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Chand Y, Jain T, Singh S. Unveiling a Comprehensive Multi-epitope Subunit Vaccine Strategy Against Salmonella subsp. enterica: Bridging Core, Subtractive Proteomics, and Immunoinformatics. Cell Biochem Biophys 2024:10.1007/s12013-024-01407-5. [PMID: 39018007 DOI: 10.1007/s12013-024-01407-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2024] [Indexed: 07/18/2024]
Abstract
Salmonella subsp. enterica (SE) presents a significant global health challenge in both developed and developing countries. Current SE vaccines have limitations, targeting specific strains and demonstrating moderate efficacy in adults, while also being unsuitable for young children and often unaffordable in regions with lower income levels where the disease is prevalent. To address these challenges, this study employed a computational approach integrating core proteomics, subtractive proteomics, and immunoinformatics to develop a universal SE vaccine and identify potential drug targets. Analysis of the core proteome of 185 SE strains revealed 1964 conserved proteins. Subtractive proteomics identified 9 proteins as potential vaccine candidates and 41 as novel drug targets. Using reverse vaccinology-based immunoinformatics, four multi-epitope-based subunit vaccine constructs (MESVCs) were designed, aiming to stimulate cytotoxic T lymphocyte, helper T lymphocyte, and linear B lymphocyte responses. These constructs underwent comprehensive evaluations for antigenicity, immunogenicity, toxicity, hydropathicity, and physicochemical properties. Predictive modeling, refinement, and validation were conducted to determine the secondary and tertiary structures of the SE-MESVCs, followed by docking studies with MHC-I, MHC-II, and TLR4 receptors. Molecular docking assessments showed favorable binding with all three receptors, with SE-MESVC-4 exhibiting the most promising binding energy. Molecular dynamics simulations confirmed the binding affinity and stability of SE-MESVC-4 with the TLR4/MD2 complex. Additionally, codon optimization and in silico cloning verified the efficient translation and successful expression of SE-MESVC-4 in Escherichia coli (E. coli) str. K12. Subsequent in silico immune simulation evaluated the efficacy of SE-MESVC-4 in triggering an effective immune response. These results suggest that SE-MESVC-4 may induce both humoral and cellular immune responses, making it a potential candidate for an effective SE vaccine. However, further experimental investigations are necessary to validate the immunogenicity and efficacy of SE-MESVC-4, bringing us closer to effectively combating SE infections.
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Affiliation(s)
- Yamini Chand
- Faculty of Biotechnology, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Tanvi Jain
- Faculty of Biotechnology, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Sachidanand Singh
- Department of Biotechnology, School of Energy and Technology, Pandit Deendayal Energy University, Gandhinagar, 382426, Gujarat, India.
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Prinčič L, Burtscher J, Sacken P, Krajnc T, Domig KJ. Clostridium strain FAM25158, a unique endospore-forming bacterium related to Clostridium tyrobutyricum and isolated from Emmental cheese shows low tolerance to salt. Front Microbiol 2024; 15:1353321. [PMID: 38414773 PMCID: PMC10897056 DOI: 10.3389/fmicb.2024.1353321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/30/2024] [Indexed: 02/29/2024] Open
Abstract
The genus Clostridium is a large and diverse group of species that can cause food spoilage, including late blowing defect (LBD) in cheese. In this study, we investigated the taxonomic status of strain FAM25158 isolated from Emmental cheese with LBD using a polyphasic taxonomic and comparative genomic approach. A 16S rRNA gene sequence phylogeny suggested affiliation to the Clostridium sensu stricto cluster, with Clostridium tyrobutyricum DSM 2637T being the closest related type strain (99.16% sequence similarity). Average Nucleotide Identity (ANI) analysis revealed that strain FAM25158 is at the species threshold with C. tyrobutyricum, with ANI values ranging from 94.70 to 95.26%, while the digital DNA-DNA hybridization values were below the recommended threshold, suggesting that FAM25158 is significantly different from C. tyrobutyricum at the genomic level. Moreover, comparative genomic analysis between FAM25158 and its four closest C. tyrobutyricum relatives revealed a diversity of metabolic pathways, with FAM25158 differing from other C. tyrobutyricum strains by the presence of genes such as scrA, srcB, and scrK, responsible for sucrose utilization, and the absence of many important functional genes associated with cold and osmolality adaptation, which was further supported by phenotypic analyses. Surprisingly, strain FAM25158 exhibited unique physiologic traits, such as an optimal growth temperature of 30°C, in contrast to its closest relatives, C. tyrobutyricum species with an optimal growth temperature of 37°C. Additionally, the growth of FAM25158 was inhibited at NaCl concentrations higher than 0.5%, a remarkable observation considering its origin from cheese. While the results of this study provide novel information on the genetic content of strain FAM25158, the relationship between its genetic content and the observed phenotype remains a topic requiring further investigation.
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Affiliation(s)
- Lucija Prinčič
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Johanna Burtscher
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Paul Sacken
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Tina Krajnc
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Konrad J Domig
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
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3
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Gong Z, Yang S, Zhang R, Wang Y, Wu X, Song L. Physiochemical and biological characteristics of fouling on landfill leachate treatment systems surface. J Environ Sci (China) 2024; 135:59-71. [PMID: 37778830 DOI: 10.1016/j.jes.2022.12.006] [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: 09/29/2022] [Revised: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 10/03/2023]
Abstract
Fouling of landfill leachate, a biofilm formation process on the surface of the collection system, migration pipeline and treatment system causes low efficiency of leachate transportation and treatment and increases cost for maintenance of those facilities. In addition, landfill leachate fouling might accumulate pathogens and antibiotic resistance genes (ARGs), posing threats to the environment. Characterization of the landfill leachate fouling and its associated environmental behavior is essential for the management of fouling. In this study, physicochemical and biological properties of landfill leachate fouling and the possible accumulation capacity of pathogens and ARGs were investigated in nitrification (aerobic condition) and denitrification (anaerobic condition) process during landfill leachate biological treatment, respectively. Results show that microbial (bacterial, archaeal, eukaryotic, and viral) community structure and function (carbon fixation, methanogenesis, nitrification and denitrification) differed in fouling under aerobic and anaerobic conditions, driven by the supplemental leachate water quality. Aerobic fouling had a higher abundance of nitrification and denitrification functional genes, while anaerobic fouling harbored a higher abundance of carbon fixation and methanogenesis genes. Both forms of leachate fouling had a higher abundance of pathogens and ARGs than the associated leachate, suggesting the accumulation capacity of fouling on biotic pollutants. Specifically, aerobic fouling harbored three orders of magnitude higher multidrug resistance genes mexD than its associated leachate. This finding provides fundamental knowledge on the biological properties of leachate fouling and suggests that leachate fouling might harbor significant pathogens and ARGs.
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Affiliation(s)
- Zhourui Gong
- School of resources and environmental engineering, Anhui University, Hefei 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi 247230, China
| | - Shu Yang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Rui Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Yangqing Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Xiaoqing Wu
- Xing Lu Huan Jing Co. LTD., Luzhou 646000, China
| | - Liyan Song
- School of resources and environmental engineering, Anhui University, Hefei 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi 247230, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
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Mesa V, Delannoy J, Ferraris L, Diancourt L, Mazuet C, Barbut F, Aires J. Core-genome multilocus sequence typing and core-SNP analysis of Clostridium neonatale strains isolated in different spatio-temporal settings. Microbiol Spectr 2023; 11:e0276623. [PMID: 37909758 PMCID: PMC10714970 DOI: 10.1128/spectrum.02766-23] [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: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Clostridium neonatale has been isolated from the fecal samples of asymptomatic neonates and cases of necrotizing enterocolitis (NEC). Taking advantage of a large collection of independent strains isolated from different spatio-temporal settings, we developed and established a cgMLST scheme for the molecular typing of C. neonatale. Both the cgMLST and cgSNP methods demonstrate comparable discrimination power. Results indicate geographic- and temporal- independent clustering of C. neonatale NEC-associated strains. No specific cgMLST clade of C. neonatale was genetically associated with NEC.
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Affiliation(s)
- Victoria Mesa
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Johanne Delannoy
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Laurent Ferraris
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Laure Diancourt
- Institut Pasteur, Université de Paris Cité, Centre National de Référence des Bactéries anaérobies et Botulisme, Paris, France
| | - Christelle Mazuet
- Institut Pasteur, Université de Paris Cité, Centre National de Référence des Bactéries anaérobies et Botulisme, Paris, France
| | - Frédéric Barbut
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Julio Aires
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
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Zhu M, Zhang L, Xu J, He Y. Improved understanding on biochar effect in electron supplied anaerobic soil as evidenced by dechlorination and methanogenesis processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159346. [PMID: 36228795 DOI: 10.1016/j.scitotenv.2022.159346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/03/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Research interest in biochar as an environmental remediation material has rapidly increased over the past few years. However, the effect of biochar on typical environmental processes in anaerobic soil environment has been insufficiently discussed. By regulating the electron donors with sodium acetate or pyruvate, the effects and underpinning chemical-microbiological coupling mechanisms of biochar under anaerobic conditions were disclosed. Unlike the electron limited condition, the addition of electron donors alleviated the competition for electrons among various reduction processes in the soil. The effect of biochar in regulating the electron transfer processes was lessened. But more than doubled methane emissions were resulted by the exogenous substances, especially with the synergic effect of biochar. Biochar addition increased soil environmental heterogeneity. It might indirectly affect the reductive transformation of γ-HCH via increasing the bioavailability of pollutants through adsorption and promoting the metabolism of some rare microorganisms. Anaerolineaceae, Peptococcaceae and Methanosarcina had coherent phylogenetic patterns and were likely to be the enablers for the reductive dechlorination process in flooded soil. ENVIRONMENTAL IMPLICATION: Previous studies have widely reported the performance characteristics of biochar, but its effects under anaerobic environments are not systematically understood. By regulating the electron donors, the competition for electrons among various reduction processes in the soil might be alleviated, resulting in a lessened effect of biochar in regulating the electron transfer processes. The findings presented in this study highlight the role of biochar to the dynamic changes of reduction processes under anaerobic environments. The relevant soil conditions such as the electron donors and the functional microbial groups should be adequately considered for maximizing the all-around beneficial efficiency of biochar amendments.
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Affiliation(s)
- Min Zhu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lujun Zhang
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan He
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou 310058, China.
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Socarras KM, Haslund-Gourley BS, Cramer NA, Comunale MA, Marconi RT, Ehrlich GD. Large-Scale Sequencing of Borreliaceae for the Construction of Pan-Genomic-Based Diagnostics. Genes (Basel) 2022; 13:1604. [PMID: 36140772 PMCID: PMC9498496 DOI: 10.3390/genes13091604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/03/2022] [Accepted: 09/04/2022] [Indexed: 11/16/2022] Open
Abstract
The acceleration of climate change has been associated with an alarming increase in the prevalence and geographic range of tick-borne diseases (TBD), many of which have severe and long-lasting effects-particularly when treatment is delayed principally due to inadequate diagnostics and lack of physician suspicion. Moreover, there is a paucity of treatment options for many TBDs that are complicated by diagnostic limitations for correctly identifying the offending pathogens. This review will focus on the biology, disease pathology, and detection methodologies used for the Borreliaceae family which includes the Lyme disease agent Borreliella burgdorferi. Previous work revealed that Borreliaceae genomes differ from most bacteria in that they are composed of large numbers of replicons, both linear and circular, with the main chromosome being the linear with telomeric-like termini. While these findings are novel, additional gene-specific analyses of each class of these multiple replicons are needed to better understand their respective roles in metabolism and pathogenesis of these enigmatic spirochetes. Historically, such studies were challenging due to a dearth of both analytic tools and a sufficient number of high-fidelity genomes among the various taxa within this family as a whole to provide for discriminative and functional genomic studies. Recent advances in long-read whole-genome sequencing, comparative genomics, and machine-learning have provided the tools to better understand the fundamental biology and phylogeny of these genomically-complex pathogens while also providing the data for the development of improved diagnostics and therapeutics.
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Affiliation(s)
- Kayla M. Socarras
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Benjamin S. Haslund-Gourley
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Nicholas A. Cramer
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, 1112 East Clay Street, Room 101 Health Sciences Research Building, Richmond, VA 23298, USA
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Mary Ann Comunale
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Richard T. Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, 1112 East Clay Street, Room 101 Health Sciences Research Building, Richmond, VA 23298, USA
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Garth D. Ehrlich
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, 1112 East Clay Street, Room 101 Health Sciences Research Building, Richmond, VA 23298, USA
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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Characterization of microbial communities in anaerobic acidification reactors fed with casein and/or lactose. Appl Microbiol Biotechnol 2022; 106:6301-6316. [PMID: 36008566 PMCID: PMC9468126 DOI: 10.1007/s00253-022-12132-5] [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] [Received: 04/07/2022] [Revised: 07/27/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022]
Abstract
Abstract Protein-rich agro-industrial waste streams are high in organic load and represent a major environmental problem. Anaerobic digestion is an established technology to treat these streams; however, retardation of protein degradation is frequently observed when carbohydrates are present. This study investigated the mechanism of the retardation by manipulating the carbon source fed to a complex anaerobic microbiota and linking the reactor performance to the variation of the microbial community. Two anaerobic acidification reactors were first acclimated either to casein (CAS reactor) or lactose (LAC reactor), and then fed with mixtures of casein and lactose. Results showed that when lactose was present, the microbial community acclimated to casein shifted from mainly Chloroflexi to Proteobacteria and Firmicutes, the degree of deamination in the CAS reactor decreased from 77 to 15%, and the VFA production decreased from 75 to 34% of the effluent COD. A decrease of 75% in protease activity and 90% in deamination activity of the microbiota was also observed. The microorganisms that can ferment both proteins and carbohydrates were predominant in the microbial community, and from a thermodynamical point of view, they consumed carbohydrates prior to proteins. The frequently observed negative effect of carbohydrates on protein degradation can be mainly attributed to the substrate preference of these populations. Keypoints • The presence of lactose shifted the microbial community and retarded anaerobic protein degradation. • Facultative genera were dominant in the presence and absence of lactose. • Substrate-preference caused retardation of anaerobic protein degradation. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12132-5.
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Podrzaj L, Burtscher J, Domig KJ. Comparative Genomics Provides Insights Into Genetic Diversity of Clostridium tyrobutyricum and Potential Implications for Late Blowing Defects in Cheese. Front Microbiol 2022; 13:889551. [PMID: 35722315 PMCID: PMC9201417 DOI: 10.3389/fmicb.2022.889551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
Clostridium tyrobutyricum has been recognized as the main cause of late blowing defects (LBD) in cheese leading to considerable economic losses for the dairy industry. Although differences in spoilage ability among strains of this species have been acknowledged, potential links to the genetic diversity and functional traits remain unknown. In the present study, we aimed to investigate and characterize genomic variation, pan-genomic diversity and key traits of C. tyrobutyricum by comparing the genomes of 28 strains. A comparative genomics analysis revealed an “open” pangenome comprising 9,748 genes and a core genome of 1,179 genes shared by all test strains. Among those core genes, the majority of genes encode proteins related to translation, ribosomal structure and biogenesis, energy production and conversion, and amino acid metabolism. A large part of the accessory genome is composed of sets of unique, strain-specific genes ranging from about 5 to more than 980 genes. Furthermore, functional analysis revealed several strain-specific genes related to replication, recombination and repair, cell wall, membrane and envelope biogenesis, and defense mechanisms that might facilitate survival under stressful environmental conditions. Phylogenomic analysis divided strains into two clades: clade I contained human, mud, and silage isolates, whereas clade II comprised cheese and milk isolates. Notably, these two groups of isolates showed differences in certain hypothetical proteins, transcriptional regulators and ABC transporters involved in resistance to oxidative stress. To the best of our knowledge, this is the first study to provide comparative genomics of C. tyrobutyricum strains related to LBD. Importantly, the findings presented in this study highlight the broad genetic diversity of C. tyrobutyricum, which might help us understand the diversity in spoilage potential of C. tyrobutyricum in cheese and provide some clues for further exploring the gene modules responsible for the spoilage ability of this species.
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Affiliation(s)
- Lucija Podrzaj
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Johanna Burtscher
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Konrad J Domig
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
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Bacterial communities in home-made Doushen with and without chili pepper. Food Res Int 2022; 156:111321. [PMID: 35651075 DOI: 10.1016/j.foodres.2022.111321] [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: 01/29/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/24/2022]
Abstract
Doushen is a traditional Chinese fermented soybean product prepared with sterilizated soybeans under open conditions. However, little is known on the bacterial community and their influence on the flavor of Doushen. In the present study, Doushen samples with and without chili pepper were collected to reveal the bacterial community and assess a correlation between bacterial community and VFCs in the two kinds of Doushen samples. We identified four phyla and 97 bacterial genera in the two kinds of Doushen samples. In addition, a total of 17 significantly different OTUs were detected by LEfSe (Line Discriminant Analysis (LDA) Effect Size). Results of Principal coordinates analysis (PCoA), unweighted pair-group method (UPGMA) and functional and phenotypes prediction showed that bacterial communities in the two kinds of Doushen were significantly different. Spearman correlation analysis showed that all the dominant genera, except Clostridium Sensu stricto 1, were significantly correlated with the characteristic VFCs. This study provides a theoretical basis for improving the flavour quality of traditional homemade Doushen.
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Mesa V, Monot M, Ferraris L, Popoff M, Mazuet C, Barbut F, Delannoy J, Dupuy B, Butel MJ, Aires J. Core-, pan- and accessory genome analyses of Clostridium neonatale: insights into genetic diversity. Microb Genom 2022; 8. [PMID: 35550024 PMCID: PMC9465065 DOI: 10.1099/mgen.0.000813] [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] [Indexed: 11/24/2022] Open
Abstract
Clostridium neonatale is a potential opportunistic pathogen recovered from faecal samples in cases of necrotizing enterocolitis (NEC), a gastrointestinal disease affecting preterm neonates. Although the C. neonatale species description and name validation were published in 2018, comparative genomics are lacking. In the present study, we provide the closed genome assembly of the C. neonatale ATCC BAA-265T (=250.09) reference strain with a manually curated functional annotation of the coding sequences. Pan-, core- and accessory genome analyses were performed using the complete 250.09 genome (4.7 Mb), three new assemblies (4.6–5.6 Mb), and five publicly available draft genome assemblies (4.6–4.7 Mb). The C. neonatale pan-genome contains 6840 genes, while the core-genome has 3387 genes. Pan-genome analysis revealed an ‘open’ state and genomic diversity. The strain-specific gene families ranged from five to 742 genes. Multiple mobile genetic elements were predicted, including a total of 201 genomic islands, 13 insertion sequence families, one CRISPR-Cas type I-B system and 15 predicted intact prophage signatures. Primary virulence classes including offensive, defensive, regulation of virulence-associated genes and non-specific virulence factors were identified. The presence of a tet(W/N/W) gene encoding a tetracycline resistance ribosomal protection protein and a 23S rRNA methyltransferase ermQ gene were identified in two different strains. Together, our results revealed a genetic diversity and plasticity of C. neonatale genomes and provide a comprehensive view of this species genomic features, paving the way for the characterization of its biological capabilities.
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Affiliation(s)
- Victoria Mesa
- Université de Paris, UMR-S1139, F-75006, Paris, France
| | - Marc Monot
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques, Institut Pasteur, F-75015, Paris, France.,Institut Pasteur, Université de Paris, UMR-CNRS 2001, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France
| | | | - Michel Popoff
- Institut Pasteur, Université de Paris, Centre National de Référence des Bactéries anaérobies et Botulisme, F-75015, Paris, France
| | - Christelle Mazuet
- Institut Pasteur, Université de Paris, Centre National de Référence des Bactéries anaérobies et Botulisme, F-75015, Paris, France
| | - Frederic Barbut
- Université de Paris, UMR-S1139, F-75006, Paris, France.,Assistance Publique-Hôpitaux de Paris, Hôpital saint Antoine, Infection Control Unit, F-75012, Paris, France
| | | | - Bruno Dupuy
- Institut Pasteur, Université de Paris, UMR-CNRS 2001, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France
| | | | - Julio Aires
- Université de Paris, UMR-S1139, F-75006, Paris, France
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Gut Microbiota Diversity and Overweight/Obesity in Infancy: Results from a Nested Case-control Study. Curr Med Sci 2022; 42:210-216. [PMID: 34985609 DOI: 10.1007/s11596-021-2476-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/09/2021] [Indexed: 11/03/2022]
Abstract
OBJECTIVE Childhood obesity is a major health concern worldwide. Previous studies have explored the relationship between obesity and gut microbiota. However, the results from such studies remain contradictory. METHODS In the present nested case-control study, based on a twin birth cohort study, the relationship between gut microbiota diversity and overweight/obesity in 1- and 6-month-old infants was explored. Twins were enrolled when one child had normal weight and the other child was overweight/obese at six months old. For both infants, stool samples were collected at 1 and 6 months of age. Finally, 12 twins were enrolled in the study. The gut microbiota was identified by 16S rRNA gene sequencing in the V3-V4 area. Six of the twins were monozygotic. RESULTS The results revealed that the microbiota communities of monozygotic twins were similar to those of dizygotic twins. The relative abundance (RA) of microbiota of 1-month-old twins was significantly higher than that of 6-month-old twins. However, the microbiota diversity of 1-month-old twins was significantly lower than that of 6-month-old twins. In addition, 6-month-old twins had significantly higher RA levels of Bifidobacterium and Lachnospiracea incertae sedis than 1-month-old twins. The 6-month-old group had significantly lower RA levels of Veillonella, Klebsiella, Akkermansia, Streptococcus, or Staphylococcus than the 1-month-old group. At six months, the RA level of Clostridium sensu stricto was higher in the overweight/obesity group than the normal-weight group. CONCLUSION These findings imply that changes in gut microbiota diversity during infancy may contribute to the development of obesity in early infancy.
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Pseudomonas aeruginosa Pangenome: Core and Accessory Genes of a Highly Resourceful Opportunistic Pathogen. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:3-28. [DOI: 10.1007/978-3-031-08491-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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Zou W, Ye G, Liu C, Zhang K, Li H, Yang J. Comparative genome analysis of Clostridium beijerinckii strains isolated from pit mud of Chinese strong flavor baijiu ecosystem. G3 (BETHESDA, MD.) 2021; 11:6364901. [PMID: 34542586 PMCID: PMC8527462 DOI: 10.1093/g3journal/jkab317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/26/2021] [Indexed: 12/24/2022]
Abstract
Clostridium beijerinckii is a well-known anaerobic solventogenic bacterium which inhabits a wide range of different niches. Previously, we isolated five butyrate-producing C. beijerinckii strains from pit mud (PM) of strong-flavor baijiu (SFB) ecosystems. Genome annotation of the five strains showed that they could assimilate various carbon sources as well as ammonium to produce acetate, butyrate, lactate, hydrogen, and esters but did not produce the undesirable flavors isopropanol and acetone, making them useful for further exploration in SFB production. Our analysis of the genomes of an additional 233 C. beijerinckii strains revealed an open pangenome based on current sampling and will likely change with additional genomes. The core genome, accessory genome, and strain-specific genes comprised 1567, 8851, and 2154 genes, respectively. A total of 298 genes were found only in the five C. beijerinckii strains from PM, among which only 77 genes were assigned to Clusters of Orthologous Genes categories. In addition, 15 transposase and 12 phage integrase families were found in all five C. beijerinckii strains from PM. Between 18 and 21 genome islands were predicted for the five C. beijerinckii genomes. The existence of a large number of mobile genetic elements indicated that the genomes of the five C. beijerinckii strains evolved with the loss or insertion of DNA fragments in the PM of SFB ecosystems. This study presents a genomic framework of C. beijerinckii strains from PM that could be used for genetic diversification studies and further exploration of these strains.
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Affiliation(s)
- Wei Zou
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
| | - Guangbin Ye
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
| | - Chaojie Liu
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
| | - Kaizheng Zhang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
| | - Hehe Li
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Jiangang Yang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, Sichuan 644005, China
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14
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Yang Y, Xia R, Zhang X, Wang X, Zhou Y, Wang H, Feng Y, Lv S, Ji S. Effects of Oral Exposure to Mn-Doped ZnS Quantum Dots on Intestinal Tract and Gut Microbiota in Mice. Front Physiol 2021; 12:657266. [PMID: 34295256 PMCID: PMC8290145 DOI: 10.3389/fphys.2021.657266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/27/2021] [Indexed: 11/14/2022] Open
Abstract
Mn-doped ZnS quantum dots (QDs) with excellent optical properties have been explored in a wide range of fields. Their potential adverse effects on biological systems and human health should be evaluated before biological application. In the present study, we investigated the effect of Mn-doped ZnS QDs on the intestinal tract and gut microbiota structures at 2 h and 14 days (d) after 14 d repeated oral exposure in mice. Flame atomic absorption spectrophotometry (FAAS), histopathological examination, and transmission electron microscopy (TEM) were used to assess the absorption and toxicity of Mn-doped ZnS QDs on the intestinal tract. The 16S rRNA gene sequencing was used to evaluate the gut microbial communities. Mn-doped ZnS QDs did not accumulate in the duodenum, jejunum, ileum, or colon. The Zn content of feces was not significantly higher than in the control group. No major histological changes were found in these tissues. The intestinal microvilli remained regular, but swelling of mitochondria and endoplasmic reticulum was detected by TEM at 14 d after the last gavage. A total of 2,712 operational taxonomic units (OTUs) were generated. Mn-doped ZnS QDs treatment did not significantly change the α-diversity of Richness, Chao1, Shannon, and Simpson indexes. According to principal component analysis (PCA), Mn-doped ZnS QDs had no effect on the overall structure of the gut microbiota. No significant change occurred at the phylum level, while three genera were downregulated at 2 h and seven changed at 14 d after the last gavage. Our findings revealed that Mn-doped ZnS QDs had a little stimulation of the intestinal tract and gut microbiota, and oral administration may be a safe route for biological application (such as bioimaging and drug delivery).
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Affiliation(s)
- Yanjie Yang
- Institute of Molecular Medicine, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Ruixue Xia
- Institute of Molecular Medicine, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Xiaomei Zhang
- Institute of Molecular Medicine, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Xu Wang
- Institute of Molecular Medicine, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yuchen Zhou
- Institute of Molecular Medicine, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Honggang Wang
- Institute of Molecular Medicine, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yu Feng
- Institute of Molecular Medicine, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Shuangyu Lv
- Institute of Molecular Medicine, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Shaoping Ji
- Institute of Molecular Medicine, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
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15
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Feng Y, Duan JL, Sun XD, Ma JY, Wang Q, Li XY, Tian WX, Wang SG, Yuan XZ. Insights on the inhibition of anaerobic digestion performances under short-term exposure of metal-doped nanoplastics via Methanosarcina acetivorans. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 275:115755. [PMID: 33582639 DOI: 10.1016/j.envpol.2020.115755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/16/2020] [Accepted: 09/28/2020] [Indexed: 06/12/2023]
Abstract
Anaerobic digestion is an attractive waste treatment technology, achieving both pollution control and energy recovery. Though the inhibition of polystyrene nanoplastics in anaerobic granular sludge is well studied, no direct evidence has been found on the interaction of methanogens and nanoplastics. In this study, to characterize the location of nanoplastics, Pd-doped polystyrene nanoplastics (Pd-PS) were used to explore the inhibition mechanism of anaerobic sludge through short-term exposure to Methanosarcina acetivorans C2A. The results showed that Pd-PS inhibited the methanogenesis of the anaerobic sludge, and the methane production decreased as the Pd-PS increased, with a 14.29% reduction at the Pd-PS concentration of 2.36 × 1010 particles/mL. Also, Pd-PS interacted with the protein in the extracellular polymeric substances (EPS). Furthermore, Pd-PS inhibited the methanogenesis of M. acetivorans C2A without exhibiting an evident reduction in the growth. The inhibition of Pd-PS on methane was due to the inhibition of methane production related genes, MtaA and mcrA. These results provide potential explication for the inhibition of nanoplastics on the methanogens, which will fulfill the knowledge on the stability of methanogens under the short-term exposure of nanoplastics.
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Affiliation(s)
- Yue Feng
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, PR China; College of Mining and Safety Engineering, Shandong University of Science and Technology, Qingdao, Shandong, 266590, China
| | - Jian-Lu Duan
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, PR China
| | - Xiao-Dong Sun
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, PR China
| | - Jing-Ya Ma
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, PR China
| | - Qian Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, PR China
| | - Xiang-Yu Li
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, PR China
| | - Wei-Xuan Tian
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, PR China
| | - Shu-Guang Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, PR China
| | - Xian-Zheng Yuan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, PR China.
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16
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Rosselli R, La Porta N, Muresu R, Stevanato P, Concheri G, Squartini A. Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity. Microorganisms 2021; 9:microorganisms9020407. [PMID: 33669391 PMCID: PMC7920277 DOI: 10.3390/microorganisms9020407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/16/2022] Open
Abstract
Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N2 into ammonia (nitrogen-fixation). The pangenome of 12 nitrogen-fixing plant symbionts of the Rhizobiales was analyzed yielding total 37,364 loci, with a core genome constituting 700 genes. The percentage of core genes averaged 10.2% over single genomes, and between 5% to 7% were found to be plasmid-associated. The comparison between a representative reference genome and the core genome subset, showed the core genome highly enriched in genes for macromolecule metabolism, ribosomal constituents and overall translation machinery, while membrane/periplasm-associated genes, and transport domains resulted under-represented. The analysis of protein functions revealed that between 1.7% and 4.9% of core proteins could putatively have different functions.
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Affiliation(s)
- Riccardo Rosselli
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research, NL-1790 AB Den Burg, The Netherlands;
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 Alicante, Spain
| | - Nicola La Porta
- Department of Sustainable Agrobiosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy;
- MOUNTFOR Project Centre, European Forest Institute, 38098 San Michele all’Adige, Italy
| | - Rosella Muresu
- Institute of Animal Production Systems in Mediterranean Environments-National Research Council, 07040 Sassari, Italy;
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy; (P.S.); (G.C.)
| | - Giuseppe Concheri
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy; (P.S.); (G.C.)
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy; (P.S.); (G.C.)
- Correspondence: ; Tel.: +39-049-8272-923
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17
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Zou W, Ye G, Zhang K, Yang H, Yang J. Analysis of the core genome and pangenome of Clostridium butyricum. Genome 2020; 64:51-61. [PMID: 33105087 DOI: 10.1139/gen-2020-0072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Clostridium butyricum is an anaerobic bacterium that inhabits broad niches. Clostridium butyricum is known for its production of butyrate, 1,3-propanediol, and hydrogen. This study aimed to present a comparative pangenome analysis of 24 strains isolated from different niches. We sequenced and annotated the genome of C. butyricum 3-3 isolated from the Chinese baijiu ecosystem. The pangenome of C. butyricum was open. The core genome, accessory genome, and strain-specific genes comprised 1011, 4543, and 1473 genes, respectively. In the core genome, Carbohydrate metabolism was the largest category, and genes in the biosynthetic pathway of butyrate and glycerol metabolism were conserved (in the core or soft-core genome). Furthermore, the 1,3-propanediol operon existed in 20 strains. In the accessory genome, numerous mobile genetic elements belonging to the Replication, recombination, and repair (L) category were identified. In addition, genome islands were identified in all 24 strains, ranging from 2 (strain KNU-L09) to 53 (strain SU1), and phage sequences were found in 17 of the 24 strains. This study provides an important genomic framework that could pave the way for the exploration of C. butyricum and future studies on the genetic diversification of C. butyricum.
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Affiliation(s)
- Wei Zou
- College of Bioengineering, Sichuan University of Science & Engineering, 188, University town, Lingang District, Yibin, Sichuan 644005, China.,Research Laboratory of Baijiu Resource Microorganisms and Big data, Sichuan University of Science & Engineering, 188 University town, Lingang District, Yibin, Sichuan 644005, China
| | - Guangbin Ye
- College of Bioengineering, Sichuan University of Science & Engineering, 188, University town, Lingang District, Yibin, Sichuan 644005, China
| | - Kaizheng Zhang
- College of Bioengineering, Sichuan University of Science & Engineering, 188, University town, Lingang District, Yibin, Sichuan 644005, China
| | - Haiquan Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jiangang Yang
- College of Bioengineering, Sichuan University of Science & Engineering, 188, University town, Lingang District, Yibin, Sichuan 644005, China
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18
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Fang H, Xu JB, Nie Y, Wu XL. Pan-genomic analysis reveals that the evolution of Dietzia species depends on their living habitats. Environ Microbiol 2020; 23:861-877. [PMID: 32715552 DOI: 10.1111/1462-2920.15176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022]
Abstract
The bacterial genus Dietzia is widely distributed in various environments. The genomes of 26 diverse strains of Dietzia, including almost all the type strains, were analysed in this study. This analysis revealed a lipid metabolism gene richness, which could explain the ability of Dietzia to live in oil related environments. The pan-genome consists of 83,976 genes assigned into 10,327 gene families, 792 of which are shared by all the genomes of Dietzia. Mathematical extrapolation of the data suggests that the Dietzia pan-genome is open. Both gene duplication and gene loss contributed to the open pan-genome, while horizontal gene transfer was limited. Dietzia strains primarily gained their diverse metabolic capacity through more ancient gene duplications. Phylogenetic analysis of Dietzia isolated from aquatic and terrestrial environments showed two distinct clades from the same ancestor. The genome sizes of Dietzia strains from aquatic environments were significantly larger than those from terrestrial environments, which was mainly due to the occurrence of more gene loss events during the evolutionary progress of the strains from terrestrial environments. The evolutionary history of Dietzia was tightly coupled to environmental conditions, and iron concentrations should be one of the key factors shaping the genomes of the Dietzia lineages.
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Affiliation(s)
- Hui Fang
- College of Engineering, Peking University, Beijing, 100871, China
| | - Jin-Bo Xu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, 100871, China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing, 100871, China.,Institute of Ocean Research, Peking University, Beijing, 100871, China
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19
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Cruz-Morales P, Orellana CA, Moutafis G, Moonen G, Rincon G, Nielsen LK, Marcellin E. Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update. Genome Biol Evol 2020; 11:2035-2044. [PMID: 31076745 PMCID: PMC6656338 DOI: 10.1093/gbe/evz096] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2019] [Indexed: 12/28/2022] Open
Abstract
Clostridium is a large genus of obligate anaerobes belonging to the Firmicutes phylum of bacteria, most of which have a Gram-positive cell wall structure. The genus includes significant human and animal pathogens, causative of potentially deadly diseases such as tetanus and botulism. Despite their relevance and many studies suggesting that they are not a monophyletic group, the taxonomy of the group has largely been neglected. Currently, species belonging to the genus are placed in the unnatural order defined as Clostridiales, which includes the class Clostridia. Here, we used genomic data from 779 strains to study the taxonomy and evolution of the group. This analysis allowed us to 1) confirm that the group is composed of more than one genus, 2) detect major differences between pathogens classified as a single species within the group of authentic Clostridium spp. (sensu stricto), 3) identify inconsistencies between taxonomy and toxin evolution that reflect on the pervasive misclassification of strains, and 4) identify differential traits within central metabolism of members of what has been defined earlier and confirmed by us as cluster I. Our analysis shows that the current taxonomic classification of Clostridium species hinders the prediction of functions and traits, suggests a new classification for this fascinating class of bacteria, and highlights the importance of phylogenomics for taxonomic studies.
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Affiliation(s)
- Pablo Cruz-Morales
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia.,Joint BioEnergy Institute, Emeryville, CA
| | - Camila A Orellana
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | | | | | | | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
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20
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Todorov SD, Kang HJ, Ivanova IV, Holzapfel WH. Bacteriocins From LAB and Other Alternative Approaches for the Control of Clostridium and Clostridiodes Related Gastrointestinal Colitis. Front Bioeng Biotechnol 2020; 8:581778. [PMID: 33042979 PMCID: PMC7517946 DOI: 10.3389/fbioe.2020.581778] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
The gut microbiome is considered as a promising target for future non-conventional therapeutic treatment of inflammatory and infectious diseases. The search for appropriate safe and beneficial (lactic acid bacterial and other) putative probiotic strains and/or their antimicrobial metabolites represents a challenging approach for combating several problematic and emerging infections. The process of selecting suitable strains, especially of lactic acid bacteria (LAB) with superior properties, has been accelerated and intensified during the past two decades, also thanks to recent developments in lab techniques. Currently, special focus is on the potential of antimicrobial metabolites produced by some LAB strains and their application as active therapeutic agents. The vision is to develop a scientific basis for 'biotherapeutics' as alternative to conventional approaches in both human and veterinary medicine. Consequently, innovative and promising applications of LAB to the therapeutic practice are presently emerging. An overview of the existing literature indicates that some antimicrobial metabolites such as bacteriocins, widely produced by different bacterial species including LAB, are promising biotherapeutic agents for controlling infections caused by potential pathogens, such as Clostridium and Clostridiodes. Non-conventional, safe and well designed therapeutic treatments may contribute to the improvement of gut dysbiotic conditions. Thereby gut homeostasis can be restored and inflammatory conditions such as gastrointestinal colitis ameliorated. Combining the knowledge on the production, characterization and application of bacteriocins from probiotic LAB, together with their antibacterial properties, appears to be a promising and novel approach in biotherapy. In this overview, different scenarios for the control of Clostridium spp. by application of bacteriocins as therapeutic agents, also in synergistic combination with antibiotics, will be discussed.
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Affiliation(s)
- Svetoslav D. Todorov
- Advanced Green Energy and Environment Institute (AGEE), Handong Global University, Pohang, South Korea
| | - Hye-Ji Kang
- Advanced Green Energy and Environment Institute (AGEE), Handong Global University, Pohang, South Korea
- HEM Inc., Handong Global University, Pohang, South Korea
| | - Iskra V. Ivanova
- Department of General and Applied Microbiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Wilhelm H. Holzapfel
- Advanced Green Energy and Environment Institute (AGEE), Handong Global University, Pohang, South Korea
- HEM Inc., Handong Global University, Pohang, South Korea
- *Correspondence: Wilhelm H. Holzapfel,
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21
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Yang C, Kennes YM, Lepp D, Yin X, Wang Q, Yu H, Yang C, Gong J, Diarra MS. Effects of encapsulated cinnamaldehyde and citral on the performance and cecal microbiota of broilers vaccinated or not vaccinated against coccidiosis. Poult Sci 2019; 99:936-948. [PMID: 32029170 PMCID: PMC7587813 DOI: 10.1016/j.psj.2019.10.036] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/15/2019] [Accepted: 10/15/2019] [Indexed: 01/08/2023] Open
Abstract
This study investigated the effects of encapsulated cinnamaldehyde (CIN) and citral (CIT) alone or in combination (CIN + CIT) on the growth performance and cecal microbiota of nonvaccinated broilers and broilers vaccinated against coccidiosis. Vaccinated (1,600) and nonvaccinated (1,600) 0-day-old male Cobb500 broilers were randomly allocated to 5 treatments: basal diet (control) and basal diet supplemented with bacitracin (BAC, 55 ppm), CIN (100 ppm), CIT (100 ppm), and CIN (100 ppm) + CIT (100 ppm). In general, body weight (BW) and feed conversion ratio were significantly improved in birds treated with BAC, CIN, CIT, and CIN + CIT (P < 0.05) but were all decreased in vaccinated birds compared with nonvaccinated birds (P < 0.05). Significant interactions (P < 0.05) between vaccination and treatments for average daily gain during the periods of starter (day 0–9) and BW on day 10 were noted. Broilers receiving vaccines (P < 0.01) or feed supplemented with BAC, CIN, CIT, or CIN + CIT (P < 0.01) showed reductions in mortality rate from day 0 to 28. The incidences of minor coccidiosis were higher (P < 0.05) in vaccinated birds than in nonvaccinated birds. Diet supplementation with BAC or tested encapsulated essential oils showed comparable effects on the coccidiosis incidences. Similar to BAC, CIN and its combination with CIT reduced both incidence and severity of necrotic enteritis (P < 0.05). No treatment effects were observed on the cecal microbiota at the phyla level. At the genus level, significant differences between vaccination and treatment groups were observed for 5 (Lactobacillus, Ruminococcus, Faecalibacterium, Enterococcus, and Clostridium) of 40 detected genera (P < 0.05). The genus Lactobacillus was more abundant in broilers fed with CIT, while Clostridium and Enterococcus were less abundant in broilers fed with CIN, CIT, or CIN + CIT in both the vaccinated and nonvaccinated groups. Results from this study suggested that CIN alone or in combination with CIT in feed could improve chicken growth performance to the level comparable with BAC and alter cecal microbiota composition.
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Affiliation(s)
- Chongwu Yang
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, Ontario, Canada N1G 5C9; Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Yan Martel Kennes
- Centre de recherche en sciences animales de Deschambault, Deschambault, 120-A, chemin du Roy, Canada QC G0A 1S0
| | - Dion Lepp
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, Ontario, Canada N1G 5C9
| | - Xianhua Yin
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, Ontario, Canada N1G 5C9
| | - Qi Wang
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, Ontario, Canada N1G 5C9
| | - Hai Yu
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, Ontario, Canada N1G 5C9
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Joshua Gong
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, Ontario, Canada N1G 5C9.
| | - Moussa S Diarra
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, Ontario, Canada N1G 5C9.
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22
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Dong TS, Chang HH, Hauer M, Lagishetty V, Katzka W, Rozengurt E, Jacobs JP, Eibl G. Metformin alters the duodenal microbiome and decreases the incidence of pancreatic ductal adenocarcinoma promoted by diet-induced obesity. Am J Physiol Gastrointest Liver Physiol 2019; 317:G763-G772. [PMID: 31545922 PMCID: PMC6962494 DOI: 10.1152/ajpgi.00170.2019] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/11/2019] [Accepted: 09/15/2019] [Indexed: 01/31/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC)'s growing incidence has been linked to the rise in obesity and type 2 diabetes mellitus. In previous work, we have shown that metformin can prevent the increased incidence of PDAC in a KrasG12D mouse model subjected to a diet high in fat and calories (HFCD). One potential way that metformin can affect the host is through alterations in the gut microbiome. Therefore, we investigated microbial associations with PDAC development and metformin use in the same mouse model. Lox-Stop-Lox Kras G12D/+ (LSL-Kras G12D/+); p48-Cre (KC) mice were given control diet, HFCD, or HFCD with 5 mg/mL metformin in drinking water for 3 mo. At the end of the 3 mo, 16S rRNA sequencing was performed to characterize microbiome composition of duodenal mucosal, duodenal luminal, and cecal luminal samples. KC mice on an HFCD demonstrated depletion of intact acini and formation of advanced pancreatic intraepithelial neoplasia. This effect was completely abrogated by metformin treatment. HFCD was associated with significant changes in microbial composition and diversity in the duodenal mucosa and lumen, much of which was prevented by metformin. In particular, Clostridium sensu stricto was negatively correlated with percent intact acini and seemed to be inhibited by the addition of metformin while on an HFCD. Administration of metformin eliminated PDAC formation in KC mice. This change was associated with significant microbial changes in both the mucosal and luminal microbiome of the duodenum. This suggests that the microbiome may be a potential mediator of the chemopreventive effects of metformin.NEW & NOTEWORTHY Pancreatic ductal adenocarcinoma (PDAC)'s growing incidence has been linked to the rise in obesity and type 2 diabetes mellitus. Administration of metformin eliminated PDAC formation in KC mice with diet-induced obesity. This change was associated with significant microbial changes in both the mucosal and luminal microbiome of the duodenum. This suggests that the microbiome may be a potential mediator of the chemopreventive effects of metformin.
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Affiliation(s)
- Tien S Dong
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, California
| | - Hui-Hua Chang
- CURE: Digestive Diseases Research Center, David Geffen School of Medicine at the University of California, Los Angeles, California
- Department of Surgery, David Geffen School of Medicine at the University of California, Los Angeles, California
| | - Meg Hauer
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, California
- CURE: Digestive Diseases Research Center, David Geffen School of Medicine at the University of California, Los Angeles, California
- University of California Los Angeles Microbiome Center, David Geffen School of Medicine at the University of California, Los Angeles, California
| | - Venu Lagishetty
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, California
- CURE: Digestive Diseases Research Center, David Geffen School of Medicine at the University of California, Los Angeles, California
- University of California Los Angeles Microbiome Center, David Geffen School of Medicine at the University of California, Los Angeles, California
| | - William Katzka
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, California
- CURE: Digestive Diseases Research Center, David Geffen School of Medicine at the University of California, Los Angeles, California
- University of California Los Angeles Microbiome Center, David Geffen School of Medicine at the University of California, Los Angeles, California
| | - Enrique Rozengurt
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, California
- CURE: Digestive Diseases Research Center, David Geffen School of Medicine at the University of California, Los Angeles, California
- Division of Gastroenterology, Hepatology, and Parenteral Nutrition, Veterans' Affairs Greater Los Angeles Healthcare System, Los Angeles, California
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, California
- CURE: Digestive Diseases Research Center, David Geffen School of Medicine at the University of California, Los Angeles, California
- University of California Los Angeles Microbiome Center, David Geffen School of Medicine at the University of California, Los Angeles, California
- Division of Gastroenterology, Hepatology, and Parenteral Nutrition, Veterans' Affairs Greater Los Angeles Healthcare System, Los Angeles, California
| | - Guido Eibl
- CURE: Digestive Diseases Research Center, David Geffen School of Medicine at the University of California, Los Angeles, California
- Department of Surgery, David Geffen School of Medicine at the University of California, Los Angeles, California
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23
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Matteoli FP, Passarelli-Araujo H, Pedrosa-Silva F, Olivares FL, Venancio TM. Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of bla CTX-M-55, bla NDM-5 and bla IMI-1, along with sophisticated iron acquisition strategies. Genomics 2019; 112:1182-1191. [PMID: 31279858 DOI: 10.1016/j.ygeno.2019.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 01/22/2023]
Abstract
Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. We report the genome of a non-clinical E. bugandensis strain, which was integrated with publicly available genomes to study the pangenome and general population structure of E. bugandensis. Core- and whole-genome multilocus sequence typing allowed the detection of five E. bugandensis phylogroups (PG-A to E), which contain important antimicrobial resistance and virulence determinants. We uncovered several extended-spectrum β-lactamases, including blaCTX-M-55 and blaNDM-5, present in an IncX replicon type plasmid, described here for the first time in E. bugandensis. Genetic context analysis of blaNDM-5 revealed the resemblance of this plasmid with other IncX plasmids from other bacteria from the same country. Three distinctive siderophore producing operons were found in E. bugandensis: enterobactin (ent), aerobactin (iuc/iut), and salmochelin (iro). Our findings provide novel insights on the lifestyle, physiology, antimicrobial, and virulence profiles of E. bugandensis.
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Affiliation(s)
- Filipe P Matteoli
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Hemanoel Passarelli-Araujo
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil; Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Fabio L Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), UENF, Brazil; Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, UENF, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil.
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24
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Yu HY, Meade A, Liu SJ. Phylogeny of Clostridium spp. Based on Conservative Genes and Comparisons with Other Trees. Microbiology (Reading) 2019. [DOI: 10.1134/s002626171904012x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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25
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Cebrián R, Macia-Valero A, Jati AP, Kuipers OP. Design and Expression of Specific Hybrid Lantibiotics Active Against Pathogenic Clostridium spp. Front Microbiol 2019; 10:2154. [PMID: 31616392 PMCID: PMC6768957 DOI: 10.3389/fmicb.2019.02154] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/02/2019] [Indexed: 12/15/2022] Open
Abstract
Clostridium difficile has been reported as the most common cause of nosocomial diarrhea (antibiotic-associated diarrhea), resulting in significant morbidity and mortality in hospitalized patients. The resistance of the clostridial spores to antibiotics and their side effects on the gut microbiota are two factors related to the emergence of infection and its relapses. Lantibiotics provide an innovative alternative for cell growth inhibition due to their dual mechanism of action (membrane pore-forming and cell wall synthesis inhibition) and low resistance rate. Based on the fact that bacteriocins are usually active against bacteria closely related to the producer strains, a new dual approach combining genome mining and synthetic biology was performed, by designing new lantibiotics with high activity and specificity toward Clostridium. We first attempted the heterologous expression of putative lantibiotics identified following Clostridium genome mining. Subsequently, we designed new hybrid lantibiotics combining the start or end of the putative clostridial peptides and the start or end parts of nisin. The designed peptides were cloned and expressed using the nisin biosynthetic machinery in Lactococcus lactis. From the 20 initial peptides, only 1 fulfilled the requirements established in this work to be considered as a good candidate: high heterologous production level and high specificity/activity against clostridial species. The high specificity and activity observed for the peptide AMV10 makes it an interesting candidate as an alternative to traditional antibiotics in the treatment of C. difficile infections, avoiding side effects and protecting the normal gut microbiota.
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26
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Abram KZ, Udaondo Z. Towards a better metabolic engineering reference: the microbial chassis. Microb Biotechnol 2018; 13:17-18. [PMID: 30589218 PMCID: PMC6922515 DOI: 10.1111/1751-7915.13363] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 12/12/2018] [Indexed: 12/01/2022] Open
Affiliation(s)
- Kaleb Z Abram
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
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27
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Wu Y, Zaiden N, Cao B. The Core- and Pan-Genomic Analyses of the Genus Comamonas: From Environmental Adaptation to Potential Virulence. Front Microbiol 2018; 9:3096. [PMID: 30619175 PMCID: PMC6299040 DOI: 10.3389/fmicb.2018.03096] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/29/2018] [Indexed: 01/30/2023] Open
Abstract
Comamonas is often reported to be one of the major members of microbial communities in various natural and engineered environments. Versatile catabolic capabilities of Comamonas have been studied extensively in the last decade. In contrast, little is known about the ecological roles and adaptation of Comamonas to different environments as well as the virulence of potentially pathogenic Comamonas strains. In this study, we provide genomic insights into the potential ecological roles and virulence of Comamonas by analysing the entire gene set (pangenome) and the genes present in all genomes (core genome) using 34 genomes of 11 different Comamonas species. The analyses revealed that the metabolic pathways enabling Comamonas to acquire energy from various nutrient sources are well conserved. Genes for denitrification and ammonification are abundant in Comamonas, suggesting that Comamonas plays an important role in the nitrogen biogeochemical cycle. They also encode sophisticated redox sensory systems and diverse c-di-GMP controlling systems, allowing them to be able to effectively adjust their biofilm lifestyle to changing environments. The virulence factors in Comamonas were found to be highly species-specific. The conserved strategies used by potentially pathogenic Comamonas for surface adherence, motility control, nutrient acquisition and stress tolerance were also revealed.
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Affiliation(s)
- Yichao Wu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Norazean Zaiden
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
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28
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Zou W, Ye G, Zhang K. Diversity, Function, and Application of Clostridium in Chinese Strong Flavor Baijiu Ecosystem: A Review. J Food Sci 2018; 83:1193-1199. [PMID: 29660763 DOI: 10.1111/1750-3841.14134] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 03/01/2018] [Indexed: 12/30/2022]
Abstract
Baijiu is a Chinese traditional distilled liquor with an annual yield over 13.12 million tons. Strong flavor baijiu (SFB) also called Luzhou-flavor liquor, takes account for > 70% of the total baijiu produced. SFB is produced by an open solid fermentation process with a complex microbial ecosystem. Clostridium is one of the most important microorganisms for the formation of the main flavor compounds of SFB, such as ethyl caproate. In this paper, we review current research progress on the Clostridium in the SFB ecosystem, focusing on the species diversity, physiological and metabolic features along with interspecies interactions. Systems biology approaches for the study of Clostridium from SFB ecosystems were discussed and explored. Furthermore, current applications of Clostridium in SFB production were discussed. PRACTICAL APPLICATION Strong flavor baijiu (SFB) accounts for more than 70% of total yield of Chinese baijiu, which exists for hundreds of years. Clostridium is common in SFB ecosystem and identified to be one of main contributors of flavor compounds in SFB. Study on the Clostridium from SFB ecosystem is not only helpful for the understanding of flavor compounds formation mechanism, but also the improvement of SFB quality. This study focuses on the current researches on the Clostridium species in SFB ecosystem, including the species diversity, physiological and metabolic features, and applications.
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Affiliation(s)
- Wei Zou
- the College of Bioengineering, Sichuan Univ. of Science & Engineering, 180 Xueyuan Road, Zigong, Sichuan 643000, China
| | - Guangbin Ye
- the College of Bioengineering, Sichuan Univ. of Science & Engineering, 180 Xueyuan Road, Zigong, Sichuan 643000, China
| | - Kaizheng Zhang
- the College of Bioengineering, Sichuan Univ. of Science & Engineering, 180 Xueyuan Road, Zigong, Sichuan 643000, China
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29
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Gyulev IS, Willson BJ, Hennessy RC, Krabben P, Jenkinson ER, Thomas GH. Part by Part: Synthetic Biology Parts Used in Solventogenic Clostridia. ACS Synth Biol 2018; 7:311-327. [PMID: 29186949 DOI: 10.1021/acssynbio.7b00327] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solventogenic Clostridia are of interest to the chemical industry because of their natural ability to produce chemicals such as butanol, acetone and ethanol from diverse feedstocks. Their use as whole cell factories presents multiple metabolic engineering targets that could lead to improved sustainability and profitability of Clostridium industrial processes. However, engineering efforts have been held back by the scarcity of genetic and synthetic biology tools. Over the past decade, genetic tools to enable transformation and chromosomal modifications have been developed, but the lack of a broad palette of synthetic biology parts remains one of the last obstacles to the rapid engineered improvement of these species for bioproduction. We have systematically reviewed existing parts that have been used in the modification of solventogenic Clostridia, revealing a narrow range of empirically chosen and nonengineered parts that are in current use. The analysis uncovers elements, such as promoters, transcriptional terminators and ribosome binding sites where increased fundamental knowledge is needed for their reliable use in different applications. Together, the review provides the most comprehensive list of parts used and also presents areas where an improved toolbox is needed for full exploitation of these industrially important bacteria.
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Affiliation(s)
- Ivan S. Gyulev
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Benjamin J. Willson
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Rosanna C. Hennessy
- Department
of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Preben Krabben
- Green Biologics Limited, Milton Park, Abingdon, Oxfordshire OX14 4RU, United Kingdom
| | | | - Gavin H. Thomas
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
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30
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Pan-Cellulosomics of Mesophilic Clostridia: Variations on a Theme. Microorganisms 2017; 5:microorganisms5040074. [PMID: 29156585 PMCID: PMC5748583 DOI: 10.3390/microorganisms5040074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 11/17/2022] Open
Abstract
The bacterial cellulosome is an extracellular, multi-enzyme machinery, which efficiently depolymerizes plant biomass by degrading plant cell wall polysaccharides. Several cellulolytic bacteria have evolved various elaborate modular architectures of active cellulosomes. We present here a genome-wide analysis of a dozen mesophilic clostridia species, including both well-studied and yet-undescribed cellulosome-producing bacteria. We first report here, the presence of cellulosomal elements, thus expanding our knowledge regarding the prevalence of the cellulosomal paradigm in nature. We explored the genomic organization of key cellulosome components by comparing the cellulosomal gene clusters in each bacterial species, and the conserved sequence features of the specific cellulosomal modules (cohesins and dockerins), on the background of their phylogenetic relationship. Additionally, we performed comparative analyses of the species-specific repertoire of carbohydrate-degrading enzymes for each of the clostridial species, and classified each cellulosomal enzyme into a specific CAZy family, thus indicating their putative enzymatic activity (e.g., cellulases, hemicellulases, and pectinases). Our work provides, for this large group of bacteria, a broad overview of the blueprints of their multi-component cellulosomal complexes. The high similarity of their scaffoldin clusters and dockerin-based recognition residues suggests a common ancestor, and/or extensive horizontal gene transfer, and potential cross-species recognition. In addition, the sporadic spatial organization of the numerous dockerin-containing genes in several of the genomes, suggests the importance of the cellulosome paradigm in the given bacterial species. The information gained in this work may be utilized directly or developed further by genetically engineering and optimizing designer cellulosome systems for enhanced biotechnological biomass deconstruction and biofuel production.
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31
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Bremer E. Clostridium difficile: A bad bug goes into defensive mode. Environ Microbiol 2017; 19:2523-2528. [PMID: 28447375 DOI: 10.1111/1462-2920.13776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von Frisch Str. 8, Marburg, D-35043, Germany.,LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, Marburg, D-35043, Germany
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