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Yang Y, He J, Wang Y, Liang L, Zhang Z, Tan X, Tao S, Wu Z, Dong M, Zheng J, Zhang H, Feng S, Cheng W, Chen Q, Wei H. Whole intestinal microbiota transplantation is more effective than fecal microbiota transplantation in reducing the susceptibility of DSS-induced germ-free mice colitis. Front Immunol 2023; 14:1143526. [PMID: 37234168 PMCID: PMC10206398 DOI: 10.3389/fimmu.2023.1143526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is an emerging and effective therapy for the treatment of inflammatory bowel disease (IBD). Previous studies have reported that compared with FMT, whole intestinal microbiota transplantation (WIMT) can more precisely replicate the community structure and reduce the inflammatory response of the host. However, it remains unclear whether WIMT is more effective in alleviating IBD. To examine the efficacy of WIMT and FMT in the intervention of IBD, GF (Germ-free) BALB/c mice were pre-colonized with whole intestinal microbiota or fecal microbiota before being treated with dextran sodium sulfate (DSS). As expected, the symptoms of colitis were alleviated by both WIMT and FMT, as demonstrated by the prevention of body weight loss and decreased the Disease activity index and histological scores in mice. However, WIMT's anti-inflammatory effect was superior to that of FMT. In addition, the inflammatory markers myeloperoxidase (MPO) and eosinophil peroxidase were dramatically downregulated by WIMT and FMT. Furthermore, the use of two different types of donors facilitated the regulation of cytokine homeostasis in colitis mice; the level of the pro-inflammatory cytokine IL-1β in the WIMT group was significantly lower than that in the FMT group, while the level of the anti-inflammatory factor IL-10 was significantly higher than that in the FMT group. Both groups showed enhanced expression of occludin to protect the intestinal barrier in comparison with the DSS group, and the WIMT group demonstrated considerably increased levels of ZO-1. The sequencing results showed that the WIMT group was highly enriched in Bifidobacterium, whereas the FMT group was significantly enriched in Lactobacillus and Ochrobactrum. Correlation analysis revealed that Bifidobacterium was negatively correlated with TNF-α, whereas Ochrobactrum was positively correlated with MPO and negatively correlated with IL-10, which might be related to different efficacies. Functional prediction using PICRUSt2 revealed that the FMT group was considerably enriched in the L-arginine biosynthesis I and L-arginine biosynthesis IV pathway, whereas the WIMT group was enriched in the L-lysine fermentation to acetate and butanoate pathway. In conclusion, the symptoms of colitis were subsided to varying degrees by the two different types of donors, with the WIMT group being more effective than the FMT group. This study provides new information on clinical interventions for IBD.
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Affiliation(s)
- Yapeng Yang
- Central Laboratory, Clinical Medicine Scientific and Technical Innovation Park, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinhui He
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuqing Wang
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lifeng Liang
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zeyue Zhang
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiang Tan
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shiyu Tao
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhifeng Wu
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Miaomiao Dong
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jixia Zheng
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shuaifei Feng
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wei Cheng
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qiyi Chen
- Intestinal Microenvironment Treatment Center, Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Hong Wei
- Central Laboratory, Clinical Medicine Scientific and Technical Innovation Park, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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Ruiz-Ojeda FJ, Plaza-Diaz J, Morales J, Álvarez-Calatayud G, Climent E, Silva Á, Martinez-Blanch JF, Enrique M, Tortajada M, Ramon D, Alvarez B, Chenoll E, Gil Á. Effects of a Novel Infant Formula on the Fecal Microbiota in the First Six Months of Life: The INNOVA 2020 Study. Int J Mol Sci 2023; 24:3034. [PMID: 36769356 PMCID: PMC9917896 DOI: 10.3390/ijms24033034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Exclusive breastfeeding is highly recommended for infants for at least the first six months of life. However, for some mothers, it may be difficult or even impossible to do so. This can lead to disturbances in the gut microbiota, which in turn may be related to a higher incidence of acute infectious diseases. Here, we aimed to evaluate whether a novel starting formula versus a standard formula provides a gut microbiota composition more similar to that of breastfed infants in the first 6 months of life. Two hundred and ten infants (70/group) were enrolled in the study and completed the intervention until 12 months of age. For the intervention period, infants were divided into three groups: Group 1 received formula 1 (INN) with a lower amount of protein, a proportion of casein to whey protein ratio of about 70/30 by increasing the content of α-lactalbumin, and with double the amount of docosahexaenoic acid/arachidonic acid than the standard formula; INN also contained a thermally inactivated postbiotic (Bifidobacterium animalis subsp. lactis). Group 2 received the standard formula (STD) and the third group was exclusively breastfed (BF) for exploratory analysis. During the study, visits were made at 21 days, 2, 4, and 6 months of age, with ±3 days for the visit at 21 days of age, ±1 week for the visit at 2 months, and ±2 weeks for the others. Here, we reveal how consuming the INN formula promotes a similar gut microbiota composition to those infants that were breastfed in terms of richness and diversity, genera, such as Bacteroides, Bifidobacterium, Clostridium, and Lactobacillus, and calprotectin and short-chain fatty acid levels at 21 days, 2 and 6 months. Furthermore, we observed that the major bacteria metabolic pathways were more alike between the INN formula and BF groups compared to the STD formula group. Therefore, we assume that consumption of the novel INN formula might improve gut microbiota composition, promoting a healthier intestinal microbiota more similar to that of an infant who receives exclusively human milk.
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Affiliation(s)
- Francisco Javier Ruiz-Ojeda
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Center Munich, Neuherberg, 85764 Munich, Germany
- Institute of Nutrition and Food Technology “José Mataix”, Centre of Biomedical Research, University of Granada, Avda. del Conocimiento s/n., 18016 Armilla, Spain
| | - Julio Plaza-Diaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Javier Morales
- Product Development Department, Alter Farmacia SA, 28880 Madrid, Spain
| | | | - Eric Climent
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Ángela Silva
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | | | - María Enrique
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Marta Tortajada
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Daniel Ramon
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Beatriz Alvarez
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Empar Chenoll
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 Paterna, Spain
| | - Ángel Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix”, Centre of Biomedical Research, University of Granada, Avda. del Conocimiento s/n., 18016 Armilla, Spain
- CIBEROBN, CIBER Physiopathology of Obesity and Nutrition, Instituto de Salud Carlos III, 28029 Madrid, Spain
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Deep Learning for Rapid Identification of Microbes Using Metabolomics Profiles. Metabolites 2021; 11:metabo11120863. [PMID: 34940621 PMCID: PMC8704490 DOI: 10.3390/metabo11120863] [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: 12/03/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022] Open
Abstract
Rapid detection of viable microbes remains a challenge in fields such as microbial food safety. We here present the application of deep learning algorithms to the rapid detection of pathogenic and non-pathogenic microbes using metabolomics data. Microbes were incubated for 4 h in a protein-free defined medium, followed by 1D 1H nuclear magnetic resonance (NMR) spectroscopy measurements. NMR spectra were analyzed by spectral binning in an untargeted metabolomics approach. We trained multilayer ("deep") artificial neural networks (ANN) on the data and used the resulting models to predict spectra of unknown microbes. ANN predicted unknown microbes in this laboratory setting with an average accuracy of 99.2% when using a simple feature selection method. We also describe learning behavior of the employed ANN and the optimization strategies that worked well with these networks for our datasets. Performance was compared to other current data analysis methods, and ANN consistently scored higher than random forest models and support vector machines, highlighting the potential of deep learning in metabolomics data analysis.
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Anaerobic Growth of Listeria monocytogenes on Rhamnose Is Stimulated by Vitamin B 12 and Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization. mSphere 2021; 6:e0043421. [PMID: 34287006 PMCID: PMC8386454 DOI: 10.1128/msphere.00434-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The foodborne pathogen Listeria monocytogenes can form proteinaceous organelles called bacterial microcompartments (BMCs) that optimize the utilization of substrates, such as 1,2-propanediol, and confer an anaerobic growth advantage. Rhamnose is a deoxyhexose sugar abundant in a range of environments, including the human intestine, and can be degraded in anaerobic conditions into 1,2-propanediol, next to acetate and lactate. Rhamnose-derived 1,2-propanediol was found to link with BMCs in some human pathogens such as Salmonella enterica, but the involvement of BMCs in rhamnose metabolism and potential physiological effects on L. monocytogenes are still unknown. In this study, we first test the effect of rhamnose uptake and utilization on anaerobic growth of L. monocytogenes EGDe without or with added vitamin B12, followed by metabolic analysis. We show that vitamin B12-dependent activation of pdu stimulates metabolism and anaerobic growth of L. monocytogenes EGDe on rhamnose via 1,2-propanediol degradation into 1-propanol and propionate. Transmission electron microscopy of pdu-induced cells shows that BMCs are formed, and additional proteomics experiments confirm expression of pdu BMC shell proteins and enzymes. Finally, we discuss the physiological effects and energy efficiency of L. monocytogenespdu BMC-driven anaerobic rhamnose metabolism and the impact on competitive fitness in environments such as the human intestine. IMPORTANCEListeria monocytogenes is a foodborne pathogen causing severe illness and, as such, it is crucial to understand the molecular mechanisms contributing to its survival strategy and pathogenicity. Rhamnose is a deoxyhexose sugar abundant in a range of environments, including the human intestine, and can be degraded in anaerobic conditions into 1,2-propanediol. In our previous study, the utilization of 1,2-propanediol (pdu) in L. monocytogenes was proved to be metabolized in bacterial microcompartments (BMCs), which are self-assembling subcellular proteinaceous structures and analogs of eukaryotic organelles. Here, we show that the vitamin B12-dependent activation of pdu stimulates metabolism and anaerobic growth of L. monocytogenes EGDe on rhamnose via BMC-dependent 1,2-propanediol utilization. Combined with metabolic and proteomics analysis, our discussion on the physiological effects and energy efficiency of BMC-driven rhamnose metabolism shed new light to understand the impact on L. monocytogenes competitive fitness in ecosystems such as the human intestine.
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Dank A, Zeng Z, Boeren S, Notebaart RA, Smid EJ, Abee T. Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization of Propionibacterium freudenreichii. Front Microbiol 2021; 12:679827. [PMID: 34054787 PMCID: PMC8149966 DOI: 10.3389/fmicb.2021.679827] [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: 03/12/2021] [Accepted: 04/16/2021] [Indexed: 12/28/2022] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous prokaryotic organelles that enable the utilization of substrates such as 1,2-propanediol and ethanolamine. BMCs are mostly linked to the survival of particular pathogenic bacteria by providing a growth advantage through utilization of 1,2-propanediol and ethanolamine which are abundantly present in the human gut. Although a 1,2-propanediol utilization cluster was found in the probiotic bacterium Propionibacterium freudenreichii, BMC-mediated metabolism of 1,2-propanediol has not been demonstrated experimentally in P. freudenreichii. In this study we show that P. freudenreichii DSM 20271 metabolizes 1,2-propanediol in anaerobic conditions to propionate and 1-propanol. Furthermore, 1,2-propanediol induced the formation of BMCs, which were visualized by transmission electron microscopy and resembled BMCs found in other bacteria. Proteomic analysis of 1,2-propanediol grown cells compared to L-lactate grown cells showed significant upregulation of proteins involved in propanediol-utilization (pdu-cluster), DNA repair mechanisms and BMC shell proteins while proteins involved in oxidative phosphorylation were down-regulated. 1,2-Propanediol utilizing cells actively produced vitamin B12 (cobalamin) in similar amounts as cells growing on L-lactate. The ability to metabolize 1,2-propanediol may have implications for human gut colonization and modulation, and can potentially aid in delivering propionate and vitamin B12in situ.
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Affiliation(s)
- Alexander Dank
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Zhe Zeng
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, Netherlands
| | - Richard A Notebaart
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
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Unravelling the Molecular Mechanisms Underlying the Protective Effect of Lactate on the High-Pressure Resistance of Listeria monocytogenes. Biomolecules 2021; 11:biom11050677. [PMID: 33946460 PMCID: PMC8147161 DOI: 10.3390/biom11050677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/16/2021] [Accepted: 04/27/2021] [Indexed: 12/22/2022] Open
Abstract
Formulations with lactate as an antimicrobial and high-pressure processing (HPP) as a lethal treatment are combined strategies used to control L. monocytogenes in cooked meat products. Previous studies have shown that when HPP is applied in products with lactate, the inactivation of L. monocytogenes is lower than that without lactate. The purpose of the present work was to identify the molecular mechanisms underlying the piezo-protection effect of lactate. Two L. monocytogenes strains (CTC1034 and EGDe) were independently inoculated in a cooked ham model medium without and with 2.8% potassium lactate. Samples were pressurized at 400 MPa for 10 min at 10 °C. Samples were subjected to RNA extraction, and a shotgun transcriptome sequencing was performed. The short exposure of L. monocytogenes cells to lactate through its inoculation in a cooked ham model with lactate 1h before HPP promoted a shift in the pathogen’s central metabolism, favoring the metabolism of propanediol and ethanolamine together with the synthesis of the B12 cofactor. Moreover, the results suggest an activated methyl cycle that would promote modifications in membrane properties resulting in an enhanced resistance of the pathogen to HPP. This study provides insights on the mechanisms developed by L. monocytogenes in response to lactate and/or HPP and sheds light on the understanding of the piezo-protective effect of lactate.
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Monedeiro F, Monedeiro-Milanowski M, Ratiu IA, Brożek B, Ligor T, Buszewski B. Needle Trap Device-GC-MS for Characterization of Lung Diseases Based on Breath VOC Profiles. Molecules 2021; 26:molecules26061789. [PMID: 33810121 PMCID: PMC8004837 DOI: 10.3390/molecules26061789] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 01/08/2023] Open
Abstract
Volatile organic compounds (VOCs) have been assessed in breath samples as possible indicators of diseases. The present study aimed to quantify 29 VOCs (previously reported as potential biomarkers of lung diseases) in breath samples collected from controls and individuals with lung cancer, chronic obstructive pulmonary disease and asthma. Besides that, global VOC profiles were investigated. A needle trap device (NTD) was used as pre-concentration technique, associated to gas chromatography-mass spectrometry (GC-MS) analysis. Univariate and multivariate approaches were applied to assess VOC distributions according to the studied diseases. Limits of quantitation ranged from 0.003 to 6.21 ppbv and calculated relative standard deviations did not exceed 10%. At least 15 of the quantified targets presented themselves as discriminating features. A random forest (RF) method was performed in order to classify enrolled conditions according to VOCs' latent patterns, considering VOCs responses in global profiles. The developed model was based on 12 discriminating features and provided overall balanced accuracy of 85.7%. Ultimately, multinomial logistic regression (MLR) analysis was conducted using the concentration of the nine most discriminative targets (2-propanol, 3-methylpentane, (E)-ocimene, limonene, m-cymene, benzonitrile, undecane, terpineol, phenol) as input and provided an average overall accuracy of 95.5% for multiclass prediction.
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Affiliation(s)
- Fernanda Monedeiro
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, 4 Wileńska St., 87-100 Toruń, Poland; (F.M.); (M.M.-M.); (I.-A.R.); (B.B.)
| | - Maciej Monedeiro-Milanowski
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, 4 Wileńska St., 87-100 Toruń, Poland; (F.M.); (M.M.-M.); (I.-A.R.); (B.B.)
| | - Ileana-Andreea Ratiu
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, 4 Wileńska St., 87-100 Toruń, Poland; (F.M.); (M.M.-M.); (I.-A.R.); (B.B.)
- “Raluca Ripan” Institute for Research in Chemistry, Babeş-Bolyai University, 30 Fântânele St., RO-400294 Cluj-Napoca, Romania
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarina St., 87-100 Toruń, Poland
| | - Beata Brożek
- Department of Lung Diseases, Provincial Polyclinic Hospital in Toruń, 4 Krasińskiego St., 87-100 Toruń, Poland;
| | - Tomasz Ligor
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, 4 Wileńska St., 87-100 Toruń, Poland; (F.M.); (M.M.-M.); (I.-A.R.); (B.B.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarina St., 87-100 Toruń, Poland
- Correspondence: ; Tel.: +48-(56)-665-60-58
| | - Bogusław Buszewski
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, 4 Wileńska St., 87-100 Toruń, Poland; (F.M.); (M.M.-M.); (I.-A.R.); (B.B.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarina St., 87-100 Toruń, Poland
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Anast JM, Bobik TA, Schmitz-Esser S. The Cobalamin-Dependent Gene Cluster of Listeria monocytogenes: Implications for Virulence, Stress Response, and Food Safety. Front Microbiol 2020; 11:601816. [PMID: 33240255 PMCID: PMC7677406 DOI: 10.3389/fmicb.2020.601816] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/19/2020] [Indexed: 12/21/2022] Open
Abstract
Several genes of the eut, pdu, and cob/cbi operons are responsible for the metabolism of ethanolamine (EA) and 1,2-propanediol (PD) and are essential during the pathogenic lifecycles of various enteric pathogens. Studies concerning EA and PD metabolism have primarily focused on bacterial genera from the family Enterobacteriaceae, especially the genus Salmonella. Listeria monocytogenes is a member of the Firmicutes phylum and is the causative agent of the rare but highly fatal foodborne disease listeriosis. The eut, pdu, and cob/cbi operons are organized as a single large locus collectively referred to as the cobalamin-dependent gene cluster (CDGC). The CDGC is well conserved in L. monocytogenes; however, functional characterization of the genes in this cluster and how they may contribute to Listeria virulence and stress tolerance in food production environments is highly limited. Previous work suggests that the degradation pathway of PD is essential for L. monocytogenes establishment in the gastrointestinal tract. In contrast, EA metabolism may be more important during intracellular replication. Other studies indicate that the CDGC is utilized when L. monocytogenes is exposed to food and food production relevant stress conditions. Perhaps most noteworthy, L. monocytogenes exhibits attenuated growth at cold temperatures when a key EA utilization pathway gene was deleted. This review aims to summarize the current knowledge of these pathways in L. monocytogenes and their significance in virulence and stress tolerance, especially considering recent developments.
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Affiliation(s)
- Justin M Anast
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States.,Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Thomas A Bobik
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Stephan Schmitz-Esser
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States.,Department of Animal Science, Iowa State University, Ames, IA, United States
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Kaszoni-Rückerl I, Mustedanagic A, Muri-Klinger S, Brugger K, Wagner KH, Wagner M, Stessl B. Predominance of Distinct Listeria Innocua and Listeria Monocytogenes in Recurrent Contamination Events at Dairy Processing Facilities. Microorganisms 2020; 8:E234. [PMID: 32050536 PMCID: PMC7074772 DOI: 10.3390/microorganisms8020234] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/24/2020] [Accepted: 02/06/2020] [Indexed: 12/25/2022] Open
Abstract
: The genus Listeria now comprises up to now 21 recognized species and six subspecies, with L. monocytogenes and L. innocua as the most prevalent sensu stricto associated species. Reports focusing on the challenges in Listeria detection and confirmation are available, especially from food-associated environmental samples. L. innocua is more prevalent in the food processing environment (FPE) than L. monocytogenes and has been shown to have a growth advantage in selective enrichment and agar media. Until now, the adaptive nature of L. innocua in FPEs has not been fully elucidated and potential persistence in the FPE has not been observed. Therefore, the aim of this study is to characterize L. innocua (n = 139) and L. monocytogenes (n = 81) isolated from FPEs and cheese products collected at five dairy processing facilities (A-E) at geno- and phenotypic levels. Biochemical profiling was conducted for all L. monocytogenes and the majority of L. innocua (n = 124) isolates and included a rhamnose positive reaction. L. monocytogenes isolates were most frequently confirmed as PCR-serogroups 1/2a, 3a (95%). Pulsed-field gel electrophoresis (PFGE)-typing, applying the restriction enzymes AscI, revealed 33 distinct Listeria PFGE profiles with a Simpson's Index of Diversity of 0.75. Multi-locus sequence typing (MLST) resulted in 27 STs with seven new L. innocua local STs (ST1595 to ST1601). L. innocua ST1597 and ST603 and L. monocytogenes ST121 and ST14 were the most abundant genotypes in dairy processing facilities A-E over time. Either SSI-1 (ST14) or SSI-2 (ST121, all L. innocua) were present in successfully FPE-adapted strains. We identified housekeeping genes common in Listeria isolates and L. monocytogenes genetic lineage III. Wherever there are long-term contamination events of L. monocytogenes and other Listeria species, subtyping methods are helpful tools to identify niches of high risk.
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Affiliation(s)
- Irene Kaszoni-Rückerl
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department of Farm Animal and Public Health in Veterinary Medicine Department of Veterinary Public Health and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (I.K.-R.); (S.M.-K.); (M.W.)
- Department of Nutritional Sciences, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria;
| | - Azra Mustedanagic
- Austrian Competence Center for Feed and Food Quality, Safety and Innovation (FFOQSI), Technopark C, 3430 Tulln, Austria;
| | - Sonja Muri-Klinger
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department of Farm Animal and Public Health in Veterinary Medicine Department of Veterinary Public Health and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (I.K.-R.); (S.M.-K.); (M.W.)
| | - Katharina Brugger
- Unit of Veterinary Public Health and Epidemiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department of Farm Animal and Public Health in Veterinary Medicine Department of Veterinary Public Health and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria;
| | - Karl-Heinz Wagner
- Department of Nutritional Sciences, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria;
| | - Martin Wagner
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department of Farm Animal and Public Health in Veterinary Medicine Department of Veterinary Public Health and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (I.K.-R.); (S.M.-K.); (M.W.)
- Austrian Competence Center for Feed and Food Quality, Safety and Innovation (FFOQSI), Technopark C, 3430 Tulln, Austria;
| | - Beatrix Stessl
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department of Farm Animal and Public Health in Veterinary Medicine Department of Veterinary Public Health and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (I.K.-R.); (S.M.-K.); (M.W.)
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10
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Zeng Z, Smid EJ, Boeren S, Notebaart RA, Abee T. Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization Stimulates Anaerobic Growth of Listeria monocytogenes EGDe. Front Microbiol 2019; 10:2660. [PMID: 31803170 PMCID: PMC6873790 DOI: 10.3389/fmicb.2019.02660] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/31/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles that optimize specific metabolic pathways referred to as metabolosomes involving transient production of toxic volatile metabolites such as aldehydes. Previous bioinformatics analysis predicted the presence of BMCs in 23 bacterial phyla including foodborne pathogens and a link with gene clusters for the utilization of host-derived substrates such as 1,2-propanediol utilization, i.e., the Pdu cluster. Although, transcriptional regulation of the Pdu cluster and its role in Listeria monocytogenes virulence in animal models have recently been reported, the experimental identification and the physiological role of BMCs in L. monocytogenes is still unexplored. Here, we ask whether BMCs could enable utilization of 1,2-propanediol (Pd) in L. monocytogenes under anaerobic conditions. Using L. monocytogenes EGDe as a model strain, we could demonstrate efficient utilization of Pd with concomitant production of 1-propanol and propionate after 24 h of anaerobic growth, while the utilization was significantly reduced in aerobic conditions. In line with this, expression of genes encoding predicted shell proteins and the signature enzyme propanediol dehydratase is upregulated more than 20-fold in cells anaerobically grown in Pdu-induced versus non-induced control conditions. Additional proteomics analysis confirmed the presence of BMC shell proteins and Pdu enzymes in cells that show active degradation of Pd. Furthermore, using transmission electron microscopy, BMC structures have been detected in these cells linking gene expression, protein composition, and BMCs to activation of the Pdu cluster in anaerobic growth of L. monocytogenes. Studies in defined minimal medium with Pd as an energy source showed a significant increase in cell numbers, indicating that Pdu and the predicted generation of ATP in the conversion of propionyl-phosphate to the end product propionate can support anaerobic growth of L. monocytogenes. Our findings may suggest a role for BMC-dependent utilization of Pd in L. monocytogenes growth, transmission, and interaction with the human host.
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Affiliation(s)
- Zhe Zeng
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, Netherlands
| | - Richard A Notebaart
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Tjakko Abee
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
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11
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Wade Y, Daniel RA, Leak DJ. Heterologous Microcompartment Assembly in Bacillaceae: Establishing the Components Necessary for Scaffold Formation. ACS Synth Biol 2019; 8:1642-1654. [PMID: 31242391 DOI: 10.1021/acssynbio.9b00155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial microcompartments (BMCs) are organelles that host specific biochemical reactions for both anabolic and catabolic functions. Engineered morphologically diverse BMCs bearing heterologous enzymatic pathways have shown enhanced productivity for commodity chemicals, which makes BMCs an important focus for metabolic engineering. Gaining control of BMC assembly and incorporation of a heterologous enzymatic cargo has yet to be achieved in thermophiles. Herein, we address this by first conducting a detailed bioinformatic analysis of the propanediol utilization (pdu) operon in the thermophile Parageobacillus thermoglucosidasius. We then demonstrated, in vivo, the ability to assemble the native BMCs at an elevated temperature of 60 °C. Heterologous expression of Pdu shell proteins from P. thermoglucosidasius in Bacillus subtilis resulted in the assembly of a single tubular BMC with an average length of 1.4 μm; BMCs assembled after a 20 min induction of expression of the shell operons. Moreover, we show that it is possible to target the monomeric superfolder GFP (msfGFP) to the interior of the compartment by fusion of an N-terminal sequence of the propanediol utilization protein (PduP) of at least 24 amino acids. This study establishes the feasibility of constructing cell factories for small molecules in industrially important Bacillus and Geobacillus spp. by heterologous cargo-carrying BMC production and assembly. Additionally, the study provides experimental confirmation that BMCs are produced in thermophilic bacteria, which opens a path for future research on repurposing the native organelles to provide new functionality at elevated temperatures.
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Affiliation(s)
- Yana Wade
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle-upon-Tyne, NE2 4AX, U.K
| | - Richard A. Daniel
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle-upon-Tyne, NE2 4AX, U.K
| | - David J. Leak
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K
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12
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Liu Y, Orsi RH, Gaballa A, Wiedmann M, Boor KJ, Guariglia-Oropeza V. Systematic review of the Listeria monocytogenes σB regulon supports a role in stress response, virulence and metabolism. Future Microbiol 2019; 14:801-828. [DOI: 10.2217/fmb-2019-0072] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: Among the alternative sigma factors of Listeria monocytogenes, σB controls the largest regulon. The aim of this study was to perform a comprehensive review of σB-regulated genes, and the functions they confer. Materials & methods: A systematic search of PubMed and Web of Knowledge was carried out to identify members of the σB regulon based on experimental evidence of σB-dependent transcription and presence of a consensus σB-dependent promoter. Results: The literature review identified σB-dependent transcription units encompassing 304 genes encoding different functions including stress response and virulence. Conclusion: Our review supports the well-known roles of σB in virulence and stress response and provides new insight into novel roles for σB in metabolism and overall resilience of L. monocytogenes.
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Affiliation(s)
- Yichang Liu
- Department of Food Science, Cornell University, Ithaca, NY 14850, USA
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, NY 14850, USA
| | - Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY 14850, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14850, USA
| | - Kathryn J Boor
- Department of Food Science, Cornell University, Ithaca, NY 14850, USA
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13
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Schardt J, Jones G, Müller-Herbst S, Schauer K, D'Orazio SEF, Fuchs TM. Comparison between Listeria sensu stricto and Listeria sensu lato strains identifies novel determinants involved in infection. Sci Rep 2017; 7:17821. [PMID: 29259308 PMCID: PMC5736727 DOI: 10.1038/s41598-017-17570-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/28/2017] [Indexed: 01/01/2023] Open
Abstract
The human pathogen L. monocytogenes and the animal pathogen L. ivanovii, together with four other species isolated from symptom-free animals, form the “Listeria sensu stricto” clade. The members of the second clade, “Listeria sensu lato”, are believed to be solely environmental bacteria without the ability to colonize mammalian hosts. To identify novel determinants that contribute to infection by L. monocytogenes, the causative agent of the foodborne disease listeriosis, we performed a genome comparison of the two clades and found 151 candidate genes that are conserved in the Listeria sensu stricto species. Two factors were investigated further in vitro and in vivo. A mutant lacking an ATP-binding cassette transporter exhibited defective adhesion and invasion of human Caco-2 cells. Using a mouse model of foodborne L. monocytogenes infection, a reduced number of the mutant strain compared to the parental strain was observed in the small intestine and the liver. Another mutant with a defective 1,2-propanediol degradation pathway showed reduced persistence in the stool of infected mice, suggesting a role of 1,2-propanediol as a carbon and energy source of listeriae during infection. These findings reveal the relevance of novel factors for the colonization process of L. monocytogenes.
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Affiliation(s)
- Jakob Schardt
- ZIEL-Institute for Food & Health, and Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Grant Jones
- Department of Microbiology, Immunology, & Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
| | - Stefanie Müller-Herbst
- ZIEL-Institute for Food & Health, and Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Kristina Schauer
- Lehrstuhl für Hygiene und Technologie der Milch, Tiermedizinische Fakultät, Ludwig-Maximilians-Universität München, Schönleutner Str. 8, 85764, Oberschleißheim, Germany
| | - Sarah E F D'Orazio
- Department of Microbiology, Immunology, & Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
| | - Thilo M Fuchs
- ZIEL-Institute for Food & Health, and Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany. .,Friedrich-Loeffler-Institut, Institut für Molekulare Pathogenese, Naumburger Str. 96a, 07743, Jena, Germany.
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14
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Liu Y, Orsi RH, Boor KJ, Wiedmann M, Guariglia-Oropeza V. Home Alone: Elimination of All but One Alternative Sigma Factor in Listeria monocytogenes Allows Prediction of New Roles for σ B. Front Microbiol 2017; 8:1910. [PMID: 29075236 PMCID: PMC5641562 DOI: 10.3389/fmicb.2017.01910] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 09/19/2017] [Indexed: 11/13/2022] Open
Abstract
Among Listeria monocytogenes' four alternative σ factors, σB controls the largest regulon. As σB-dependent transcription of some genes may be masked by overlaps among regulons, and as some σB-dependent genes are expressed only under very specific conditions, we hypothesized that the σB regulon is not yet fully defined. To further extend our understanding of the σB regulon, we used RNA-seq to identify σB-dependent genes in an L. monocytogenes strain that expresses σB following rhamnose induction, and in which genes encoding the other alternative sigma factors have been deleted. Analysis of RNA-seq data with multiple bioinformatics approaches, including a sliding window method that detects differentially transcribed 5' untranslated regions (UTRs), identified 105 σB-dependent transcription units (TUs) comprising 201 genes preceded by σB-dependent promoters. Of these 105 TUs, 7 TUs comprising 15 genes had not been identified previously as σB-dependent. An additional 23 genes not reported previously as σB-dependent were identified in 9 previously recognized σB-dependent TUs. Overall, 38 of these 201 genes had not been identified previously as members of the L. monocytogenes σB regulon. These newly identified σB-dependent genes encode proteins annotated as being involved in transcriptional regulation, oxidative and osmotic stress response, and in metabolism of energy, carbon and nucleotides. In total, 18 putative σB-dependent promoters were newly identified. Interestingly, a number of genes previously identified as σB-dependent did not show significant evidence for σB-dependent transcription in our experiments. Based on promoter analyses, a number of these genes showed evidence for co-regulation by σB and other transcriptional factors, suggesting that some σB-dependent genes require additional transcriptional regulators along with σB for transcription. Over-expression of a single alternative sigma factor in the absence of all other alternative sigma factors allowed us to: (i) identify new σB-dependent functions in L. monocytogenes, such as regulation of genes involved in 1,2-propanediol utilization (LMRG_00594-LMRG_00611) and biosynthesis of pyrimidine nucleotides (LMRG_00978-LMRG_00985); and (ii) identify new σB-dependent genes involved in stress response and pathogenesis functions. These data further support that σB not only regulates stress response functions, but also plays a broad role in L. monocytogenes homeostasis and resilience.
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Affiliation(s)
- Yichang Liu
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Kathryn J Boor
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
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15
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Upadhyay A, Arsi K, Wagle BR, Upadhyaya I, Shrestha S, Donoghue AM, Donoghue DJ. Trans-Cinnamaldehyde, Carvacrol, and Eugenol Reduce Campylobacter jejuni Colonization Factors and Expression of Virulence Genes in Vitro. Front Microbiol 2017; 8:713. [PMID: 28487683 PMCID: PMC5403884 DOI: 10.3389/fmicb.2017.00713] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/06/2017] [Indexed: 11/13/2022] Open
Abstract
Campylobacter jejuni is a major foodborne pathogen that causes severe gastroenteritis in humans characterized by fever, diarrhea, and abdominal cramps. In the human gut, Campylobacter adheres and invades the intestinal epithelium followed by cytolethal distending toxin mediated cell death, and enteritis. Reducing the attachment and invasion of Campylobacter to intestinal epithelium and expression of its virulence factors such as motility and cytolethal distending toxin (CDT) production could potentially reduce infection in humans. This study investigated the efficacy of sub-inhibitory concentrations (SICs, concentration not inhibiting bacterial growth) of three GRAS (generally recognized as safe) status phytochemicals namely trans-cinnamaldehyde (TC; 0.005, 0.01%), carvacrol (CR; 0.001, 0.002%), and eugenol (EG; 0.005, 0.01%) in reducing the attachment, invasion, and translocation of C. jejuni on human intestinal epithelial cells (Caco-2). Additionally, the effect of these phytochemicals on Campylobacter motility and CDT production was studied using standard bioassays and gene expression analysis. All experiments had duplicate samples and were replicated three times on three strains (wild type S-8, NCTC 11168, 81-176) of C. jejuni. Data were analyzed using ANOVA with GraphPad ver. 6. Differences between the means were considered significantly different at P < 0.05. The majority of phytochemical treatments reduced C. jejuni adhesion, invasion, and translocation of Caco-2 cells (P < 0.05). In addition, the phytochemicals reduced pathogen motility and production of CDT in S-8 and NCTC 11168 (P < 0.05). Real-time quantitative PCR revealed that phytochemicals reduced the transcription of select C. jejuni genes critical for infection in humans (P < 0.05). Results suggest that TC, CR, and EG could potentially be used to control C. jejuni infection in humans.
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Affiliation(s)
- Abhinav Upadhyay
- Department of Poultry Science, University of ArkansasFayetteville, AR, USA
| | - Komala Arsi
- Department of Poultry Science, University of ArkansasFayetteville, AR, USA
| | - Basanta R Wagle
- Department of Poultry Science, University of ArkansasFayetteville, AR, USA
| | - Indu Upadhyaya
- Department of Poultry Science, University of ArkansasFayetteville, AR, USA
| | - Sandip Shrestha
- Department of Poultry Science, University of ArkansasFayetteville, AR, USA
| | - Ann M Donoghue
- Poultry Production and Product Safety Research Unit, Agricultural Research Service (USDA)Fayetteville, AR, USA
| | - Dan J Donoghue
- Department of Poultry Science, University of ArkansasFayetteville, AR, USA
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16
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Louis P, Flint HJ. Formation of propionate and butyrate by the human colonic microbiota. Environ Microbiol 2016; 19:29-41. [PMID: 27928878 DOI: 10.1111/1462-2920.13589] [Citation(s) in RCA: 1445] [Impact Index Per Article: 180.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/21/2016] [Indexed: 12/11/2022]
Abstract
The human gut microbiota ferments dietary non-digestible carbohydrates into short-chain fatty acids (SCFA). These microbial products are utilized by the host and propionate and butyrate in particular exert a range of health-promoting functions. Here an overview of the metabolic pathways utilized by gut microbes to produce these two SCFA from dietary carbohydrates and from amino acids resulting from protein breakdown is provided. This overview emphasizes the important role played by cross-feeding of intermediary metabolites (in particular lactate, succinate and 1,2-propanediol) between different gut bacteria. The ecophysiology, including growth requirements and responses to environmental factors, of major propionate and butyrate producing bacteria are discussed in relation to dietary modulation of these metabolites. A detailed understanding of SCFA metabolism by the gut microbiota is necessary to underpin effective strategies to optimize SCFA supply to the host.
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Affiliation(s)
- Petra Louis
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, Foresterhill, UK
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, Foresterhill, UK
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17
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Polymorphic variation in susceptibility and metabolism of triclosan-resistant mutants of Escherichia coli and Klebsiella pneumoniae clinical strains obtained after exposure to biocides and antibiotics. Antimicrob Agents Chemother 2015; 59:3413-23. [PMID: 25824225 DOI: 10.1128/aac.00187-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/21/2015] [Indexed: 01/08/2023] Open
Abstract
Exposure to biocides may result in cross-resistance to other antimicrobials. Changes in biocide and antibiotic susceptibilities, metabolism, and fitness costs were studied here in biocide-selected Escherichia coli and Klebsiella pneumoniae mutants. E. coli and K. pneumoniae mutants with various degrees of triclosan susceptibility were obtained after exposure to triclosan (TRI), benzalkonium chloride (BKC), chlorhexidine (CHX) or sodium hypochlorite (SHC), and ampicillin or ciprofloxacin. Alterations in antimicrobial susceptibility and metabolism in mutants were tested using Phenotype MicroArrays. The expression of AcrAB pump and global regulators (SoxR, MarA, and RamA) was measured by quantitative reverse transcription-PCR (qRT-PCR), and the central part of the fabI gene was sequenced. The fitness costs of resistance were assessed by a comparison of relative growth rates. Triclosan-resistant (TRI(r)) and triclosan-hypersusceptible (TRI(hs)) mutants of E. coli and K. pneumoniae were obtained after selection with biocides and/or antibiotics. E. coli TRI(r) mutants, including those with mutations in the fabI gene or in the expression of acrB, acrF, and marA, exhibited changes in susceptibility to TRI, CHX, and antibiotics. TRI(r) mutants for which the TRI MIC was high presented improved metabolism of carboxylic acids, amino acids, and carbohydrates. In TRI(r) mutants, resistance to one antimicrobial provoked hypersusceptibility to another one(s). TRI(r) mutants had fitness costs, particularly marA-overexpressing (E. coli) or ramA-overexpressing (K. pneumoniae) mutants. TRI, BKC, and CIP exposure frequently yielded TRI(r) mutants exhibiting alterations in AraC-like global regulators (MarA, SoxR, and RamA), AcrAB-TolC, and/or FabI, and influencing antimicrobial susceptibility, fitness, and metabolism. These various phenotypes suggest a trade-off of different selective processes shaping the evolution toward antibiotic/biocide resistance and influencing other adaptive traits.
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18
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Tirumalai PS. Metabolic gene expression shift by Listeria monocytogenes in coculture biofilms. Can J Microbiol 2015; 61:327-34. [PMID: 25776109 DOI: 10.1139/cjm-2014-0704] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Coculture communities of microbes are more realistic and common in nature than in laboratory-grown pure cultures. In a mixed community, when resources with a potential role in growth are shared, conflict (as a consequence of competition) or cooperation is certain. In our study, this situation of conflict and cooperation was explored to understand the population dynamics and community behavior of Listeria monocytogenes. The social behavioral response of L. monocytogenes to the presence of Bacillus subtilis was studied in terms of divergence in gene expression of L. monocytogenes. It is evident from the results that social behavior of L. monocytogenes changes from competition for survival in broth to cooperation and coexistence in biofilm. Furthermore, the gene expression pattern is clearly indicative of L. monocytogenes switching from aerobic to fermentative metabolism in broth and biofilm conditions, respectively.
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Affiliation(s)
- Prem Saran Tirumalai
- Environmental and Advanced Parasitology Laboratory, Department of Zoology, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra, India
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19
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Axen SD, Erbilgin O, Kerfeld CA. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput Biol 2014; 10:e1003898. [PMID: 25340524 PMCID: PMC4207490 DOI: 10.1371/journal.pcbi.1003898] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/09/2014] [Indexed: 01/21/2023] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found in seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful for design of genetic modules for introducing BMCs in bioengineering applications. Some enzymatic transformations have undesirable side reactions, produce toxic or volatile intermediates, or are inefficient; these shortcomings can be alleviated through their sequestration with their substrates in a confined space, as in the membrane-bound organelles of eukaryotes. Recently, it was discovered that bacteria also form organelles–bacterial microcompartments (BMCs)–composed of a protein shell that surrounds functionally related enzymes. BMCs long evaded detection because they typically form only in the presence of the substrate they metabolize, and they can only be visualized by electron microscopy. A few BMCs have been experimentally characterized; they have diverse functions in CO2 fixation, pathogenesis, and niche colonization. While the encapsulated enzymes differ among functionally distinct BMCs, the shell architecture is conserved. This enables their detection computationally, as genes for shell proteins are typically nearby genes for the encapsulated enzymes. We developed a novel algorithm to comprehensively identify and categorize BMCs in sequenced bacterial genomes. We show that BMCs are often encoded adjacent to genes that play supporting roles to the organelle's function. Our results provide the first glimpse of the extent of BMC metabolic diversity and will inform design of genetic modules encoding BMCs for introduction of new metabolic functions in a plug-and-play approach.
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Affiliation(s)
- Seth D. Axen
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Onur Erbilgin
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Cheryl A. Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
- DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Berkeley Synthetic Biology Institute, Berkeley, California, United States of America
- * E-mail: ,
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20
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Hoelzle RD, Virdis B, Batstone DJ. Regulation mechanisms in mixed and pure culture microbial fermentation. Biotechnol Bioeng 2014; 111:2139-54. [DOI: 10.1002/bit.25321] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/19/2014] [Accepted: 06/25/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Robert D. Hoelzle
- Advanced Water Management Centre; The University of Queensland; Brisbane QLD 4072 Australia
| | - Bernardino Virdis
- Advanced Water Management Centre; The University of Queensland; Brisbane QLD 4072 Australia
- Centre for Microbial Electrosynthesis; The University of Queensland; Brisbane QLD 4072 Australia
| | - Damien J. Batstone
- Advanced Water Management Centre; The University of Queensland; Brisbane QLD 4072 Australia
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21
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Saraoui T, Parayre S, Guernec G, Loux V, Montfort J, Le Cam A, Boudry G, Jan G, Falentin H. A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment. BMC Genomics 2013; 14:911. [PMID: 24365073 PMCID: PMC3880035 DOI: 10.1186/1471-2164-14-911] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 12/11/2013] [Indexed: 02/08/2023] Open
Abstract
Background Propionibacterium freudenreichii is a food grade bacterium consumed both in cheeses and in probiotic preparations. Its promising probiotic potential, relying largely on the active release of beneficial metabolites within the gut as well as the expression of key surface proteins involved in immunomodulation, deserves to be explored more deeply. Adaptation to the colon environment is requisite for the active release of propionibacterial beneficial metabolites and constitutes a bottleneck for metabolic activity in vivo. Mechanisms allowing P. freudenreichii to adapt to digestive stresses have been only studied in vitro so far. Our aim was therefore to study P. freudenreichii metabolic adaptation to intra-colonic conditions in situ. Results We maintained a pure culture of the type strain P. freudenreichii CIRM BIA 1, contained in a dialysis bag, within the colon of vigilant piglets during 24 hours. A transcriptomic analysis compared gene expression to identify the metabolic pathways induced by this environment, versus control cultures maintained in spent culture medium. We observed drastic changes in the catabolism of sugars and amino-acids. Glycolysis, the Wood-Werkman cycle and the oxidative phosphorylation pathways were down-regulated but induction of specific carbohydrate catabolisms and alternative pathways were induced to produce NADH, NADPH, ATP and precursors (utilizing of propanediol, gluconate, lactate, purine and pyrimidine and amino-acids). Genes involved in stress response were down-regulated and genes specifically expressed during cell division were induced, suggesting that P. freudenreichii adapted its metabolism to the conditions encountered in the colon. Conclusions This study constitutes the first molecular demonstration of P. freudenreichii activity and physiological adaptation in vivo within the colon. Our data are likely specific to our pig microbiota composition but opens an avenue towards understanding probiotic action within the gut in further studies comparing bacterial adaptation to different microbiota.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hélène Falentin
- INRA, UMR1253, Science et Technologie du Lait et de l'Œuf, F 35042 Rennes, France.
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Kumar V, Ashok S, Park S. Recent advances in biological production of 3-hydroxypropionic acid. Biotechnol Adv 2013; 31:945-61. [DOI: 10.1016/j.biotechadv.2013.02.008] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/13/2013] [Accepted: 02/24/2013] [Indexed: 11/16/2022]
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Fieseler L, Schmitter S, Teiserskas J, Loessner MJ. Rhamnose-inducible gene expression in Listeria monocytogenes. PLoS One 2012; 7:e43444. [PMID: 22927968 PMCID: PMC3425472 DOI: 10.1371/journal.pone.0043444] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/20/2012] [Indexed: 12/02/2022] Open
Abstract
Acid production from rhamnose is a characteristic phenotype of Listeria monocytogenes. We report the identification of the rhamnose transport and utilization operon located at lmo2846 to lmo2851, including the rhamnose-dependent promoter Prha. Expression of reporter genes under control of Prha on a single copy integration vector demonstrated its suitability for inducible gene expression in L. monocytogenes. Transcription initiation from Prha is dose dependent, and a concentration as low as 100 µM rhamnose was found sufficient for induction. Moreover, Prha is subject to glucose catabolite repression, which provides additional options for strict control of expression. Infection of human THP1 macrophages revealed that Prha is repressed in intracellular L. monocytogenes, which is explained by the absence of rhamnose in the cytosol and possible interference by catabolite repression. The Prha promoter provides a novel and useful tool for triggering gene expression in extracellular L. monocytogenes, whereas intracellular conditions prevent transcription from this promoter.
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Affiliation(s)
- Lars Fieseler
- Institute of Food, Nutrition, and Health, ETH Zurich, Zurich, Switzerland
| | - Sibylle Schmitter
- Institute of Food, Nutrition, and Health, ETH Zurich, Zurich, Switzerland
| | | | - Martin J. Loessner
- Institute of Food, Nutrition, and Health, ETH Zurich, Zurich, Switzerland
- * E-mail:
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Luo LH, Kim CH, Heo SY, Oh BR, Hong WK, Kim S, Kim DH, Seo JW. Production of 3-hydroxypropionic acid through propionaldehyde dehydrogenase PduP mediated biosynthetic pathway in Klebsiella pneumoniae. BIORESOURCE TECHNOLOGY 2012; 103:1-6. [PMID: 22018749 DOI: 10.1016/j.biortech.2011.09.099] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/20/2011] [Accepted: 09/23/2011] [Indexed: 05/31/2023]
Abstract
The pduP gene encodes a propionaldehyde dehydrogenase (PduP) was investigated for the role in 3-hydroxypropionic acid (3-HP) glycerol metabolism in Klebsiella pneumoniae. The enzyme assay showed that cell extracts from a pduP mutant strain lacked measurable dehydrogenase activity. Additionally, the mutant strain accumulated the cytotoxic intermediate metabolite 3-hydroxypropionaldehyde (3-HPA), causing both cell death and a lower final 3-HP titer. Ectopic expression of pduP restored normal cell growth to mutant. The enzymatic property of recombinant protein from Escherichia coli was examined, exhibiting a broad substrate specificity, being active on 3-HPA. The present work is thus the first to demonstrate the role of PduP in glycerol metabolism and biosynthesis of 3-HP.
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Affiliation(s)
- Lian Hua Luo
- Microbe-based Fusion Technology Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk 580-185, South Korea
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