potential pathogenicity and disease outbreaks. Because strains derived from diseased fish and dairy products are considered potentially virulent and beneficial, respectively, their genotypic and phenotypic characteristics have attracted considerable attention. A genome-wide comparison of 30 genome sequences (13, 3, and 14 strains from diseased aquatic animals, dairy products, and processed food, respectively) was carried out. Additionally, one dairy and two nondairy strains were incubated in nutrient-rich (diluted liquid media) and nutrient-deficient environments (PBS) at pH 10 to compare their alkaline resistance in accordance with different nutritional environments by measuring their optical density and viable bacterial cell counts. Interestingly, only dairy strains carried 11 shared accessory genes, and 8 genes were strongly involved in the V-type ATPase gene cluster. Given that V-type ATPase contributes to resistance to alkaline pH and salts using proton motive force generated via sodium translocation across the membrane, C. maltaromaticum with a V-type ATPase might use nutrients in food under high pH. Indeed, the dairy strain carrying the V-type ATPase exhibited the highest alkaline resistance only in the nutrient-rich environment with significant upregulation of V-type ATPase expression. These results suggest that the gene cluster of V-type ATPase and increased alkaline resistance of dairy strains facilitate adaptation in the long-term ripening of alkaline dairy products.
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17
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Bagon BB, Valeriano VDV, Oh JK, Pajarillo EAB, Lee JY, Kang DK. Exoproteome Perspective on the Bile Stress Response of Lactobacillus johnsonii. Proteomes 2021; 9:proteomes9010010. [PMID: 33578796 PMCID: PMC7931105 DOI: 10.3390/proteomes9010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
Probiotics must not only exert a health-promoting effect but also be capable of adapting to the harsh environment of the gastrointestinal (GI) tract. Probiotics in the GI tract must survive the cell wall-disrupting effect of bile acids. We investigated the exoproteome of Lactobacillus johnsonii PF01 and C1-10 under bile stress. A comparative analysis revealed the similarities between the two L. johnsonii exoproteomes, as well as their different responses to bile. The large number of metabolic proteins in L. johnsonii revealed its metabolic adaptation to meet protein synthesis requirements under bile stress. In addition, cell wall modifications occurred in response to bile. Furthermore, some extracellular proteins of L. johnsonii may have moonlighting function in the presence of bile. Enolase, L-lactate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, triosephosphate isomerase, 50s ribosomal protein L7/L12, and cellobiose-specific phosphotransferase system (PTS) sugar transporter were significantly upregulated under bile stress, suggesting a leading role in the collective bile stress response of L. johnsonii from its exoproteome perspective.
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Affiliation(s)
- Bernadette B. Bagon
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea; (B.B.B.); (V.D.V.V.); (J.K.O.); (E.A.B.P.)
| | - Valerie Diane V. Valeriano
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea; (B.B.B.); (V.D.V.V.); (J.K.O.); (E.A.B.P.)
| | - Ju Kyoung Oh
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea; (B.B.B.); (V.D.V.V.); (J.K.O.); (E.A.B.P.)
| | - Edward Alain B. Pajarillo
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea; (B.B.B.); (V.D.V.V.); (J.K.O.); (E.A.B.P.)
| | - Ji Yoon Lee
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea;
| | - Dae-Kyung Kang
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea; (B.B.B.); (V.D.V.V.); (J.K.O.); (E.A.B.P.)
- Correspondence:
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18
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Taniguchi M, Nambu M, Katakura Y, Yamasaki-Yashiki S. Adhesion mechanisms of Bifidobacterium animalis subsp. lactis JCM 10602 to dietary fiber. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2021; 40:59-64. [PMID: 33520570 PMCID: PMC7817516 DOI: 10.12938/bmfh.2020-003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 09/07/2020] [Indexed: 12/18/2022]
Abstract
Adherence of probiotics to dietary fibers present in the intestinal tract may affect
adhesion to intestinal epithelial cells. The properties of the adhesion of bifidobacteria
to mucin or epithelial cells have been well studied; however, adhesion of bifidobacteria
to dietary fiber has not been investigated. The adhesion ratio of six
Bifidobacterium strains to cellulose and chitin was examined; among the
strains, Bifidobacterium animalis subsp. lactis JCM
10602 showed high adherence to both cellulose and chitin, and two strains showed high
adherence to only chitin. The ratios of adhesion of B. animalis to
cellulose and chitin were positively and negatively correlated with ionic strength,
respectively. These data suggest that hydrophobic and electrostatic interactions are
involved in the adhesion to cellulose and chitin, respectively. The adhesion ratios of the
cells in the late logarithmic phase to cellulose and chitin decreased by approximately 40%
and 70% of the cells in the early logarithmic phase, respectively. Furthermore, the
adhesion ratio to cellulose decreased with increasing bile concentration regardless of the
culture phase of the cells. On the other hand, the adhesion ratio to chitin of cells in
the early logarithmic phase decreased with increasing bile concentration; however, that of
cells in the late logarithmic phase increased slightly, suggesting that adhesins differ
depending on the culture phase. Our results indicated the importance of considering
adhesion to both dietary fibers and the intestinal mucosa when using bifidobacteria as
probiotics.
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Affiliation(s)
- Maria Taniguchi
- Chemistry, Materials and Bioengineering Major, Graduate School of Science and Engineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Minori Nambu
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Yoshio Katakura
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Shino Yamasaki-Yashiki
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
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Gao Y, Liu Y, Ma F, Sun M, Mu G, Tuo Y. Global transcriptomic and proteomics analysis of Lactobacillus plantarum Y44 response to 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress. J Proteomics 2020; 226:103903. [PMID: 32682107 DOI: 10.1016/j.jprot.2020.103903] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/23/2020] [Accepted: 07/11/2020] [Indexed: 12/22/2022]
Abstract
Our previous study demonstrated that Lactobacillus plantarum Y44 exhibited antioxidant activity. However, the physiological characteristics of L. plantarum Y44 exposure to oxidative stress was not clear. In this research, the differentially expressed proteins and genes in L. plantarum Y44 under 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress at different concentrations were studied by using integrated transcriptomic and proteomic methods. Under 100 mM AAPH stress condition, 1139 differentially expressed genes (DEGs, 546 up-regulated and 593 down-regulated) and 329 differentially expressed proteins (DEPs, 127 up-regulated and 202 down-regulated) were observed. Under 200 mM AAPH stress condition, 1526 DEGs (751 up-regulated and 775 down-regulated) and 382 DEPs (139 up-regulated and 243 down-regulated) were observed. Overall, we found that L. plantarum Y44 fought against AAPH induced oxidative stress by up-regulating antioxidant enzymes and DNA repair proteins, such as ATP-dependent DNA helicase RuvA, adenine DNA glycosylase, single-strand DNA-binding protein SSB, DNA-binding ferritin-like protein DPS, thioredoxin reductase, protein-methionine-S-oxide reductase and glutathione peroxidase. Additionally, cell envelope composition of L. plantarum Y44 was highly remodeled by accelerating peptidoglycan and teichoic-acid (LTA) biosynthesis and modulating the fatty acids (FA) composition to achieve a higher ratio of unsaturated/saturated fatty acids (UFAs/SFAs) against AAPH stress. Moreover, metabolism processes including carbohydrate metabolism, amino acid biosynthesis, and nucleotide metabolism altered to respond to AAPH-induced damage. Altogether, our findings allow us to facilitate a better understanding of L. plantarum Y44 against oxidative stress. SIGNIFICANCE: This study represents an integrated proteomic and transcriptomic analysis of Lactobacillus plantarum Y44 response to 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress. Differentially expressed proteins and genes were identified between the proteome and transcriptome of L. plantarum Y44 under different AAPH stress. AAPH-induced response of L. plantarum Y44 appears to be primarily based on ROS scavenging, DNA repair, highly remodeled cell surface and specific metabolic processes. The knowledge about these proteomes and transcriptomes provides significant insights into the oxidative stress response of Lactobacillus plantarum.
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Affiliation(s)
- Yuan Gao
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Yujun Liu
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China
| | - Fenglian Ma
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Mengying Sun
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Guangqing Mu
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China.
| | - Yanfeng Tuo
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China.
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Kelly SM, Lanigan N, O'Neill IJ, Bottacini F, Lugli GA, Viappiani A, Turroni F, Ventura M, van Sinderen D. Bifidobacterial biofilm formation is a multifactorial adaptive phenomenon in response to bile exposure. Sci Rep 2020; 10:11598. [PMID: 32665665 PMCID: PMC7360559 DOI: 10.1038/s41598-020-68179-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
In the current study, we show that biofilm formation by various strains and species belonging to Bifidobacterium, a genus that includes gut commensals with reported health-promoting activities, is induced by high concentrations of bile (0.5% (w/v) or higher) and individual bile salts (20 mM or higher), rather than by acid or osmotic stress. The transcriptomic response of a bifidobacterial prototype Bifidobacterium breve UCC2003 to such high bile concentrations was investigated and a random transposon bank of B. breve UCC2003 was screened for mutants that affect biofilm formation in order to identify genes involved in this adaptive process. Eleven mutants affected in their ability to form a biofilm were identified, while biofilm formation capacity of an insertional mutation in luxS and an exopolysaccharide (EPS) negative B. breve UCC2003 was also studied. Reduced capacity to form biofilm also caused reduced viability when exposed to porcine bile. We propose that bifidobacterial biofilm formation is an adaptive response to high concentrations of bile in order to avoid bactericidal effects of high bile concentrations in the gastrointestinal environment. Biofilm formation appears to be a multi-factorial process involving EPS production, proteins and extracellular DNA release, representing a crucial strategy in response to bile stress in order to enhance fitness in the gut environment.
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Affiliation(s)
- Sandra M Kelly
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Noreen Lanigan
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Ian J O'Neill
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Western Road, Cork, Ireland. .,APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland.
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21
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Kameda M, Abiko Y, Washio J, Tanner ACR, Kressirer CA, Mizoguchi I, Takahashi N. Sugar Metabolism of Scardovia wiggsiae, a Novel Caries-Associated Bacterium. Front Microbiol 2020; 11:479. [PMID: 32269556 PMCID: PMC7109253 DOI: 10.3389/fmicb.2020.00479] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/05/2020] [Indexed: 12/25/2022] Open
Abstract
Scardovia wiggsiae has been detected from caries in children and adolescents and has been suggested to be a caries-associated microorganism. To investigate the cariogenic potential of S. wiggsiae, we examined carbohydrate metabolism and acid productivity, the fluoride sensitivity of carbohydrate metabolism and the mechanism by which fluoride inhibits carbohydrate metabolism, and the acid sensitivity of carbohydrate metabolism in this bacterium. S. wiggsiae metabolized glucose and reduced the environmental pH to 3.5. It mainly produced acetic acid from glucose, together with small amounts of lactic and formic acid. The 50% inhibitory concentration of fluoride for acid production was 8.0 mM at pH 7.0 and 1.5 mM at pH 5.5, which were much higher than those of representative caries-associated bacteria, such as Streptococcus mutans. Metabolomic profiles showed the accumulation of 3-phosphoglycerate and a marked reduction in the pyruvate concentration in the presence of fluoride, suggesting that fluoride inhibits the latter half of glycolysis, including enolase activity. Enolase activity was inhibited by fluoride in S. wiggsiae, but it was more fluoride-tolerant than the enolase activity of S. mutans. Unlike in S. mutans, lactic acid did not inhibit acid production by S. wiggsiae at acidic pH. These results indicate that S. wiggsiae exhibits high acid production and tolerance to fluoride and lactic acid. S. wiggsiae possesses a unique metabolic pathway, the F6PPK shunt, which might allow it to avoid the lactate-formate pathway, including fluoride-sensitive enolase activity, and enable metabolic flow to the fluoride-tolerant acetate pathway. The fluoride tolerance of S. wiggsiae's enolase activity also increases the fluoride tolerance of its carbohydrate metabolism. The lactic acid tolerance of S. wiggsiae's acid production might result in S. wiggsiae having high acidogenic and aciduric potential and make it ecologically competitive in acidic environments, such as caries lesions, where lactic acid predominates.
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Affiliation(s)
- Mai Kameda
- Division of Orthodontics and Dentofacial Orthopaedics, Tohoku University Graduate School of Dentistry, Sendai, Japan
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Yuki Abiko
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Jumpei Washio
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Anne C. R. Tanner
- Forsyth Institute, Cambridge, MA, United States
- Harvard School of Dental Medicine, Boston, MA, United States
| | - Christine A. Kressirer
- Forsyth Institute, Cambridge, MA, United States
- Harvard School of Dental Medicine, Boston, MA, United States
| | - Itaru Mizoguchi
- Division of Orthodontics and Dentofacial Orthopaedics, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Nobuhiro Takahashi
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
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22
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Ali SA, Singh P, Tomar SK, Mohanty AK, Behare P. Proteomics fingerprints of systemic mechanisms of adaptation to bile in Lactobacillus fermentum. J Proteomics 2019; 213:103600. [PMID: 31805390 DOI: 10.1016/j.jprot.2019.103600] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 11/17/2019] [Accepted: 11/28/2019] [Indexed: 12/17/2022]
Abstract
Lactobacillus fermentum is a natural resident of the human GIT and is used as a probiotic. A unique property of L. fermentum is its ability to tolerate, colonize, and survive in the harsh conditions of bile, which facilitates transient colonization of the host colon. In the current study, we investigated the key mechanisms of action involved in bacterial survival in the presence of bile, using high-resolution mass spectrometry. A total of 1071 proteins were identified, among which 378 were up-regulated and 368 down-regulated by ≥2-fold (t-test, p < .05). Differentially regulated proteins comprised both intracellular and surface-exposed (i.e., membrane) proteins (p < .01, t-test for total proteome analysis; p < .05, t-test for membrane proteome analysis). These alterations strengthen the cell envelope and also mediate bile efflux by adjusting carbohydrate metabolic pathways and prevention of protein misfolding. These processes are mainly involved in the active removal of bile salts or amelioration of its adverse effects on cells. Further investigation of mRNA transcript expression levels of selected proteins by quantitative reverse transcriptase-PCR verified the proteomic data. Together, our proteomics findings reveal the roles of post-stress recovery proteins and highlight the interacting pathways responsible for bacterial cell tolerance to bile stress. BIOLOGICAL SIGNIFICANCE: Our intestinal tract is a nutrient-rich milieu crowded with up to 100 trillion (1014) of microbes. The fact that we are born germ-free describes that these microbes must colonize our intestinal tract from outside. However, their survival is also complicated because of hazardous conditions in the gut due to the presence of bile acid and others, which exerts a deleterious effect on the beneficial microbial load. While there was limited information available describing the comprehensive mechanism of survival? Furthermore, the imbalance of these micro floras leads to numerous disease conditions. It explains the need for enhanced understanding of host-microbe interactions in the colon. The present study majorly focuses on identifying "how microbes respond to environmental stressors" in this context, particularly bile acid response. This work addresses a fascinating cellular mechanism involved in the complex changes of bile induction in the microbial system; in this case, L. fermentum NCDC 605 a well established probiotic organism. In this article, we decipher the characteristic adaptation mechanism adjusted by probiotics in the harsh condition of 1.2% bile. The generated new knowledge will also improve the potential therapeutic efficacy of probiotics strains in clinical trials for patients of inflammatory bowel diseases (IBD) and related disorders.
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Affiliation(s)
- Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Haryana, India.
| | - Parul Singh
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Haryana, India
| | - Sudhir K Tomar
- National Collection of Dairy Cultures (NCDC) lab, Dairy Microbiology Division, National Dairy Research Institute, Haryana, India
| | - Ashok K Mohanty
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Haryana, India
| | - Pradip Behare
- National Collection of Dairy Cultures (NCDC) lab, Dairy Microbiology Division, National Dairy Research Institute, Haryana, India.
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23
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Manome A, Abiko Y, Kawashima J, Washio J, Fukumoto S, Takahashi N. Acidogenic Potential of Oral Bifidobacterium and Its High Fluoride Tolerance. Front Microbiol 2019; 10:1099. [PMID: 31156604 PMCID: PMC6532017 DOI: 10.3389/fmicb.2019.01099] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/30/2019] [Indexed: 12/23/2022] Open
Abstract
Bifidobacterium is frequently detected in early childhood caries and white spot lesions, indicating that it is a novel caries-associated bacterium. Bifidobacterium is known to possess a unique metabolic pathway, the “bifid shunt,” which might give it cariogenic potential by increasing its acid production. Thus, we evaluated the acid-producing activity of Bifidobacterium and its sensitivity to fluoride, a caries preventive reagent. Bifidobacterium longum, Bifidobacterium dentium, and Streptococcus mutans were used. Acid-producing activity was measured using a pH-stat in the absence and presence of fluoride under anaerobic conditions. Furthermore, metabolomic analysis was performed to elucidate the mechanism underlying the inhibitory effects of fluoride. The acid production of Bifidobacterium at pH 5.5 was as high as that seen at pH 7.0, indicating that Bifidobacterium has high cariogenic potential, although it produced less acid than S. mutans. In addition, Bifidobacterium produced acid in the absence of extracellular carbohydrates, suggesting that it can store intracellular polysaccharides. Bifidobacterium produced more acid from lactose than from glucose. Bifidobacterium mainly produced acetate, whereas S. mutans mainly produced lactate. The 50% inhibitory concentration (IC50) of fluoride for acid production was 6.0–14.2 times higher in Bifidobacterium than in S. mutans. Fluoride inhibited enolase in the glycolysis, resulting in the intracellular accumulation of 3-phosphoenolpyruvate, glucose 6-phosphate, and erythrose 4-phosphate. However, the bifid shunt provides a bypass pathway that can be used to produce acetate, suggesting that Bifidobacterium is able to metabolize carbohydrates in the presence of fluoride. It is suggested that its exclusive acetate production contributes to the pathogenesis of dental caries.
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Affiliation(s)
- Ayumi Manome
- Division of Pediatric Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan.,Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Yuki Abiko
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Junko Kawashima
- Division of Community Oral Health Science, Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Jumpei Washio
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Satoshi Fukumoto
- Division of Pediatric Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Nobuhiro Takahashi
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
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24
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Zhou L, Wang L, Tian P, Bao T, Li L, Zhao X. The LiaFSR and BsrXRS Systems Contribute to Bile Salt Resistance in Enterococcus faecium Isolates. Front Microbiol 2019; 10:1048. [PMID: 31134041 PMCID: PMC6522849 DOI: 10.3389/fmicb.2019.01048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/25/2019] [Indexed: 11/23/2022] Open
Abstract
Two-component systems (TCSs) are dominant regulating components in bacteria for responding to environmental stimuli. However, little information is available on how TCSs in Enterococcus faecium respond to bile salts - an important environmental stimulus for intestinal bacteria. In this study, the gene expression of 2 TCSs, BsrXRS and LiaFSR, was positively correlated with survival rates of different E. faecium isolates during exposure to ox gall. Moreover, gene disruptions of bsrR, bsrS, liaS, and liaR significantly reduced the survival rates of E. faecium in the presence of ox gall. Finally, EMSA results indicated that BsrR functioned as a transcription regulator for expression of its own gene as well as lipoate-protein ligase A (lplA). Additional 27 potential target genes by BsrR were revealed through in silico analyses. These findings suggest that BsrXRS and LiaFSR systems play important roles in bile salt resistance in E. faecium.
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Affiliation(s)
- Luoxiong Zhou
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Lihong Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Ping Tian
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Tingting Bao
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Lianbin Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xin Zhao
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
- Department of Animal Science, McGill University, Montreal, QC, Canada
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25
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Lu J, Cui L, Lin S, Hao L, Cao N, Yi J, Liu X, Lu L, Kang Q. Short communication: Global transcriptome analysis of Lactococcus lactis ssp. lactis in response to gradient freezing. J Dairy Sci 2019; 102:3933-3938. [PMID: 30852017 DOI: 10.3168/jds.2018-15972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/07/2019] [Indexed: 11/19/2022]
Abstract
Lactic acid bacteria are often preserved as starter cultures by freezing to extend shelf stability as well as maintain cell viability and acidification activity. Previous studies showed that the endocyte extracted from gradient-freezing pretreated cells could act as lyoprotectant in the lyophilization process of Lactococcus lactis ssp. lactis. In this study, the molecular mechanisms of L. lactis in response to gradient freezing exposure are described using high-throughput sequencing. Nineteen of 56 genes were upregulated after gradient freezing, whereas 37 genes were downregulated. Further validation results of quantitative real-time PCR experiments were consistent with the RNA sequencing. Gene Ontology (http://www.geneontology.org/) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG; https://www.genome.jp/kegg/) pathway were used to analyze the differentially expressed genes. Several pathways, such as glutathione metabolism, ATP-binding cassette transport, metabolism of cell wall and cell membrane components, and stress response-related pathways, were affected by gradient freezing. Six genes relevant to freezing stress response were selected for quantitative real-time PCR, including 3 upregulated genes (hisK, eutD, dukA) and 3 downregulated genes (als, yedF, pepN). The Gene Ontology enrichment and KEGG pathway analyses showed these genes may influence stress response-related pathways, improving the survival of the L. lactis under freezing stress. The identification of these genes deepened an understanding about their response under freezing stress, helping us find potential genes or pathways related to gradient freezing for further research on lyoprotectants.
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Affiliation(s)
- Jike Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.
| | - Lianming Cui
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Songyang Lin
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Limin Hao
- The Quartermaster Equipment Institute, Academy of Military Sciences PLA China, Beijing 100010, China
| | - Nana Cao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Juanjuan Yi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xin Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Laizheng Lu
- Zhengzhou Mindtek Biotechnology Co. Ltd., Zhengzhou, Henan 450001, China
| | - Qiaozhen Kang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.
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26
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Dynamic distribution of gallbladder microbiota in rabbit at different ages and health states. PLoS One 2019; 14:e0211828. [PMID: 30716131 PMCID: PMC6361460 DOI: 10.1371/journal.pone.0211828] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 01/22/2019] [Indexed: 12/12/2022] Open
Abstract
The internal environment of the gallbladder has been considered extremely unfavorable for bacterial growth, and the microbial profile of the gallbladder still unknown. By high-throughput sequencing of the bacterial 16S rRNA gene, we studied the microbial profile of the gallbladder from healthy rabbits before and after weaning. Moreover, we investigated the difference of microbiota between the gallbladder and gut. Our results showed that the gallbladder was dominantly populated by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria in the phylum throughout the developmental stages of rabbits. The adult rabbits showed higher species richness and exhibited higher bacterial diversity than rabbits before weaning based on the results of alpha diversity. Beta diversity analyses indicated differences in the bacterial community composition between different developmental stages. In the comparison of the gallbladder and feces, Firmicutes and Bacteroidetes were dominant in the phylum, as they were present in about 61% and 21% of the feces, respectively. Conversely, in the gallbladder, Firmicutes was the most dominant (about 41%), and Bacteroidetes and Proteobacteria were present in about 16% and 22% of the gallbladder, respectively. The Unweighted UniFrac Principal Coordinate Analysis results illustrated samples clustered into 2 categories: the gallbladder and feces. Our study might provide a foundation for knowledge on gallbladder microbiota for the first time and a basis for further studies on gallbladder and intestinal health.
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27
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28
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Xu Q, Zhai Z, An H, Yang Y, Yin J, Wang G, Ren F, Hao Y. The MarR Family Regulator BmrR Is Involved in Bile Tolerance of Bifidobacterium longum BBMN68 via Controlling the Expression of an ABC Transporter. Appl Environ Microbiol 2019; 85:e02453-18. [PMID: 30478236 PMCID: PMC6344635 DOI: 10.1128/aem.02453-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022] Open
Abstract
In order to colonize the human gastrointestinal tract and exert their beneficial effects, bifidobacteria must effectively cope with toxic bile salts in the intestine; however, the molecular mechanism underlying bile tolerance is poorly understood. In this study, heterologous expression of a MarR family transcriptional regulator, BmrR, significantly reduced the ox bile resistance of Lactococcus lactis NZ9000, suggesting that BmrR might play a role in the bile stress response. In silico analysis combined with reverse transcription-PCR assays demonstrated that bmrR was cotranscribed with bmrA and bmrB, which encoded multidrug resistance (MDR) ABC transporters. Promoter prediction and electrophoretic mobility shift assays revealed that BmrR could autoregulate the bmrRAB operon by binding to the bmr box (ATTGTTG-6nt-CAACAAT) in the promoter region. Moreover, heterologous expression of bmrA and bmrB in L. lactis yielded 20.77-fold higher tolerance to 0.10% ox bile, compared to the wild-type strain. In addition, ox bile could disrupt the DNA binding activity of BmrR as a ligand. Taken together, our findings indicate that the bmrRAB operon is autoregulated by the transcriptional regulator BmrR and ox bile serves as an inducer to activate the bile efflux transporter BmrAB in response to bile stress in Bifidobacterium longum BBMN68.IMPORTANCE Bifidobacteria are natural inhabitants of the human intestinal tract. Some bifidobacterial strains are used as probiotics in fermented dairy production because of their health-promoting effects. Following consumption, bifidobacteria colonize the lower intestinal tract, where the concentrations of bile salts remain nearly 0.05% to 2.0%. Bile salts, as detergent-like antimicrobial compounds, can cause cellular membrane disruption, protein misfolding, and DNA damage. Therefore, tolerance to physiological bile stress is indeed essential for bifidobacteria to survive and to exert probiotic effects in the gastrointestinal tract. In B. longum BBMN68, the MarR-type regulator BmrR was involved in the bile stress response by autoregulating the bmrRAB operon, and ox bile as an inducer could increase the expression of the BmrAB transporter to enhance the bile tolerance of BBMN68. Our study represents a functional analysis of the bmrRAB operon in the bile stress response, which will provide new insights into bile tolerance mechanisms in Bifidobacterium and other bacteria.
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Affiliation(s)
- Qi Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zhengyuan Zhai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Department of Food Science and Technology, University of California, Davis, Davis, California, USA
| | - Haoran An
- Center for Infectious Disease Research, Tsinghua-Peking Joint Center for Life Science, School of Medicine, Tsinghua University, Beijing, China
| | - Yang Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jia Yin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Guohong Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Fazheng Ren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Functional Dairy, Beijing, China
| | - Yanling Hao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Functional Dairy, Beijing, China
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29
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Mauras A, Chain F, Faucheux A, Ruffié P, Gontier S, Ryffel B, Butel MJ, Langella P, Bermúdez-Humarán LG, Waligora-Dupriet AJ. A New Bifidobacteria Expression SysTem (BEST) to Produce and Deliver Interleukin-10 in Bifidobacterium bifidum. Front Microbiol 2018; 9:3075. [PMID: 30622516 PMCID: PMC6308194 DOI: 10.3389/fmicb.2018.03075] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 11/29/2018] [Indexed: 12/17/2022] Open
Abstract
In the last years there has been a growing interest in the use of genetically modified bacteria to deliver molecules of therapeutic interest at mucosal surfaces. Due to the well-recognized probiotic properties of some strains, bifidobacteria represent excellent candidates for the development of live vehicles to produce and deliver heterologous proteins at mucosal surfaces. However, very few studies have considered this genus because of its complexity to be genetically manipulated. In this work, we report the development of a new Bifidobacteria Expression SysTem (BEST) allowing the production of heterologous proteins in Bifidobacterium bifidum. This system is based on: i) the broad host range plasmid pWV01, ii) a stress-inducible promoter, and iii) two different signal peptides (SPs) one issued from Lactococcus lactis (SPExp4) and issued from Bifidobacterium longum (SPBL1181). The functionality of BEST system was validated by cloning murine interleukin-10 (IL-10) and establishing the resulting plasmids (i.e., pBESTExp4:IL-10 and pBESTBL1181:IL-10) in the strain of B. bifidum BS42. We then demonstrated in vitro that recombinant B. bifidum BS42 harboring pBESTBL1181:IL-10 plasmid efficiently secreted IL-10 and that this secretion was significantly higher (sevenfold) than its counterpart B. bifidum BS42 harboring pBESTExp4:IL-10 plasmid. Finally, we validated in vivo that recombinant B. bifidum strains producing IL-10 using BEST system efficiently delivered this cytokine at mucosal surfaces and exhibit beneficial effects in a murine model of low-grade intestinal inflammation.
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Affiliation(s)
- Aurélie Mauras
- EA 4065, Ecosystème Intestinal, Probiotiques, Antibiotiques, Faculté de Pharmacie de Paris, DHU Risques et Grossesse, Université Paris Descartes, Paris, France
| | - Florian Chain
- INRA, Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Aurélie Faucheux
- EA 4065, Ecosystème Intestinal, Probiotiques, Antibiotiques, Faculté de Pharmacie de Paris, DHU Risques et Grossesse, Université Paris Descartes, Paris, France
| | - Pauline Ruffié
- INRA, Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sophie Gontier
- INRA, Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Bernhard Ryffel
- UMR 7355 CNRS, Laboratory of Experimental and Molecular Immunology and Neurogenetics, University of Orleans, Orleans, France
| | - Marie-José Butel
- EA 4065, Ecosystème Intestinal, Probiotiques, Antibiotiques, Faculté de Pharmacie de Paris, DHU Risques et Grossesse, Université Paris Descartes, Paris, France
| | - Philippe Langella
- INRA, Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Luis G Bermúdez-Humarán
- INRA, Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Anne-Judith Waligora-Dupriet
- EA 4065, Ecosystème Intestinal, Probiotiques, Antibiotiques, Faculté de Pharmacie de Paris, DHU Risques et Grossesse, Université Paris Descartes, Paris, France
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30
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Zuo F, Yu R, Xiao M, Khaskheli GB, Sun X, Ma H, Ren F, Zhang B, Chen S. Transcriptomic analysis of Bifidobacterium longum subsp. longum BBMN68 in response to oxidative shock. Sci Rep 2018; 8:17085. [PMID: 30459453 PMCID: PMC6244367 DOI: 10.1038/s41598-018-35286-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 10/18/2018] [Indexed: 02/08/2023] Open
Abstract
Bifidobacterium longum strain BBMN68 is sensitive to low concentrations of oxygen. A transcriptomic study was performed to identify candidate genes for B. longum BBMN68's response to oxygen treatment (3%, v/v). Expression of genes and pathways of B. longum BBMN68 involved in nucleotide metabolism, amino acid transport, protein turnover and chaperones increased, and that of carbohydrate metabolism, translation and biogenesis decreased to adapt to the oxidative stress. Notably, expression of two classes of ribonucleotide reductase (RNR), which are important for deoxyribonucleotide biosynthesis, was rapidly and persistently induced. First, the class Ib RNR NrdHIEF was immediately upregulated after 5 min oxygen exposure, followed by the class III RNR NrdDG, which was upregulated after 20 min of exposure. The upregulated expression of branched-chain amino acids and tetrahydrofolate biosynthesis-related genes occurred in bifidobacteria in response to oxidative stress. These change toward to compensate for DNA and protein damaged by reactive oxygen species (ROS). In addition, oxidative stress resulted in improved B. longum BBMN68 cell hydrophobicity and autoaggregation. These results provide a rich resource for our understanding of the response mechanisms to oxidative stress in bifidobacteria.
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Affiliation(s)
- Fanglei Zuo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691, Stockholm, Sweden
| | - Rui Yu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Man Xiao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Gul Bahar Khaskheli
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Xiaofei Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Huiqin Ma
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
| | - Fazheng Ren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Bing Zhang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Shangwu Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China. .,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.
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31
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Bustos AY, Font de Valdez G, Fadda S, Taranto MP. New insights into bacterial bile resistance mechanisms: the role of bile salt hydrolase and its impact on human health. Food Res Int 2018; 112:250-262. [DOI: 10.1016/j.foodres.2018.06.035] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/14/2018] [Accepted: 06/18/2018] [Indexed: 01/18/2023]
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32
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Ma X, Wang G, Zhai Z, Zhou P, Hao Y. Global Transcriptomic Analysis and Function Identification of Malolactic Enzyme Pathway of Lactobacillus paracasei L9 in Response to Bile Stress. Front Microbiol 2018; 9:1978. [PMID: 30210466 PMCID: PMC6119781 DOI: 10.3389/fmicb.2018.01978] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/06/2018] [Indexed: 12/11/2022] Open
Abstract
Tolerance to bile stress is crucial for Lactobacillus paracasei to survive in the intestinal tract and exert beneficial actions. In this work, global transcriptomic analysis revealed that 104 genes were significantly changed (log2FoldChange > 1.5, P < 0.05) in detected transcripts of L. paracasei L9 when exposed to 0.13% Ox-bile. The different expressed genes involved in various biological processes, including carbon source utilization, amino acids and peptide metabolism processes, transmembrane transport, transcription factors, and membrane proteins. It is noteworthy that gene mleS encoding malolactic enzyme (MLE) was 2.60-fold up-regulated. Meanwhile, L-malic acid was proved to enhance bile tolerance, which could be attributed to the intracellular alkalinization caused by MLE pathway. In addition, membrane vesicles were observed under bile stress, suggesting a disturbance in membrane charge without L-malic acid. Then, genetic and physiological experiments revealed that MLE pathway enhanced the bile tolerance by maintaining a membrane balance in L. paracasei L9, which will provide new insight into the molecular basis of MLE pathway involved in bile stress response in Lactic acid bacteria.
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Affiliation(s)
- Xiayin Ma
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, China Agricultural University, Beijing, China
| | - Guohong Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, China Agricultural University, Beijing, China
| | - Zhengyuan Zhai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, China Agricultural University, Beijing, China
| | - Pengyu Zhou
- Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, China Agricultural University, Beijing, China
| | - Yanling Hao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, China Agricultural University, Beijing, China
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33
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Navone L, McCubbin T, Gonzalez-Garcia RA, Nielsen LK, Marcellin E. Genome-scale model guided design of Propionibacterium for enhanced propionic acid production. Metab Eng Commun 2018; 6:1-12. [PMID: 29255672 PMCID: PMC5725212 DOI: 10.1016/j.meteno.2017.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/12/2017] [Accepted: 11/20/2017] [Indexed: 12/17/2022] Open
Abstract
Production of propionic acid by fermentation of propionibacteria has gained increasing attention in the past few years. However, biomanufacturing of propionic acid cannot compete with the current oxo-petrochemical synthesis process due to its well-established infrastructure, low oil prices and the high downstream purification costs of microbial production. Strain improvement to increase propionic acid yield is the best alternative to reduce downstream purification costs. The recent generation of genome-scale models for a number of Propionibacterium species facilitates the rational design of metabolic engineering strategies and provides a new opportunity to explore the metabolic potential of the Wood-Werkman cycle. Previous strategies for strain improvement have individually targeted acid tolerance, rate of propionate production or minimisation of by-products. Here we used the P. freudenreichii subsp. shermanii and the pan-Propionibacterium genome-scale metabolic models (GEMs) to simultaneously target these combined issues. This was achieved by focussing on strategies which yield higher energies and directly suppress acetate formation. Using P. freudenreichii subsp. shermanii, two strategies were assessed. The first tested the ability to manipulate the redox balance to favour propionate production by over-expressing the first two enzymes of the pentose-phosphate pathway (PPP), Zwf (glucose-6-phosphate 1-dehydrogenase) and Pgl (6-phosphogluconolactonase). Results showed a 4-fold increase in propionate to acetate ratio during the exponential growth phase. Secondly, the ability to enhance the energy yield from propionate production by over-expressing an ATP-dependent phosphoenolpyruvate carboxykinase (PEPCK) and sodium-pumping methylmalonyl-CoA decarboxylase (MMD) was tested, which extended the exponential growth phase. Together, these strategies demonstrate that in silico design strategies are predictive and can be used to reduce by-product formation in Propionibacterium. We also describe the benefit of carbon dioxide to propionibacteria growth, substrate conversion and propionate yield.
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Affiliation(s)
- Laura Navone
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Australia
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Australia
| | | | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, Australia
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Yahav S, Berkovich Z, Ostrov I, Reifen R, Shemesh M. Encapsulation of beneficial probiotic bacteria in extracellular matrix from biofilm-forming Bacillus subtilis. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2018; 46:974-982. [PMID: 29806505 DOI: 10.1080/21691401.2018.1476373] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Probiotics, live microbial supplements, are often incorporated into foods and beverages to provide putative health benefits. To ensure their beneficial effects, these organisms must survive processing and storage of food, its passage through the upper gastrointestinal tract (GIT), and subsequent chemical ingestion processes until they reach their target organ. However, there is considerable loss of viability of probiotic bacteria in the acidic conditions of the stomach and the high bile concentration in the small intestine. Bacillus subtilis, a spore-forming non-pathogenic bacterium, recently has gained interest in its probiotic properties; it can effectively maintain a favorable balance of microflora in the GIT. In addition, B. subtilis produces an extracellular matrix that protects it from stressful environments. We suggested that the extracellular matrix produced by B. subtilis could protect other probiotic bacteria and therefore potentially could be used as a vehicle for delivering viable probiotic cells to humans. Therefore, we developed a novel cultivation system that enables co-culturing of B. subtilis along with probiotic lactic acid bacteria (LAB) by increasing production of the extracellular matrix by B. subtilis cells. Moreover, we showed that B. subtilis improved survivability of LAB during food preparation, storage and ingestion. Therefore, we believe that the results of our study will provide a novel technique of using a natural system for preservation and delivery of probiotics to humans.
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Affiliation(s)
- Sagit Yahav
- a Department of Food Quality and Safety , Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization, Volcani Center , Rishon LeZion , Israel.,b The Robert H. Smith Faculty of Agriculture , Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem , Rehovot , Israel
| | - Zipi Berkovich
- b The Robert H. Smith Faculty of Agriculture , Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem , Rehovot , Israel
| | - Ievgeniia Ostrov
- a Department of Food Quality and Safety , Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization, Volcani Center , Rishon LeZion , Israel.,c Biofilm Research Laboratory , Hebrew University-Hadassah , Jerusalem , Israel
| | - Ram Reifen
- b The Robert H. Smith Faculty of Agriculture , Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem , Rehovot , Israel
| | - Moshe Shemesh
- a Department of Food Quality and Safety , Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization, Volcani Center , Rishon LeZion , Israel
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35
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Pérez Montoro B, Benomar N, Caballero Gómez N, Ennahar S, Horvatovich P, Knapp CW, Alonso E, Gálvez A, Abriouel H. Proteomic analysis of Lactobacillus pentosus for the identification of potential markers of adhesion and other probiotic features. Food Res Int 2018; 111:58-66. [PMID: 30007721 DOI: 10.1016/j.foodres.2018.04.072] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/25/2018] [Accepted: 04/28/2018] [Indexed: 11/19/2022]
Abstract
We analyzed the adhesion capacity to mucus of 31 Lactobacillus pentosus strains isolated from naturally fermented Aloreña green table olives using an immobilized mucin model. On the basis of their adhesive capacity to mucin, three phenotypes were selected for cell-wall protein proteomic analysis to pinpoint proteins involved in the adhesion process: the highly adhesive L. pentosus CF1-43 N (73.49% of adhesion ability), the moderately adhesive L. pentosus CF1-37 N (49.56% of adhesion ability) and the poorly adhesive L. pentosus CF2-20P (32.79% of adhesion ability). The results revealed four moonlighting proteins over-produced in the highly adhesive L. pentosus CF1-43 N, which were under/not produced in the other two L. pentosus strains (CF1-37 N and CF2-20P). These proteins were involved in glycolytic pathway (phosphoglycerate mutase and glucosamine-6-phosphate deaminase), stress response (small heat shock protein) and transcription (transcription elongation factor GreA). Furthermore, the relative fold change in gene expression analysis showed significant up-regulation of the genes coding for these four moonlighting proteins in the highly adhesive L. pentosus CF1-43 N versus the poorly adhesive L. pentosus CF2-20P and also in response to mucin for 20 h which clearly indicate the significant role of these genes in the adhesion capacity of L. pentosus. Thus, these proteins could be used as biomarkers for mucus adhesion in L. pentosus. On the other hand, mucin exposure induced other probiotic effects in L. pentosus strains, enhancing their co-aggregation ability with pathogens and possible inactivation.
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Affiliation(s)
- Beatriz Pérez Montoro
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Natacha Caballero Gómez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Said Ennahar
- Equipe de Chimie Analytique des Molécules Bio-Actives, UMR 7178, IPHC-DSA, CNRS, Université de Strasbourg, Illkirch-Graffenstaden 67400, France
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Centre for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Charles W Knapp
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Esther Alonso
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Antonio Gálvez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain.
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36
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Turroni F, Milani C, Duranti S, Ferrario C, Lugli GA, Mancabelli L, van Sinderen D, Ventura M. Bifidobacteria and the infant gut: an example of co-evolution and natural selection. Cell Mol Life Sci 2018; 75:103-118. [PMID: 28983638 PMCID: PMC11105234 DOI: 10.1007/s00018-017-2672-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut. Among the most abundant members of the infant microbiota are species belonging to the Bifidobacterium genus, which are believed to confer beneficial effects upon their host. Bifidobacteria may be acquired directly from the mother by vertical transmission and their persistence in the infant gut is associated with their saccharolytic activity toward glycans that are abundant in the infant gut. Here, we discuss the establishment of the infant gut microbiota and the contribution of bifidobacteria to this early life microbial consortium.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
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37
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Pinto E, Anselmo M, Calha M, Bottrill A, Duarte I, Andrew PW, Faleiro ML. The intestinal proteome of diabetic and control children is enriched with different microbial and host proteins. MICROBIOLOGY-SGM 2017; 163:161-174. [PMID: 28270263 DOI: 10.1099/mic.0.000412] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this study, the intestinal microbial proteome of children with established type 1 diabetes (T1D) was compared with the proteome of healthy children (Control) with the aim to identify differences in the activity of the intestinal microbiota that not only will contribute to a deeper knowledge of the functionality of the gut in these children but also may provide new approaches to improve the control of the disease. Faecal protein extracts collected from three T1D children (aged 9.3±0.6 years) and three Control children (aged 9.3±1.5 years) were analysed using a combination of 2D gel electrophoresis and spectral counting. The results evidenced markedly differences between the intestinal proteome of T1D children and the Control. The T1D microbial intestinal proteome was enriched with proteins of clostridial cluster XVa and cluster IV and Bacteroides. In contrast, the Control proteome was enriched with bifidobacterial proteins. In both groups, proteins with moonlight function were observed. Human proteins also distinguished the two groups with T1D children depleted in exocrine pancreatic enzymes.
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Affiliation(s)
- Elsa Pinto
- Faculdade de Ciências e Tecnologia, Centro de Investigação em Biomedicina, Universidade do Algarve Campus de Gambelas, 8005-139 Faro, Portugal
| | - Marisol Anselmo
- Núcleo de Diabetologia, Nutrição e Doenças Metabólicas (NDNDM) do Hospital de Faro, 8000-386 Faro, Portugal
| | - Manuela Calha
- Núcleo de Diabetologia, Nutrição e Doenças Metabólicas (NDNDM) do Hospital de Faro, 8000-386 Faro, Portugal
| | - Andrew Bottrill
- Protein and Nucleic Acid Chemistry Laboratory (PNACL), University of Leicester, Leicester LE1 7RH, UK
| | - Isabel Duarte
- Faculdade de Ciências e Tecnologia, Centro de Investigação em Biomedicina, Universidade do Algarve Campus de Gambelas, 8005-139 Faro, Portugal
| | - Peter W Andrew
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 7RH, UK
| | - Maria L Faleiro
- Faculdade de Ciências e Tecnologia, Centro de Investigação em Biomedicina, Universidade do Algarve Campus de Gambelas, 8005-139 Faro, Portugal
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38
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Proteomic analysis of food borne pathogens following the mode of action of the disinfectants based on pyridoxal oxime derivatives. Food Res Int 2017; 99:560-570. [DOI: 10.1016/j.foodres.2017.06.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/08/2017] [Accepted: 06/05/2017] [Indexed: 01/11/2023]
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39
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Chen MJ, Tang HY, Chiang ML. Effects of heat, cold, acid and bile salt adaptations on the stress tolerance and protein expression of kefir-isolated probiotic Lactobacillus kefiranofaciens M1. Food Microbiol 2017; 66:20-27. [DOI: 10.1016/j.fm.2017.03.020] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/23/2017] [Accepted: 03/28/2017] [Indexed: 01/01/2023]
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40
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Label-free quantitative proteomic analysis of Lactobacillus fermentum NCDC 400 during bile salt exposure. J Proteomics 2017; 167:36-45. [DOI: 10.1016/j.jprot.2017.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 07/19/2017] [Accepted: 08/07/2017] [Indexed: 11/20/2022]
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41
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Castro-Bravo N, Hidalgo-Cantabrana C, Rodriguez-Carvajal MA, Ruas-Madiedo P, Margolles A. Gene Replacement and Fluorescent Labeling to Study the Functional Role of Exopolysaccharides in Bifidobacterium animalis subsp. lactis. Front Microbiol 2017; 8:1405. [PMID: 28790996 PMCID: PMC5524739 DOI: 10.3389/fmicb.2017.01405] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/11/2017] [Indexed: 01/01/2023] Open
Abstract
An extracellular layer of exopolysaccharides (EPS) covers the surface of some Bifidobacterium animalis subsp. lactis strains, which could be of relevance for its probiotic performance. In order to understand the functional characteristics of B. animalis subsp. lactis, two isogenic strains that differ in their EPS-producing phenotype, due to a single mutation in the gene Balat_1410, were studied. By means of a double crossover recombination strategy, successfully used for the first time in bifidobacteria, Balat_1410 in the type strain B. animalis subsp. lactis DSM10140 was replaced by a mutated gene containing a non-synonymous mutation previously associated with the appearance of a mucoid-ropy phenotype. Nuclear magnetic resonance and SEC-MALS analyses showed that the novel strain harboring the mutation acquired a ropy phenotype, due to the production of a high molecular weight (HMW)-EPS that is not produced in the wild-type strain. Fluorescence labeling of both strains with two fluorescent proteins, m-Cherry and Green Fluorescent Protein, was achieved by expressing the corresponding genes under the control of a native selected promoter (the elongation factor Tu promoter). Remarkably, qualitative and quantitative fluorescence analyses demonstrated that the ropy strain displays a lower capability to adhere to human intestinal epithelial cells. In addition, the presence of the HMW-EPS reduced the capability of the producing strain to form biofilms upon three different abiotic surfaces. This work also highlights the fact that different EPS confer variable functional characteristics to the bifidobacterial surface, which may be relevant for the performance of B. animalis subsp. lactis as a probiotic. The construction of molecular tools allowing the functional characterization of surface structures in next generation probiotics is still a challenging issue that deserves further attention, given the relevant role that such molecules must play in the interaction with the host.
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Affiliation(s)
- Nuria Castro-Bravo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | - Claudio Hidalgo-Cantabrana
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | | | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
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42
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López M, Blasco L, Gato E, Perez A, Fernández-Garcia L, Martínez-Martinez L, Fernández-Cuenca F, Rodríguez-Baño J, Pascual A, Bou G, Tomás M. Response to Bile Salts in Clinical Strains of Acinetobacter baumannii Lacking the AdeABC Efflux Pump: Virulence Associated with Quorum Sensing. Front Cell Infect Microbiol 2017; 7:143. [PMID: 28536672 PMCID: PMC5423435 DOI: 10.3389/fcimb.2017.00143] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 04/06/2017] [Indexed: 11/17/2022] Open
Abstract
Introduction:Acinetobacter baumannii is an opportunistic nosocomial pathogen associated with multiple infections. This pathogen usually colonizes (first stage of microbial infection) host tissues that are in contact with the external environment. As one of the sites of entry in human hosts is the gastrointestinal tract, the pathogen must be capable of tolerating bile salts. However, studies analyzing the molecular characteristics involved in the response to bile salts in clinical strains of A. baumannii are scarce. Material and Methods: Microbiological and transcriptional studies (arrays and RT-PCR) in the response to bile salts were carried out in isogenic (A. baumanni ΔadeB ATCC 17978 and A. baumannii ΔadeL ATCC 17978) and clinical strains from clone ST79/PFGE-HUI-1 which is characterized by lacking the AdeABC efflux pump and by overexpression the AdeFGH efflux pump. Results and Discussion: In presence of bile salts, in addition to the glutamate/aspartate transporter were found overexpressed in A. baumannii ΔadeB ATCC 17978, the virulence factors (surface motility, biofilm, and Type VI Secretion System) which are associated with activation of the Quorum Sensing system. Overexpression of these factors was confirmed in clinical strains of clone ST79/PFGE-HUI-1. Conclusions: This the first study about the adaptive response to bile salts investigating the molecular and microbiological characteristics in response to bile salts of an isogenic model of A. baumannii ATCC 17978 and clinical isolates of A. baumannii (clinical strains of ST79/PFGE-HUI-1) lacking the main RND efflux pump (AdeABC). Clinical isolates of A. baumannii lacking the AdeABC efflux pump (clone ST79/PFGE-HUI-1) displayed a new clinical profile (increased invasiveness) possibly associated with the response to stress conditions (such as the presence of bile salts).
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Affiliation(s)
- Maria López
- Department of Microbiology, Complejo Hospitalario Universitario A Coruña-INIBICLa Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Hospital Virgen MacarenaSeville, Spain
| | - Lucia Blasco
- Department of Microbiology, Complejo Hospitalario Universitario A Coruña-INIBICLa Coruña, Spain
| | - Eva Gato
- Department of Microbiology, Complejo Hospitalario Universitario A Coruña-INIBICLa Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Hospital Virgen MacarenaSeville, Spain
| | - Astrid Perez
- Department of Microbiology, Complejo Hospitalario Universitario A Coruña-INIBICLa Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Hospital Virgen MacarenaSeville, Spain
| | - Laura Fernández-Garcia
- Department of Microbiology, Complejo Hospitalario Universitario A Coruña-INIBICLa Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Hospital Virgen MacarenaSeville, Spain
| | - Luis Martínez-Martinez
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Hospital Virgen MacarenaSeville, Spain
- Department of Clinical Microbiology, Hospital Universitario Marqués de Valdecilla-IFIMAVSantander, Spain
- Departament of Molecular Biology, University of CantabriaSantander, Spain
| | - Felipe Fernández-Cuenca
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Hospital Virgen MacarenaSeville, Spain
- Department of Microbiology and Infectious Diseases, Hospital Universitario Virgen MacarenaSeville, Spain
- Department of Medicine, Universidad de SevilleSeville, Spain
| | - Jesús Rodríguez-Baño
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Hospital Virgen MacarenaSeville, Spain
- Department of Microbiology and Infectious Diseases, Hospital Universitario Virgen MacarenaSeville, Spain
- Department of Medicine, Universidad de SevilleSeville, Spain
| | - Alvaro Pascual
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Hospital Virgen MacarenaSeville, Spain
- Department of Microbiology and Infectious Diseases, Hospital Universitario Virgen MacarenaSeville, Spain
- Department of Medicine, Universidad de SevilleSeville, Spain
| | - German Bou
- Department of Microbiology, Complejo Hospitalario Universitario A Coruña-INIBICLa Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Hospital Virgen MacarenaSeville, Spain
| | - Maria Tomás
- Department of Microbiology, Complejo Hospitalario Universitario A Coruña-INIBICLa Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015), Hospital Virgen MacarenaSeville, Spain
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43
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Heat Acclimation of Bifidobacterium longum and Proteomic Changes Behind It. Probiotics Antimicrob Proteins 2017; 9:255-261. [DOI: 10.1007/s12602-017-9251-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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44
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High-resolution mass spectrometry-based global proteomic analysis of probiotic strains Lactobacillus fermentum NCDC 400 and RS2. J Proteomics 2017; 152:121-130. [DOI: 10.1016/j.jprot.2016.10.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/22/2016] [Accepted: 10/26/2016] [Indexed: 02/07/2023]
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45
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Wei S, Bian Y, Zhao Q, Chen S, Mao J, Song C, Cheng K, Xiao Z, Zhang C, Ma W, Zou H, Ye M, Dai S. Salinity-Induced Palmella Formation Mechanism in Halotolerant Algae Dunaliella salina Revealed by Quantitative Proteomics and Phosphoproteomics. FRONTIERS IN PLANT SCIENCE 2017; 8:810. [PMID: 28588593 PMCID: PMC5441111 DOI: 10.3389/fpls.2017.00810] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/30/2017] [Indexed: 05/05/2023]
Abstract
Palmella stage is critical for some unicellular algae to survive in extreme environments. The halotolerant algae Dunaliella salina is a good single-cell model for studying plant adaptation to high salinity. To investigate the molecular adaptation mechanism in salinity shock-induced palmella formation, we performed a comprehensive physiological, proteomics and phosphoproteomics study upon palmella formation of D. salina using dimethyl labeling and Ti4+-immobilized metal ion affinity chromatography (IMAC) proteomic approaches. We found that 151 salinity-responsive proteins and 35 salinity-responsive phosphoproteins were involved in multiple signaling and metabolic pathways upon palmella formation. Taken together with photosynthetic parameters and enzyme activity analyses, the patterns of protein accumulation and phosphorylation level exhibited the mechanisms upon palmella formation, including dynamics of cytoskeleton and cell membrane curvature, accumulation and transport of exopolysaccharides, photosynthesis and energy supplying (i.e., photosystem II stability and activity, cyclic electron transport, and C4 pathway), nuclear/chloroplastic gene expression regulation and protein processing, reactive oxygen species homeostasis, and salt signaling transduction. The salinity-responsive protein-protein interaction (PPI) networks implied that signaling and protein synthesis and fate are crucial for modulation of these processes. Importantly, the 3D structure of phosphoprotein clearly indicated that the phosphorylation sites of eight proteins were localized in the region of function domain.
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Affiliation(s)
- Sijia Wei
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field, Alkali Soil Natural Environmental Science Center, Ministry of Education, Northeast Forestry UniversityHarbin, China
| | - Yangyang Bian
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of SciencesDalian, China
| | - Qi Zhao
- College of Life and Environmental Sciences, Shanghai Normal UniversityShanghai, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, Unites States
| | - Jiawei Mao
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of SciencesDalian, China
| | - Chunxia Song
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of SciencesDalian, China
| | - Kai Cheng
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of SciencesDalian, China
| | - Zhen Xiao
- College of Life and Environmental Sciences, Shanghai Normal UniversityShanghai, China
| | - Chuanfang Zhang
- College of Life and Environmental Sciences, Shanghai Normal UniversityShanghai, China
| | - Weimin Ma
- College of Life and Environmental Sciences, Shanghai Normal UniversityShanghai, China
| | - Hanfa Zou
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of SciencesDalian, China
| | - Mingliang Ye
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of SciencesDalian, China
- *Correspondence: Mingliang Ye
| | - Shaojun Dai
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field, Alkali Soil Natural Environmental Science Center, Ministry of Education, Northeast Forestry UniversityHarbin, China
- College of Life and Environmental Sciences, Shanghai Normal UniversityShanghai, China
- Shaojun Dai
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46
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Ruiz L, Hidalgo C, Blanco-Míguez A, Lourenço A, Sánchez B, Margolles A. Tackling probiotic and gut microbiota functionality through proteomics. J Proteomics 2016; 147:28-39. [DOI: 10.1016/j.jprot.2016.03.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/19/2016] [Accepted: 03/10/2016] [Indexed: 12/24/2022]
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47
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Integrated transcriptomic and proteomic analysis of the bile stress response in probiotic Lactobacillus salivarius LI01. J Proteomics 2016; 150:216-229. [PMID: 27585996 DOI: 10.1016/j.jprot.2016.08.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/24/2016] [Accepted: 08/25/2016] [Indexed: 12/11/2022]
Abstract
Lactobacillus salivarius LI01, isolated from healthy humans, has demonstrated probiotic properties in the prevention and treatment of liver failure. Tolerance to bile stress is crucial to allow lactobacilli to survive in the gastrointestinal tract and exert their benefits. In this work, we used a Digital Gene Expression transcriptomic and iTRAQ LC-MS/MS proteomic approach to examine the characteristics of LI01 in response to bile stress. Using culture medium with or without 0.15% ox bile, 591 differentially transcribed genes and 347 differentially expressed proteins were detected in LI01. Overall, we found the bile resistance of LI01 to be based on a highly remodeled cell envelope and a reinforced bile efflux system rather than on the activity of bile salt hydrolases. Additionally, some differentially expressed genes related to regulatory systems, the general stress response and central metabolism processes, also play roles in stress sensing, bile-induced damage prevention and energy efficiency. Moreover, bile salts appear to enhance proteolysis and amino acid uptake (especially aromatic amino acids) by LI01, which may support the liver protection properties of this strain. Altogether, this study establishes a model of global response mechanism to bile stress in L. salivarius LI01. BIOLOGICAL SIGNIFICANCE L. salivarius strain LI01 exhibits not only antibacterial and antifungal properties but also exerts a good health-promoting effect in acute liver failure. As a potential probiotic strain, the bile-tolerance trait of strain LI01 is important, though this has not yet been explored. In this study, an analysis based on DGE and iTRAQ was performed to investigate the gene expression in strain LI01 under bile stress at the mRNA and protein levels, respectively. To our knowledge, this work also represents the first combined transcriptomic and proteomic analysis of the bile stress response mechanism in L. salivarius.
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48
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Arboleya S, Stanton C, Ryan CA, Dempsey E, Ross PR. Bosom Buddies: The Symbiotic Relationship Between Infants and Bifidobacterium longum ssp. longum and ssp. infantis. Genetic and Probiotic Features. Annu Rev Food Sci Technol 2016; 7:1-21. [PMID: 26934170 DOI: 10.1146/annurev-food-041715-033151] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The intestinal microbiota is a complex community that plays an important role in human health from the initial steps of its establishment. Its microbial composition has been suggested to result from selective pressures imposed by the host and is modulated by competition among its members. Bifidobacterium longum is one of the most abundant species of the Bifidobacterium genus in the gut microbiota of healthy breast-fed infants and adults. The recent advancements of 'omics techniques have facilitated the genetic and functional studies of different gut microbiota members. They have revealed the complex genetic pathways used to metabolize different compounds that likely contribute to the competitiveness and persistence of B. longum in the colon. The discovery of a genomic island in B. longum ssp. infantis that encodes specific enzymes for the metabolism of human milk oligosaccharides suggests a specific ecological adaptation. Moreover, B. longum is widely used as probiotic, and beneficial effects in infant health have been reported in several studies.
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Affiliation(s)
- Silvia Arboleya
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; ,
| | - Catherine Stanton
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; ,
| | - C Anthony Ryan
- Department of Paediatrics and Child Health, University College Cork, Ireland.,Irish Centre for Fetal and Neonatal Translational Research (INFANT), Cork, Ireland; ,
| | - Eugene Dempsey
- Department of Paediatrics and Child Health, University College Cork, Ireland.,Irish Centre for Fetal and Neonatal Translational Research (INFANT), Cork, Ireland; ,
| | - Paul R Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; , .,School of Microbiology, University College Cork, Cork, Ireland;
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49
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Rios-Covián D, Sánchez B, Cuesta I, Cueto-Díaz S, Hernández-Barranco A, Gueimonde M, De los Reyes-Gavilán C. Glucolytic fingerprinting reveals metabolic groups within the genus Bifidobacterium: an exploratory study. Benef Microbes 2016; 7:265-73. [DOI: 10.3920/bm2015.0129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Microorganisms of the genus Bifidobacterium are inhabitants of diverse niches including the digestive tract of humans and animals. The species Bifidobacterium adolescentis, Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium breve and Bifidobacterium longum have qualified presumption of safety status granted by EFSA and several strains are considered probiotic, and are being included in functional dairy fermented products. In the present work we carried out a preliminary exploration of general metabolic characteristics and organic acid production profiles of a reduced number of strains selected from these and other species of the genus Bifidobacterium. The use of resting cells allowed obtaining metabolic fingerprints without interference of metabolites accumulated during growth in culture media. Acetic acid was the most abundant organic acid formed per mol of glucose consumed (from 1.07±0.03 to 1.71±0.22 mol) followed by lactic acid (from 0.34±0.06 to 0.90±0.12 mol), with moderate differences in production among strains; pyruvic, succinic and formic acids were also produced at considerably lower proportions, with variability among strains. The acetic to lactic acid ratio showed lower values in stationary phase as regard to the exponential phase for most, but not all, the microorganisms; this was due to a decrease in acetic acid molar proportions together with increases of lactic acid proportions in stationary phase. A linear discriminant analysis allowed to cluster strains into species with 51-100% probability, evidencing different metabolic profiles, according to the relative production of organic acids from glucose by resting cells, of microorganisms collected at the exponential phase of growth. Looking for a single metabolic marker that could adequately discriminate metabolic groups, we found that groups established by the acetic to lactic acid ratio fit well with differences previously evidenced by the discriminant analysis. The proper establishment of metabolic groups within the genus Bifidobacterium could help to select the best suited probiotic strains for specific applications.
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Affiliation(s)
- D. Rios-Covián
- Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - B. Sánchez
- Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - I. Cuesta
- Scientific and Technical Facilities, IPLA-CSIC, Paseo Rio Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - S. Cueto-Díaz
- Scientific and Technical Facilities, University of Oviedo, Fernando Bonguera s/n, 33006 Oviedo, Spain
| | - A.M. Hernández-Barranco
- Scientific and Technical Facilities, IPLA-CSIC, Paseo Rio Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - M. Gueimonde
- Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - C.G. De los Reyes-Gavilán
- Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300 Villaviciosa, Asturias, Spain
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50
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Rios-Covián D, Sánchez B, Martínez N, Cuesta I, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Gueimonde M. A proteomic approach towards understanding the cross talk between Bacteroides fragilis and Bifidobacterium longum in coculture. Can J Microbiol 2016; 62:623-8. [PMID: 27156738 DOI: 10.1139/cjm-2015-0804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A better understanding of the interactions among intestinal microbes is needed to decipher the complex cross talk that takes place within the human gut. Bacteroides and Bifidobacterium genera are among the most relevant intestinal bacteria, and it has been previously reported that coculturing of these 2 microorganisms affects their survival. Therefore, coculturing of Bifidobacterium longum NB667 and Bacteroides fragilis DSMZ2151 was performed with the aim of unravelling the mechanisms involved in their interaction. To this end, we applied proteomic (2D-DIGE) analyses, and by chromatographic techniques we quantified the bacterial metabolites produced during coincubation. Coculture stimulated the growth of B. longum, retarding that of B. fragilis, with concomitant changes in the production of some proteins and metabolites of both bacteria. The combined culture promoted upregulation of the bifidobacterial pyruvate kinase and downregulation of the Bacteroides phosphoenolpyruvate carboxykinase - 2 enzymes involved in the catabolism of carbohydrates. Moreover, B. fragilis FKBP-type peptidyl-prolyl cis-trans isomerase, a protein with chaperone-like activity, was found to be overproduced in coculture, suggesting the induction of a stress response in this microorganism. This study provides mechanistic data to deepen our understanding of the interaction between Bacteroides and Bifidobacterium intestinal populations.
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Affiliation(s)
- David Rios-Covián
- a Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Borja Sánchez
- a Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Noelia Martínez
- a Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Isabel Cuesta
- b Scientific and Technical Facilities, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Ana M Hernández-Barranco
- b Scientific and Technical Facilities, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Clara G de Los Reyes-Gavilán
- a Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Miguel Gueimonde
- a Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
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