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Elechi JOG, Sirianni R, Conforti FL, Cione E, Pellegrino M. Food System Transformation and Gut Microbiota Transition: Evidence on Advancing Obesity, Cardiovascular Diseases, and Cancers-A Narrative Review. Foods 2023; 12:2286. [PMID: 37372497 DOI: 10.3390/foods12122286] [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: 04/06/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Food, a vital component of our daily life, is fundamental to our health and well-being, and the knowledge and practices relating to food have been passed down from countless generations of ancestors. Systems may be used to describe this extremely extensive and varied body of agricultural and gastronomic knowledge that has been gathered via evolutionary processes. The gut microbiota also underwent changes as the food system did, and these alterations had a variety of effects on human health. In recent decades, the gut microbiome has gained attention due to its health benefits as well as its pathological effects on human health. Many studies have shown that a person's gut microbiota partially determines the nutritional value of food and that diet, in turn, shapes both the microbiota and the microbiome. The current narrative review aims to explain how changes in the food system over time affect the makeup and evolution of the gut microbiota, advancing obesity, cardiovascular disease (CVD), and cancer. After a brief discussion of the food system's variety and the gut microbiota's functions, we concentrate on the relationship between the evolution of food system transformation and gut microbiota system transition linked to the increase of non-communicable diseases (NCDs). Finally, we also describe sustainable food system transformation strategies to ensure healthy microbiota composition recovery and maintain the host gut barrier and immune functions to reverse advancing NCDs.
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Affiliation(s)
- Jasper Okoro Godwin Elechi
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Rosa Sirianni
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Francesca Luisa Conforti
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Erika Cione
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Michele Pellegrino
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
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2
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Kugarajah V, Nisha KN, Jayakumar R, Sahabudeen S, Ramakrishnan P, Mohamed SB. Significance of microbial genome in environmental remediation. Microbiol Res 2023; 271:127360. [PMID: 36931127 DOI: 10.1016/j.micres.2023.127360] [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: 12/27/2022] [Revised: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 03/11/2023]
Abstract
Environmental pollutants seriously threaten the ecosystem and health of various life forms, particularly with the rapid industrialization and emerging population. Conventionally physical and chemical strategies are being opted for the removal of these pollutants. Bioremediation, through several advancements, has been a boon to combat the existing threat faced today. Microbes with enzymes degrade various pollutants and utilize them as a carbon and energy source. With the existing demand and through several research explorations, Genetically Engineered Microorganisms (GEMs) have paved to be a successful approach to abate pollution through bioremediation. The genome of the microbe determines its biodegradative nature. Thus, methods including pure culture techniques and metagenomics are used for analyzing the genome of microbes, which provides information about catabolic genes. The information obtained along with the aid of biotechnology helps to construct GEMs that are cost-effective and safer thereby exhibiting higher degradation of pollutants. The present review focuses on the role of microbes in the degradation of environmental pollutants, role of evolution in habitat and adaptation of microbes, microbial degenerative genes, their pathways, and the efficacy of recombinant DNA (rDNA) technology for creating GEMs for bioremediation. The present review also provides a gist of existing GEMs for bioremediation and their limitations, thereby providing a future scope of implementation of these GEMs for a sustainable environment.
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Affiliation(s)
- Vaidhegi Kugarajah
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India
| | | | - R Jayakumar
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India
| | - S Sahabudeen
- Department of Biotechnology, SRM Institute of Science and Technology, Kanchipuram Dist, Kattankulathur, Tamil Nadu, India; Medical Team, Doctoral Institute for Evidence Based Policy, Tokyo, Japan
| | - P Ramakrishnan
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India.
| | - S B Mohamed
- Department of Materials Science, School of Technology, Central University of Tamil Nadu, Thiruvarur 610005, Tamil Nadu, India.
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3
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Alkatheri AH, Yap PSX, Abushelaibi A, Lai KS, Cheng WH, Erin Lim SH. Microbial Genomics: Innovative Targets and Mechanisms. Antibiotics (Basel) 2023; 12:antibiotics12020190. [PMID: 36830101 PMCID: PMC9951906 DOI: 10.3390/antibiotics12020190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Multidrug resistance (MDR) has become an increasing threat to global health because bacteria can develop resistance to antibiotics over time. Scientists worldwide are searching for new approaches that go beyond traditional antibiotic discovery and development pipelines. Advances in genomics, however, opened up an unexplored therapeutic opportunity for the discovery of new antibacterial agents. Genomic approaches have been used to discover several novel antibiotics that target critical processes for bacterial growth and survival, including histidine kinases (HKs), LpxC, FabI, peptide deformylase (PDF), and aminoacyl-tRNA synthetases (AaRS). In this review, we will discuss the use of microbial genomics in the search for innovative and promising drug targets as well as the mechanisms of action for novel antimicrobial agents. We will also discuss future directions on how the utilization of the microbial genomics approach could improve the odds of antibiotic development having a more successful outcome.
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Affiliation(s)
- Asma Hussain Alkatheri
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Polly Soo-Xi Yap
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor 47500, Malaysia
| | - Aisha Abushelaibi
- Office of Campus Director, Abu Dhabi Colleges, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Wan-Hee Cheng
- Faculty of Health and Life Sciences, INTI International University, Persiaran Perdana BBN, Nilai 71800, Malaysia
| | - Swee-Hua Erin Lim
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
- Correspondence:
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Martin CS, Jubelin G, Darsonval M, Leroy S, Leneveu-Jenvrin C, Hmidene G, Omhover L, Stahl V, Guillier L, Briandet R, Desvaux M, Dubois-Brissonnet F. Genetic, physiological, and cellular heterogeneities of bacterial pathogens in food matrices: Consequences for food safety. Compr Rev Food Sci Food Saf 2022; 21:4294-4326. [PMID: 36018457 DOI: 10.1111/1541-4337.13020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 01/28/2023]
Abstract
In complex food systems, bacteria live in heterogeneous microstructures, and the population displays phenotypic heterogeneities at the single-cell level. This review provides an overview of spatiotemporal drivers of phenotypic heterogeneity of bacterial pathogens in food matrices at three levels. The first level is the genotypic heterogeneity due to the possibility for various strains of a given species to contaminate food, each of them having specific genetic features. Then, physiological heterogeneities are induced within the same strain, due to specific microenvironments and heterogeneous adaptative responses to the food microstructure. The third level of phenotypic heterogeneity is related to cellular heterogeneity of the same strain in a specific microenvironment. Finally, we consider how these phenotypic heterogeneities at the single-cell level could be implemented in mathematical models to predict bacterial behavior and help ensure microbiological food safety.
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Affiliation(s)
- Cédric Saint Martin
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France.,Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Grégory Jubelin
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Maud Darsonval
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Charlène Leneveu-Jenvrin
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France.,Association pour le Développement de l'Industrie de la Viande (ADIV), Clermont-Ferrand, France
| | - Ghaya Hmidene
- Risk Assessment Department, ANSES, Maisons-Alfort, France
| | - Lysiane Omhover
- Aerial, Technical Institute of Agro-Industry, Illkirch, France
| | - Valérie Stahl
- Aerial, Technical Institute of Agro-Industry, Illkirch, France
| | | | - Romain Briandet
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
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Shibata K, Shimizu T, Nakahara M, Ito E, Legoux F, Fujii S, Yamada Y, Furutani-Seiki M, Lantz O, Yamasaki S, Watarai M, Shirai M. The intracellular pathogen Francisella tularensis escapes from adaptive immunity by metabolic adaptation. Life Sci Alliance 2022; 5:5/10/e202201441. [PMID: 35667686 PMCID: PMC9170078 DOI: 10.26508/lsa.202201441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
This study shows that metabolic adaptation allows the intracellular bacterial pathogen Francisella tularensis to escape recognition by the host adaptive immunity. Intracellular pathogens lose many metabolic genes during their evolution from free-living bacteria, but the pathogenic consequences of their altered metabolic programs on host immunity are poorly understood. Here, we show that a pathogenic strain of Francisella tularensis subsp. tularensis (FT) has five amino acid substitutions in RibD, a converting enzyme of the riboflavin synthetic pathway responsible for generating metabolites recognized by mucosal-associated invariant T (MAIT) cells. Metabolites from a free-living strain, F. tularensis subsp. novicida (FN), activated MAIT cells in a T-cell receptor (TCR)–dependent manner, whereas introduction of FT-type ribD to the free-living strain was sufficient to attenuate this activation in both human and mouse MAIT cells. Intranasal infection in mice showed that the ribDFT-expressing FN strain induced impaired Th1-type MAIT cell expansion and resulted in reduced bacterial clearance and worsened survival compared with the wild-type free-living strain FN. These results demonstrate that F. tularensis can acquire immune evasion capacity by alteration of metabolic programs during evolution.
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Affiliation(s)
- Kensuke Shibata
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan .,Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Ophthalmology, Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takashi Shimizu
- Joint Faculty of Veterinary Medicine, Laboratory of Veterinary Public Health, Yamaguchi University, Yamaguchi, Japan
| | - Mashio Nakahara
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Emi Ito
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | | | - Shotaro Fujii
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Yuka Yamada
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Makoto Furutani-Seiki
- Systems Biochemistry in Pathology and Regeneration, Graduate School of Medicine, Yamaguchi University, Ube, Japan
| | - Olivier Lantz
- INSERM U932, PSL University, Laboratoire d'Immunologie Clinique, Centre d'Investigation Clinique en Biothérapie, Institut Curie (CIC-BT1428), Paris, France
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Division of Molecular Design, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Masahisa Watarai
- Joint Faculty of Veterinary Medicine, Laboratory of Veterinary Public Health, Yamaguchi University, Yamaguchi, Japan
| | - Mutsunori Shirai
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
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Sharma A, Timilsina S, Abrahamian P, Minsavage GV, Colee J, Ojiambo PS, Goss EM, Vallad GE, Jones JB. Need for speed: bacterial effector XopJ2 is associated with increased dispersal velocity of Xanthomonas perforans. Environ Microbiol 2021; 23:5850-5865. [PMID: 33891376 PMCID: PMC8597037 DOI: 10.1111/1462-2920.15541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/20/2021] [Indexed: 11/28/2022]
Abstract
Bacterial spot caused by Xanthomonas perforans (Xp) is an economically important disease in tomato. Previous studies have shown that the recently isolated Xp strains have acquired and retained the effector gene, xopJ2, which has been reported to increase fitness of the pathogen in the field. To elucidate the fitness benefit of xopJ2, we quantified the effect of xopJ2 on the dispersal and evolution of Xp populations on tomato. We compared movement of two wild-type Xp strains expressing xopJ2 to their respective xopJ2 mutants when co-inoculated in the field. We developed a binary logistic model to predict the presence of Xp over spatial and temporal dimensions with or without xopJ2. Based on the model, wild-type bacteria were dispersed approximately three times faster than the xopJ2 mutants. In a simulation experiment, the selective advantage due to increased dispersal velocity led to an increase in the frequency of xopJ2 gene in the Xp population and its apparent fixation within 10 to 12 cropping seasons of the tomato crop. Our results show that the presence of a single gene can affect the dispersal of a bacterial pathogen and significantly alter its population dynamics.
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Affiliation(s)
- Anuj Sharma
- Department of Plant PathologyUniversity of FloridaGainesvilleFloridaUSA
| | - Sujan Timilsina
- Department of Plant PathologyUniversity of FloridaGainesvilleFloridaUSA
| | - Peter Abrahamian
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
| | | | - James Colee
- Statistics Consulting Unit, Institute of Food and Agricultural SciencesUniversity of FloridaGainesvilleFloridaUSA
| | - Peter S. Ojiambo
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Erica M. Goss
- Department of Plant PathologyUniversity of FloridaGainesvilleFloridaUSA
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Gary E. Vallad
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
| | - Jeffrey B. Jones
- Department of Plant PathologyUniversity of FloridaGainesvilleFloridaUSA
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Verma S, Dutta SK, Firnberg E, Phillips L, Vinayek R, Nair PP. Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects. PLoS One 2021; 16:e0251590. [PMID: 34252073 PMCID: PMC8274925 DOI: 10.1371/journal.pone.0251590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 04/29/2021] [Indexed: 12/22/2022] Open
Abstract
Background Recurrent Clostridioides diffícile infection (RCDI) is associated with major bacterial dysbiosis and colitis. Fecal microbiota transplantation (FMT) is a highly effective therapeutic modality for RCDI. While several studies have identified bacterial species associated with resolution of symptoms in patients, characterization of the fecal microbiome at the bacterial strain level in RCDI patients before and after FMT and healthy donors, has been lacking. The aim of this study was to examine the ability of bacterial strains from healthy donors to engraft in the gastrointestinal tract of patients with RCDI following FMT. Methods Fecal samples were collected from 22 patients with RCDI before and after FMT and their corresponding healthy donors. Total DNA was extracted from each sample and analyzed by shotgun metagenomic sequencing. The Cosmos-ID analysis platform was used for taxonomic assignment of sequences and calculation of the relative abundance (RA) of bacterial species and strains. From these data, the total number of bacterial strains (BSI), Shannon diversity index, dysbiosis index (DI), and bacterial engraftment factor, were calculated for each strain. Findings A marked reduction (p<0·0001) in the RA of total and specific bacterial strains, especially from phylum Firmicutes, was observed in RCDI patients prior to FMT. This change was associated with an increase in the DI (p<0·0001) and in pathobiont bacterial strains from phylum Proteobacteria, such as Escherichia coli O157:H7 and Klebsiella pneumoniae UCI 34. BSI was significantly lower in this group of patients as compared to healthy donors and correlated with the Shannon Index. (p<0·0001). Identification and engraftment of bacterial strains from healthy donors revealed a greater diversity and higher relative abundance of short-chain fatty acid (SCFA)-producing bacterial strains, including Lachnospiraceae bacterium 5_1_63FAA_u_t, Dorea formicigenerans ATCC 27755, Anaerostipes hadrusand others, in RCDI patients after FMT. Interpretation These observations identify a group of SCFA-producing bacterial strains from healthy donors that engraft well in patients with RCDI following FMT and are associated with complete resolution of clinical symptoms and bacterial dysbiosis.
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Affiliation(s)
- Sandeep Verma
- Division of Gastroenterology, Sinai Hospital, Baltimore MD, United States of America
- * E-mail:
| | - Sudhir K. Dutta
- Division of Gastroenterology, Sinai Hospital, Baltimore MD, United States of America
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Elad Firnberg
- Division of Gastroenterology, Sinai Hospital, Baltimore MD, United States of America
| | - Laila Phillips
- Division of Gastroenterology, Sinai Hospital, Baltimore MD, United States of America
| | - Rakesh Vinayek
- Division of Gastroenterology, Sinai Hospital, Baltimore MD, United States of America
| | - Padmanabhan P. Nair
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- Noninvasive Technologies, Elkridge, MD, United States of America
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Ausuri J, Vitale GA, Coppola D, Palma Esposito F, Buonocore C, de Pascale D. Assessment of the Degradation Potential and Genomic Insights towards Phenanthrene by Dietzia psychralcaliphila JI1D. Microorganisms 2021; 9:microorganisms9061327. [PMID: 34205451 PMCID: PMC8235520 DOI: 10.3390/microorganisms9061327] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
Extreme marine environments are potential sources of novel microbial isolations with dynamic metabolic activity. Dietzia psychralcaliphila J1ID was isolated from sediments originated from Deception Island, Antarctica, grown over phenanthrene. This strain was also assessed for its emulsifying activity. In liquid media, Dietzia psychralcaliphila J1ID showed 84.66% degradation of phenanthrene examined with HPLC-PDA. The identification of metabolites by GC-MS combined with its whole genome analysis provided the pathway involved in the degradation process. Whole genome sequencing indicated a genome size of 4,216,480 bp with 3961 annotated genes. The presence of a wide range of monooxygenase and dioxygenase, as well as dehydrogenase catabolic genes provided the genomic basis for the biodegradation. The strain possesses the genetic compartments for a wide range of toxic aromatic compounds, which includes the benABCD and catABC clusters. COG2146, COG4638, and COG0654 through COG analysis confirmed the genes involved in the oxygenation reaction of the hydrocarbons by the strain. Insights into assessing the depletion of phenanthrene throughout the incubation process and the genetic components involved were obtained. This study indicates the degradation potential of the strain, which can also be further expanded to other model polyaromatic hydrocarbons.
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Affiliation(s)
- Janardhan Ausuri
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy; (J.A.); (C.B.)
| | - Giovanni Andrea Vitale
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (G.A.V.); (D.C.); (F.P.E.)
| | - Daniela Coppola
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (G.A.V.); (D.C.); (F.P.E.)
| | - Fortunato Palma Esposito
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (G.A.V.); (D.C.); (F.P.E.)
| | - Carmine Buonocore
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy; (J.A.); (C.B.)
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (G.A.V.); (D.C.); (F.P.E.)
| | - Donatella de Pascale
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy; (J.A.); (C.B.)
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (G.A.V.); (D.C.); (F.P.E.)
- Correspondence: ; Tel.: +39-081-5833-319
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Microbial colonization of the gastrointestinal tract of dairy calves - a review of its importance and relationship to health and performance. Anim Health Res Rev 2021; 22:97-108. [PMID: 34132191 DOI: 10.1017/s1466252321000062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review aims to explain how microbial colonization of the gastrointestinal tract (GIT) in young dairy calves is related to health and, consequently, to the performance of these animals. The review addresses everything from the fundamental aspects of microbial colonization to the current understanding about the microbiota manipulation to improve performance in adult animals. The ruminal microbiota is the most studied, mainly due to the high interest in the fermentative aspects, the production of short-chain fatty acids, and microbial proteins, and its effects on animal production. However, in recent years, the intestinal microbiota has gained space between studies, mainly due to the relationship to the host health and how it affects performance. Understanding how the GIT's microbiota looks like and how it is colonized may allow future studies to predict the best timing for dietary interventions as a way to manipulate it and, consequently, improve the health and performance of young ruminants.
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10
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Lee HH, Park J, Jung H, Seo YS. Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli. Microorganisms 2021; 9:1123. [PMID: 34067383 PMCID: PMC8224644 DOI: 10.3390/microorganisms9061123] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Burkholderia gladioli has high versatility and adaptability to various ecological niches. Here, we constructed a pan-genome using 14 genome sequences of B. gladioli, which originate from different niches, including gladiolus, rice, humans, and nature. Functional roles of core and niche-associated genomes were investigated by pathway enrichment analyses. Consequently, we inferred the uniquely important role of niche-associated genomes in (1) selenium availability during competition with gladiolus host; (2) aromatic compound degradation in seed-borne and crude oil-accumulated environments, and (3) stress-induced DNA repair system/recombination in the cystic fibrosis-niche. We also identified the conservation of the rhizomide biosynthetic gene cluster in all the B. gladioli strains and the concentrated distribution of this cluster in human isolates. It was confirmed the absence of complete CRISPR/Cas system in both plant and human pathogenic B. gladioli and the presence of the system in B. gladioli living in nature, possibly reflecting the inverse relationship between CRISPR/Cas system and virulence.
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Affiliation(s)
- Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
- Environmental Microbiology Research Team, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Korea
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
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11
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Mahto KU, Das S. Whole genome characterization and phenanthrene catabolic pathway of a biofilm forming marine bacterium Pseudomonas aeruginosa PFL-P1. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 206:111087. [PMID: 32871516 DOI: 10.1016/j.ecoenv.2020.111087] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 05/02/2023]
Abstract
Pseudomonas aeruginosa is a small rod shaped Gram-negative bacterium of Gammaproteobacteria class known for its metabolic versatility. P. aeruginosa PFL-P1 was isolated from Polycyclic Aromatic Hydrocarbons (PAHs) contaminated site of Paradip Port, Odisha Coast, India. The strain showed excellent biofilm formation and could retain its ability to form biofilm grown with different PAHs in monoculture as well as co-cultures. To explore mechanistic insights of PAHs metabolism, the whole genome of the strain was sequenced. Next generation sequencing unfolded a genome size of 6,333,060 bp encoding 5857 CDSs. Gene ontology distribution assigned to a total of 2862 genes, wherein 2235 genes were allocated to biological process, 1549 genes to cellular component and 2339 genes to molecular function. A total of 318 horizontally transferred genes were identified when the genome was compared with the reference genomes of P. aeruginosa PAO1 and P. aeruginosa DSM 50071. Further comparison of P. aeruginosa PFL-P1 genome with P. putida containing TOL plasmids revealed similarities in the meta cleavage pathway employed for degradation of aromatic compounds like xylene and toluene. Gene annotation and pathway analysis unveiled 145 genes involved in xenobiotic biodegradation and metabolism. The biofilm cultures of P. aeruginosa PFL-P1 could degrade ~74% phenanthrene within 120 h while degradation increased up to ~76% in co-culture condition. GC-MS analysis indicated presence of diverse metabolites indicating the involvement of multiple pathways for one of the PAHs (phenanthrene) degradation. The strain also possesses the genetic machinery to utilize diverse toxic aromatic compounds such as naphthalene, benzoate, aminobenzoate, fluorobenzoate, toluene, xylene, styrene, atrazine, caprolactam etc. Common catabolic gene clusters such as benABCD, xylXYZ and catAB were observed within the genome of P. aeruginosa PFL-P1 which play key roles in the degradation of various toxic aromatic compounds.
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Affiliation(s)
- Kumari Uma Mahto
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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12
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Tripathi P, Singh J, Lal JA, Tripathi V. Next-Generation Sequencing: An Emerging Tool for Drug Designing. Curr Pharm Des 2020; 25:3350-3357. [PMID: 31544713 DOI: 10.2174/1381612825666190911155508] [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] [Received: 08/06/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. METHOD In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. DISCUSSIONS The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. CONCLUSION Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.
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Affiliation(s)
- Pooja Tripathi
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India
| | - Jyotsna Singh
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India
| | - Jonathan A Lal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India.,Institute for Public Health Genomics, Maastricht University, Maastricht, Netherlands
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India
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13
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Bedoya-Correa CM, Rincón Rodríguez RJ, Parada-Sanchez MT. Genomic and phenotypic diversity of Streptococcus mutans. J Oral Biosci 2019; 61:22-31. [DOI: 10.1016/j.job.2018.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/29/2018] [Accepted: 11/05/2018] [Indexed: 02/03/2023]
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14
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Pilo P, Frey J. Pathogenicity, population genetics and dissemination of Bacillus anthracis. INFECTION GENETICS AND EVOLUTION 2018; 64:115-125. [PMID: 29935338 DOI: 10.1016/j.meegid.2018.06.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 12/30/2022]
Abstract
Bacillus anthracis, the etiological agent of anthrax, procures its particular virulence by a capsule and two AB type toxins: the lethal factor LF and the edema factor EF. These toxins primarily disable immune cells. Both toxins are translocated to the host cell by the adhesin-internalin subunit called protective antigen PA. PA enables LF to reach intra-luminal vesicles, where it remains active for long periods. Subsequently, LF translocates to non-infected cells, leading to inefficient late therapy of anthrax. B. anthracis undergoes slow evolution because it alternates between vegetative and long spore phases. Full genome sequence analysis of a large number of worldwide strains resulted in a robust evolutionary reconstruction of this bacterium, showing that B. anthracis is split in three main clades: A, B and C. Clade A efficiently disseminated worldwide underpinned by human activities including heavy intercontinental trade of goat and sheep hair. Subclade A.Br.WNA, which is widespread in the Northern American continent, is estimated to have split from clade A reaching the Northern American continent in the late Pleistocene epoch via the former Bering Land Bridge and further spread from Northwest southwards. An alternative hypothesis is that subclade A.Br.WNA. evolved from clade A.Br.TEA tracing it back to strains from Northern France that were assumingly dispatched by European explorers that settled along the St. Lawrence River. Clade B established mostly in Europe along the alpine axis where it evolved in association with local cattle breeds and hence displays specific geographic subclusters. Sequencing technologies are also used for forensic applications to trace unintended or criminal acts of release of B. anthracis. Under natural conditions, B. anthracis generally affects domesticated and wild ruminants in arid ecosystems. The more recently discovered B. cereus biovar anthracis spreads in tropical forests, where it threatens particularly endangered primate populations.
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Affiliation(s)
- Paola Pilo
- Institute of Veterinary Bacteriology, Vetsuisse, University of Bern, Bern, Switzerland.
| | - Joachim Frey
- Dean's Office, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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15
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Complete genome sequence of the sesame pathogen Ralstonia solanacearum strain SEPPX 05. Genes Genomics 2018; 40:657-668. [PMID: 29892946 DOI: 10.1007/s13258-018-0667-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/04/2018] [Indexed: 10/18/2022]
Abstract
Ralstonia solanacearum is a soil-borne phytopathogen associated with bacterial wilt disease of sesame. R. solanacearum is the predominant agent causing damping-off from tropical to temperate regions. Because bacterial wilt has decreased the sesame industry yield, we sequenced the SEPPX05 genome using PacBio and Illumina HiSeq 2500 systems and revealed that R. solanacearum strain SEPPX05 carries a bipartite genome consisting of a 3,930,849 bp chromosome and a 2,066,085 bp megaplasmid with 66.84% G+C content that harbors 5,427 coding sequences. Based on the whole genome, phylogenetic analysis showed that strain SEPPX05 is grouped with two phylotype I strains (EP1 and GMI1000). Pan-genomic analysis shows that R. solanacearum is a complex species with high biological diversity and was able to colonize various environments during evolution. Despite deletions, insertions, and inversions, most genes of strain SEPPX05 have relatively high levels of synteny compared with strain GMI1000. We identified 104 genes involved in virulence-related factors in the SEPPX05 genome and eight absent genes encoding T3Es of GMI1000. Comparing SEPPX05 with other species, we found highly conserved secretion systems central to modulating interactions of host bacteria. These data may provide important clues for understanding underlying pathogenic mechanisms of R. solanacearum and help in the control of sesame bacterial wilt.
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16
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Caboche S, Even G, Loywick A, Audebert C, Hot D. MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data. Genome Biol 2017; 18:233. [PMID: 29258574 PMCID: PMC5738152 DOI: 10.1186/s13059-017-1367-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/30/2017] [Indexed: 12/15/2022] Open
Abstract
The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis. MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of antibiotic susceptibility and resistance and comparing the results of several samples. MICRA is fast, producing few false-positive annotations and variant calls compared to current methods, making it a tool of great interest for fully exploiting sequencing data.
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Affiliation(s)
- Ségolène Caboche
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France. .,PEGASE-Biosciences, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, 59019, Lille, France.
| | - Gaël Even
- Genes Diffusion, 3595, Route de Tournai, 59501, Douai, France.,PEGASE-Biosciences, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, 59019, Lille, France
| | - Alexandre Loywick
- Genes Diffusion, 3595, Route de Tournai, 59501, Douai, France.,PEGASE-Biosciences, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, 59019, Lille, France
| | - Christophe Audebert
- Genes Diffusion, 3595, Route de Tournai, 59501, Douai, France.,PEGASE-Biosciences, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, 59019, Lille, France
| | - David Hot
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France.,PEGASE-Biosciences, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, 59019, Lille, France
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17
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Exploring the Genomic Diversity and Cariogenic Differences of Streptococcus mutans Strains Through Pan-Genome and Comparative Genome Analysis. Curr Microbiol 2017; 74:1200-1209. [PMID: 28717847 DOI: 10.1007/s00284-017-1305-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 07/11/2017] [Indexed: 10/19/2022]
Abstract
Pan-genome refers to the sum of genes that can be found in a given bacterial species, including the core-genome and the dispensable genome. In this study, the genomes from 183 Streptococcus mutans (S. mutans) isolates were analyzed from the pan-genome perspective. This analysis revealed that S. mutans has an "open" pan-genome, implying that there are plenty of new genes to be found as more genomes are sequenced. Additionally, S. mutans has a limited core-genome, which is composed of genes related to vital activities within the bacterium, such as metabolism and hereditary information storage or processing, occupying 35.6 and 26.6% of the core genes, respectively. We estimate the theoretical core-genome size to be about 1083 genes, which are fewer than other Streptococcus species. In addition, core genes suffer larger selection pressures in comparison to those that are less widely distributed. Not surprisingly, the distribution of putative virulence genes in S. mutans strains does not correlate with caries status, indicating that other factors are also responsible for cariogenesis. These results contribute to a more understanding of the evolutionary characteristics and dynamic changes within the genome components of the species. This also helps to form a new theoretical foundation for preventing dental caries. Furthermore, this study sets an example for analyzing large genomic datasets of pathogens from the pan-genome perspective.
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18
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Price A, Gibas C. The quantitative impact of read mapping to non-native reference genomes in comparative RNA-Seq studies. PLoS One 2017; 12:e0180904. [PMID: 28700635 PMCID: PMC5507458 DOI: 10.1371/journal.pone.0180904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/22/2017] [Indexed: 11/18/2022] Open
Abstract
Sequence read alignment to a reference genome is a fundamental step in many genomics studies. Accuracy in this fundamental step is crucial for correct interpretation of biological data. In cases where two or more closely related bacterial strains are being studied, a common approach is to simply map reads from all strains to a common reference genome, whether because there is no closed reference for some strains or for ease of comparison. The assumption is that the differences between bacterial strains are insignificant enough that the results of differential expression analysis will not be influenced by choice of reference. Genes that are common among the strains under study are used for differential expression analysis, while the remaining genes, which may fail to express in one sample or the other because they are simply absent, are analyzed separately. In this study, we investigate the practice of using a common reference in transcriptomic analysis. We analyze two multi-strain transcriptomic data sets that were initially presented in the literature as comparisons based on a common reference, but which have available closed genomic sequence for all strains, allowing a detailed examination of the impact of reference choice. We provide a method for identifying regions that are most affected by non-native alignments, leading to false positives in differential expression analysis, and perform an in depth analysis identifying the extent of expression loss. We also simulate several data sets to identify best practices for non-native reference use.
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Affiliation(s)
- Adam Price
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Cynthia Gibas
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- * E-mail:
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19
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Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems? mSystems 2016; 1:mSystems00009-16. [PMID: 27822532 PMCID: PMC5069764 DOI: 10.1128/msystems.00009-16] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/11/2016] [Indexed: 01/01/2023] Open
Abstract
The evolution of bacterial pathogens, their plasticity and ability to rapidly change and adapt to new surroundings are crucial for understanding the epidemiology and public health. With the application of genomics, it became clear that horizontal gene transfer played a key role in evolution. To understand the evolution and diversification of pathogens, we need to understand the processes that drive the horizontal gene transfer. Restriction-modification systems are thought to cause rearrangements within the chromosome, as well as act as a barrier to horizontal gene transfer. However, here we show that the correlation between restriction-modification systems and evolution in other bacterial species does not apply to Salmonella enterica subsp. enterica. In summary, from this work, we conclude that other mechanisms might be involved in controlling and shaping the evolution of Salmonella enterica subsp. enterica. Salmonella enterica subsp. enterica bacteria are highly diverse foodborne pathogens that are subdivided into more than 1,500 serovars. The diversity is believed to result from mutational evolution, as well as intra- and interspecies recombination that potentially could be influenced by restriction-modification (RM) systems. The aim of this study was to investigate whether RM systems were linked to the evolution of Salmonella enterica subsp. enterica. The study included 221 Salmonella enterica genomes, of which 68 were de novo sequenced and 153 were public available genomes from ENA. The data set covered 97 different serovars of Salmonella enterica subsp. enterica and an additional five genomes from four other Salmonella subspecies as an outgroup for constructing the phylogenetic trees. The phylogenetic trees were constructed based on multiple alignment of core genes, as well as the presence or absence of pangenes. The topology of the trees was compared to the presence of RM systems, antimicrobial resistance (AMR) genes, Salmonella pathogenicity islands (SPIs), and plasmid replicons. We did not observe any correlation between evolution and the RM systems in S. enterica subsp. enterica. However, sublineage correlations and serovar-specific patterns were observed. Additionally, we conclude that plasmid replicons, SPIs, and AMR were all better correlated to serovars than to RM systems. This study suggests a limited influence of RM systems on the evolution of Salmonella enterica subsp. enterica, which could be due to the conjugational mode of horizontal gene transfer in Salmonella. Thus, we conclude that other factors must be involved in shaping the evolution of bacteria. IMPORTANCE The evolution of bacterial pathogens, their plasticity and ability to rapidly change and adapt to new surroundings are crucial for understanding the epidemiology and public health. With the application of genomics, it became clear that horizontal gene transfer played a key role in evolution. To understand the evolution and diversification of pathogens, we need to understand the processes that drive the horizontal gene transfer. Restriction-modification systems are thought to cause rearrangements within the chromosome, as well as act as a barrier to horizontal gene transfer. However, here we show that the correlation between restriction-modification systems and evolution in other bacterial species does not apply to Salmonella enterica subsp. enterica. In summary, from this work, we conclude that other mechanisms might be involved in controlling and shaping the evolution of Salmonella enterica subsp. enterica.
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20
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Abstract
Bacteria occur ubiquitously in nature and are broadly relevant throughout the food supply chain, with diverse and variable tolerance levels depending on their origin, biological role, and impact on the quality and safety of the product as well as on the health of the consumer. With increasing knowledge of and accessibility to the microbial composition of our environments, food supply, and host-associated microbiota, our understanding of and appreciation for the ratio of beneficial to undesirable bacteria are rapidly evolving. Therefore, there is a need for tools and technologies that allow definite, accurate, and high-resolution identification and typing of various groups of bacteria that include beneficial microbes such as starter cultures and probiotics, innocuous commensals, and undesirable pathogens and spoilage organisms. During the transition from the current molecular biology-based PFGE (pulsed-field gel electrophoresis) gold standard to the increasingly accessible omics-level whole-genome sequencing (WGS) N-gen standard, high-resolution technologies such as CRISPR-based genotyping constitute practical and powerful alternatives that provide valuable insights into genome microevolution and evolutionary trajectories. Indeed, several studies have shown potential for CRISPR-based typing of industrial starter cultures, health-promoting probiotic strains, animal commensal species, and problematic pathogens. Emerging CRISPR-based typing methods open new avenues for high-resolution typing of a broad range of bacteria and constitute a practical means for rapid tracking of a diversity of food-associated microbes.
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Affiliation(s)
- Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695; .,Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Edward G Dudley
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802;
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21
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Bentley SD, Parkhill J. Genomic perspectives on the evolution and spread of bacterial pathogens. Proc Biol Sci 2015; 282:20150488. [PMID: 26702036 PMCID: PMC4707741 DOI: 10.1098/rspb.2015.0488] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/19/2015] [Indexed: 12/22/2022] Open
Abstract
Since the first complete sequencing of a free-living organism, Haemophilus influenzae, genomics has been used to probe both the biology of bacterial pathogens and their evolution. Single-genome approaches provided information on the repertoire of virulence determinants and host-interaction factors, and, along with comparative analyses, allowed the proposal of hypotheses to explain the evolution of many of these traits. These analyses suggested many bacterial pathogens to be of relatively recent origin and identified genome degradation as a key aspect of host adaptation. The advent of very-high-throughput sequencing has allowed for detailed phylogenetic analysis of many important pathogens, revealing patterns of global and local spread, and recent evolution in response to pressure from therapeutics and the human immune system. Such analyses have shown that bacteria can evolve and transmit very rapidly, with emerging clones showing adaptation and global spread over years or decades. The resolution achieved with whole-genome sequencing has shown considerable benefits in clinical microbiology, enabling accurate outbreak tracking within hospitals and across continents. Continued large-scale sequencing promises many further insights into genetic determinants of drug resistance, virulence and transmission in bacterial pathogens.
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Affiliation(s)
- Stephen D Bentley
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Julian Parkhill
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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22
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Schmedes SE, King JL, Budowle B. Correcting Inconsistencies and Errors in Bacterial Genome Metadata Using an Automated Curation Tool in Excel (AutoCurE). Front Bioeng Biotechnol 2015; 3:138. [PMID: 26442252 PMCID: PMC4566056 DOI: 10.3389/fbioe.2015.00138] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/28/2015] [Indexed: 12/24/2022] Open
Abstract
Whole-genome data are invaluable for large-scale comparative genomic studies. Current sequencing technologies have made it feasible to sequence entire bacterial genomes with relative ease and time with a substantially reduced cost per nucleotide, hence cost per genome. More than 3,000 bacterial genomes have been sequenced and are available at the finished status. Publically available genomes can be readily downloaded; however, there are challenges to verify the specific supporting data contained within the download and to identify errors and inconsistencies that may be present within the organizational data content and metadata. AutoCurE, an automated tool for bacterial genome database curation in Excel, was developed to facilitate local database curation of supporting data that accompany downloaded genomes from the National Center for Biotechnology Information. AutoCurE provides an automated approach to curate local genomic databases by flagging inconsistencies or errors by comparing the downloaded supporting data to the genome reports to verify genome name, RefSeq accession numbers, the presence of archaea, BioProject/UIDs, and sequence file descriptions. Flags are generated for nine metadata fields if there are inconsistencies between the downloaded genomes and genomes reports and if erroneous or missing data are evident. AutoCurE is an easy-to-use tool for local database curation for large-scale genome data prior to downstream analyses.
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Affiliation(s)
- Sarah E Schmedes
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center , Fort Worth, TX , USA
| | - Jonathan L King
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center , Fort Worth, TX , USA
| | - Bruce Budowle
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center , Fort Worth, TX , USA ; Center of Excellence in Genomic Medicine Research, King Abdulaziz University , Jeddah , Saudi Arabia
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23
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Larson MA, Nalbantoglu U, Sayood K, Zentz EB, Bartling AM, Francesconi SC, Fey PD, Dempsey MP, Hinrichs SH. Francisella tularensis Subtype A.II Genomic Plasticity in Comparison with Subtype A.I. PLoS One 2015; 10:e0124906. [PMID: 25918839 PMCID: PMC4412822 DOI: 10.1371/journal.pone.0124906] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/09/2015] [Indexed: 11/26/2022] Open
Abstract
Although Francisella tularensis is considered a monomorphic intracellular pathogen, molecular genotyping and virulence studies have demonstrated important differences within the tularensis subspecies (type A). To evaluate genetic variation within type A strains, sequencing and assembly of a new subtype A.II genome was achieved for comparison to other completed F. tularensis type A genomes. In contrast with the F. tularensis A.I strains (SCHU S4, FSC198, NE061598, and TI0902), substantial genomic variation was observed between the newly sequenced F. tularensis A.II strain (WY-00W4114) and the only other publically available A.II strain (WY96-3418). Genome differences between WY-00W4114 and WY96-3418 included three major chromosomal translocations, 1580 indels, and 286 nucleotide substitutions of which 159 were observed in predicted open reading frames and 127 were located in intergenic regions. The majority of WY-00W4114 nucleotide deletions occurred in intergenic regions, whereas most of the insertions and substitutions occurred in predicted genes. Of the nucleotide substitutions, 48 (30%) were synonymous and 111 (70%) were nonsynonymous. WY-00W4114 and WY96-3418 nucleotide polymorphisms were predominantly G/C to A/T allelic mutations, with WY-00W4114 having more A+T enrichment. In addition, the A.II genomes contained a considerably higher number of intact genes and longer repetitive sequences, including transposon remnants than the A.I genomes. Together these findings support the premise that F. tularensis A.II may have a fitness advantage compared to the A.I subtype due to the higher abundance of functional genes and repeated chromosomal sequences. A better understanding of the selective forces driving F. tularensis genetic diversity and plasticity is needed.
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Affiliation(s)
- Marilynn A. Larson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
| | - Ufuk Nalbantoglu
- Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Khalid Sayood
- Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Emily B. Zentz
- OpGen Inc., Gaithersburg, Maryland, United States of America
| | - Amanda M. Bartling
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | | | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Michael P. Dempsey
- United States Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, Ohio, United States of America
| | - Steven H. Hinrichs
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
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24
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Yap KP, Gan HM, Teh CSJ, Chai LC, Thong KL. Comparative genomics of closely related Salmonella enterica serovar Typhi strains reveals genome dynamics and the acquisition of novel pathogenic elements. BMC Genomics 2014; 15:1007. [PMID: 25412680 PMCID: PMC4289253 DOI: 10.1186/1471-2164-15-1007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/06/2014] [Indexed: 12/31/2022] Open
Abstract
Background Typhoid fever is an infectious disease of global importance that is caused by Salmonella enterica subsp. enterica serovar Typhi (S. Typhi). This disease causes an estimated 200,000 deaths per year and remains a serious global health threat. S. Typhi is strictly a human pathogen, and some recovered individuals become long-term carriers who continue to shed the bacteria in their faeces, thus becoming main reservoirs of infection. Results A comparative genomics analysis combined with a phylogenomic analysis revealed that the strains from the outbreak and carrier were closely related with microvariations and possibly derived from a common ancestor. Additionally, the comparative genomics analysis with all of the other completely sequenced S. Typhi genomes revealed that strains BL196 and CR0044 exhibit unusual genomic variations despite S. Typhi being generally regarded as highly clonal. The two genomes shared distinct chromosomal architectures and uncommon genome features; notably, the presence of a ~10 kb novel genomic island containing uncharacterised virulence-related genes, and zot in particular. Variations were also detected in the T6SS system and genes that were related to SPI-10, insertion sequences, CRISPRs and nsSNPs among the studied genomes. Interestingly, the carrier strain CR0044 harboured far more genetic polymorphisms (83% mutant nsSNPs) compared with the closely related BL196 outbreak strain. Notably, the two highly related virulence-determinant genes, rpoS and tviE, were mutated in strains BL196 and CR0044, respectively, which revealed that the mutation in rpoS is stabilising, while that in tviE is destabilising. These microvariations provide novel insight into the optimisation of genes by the pathogens. However, the sporadic strain was found to be far more conserved compared with the others. Conclusions The uncommon genomic variations in the two closely related BL196 and CR0044 strains suggests that S. Typhi is more diverse than previously thought. Our study has demonstrated that the pathogen is continually acquiring new genes through horizontal gene transfer in the process of host adaptation, providing novel insight into its unusual genomic dynamics. The understanding of these strains and virulence factors, and particularly the strain that is associated with the large outbreak and the less studied asymptomatic Typhi carrier in the population, will have important impact on disease control. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1007) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Kwai Lin Thong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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Gao XY, Zhi XY, Li HW, Klenk HP, Li WJ. Comparative genomics of the bacterial genus Streptococcus illuminates evolutionary implications of species groups. PLoS One 2014; 9:e101229. [PMID: 24977706 PMCID: PMC4076318 DOI: 10.1371/journal.pone.0101229] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 06/04/2014] [Indexed: 11/18/2022] Open
Abstract
Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into “species groups”. However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups.
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Affiliation(s)
- Xiao-Yang Gao
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (X-YG); (W-JL)
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Hong-Wei Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- The First Hospital of Qujing City, Qujing Affiliated Hospital of Kunming Medical University, Qujing, China
| | - Hans-Peter Klenk
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- * E-mail: (X-YG); (W-JL)
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De Maayer P, Chan WY, Rubagotti E, Venter SN, Toth IK, Birch PRJ, Coutinho TA. Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts. BMC Genomics 2014; 15:404. [PMID: 24884520 PMCID: PMC4070556 DOI: 10.1186/1471-2164-15-404] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/20/2014] [Indexed: 11/10/2022] Open
Abstract
Background Pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. Some strains have proven effective as biological control agents and plant-growth promoters, while other strains have been implicated in diseases of a broad range of plant hosts and humans. By analysing the pan-genome of eight sequenced P. ananatis strains isolated from different sources we identified factors potentially underlying its ability to colonize and interact with hosts in both the plant and animal Kingdoms. Results The pan-genome of the eight compared P. ananatis strains consisted of a core genome comprised of 3,876 protein coding sequences (CDSs) and a sizeable accessory genome consisting of 1,690 CDSs. We estimate that ~106 unique CDSs would be added to the pan-genome with each additional P. ananatis genome sequenced in the future. The accessory fraction is derived mainly from integrated prophages and codes mostly for proteins of unknown function. Comparison of the translated CDSs on the P. ananatis pan-genome with the proteins encoded on all sequenced bacterial genomes currently available revealed that P. ananatis carries a number of CDSs with orthologs restricted to bacteria associated with distinct hosts, namely plant-, animal- and insect-associated bacteria. These CDSs encode proteins with putative roles in transport and metabolism of carbohydrate and amino acid substrates, adherence to host tissues, protection against plant and animal defense mechanisms and the biosynthesis of potential pathogenicity determinants including insecticidal peptides, phytotoxins and type VI secretion system effectors. Conclusions P. ananatis has an ‘open’ pan-genome typical of bacterial species that colonize several different environments. The pan-genome incorporates a large number of genes encoding proteins that may enable P. ananatis to colonize, persist in and potentially cause disease symptoms in a wide range of plant and animal hosts. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-404) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pieter De Maayer
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria 0002, South Africa.
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27
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O'Donovan D, Corcoran GD, Lucey B, Sleator RD. Campylobacter ureolyticus: a portrait of the pathogen. Virulence 2014; 5:498-506. [PMID: 24717836 PMCID: PMC4063811 DOI: 10.4161/viru.28776] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/03/2014] [Accepted: 04/03/2014] [Indexed: 01/29/2023] Open
Abstract
Herein, we provide a brief overview of the emerging bacterial pathogen Campylobacter ureolyticus. We describe the identification of the pathogen by molecular as opposed to classical culture based diagnostics and discuss candidate reservoirs of infection. We also review the available genomic data, outlining some of the major virulence factors, and discuss how these mechanisms likely contribute to pathogenesis of the organism.
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Affiliation(s)
- Dylan O'Donovan
- Department of Biological Sciences; Cork Institute of Technology; Bishopstown, Cork, Ireland
| | - Gerard D Corcoran
- Department of Diagnostic Microbiology; Cork University Hospital; Wilton, Cork, Ireland
| | - Brigid Lucey
- Department of Biological Sciences; Cork Institute of Technology; Bishopstown, Cork, Ireland
| | - Roy D Sleator
- Department of Biological Sciences; Cork Institute of Technology; Bishopstown, Cork, Ireland
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Corteggiani Carpinelli E, Telatin A, Vitulo N, Forcato C, D'Angelo M, Schiavon R, Vezzi A, Giacometti GM, Morosinotto T, Valle G. Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion. MOLECULAR PLANT 2014; 7:323-35. [PMID: 23966634 DOI: 10.1093/mp/sst120] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nannochloropsis is rapidly emerging as a model organism for the study of biofuel production in microalgae. Here, we report a high-quality genomic assembly of Nannochloropsis gaditana, consisting of large contigs, up to 500 kbp long, and scaffolds that in most cases span the entire length of the chromosomes. We identified 10646 complete genes and characterized possible alternative transcripts. The annotation of the predicted genes and the analysis of cellular processes revealed traits relevant for the genetic improvement of this organism such as genes involved in DNA recombination, RNA silencing, and cell wall synthesis. We also analyzed the modification of the transcriptional profile in nitrogen deficiency-a condition known to stimulate lipid accumulation. While the content of lipids increased, we did not detect major changes in expression of the genes involved in their biosynthesis. At the same time, we observed a very significant down-regulation of mitochondrial gene expression, suggesting that part of the Acetyl-CoA and NAD(P)H, normally oxidized through the mitochondrial respiration, would be made available for fatty acids synthesis, increasing the flux through the lipid biosynthetic pathway. Finally, we released an information resource of the genomic data of N. gaditana, available online at www.nannochloropsis.org.
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Palmer GH, Brayton KA. Antigenic variation and transmission fitness as drivers of bacterial strain structure. Cell Microbiol 2013; 15:1969-75. [PMID: 23941262 PMCID: PMC3836861 DOI: 10.1111/cmi.12182] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/05/2013] [Accepted: 08/08/2013] [Indexed: 11/29/2022]
Abstract
Shifts in microbial strain structure underlie both emergence of new pathogens and shifts in patterns of infection and disease of known agents. Understanding the selective pressures at a population level as well as the mechanisms at the molecular level represent significant gaps in our knowledge regarding microbial epidemiology. Highly antigenically variant pathogens, which are broadly represented among microbial taxa, are most commonly viewed through the mechanistic lens of how they evade immune clearance within the host. However, equally important are mechanisms that allow pathogens to evade immunity at the population level. The selective pressure of immunity at both the level of the individual host and the population is a driver of diversification within a pathogen strain. Using Anaplasma marginale as a model highly antigenically variable bacterial pathogen, we review how immunity selects for genetic diversification in alleles encoding outer membrane proteins both within and among strains. Importantly, genomic comparisons among strains isolated from diverse epidemiological settings elucidates the counterbalancing pressures for diversification and conservation, driven by immune escape and transmission fitness, respectively, and how these shape pathogen strain structure.
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Affiliation(s)
- Guy H. Palmer
- Paul G. Allen School for Global Animal Health, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington 99164-7090
| | - Kelly A. Brayton
- Paul G. Allen School for Global Animal Health, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington 99164-7090
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30
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He X, Marco ML, Slupsky CM. Emerging aspects of food and nutrition on gut microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:9559-9574. [PMID: 24028159 DOI: 10.1021/jf4029046] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The human gastrointestinal tract contains a highly complex ecosystem that harbors various microorganisms, which together create a unique environment within each individual. There is growing awareness that dietary habits are one of the essential factors contributing to the microbial diversity and community configuration that ultimately affects human health. From an evolutionary perspective, human dietary history can be viewed as a central factor in the selection of the gut microbial community and stabilization of the mutualistic host-microbial interaction, that together drive host phenotype. Herein, current knowledge concerning the influence of major dietary macrostructure and individual food ingredients is presented. This knowledge will provide perspectives for personalized gut microbiota management and, ultimately, movement toward an era of personalized nutrition and medicine.
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Affiliation(s)
- Xuan He
- Department of Nutrition and ‡Department of Food Science and Technology, University of California , Davis, California 95616, United States
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31
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Romano JD, Coppens I. Host Organelle Hijackers: a similar modus operandi for Toxoplasma gondii and Chlamydia trachomatis: co-infection model as a tool to investigate pathogenesis. Pathog Dis 2013; 69:72-86. [PMID: 23821471 DOI: 10.1111/2049-632x.12057] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 06/11/2013] [Accepted: 06/11/2013] [Indexed: 12/27/2022] Open
Abstract
The bacterium Chlamydia trachomatis and the protozoan parasite Toxoplasma gondii are the causative agents of chlamydiosis and toxoplasmosis in humans, respectively. Both microorganisms are obligate intracellular pathogens and notorious for extensively modifying the cytoskeletal architecture and the endomembrane system of their host cells to establish productive infections. This review highlights the similar tactics developed by these two pathogens to manipulate their host cell despite their genetic unrelatedness. Using an in vitro cell culture model whereby single fibroblasts are infected by C. trachomatis and T. gondii simultaneously, thus setting up an intracellular competition, we demonstrate that the solutions to the problem of intracellular survival deployed by the parasite and the bacterium may represent an example of convergent evolution, driven by the necessity to acquire nutrients in a hostile environment.
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Affiliation(s)
- Julia D Romano
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
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Romano JD, de Beaumont C, Carrasco JA, Ehrenman K, Bavoil PM, Coppens I. A novel co-infection model with Toxoplasma and Chlamydia trachomatis highlights the importance of host cell manipulation for nutrient scavenging. Cell Microbiol 2013; 15:619-46. [PMID: 23107293 PMCID: PMC3625693 DOI: 10.1111/cmi.12060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 09/14/2012] [Accepted: 10/20/2012] [Indexed: 12/24/2022]
Abstract
Toxoplasma and Chlamydia trachomatis are obligate intracellular pathogens that have evolved analogous strategies to replicate within mammalian cells. Both pathogens are known to extensively remodel the cytoskeleton, and to recruit endocytic and exocytic organelles to their respective vacuoles. However, how important these activities are for infectivity by either pathogen remains elusive. Here, we have developed a novel co-infection system to gain insights into the developmental cycles of Toxoplasma and C. trachomatis by infecting human cells with both pathogens, and examining their respective ability to replicate and scavenge nutrients. We hypothesize that the common strategies used by Toxoplasma and Chlamydia to achieve development results in direct competition of the two pathogens for the same pool of nutrients. We show that a single human cell can harbour Chlamydia and Toxoplasma. In co-infected cells, Toxoplasma is able to divert the content of host organelles, such as cholesterol. Consequently, the infectious cycle of Toxoplasma progresses unimpeded. In contrast, Chlamydia's ability to scavenge selected nutrients is diminished, and the bacterium shifts to a stress-induced persistent growth. Parasite killing engenders an ordered return to normal chlamydial development. We demonstrate that C. trachomatis enters a stress-induced persistence phenotype as a direct result from being barred from its normal nutrient supplies as addition of excess nutrients, e.g. amino acids, leads to substantial recovery of Chlamydia growth and infectivity. Co-infection of C. trachomatis with slow growing strains of Toxoplasma or a mutant impaired in nutrient acquisition does not restrict chlamydial development. Conversely, Toxoplasma growth is halted in cells infected with the highly virulent Chlamydia psittaci. This study illustrates the key role that cellular remodelling plays in the exploitation of host intracellular resources by Toxoplasma and Chlamydia. It further highlights the delicate balance between success and failure of infection by intracellular pathogens in a co-infection system at the cellular level.
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Affiliation(s)
- Julia D. Romano
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Catherine de Beaumont
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jose A. Carrasco
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, USA
| | - Karen Ehrenman
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Patrik M. Bavoil
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, USA
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
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Nunes A, Borrego MJ, Gomes JP. Genomic features beyond Chlamydia trachomatis phenotypes: what do we think we know? INFECTION GENETICS AND EVOLUTION 2013; 16:392-400. [PMID: 23523596 DOI: 10.1016/j.meegid.2013.03.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/25/2013] [Accepted: 03/13/2013] [Indexed: 10/27/2022]
Abstract
The obligate intracellular pathogen Chlamydia trachomatis is the causative agent of the blinding trachoma and the world's leading cause of bacterial sexually transmitted infections. Despite aggressive antibacterial control measures, C. trachomatis infections have been increasing, constituting a serious public health concern due to its morbidity and socioeconomic burden. Still, very little is known about the molecular basis underlying the phenotypic disparities observed among C. trachomatis serovars in terms of tissue tropism (ocular conjunctiva, epithelial-genitalia and lymph nodes), virulence (disease outcomes) and ecological success. This is in part due to the inexistence of straightforward tools to genetically manipulate Chlamydiae and host cell-free growth systems, hampering the elucidation of the biological role of loci. The recent release of tenths of full-genome C. trachomatis sequences depict a strains clustering scenario reflecting the organ/cell-type that they preferentially infect. However, the high degree of genomic conservation implies that few genetic features are involved in phenotypic dissimilarities. The purpose of this review is to gather the most relevant data dispersed throughout the literature concerning the genotypic evidences that support niche-specific phenotypes. This review focus on chromosomal dynamics phenomena like recombination and point-mutations, essentially involving outer and inclusion membrane proteins, type III secretion effectors, and hypothetical proteins with unknown function. The scrutiny of C. trachomatis loci involved in tissue tropism, pathogenesis and ecological success is crucial for the development of disease-specific prophylaxis.
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Affiliation(s)
- Alexandra Nunes
- Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal.
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Xu X, Xu P, Ma C, Tang J, Zhang X. Gut microbiota, host health, and polysaccharides. Biotechnol Adv 2012; 31:318-37. [PMID: 23280014 DOI: 10.1016/j.biotechadv.2012.12.009] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 12/20/2012] [Accepted: 12/21/2012] [Indexed: 02/07/2023]
Abstract
The intestinal microbiota is a complicated ecosystem that influences many aspects of host physiology (i.e. diet, disease development, drug metabolism, and regulation of the immune system). It also exhibits spatial patterning and temporal dynamics. In this review, the effects of internal and external (environmental) factors on intestinal microbiota are discussed. We describe the roles of the gut microbiota in maintaining intestinal and immune system homeostasis and the relationship between gut microbiota and diseases. In particular, the contributions of polysaccharides, as the most abundant diet components in intestinal microbiota and host health are presented. Finally, perspectives for research avenues relating to gut microbiota are also discussed.
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Affiliation(s)
- Xiaofei Xu
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
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Fierce competition between Toxoplasma and Chlamydia for host cell structures in dually infected cells. EUKARYOTIC CELL 2012; 12:265-77. [PMID: 23243063 DOI: 10.1128/ec.00313-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The prokaryote Chlamydia trachomatis and the protozoan Toxoplasma gondii, two obligate intracellular pathogens of humans, have evolved a similar modus operandi to colonize their host cell and salvage nutrients from organelles. In order to gain fundamental knowledge on the pathogenicity of these microorganisms, we have established a cell culture model whereby single fibroblasts are coinfected by C. trachomatis and T. gondii. We previously reported that the two pathogens compete for the same nutrient pools in coinfected cells and that Toxoplasma holds a significant competitive advantage over Chlamydia. Here we have expanded our coinfection studies by examining the respective abilities of Chlamydia and Toxoplasma to co-opt the host cytoskeleton and recruit organelles. We demonstrate that the two pathogen-containing vacuoles migrate independently to the host perinuclear region and rearrange the host microtubular network around each vacuole. However, Toxoplasma outcompetes Chlamydia to the host microtubule-organizing center to the detriment of the bacterium, which then shifts to a stress-induced persistent state. Solely in cells preinfected with Chlamydia, the centrosomes become associated with the chlamydial inclusion, while the Toxoplasma parasitophorous vacuole displays growth defects. Both pathogens fragment the host Golgi apparatus and recruit Golgi elements to retrieve sphingolipids. This study demonstrates that the productive infection by both Chlamydia and Toxoplasma depends on the capability of each pathogen to successfully adhere to a finely tuned developmental program that aims to remodel the host cell for the pathogen's benefit. In particular, this investigation emphasizes the essentiality of host organelle interception by intravacuolar pathogens to facilitate access to nutrients.
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Hsiao WW, Li KL, Liu Z, Jones C, Fraser-Liggett CM, Fouad AF. Microbial transformation from normal oral microbiota to acute endodontic infections. BMC Genomics 2012; 13:345. [PMID: 22839737 PMCID: PMC3431219 DOI: 10.1186/1471-2164-13-345] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 07/28/2012] [Indexed: 12/24/2022] Open
Abstract
Background Endodontic infections are a leading cause of oro-facial pain and tooth loss in western countries, and may lead to severe life-threatening infections. These infections are polymicrobial with high bacterial diversity. Understanding the spatial transition of microbiota from normal oral cavities through the infected root canal to the acute periapical abscess can improve our knowledge of the pathogenesis of endodontic infections and lead to more effective treatment. We obtained samples from the oral cavity, infected root canal and periapical abscess of 8 patients (5 with localized and 3 with systemic infections). Microbial populations in these samples were analyzed using next-generation sequencing of 16S rRNA amplicons. Bioinformatics tools and statistical tests with rigorous criteria were used to elucidate the spatial transition of the microbiota from normal to diseased sites. Results On average, 10,000 partial 16S rRNA gene sequences were obtained from each sample. All sequences fell into 11 different bacterial phyla. The microbial diversity in root canal and abscess samples was significantly lower than in the oral samples. Streptococcus was the most abundant genus in oral cavities while Prevotella and Fusobacterium were most abundant in diseased samples. The microbiota community structures of root canal and abscess samples were, however, more similar to each other than to the oral cavity microbiota. Using rigorous criteria and novel bioinformatics tools, we found that Granulicatella adiacens, Eubacterium yurii, Prevotella melaninogenica, Prevotella salivae, Streptococcus mitis, and Atopobium rimae were over-represented in diseased samples. Conclusions We used a novel approach and high-throughput methodologies to characterize the microbiota associated normal and diseased oral sites in the same individuals.
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Affiliation(s)
- William Wl Hsiao
- University of Maryland School of Dentistry, Department of Endodontics, Prosthodontics and Operative Dentistry, Baltimore, MD 20201, USA
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Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia. J Bacteriol 2012; 194:3199-215. [PMID: 22505676 DOI: 10.1128/jb.00183-12] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corynebacterium diphtheriae is one of the most prominent human pathogens and the causative agent of the communicable disease diphtheria. The genomes of 12 strains isolated from patients with classical diphtheria, endocarditis, and pneumonia were completely sequenced and annotated. Including the genome of C. diphtheriae NCTC 13129, we herewith present a comprehensive comparative analysis of 13 strains and the first characterization of the pangenome of the species C. diphtheriae. Comparative genomics showed extensive synteny and revealed a core genome consisting of 1,632 conserved genes. The pangenome currently comprises 4,786 protein-coding regions and increases at an average of 65 unique genes per newly sequenced strain. Analysis of prophages carrying the diphtheria toxin gene tox revealed that the toxoid vaccine producer C. diphtheriae Park-Williams no. 8 has been lysogenized by two copies of the ω(tox)(+) phage, whereas C. diphtheriae 31A harbors a hitherto-unknown tox(+) corynephage. DNA binding sites of the tox-controlling regulator DtxR were detected by genome-wide motif searches. Comparative content analysis showed that the DtxR regulons exhibit marked differences due to gene gain, gene loss, partial gene deletion, and DtxR binding site depletion. Most predicted pathogenicity islands of C. diphtheriae revealed characteristics of horizontal gene transfer. The majority of these islands encode subunits of adhesive pili, which can play important roles in adhesion of C. diphtheriae to different host tissues. All sequenced isolates contain at least two pilus gene clusters. It appears that variation in the distributed genome is a common strategy of C. diphtheriae to establish differences in host-pathogen interactions.
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Pina-Pedrero S, Olvera A, Pérez-Simó M, Bensaid A. Genomic and antigenic characterization of monomeric autotransporters of Haemophilus parasuis: an ongoing process of reductive evolution. MICROBIOLOGY-SGM 2011; 158:436-447. [PMID: 22075024 DOI: 10.1099/mic.0.052399-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genome of the highly pathogenic Haemophilus parasuis Nagasaki strain (serovar 5) was sequenced to 99 % completion. A genomic comparison with two other pathogenic serovar 5 H. parasuis strains identified six genes per genome (bmaA1-bmaA6) encoding β-barrel monomeric autotransporters, bmaA2 and bmaA3 being pseudogenes in at least one strain. The remaining encoded proteins were predicted to belong to the subtilisin (BmaA1 and BmaA4) and cysteine (BmaA5 and BmaA6) protease families. Allelic polymorphism was detected in other H. parasuis strains by comparative genomic hybridization using microarrays. Recombination events were observed, some of them leading to gene disruption in one of the three strains, although synteny around bmaA genes was conserved. These results suggest that bmaA genes are undergoing a process of reductive evolution. To evaluate their use as potential vaccine antigens, the products of the passenger domains of bmaA1, bmaA4, bmaA5 and bmaA6 were produced in Escherichia coli as recombinant proteins. They were detected by immunoblotting using sera of colostrum-deprived piglets recovering from a sublethal infection with H. parasuis (Nagasaki). The existence of specific antibodies after infection with H. parasuis also demonstrated in vivo expression. Using proteomics, only BmaA6 was detected in the in vitro-grown Nagasaki strain. Interestingly, the translocator domain was found in the outer membrane, while the passenger domain was located in supernatants. These results indicate that BmaA proteins could be considered as immunogen candidates to improve H. parasuis vaccines. However, their capacity to confer protective immunity needs to be studied further.
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Affiliation(s)
- Sonia Pina-Pedrero
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Alex Olvera
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Marta Pérez-Simó
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Albert Bensaid
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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Microbial systematics in the post-genomics era. Antonie van Leeuwenhoek 2011; 101:45-54. [DOI: 10.1007/s10482-011-9663-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 10/15/2011] [Indexed: 10/16/2022]
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Affiliation(s)
- David A Relman
- Department of Medicine, Stanford University, Stanford, California, USA.
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Mahmoud A, Zerhouni E. Neglected tropical diseases: moving beyond mass drug treatment to understanding the science. Health Aff (Millwood) 2011; 28:1726-33. [PMID: 19887413 DOI: 10.1377/hlthaff.28.6.1726] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Neglected tropical diseases (NTDs) represent a major health burden in many developing countries. To date, global efforts to control thirteen parasitic and bacterial infections that affect more than 1.4 billion people have relied on mass drug administration. This singular approach should now be expanded to a more comprehensive suite of tools including coordinated community-based programs, vector control, local training, education, and environmental change. In addition, an intensive basic research agenda is urgently needed to develop effective diagnostic, preventive, and therapeutic interventions to stay one step ahead of the evolutionary adaptation tactics of disease-causing microbes and parasites.
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Affiliation(s)
- Adel Mahmoud
- Department of Molecular Biology and Woodrow Wilson School, Princeton University
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Abstract
Bacterial gene content variation during the course of evolution has been widely acknowledged and its pattern has been actively modeled in recent years. Gene truncation or gene pseudogenization also plays an important role in shaping bacterial genome content. Truncated genes could also arise from small-scale lateral gene transfer events. Unfortunately, the information of truncated genes has not been considered in any existing mathematical models on gene content variation. In this study, we developed a model to incorporate truncated genes. Maximum-likelihood estimates (MLEs) of the new model reveal fast rates of gene insertions/deletions on recent branches, suggesting a fast turnover of many recently transferred genes. The estimates also suggest that many truncated genes are in the process of being eliminated from the genome. Furthermore, we demonstrate that the ignorance of truncated genes in the estimation does not lead to a systematic bias but rather has a more complicated effect. Analysis using the new model not only provides more accurate estimates on gene gains/losses (or insertions/deletions), but also reduces any concern of a systematic bias from applying simplified models to bacterial genome evolution. Although not a primary purpose, the model incorporating truncated genes could be potentially used for phylogeny reconstruction using gene family content.
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Havelaar AH, Brul S, de Jong A, de Jonge R, Zwietering MH, ter Kuile BH. Future challenges to microbial food safety. Int J Food Microbiol 2010; 139 Suppl 1:S79-94. [DOI: 10.1016/j.ijfoodmicro.2009.10.015] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 10/09/2009] [Accepted: 10/14/2009] [Indexed: 11/29/2022]
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Affiliation(s)
- M Begley
- Food for Health Ireland, University College Cork, Cork, Ireland
| | - Colin Hill
- Food for Health Ireland, University College Cork, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland; ,
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Maruyama F, Kobata M, Kurokawa K, Nishida K, Sakurai A, Nakano K, Nomura R, Kawabata S, Ooshima T, Nakai K, Hattori M, Hamada S, Nakagawa I. Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content. BMC Genomics 2009; 10:358. [PMID: 19656368 PMCID: PMC2907686 DOI: 10.1186/1471-2164-10-358] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 08/05/2009] [Indexed: 11/20/2022] Open
Abstract
Background Streptococcus mutans is the major pathogen of dental caries, and it occasionally causes infective endocarditis. While the pathogenicity of this species is distinct from other human pathogenic streptococci, the species-specific evolution of the genus Streptococcus and its genomic diversity are poorly understood. Results We have sequenced the complete genome of S. mutans serotype c strain NN2025, and compared it with the genome of UA159. The NN2025 genome is composed of 2,013,587 bp, and the two strains show highly conserved core-genome. However, comparison of the two S. mutans strains showed a large genomic inversion across the replication axis producing an X-shaped symmetrical DNA dot plot. This phenomenon was also observed between other streptococcal species, indicating that streptococcal genetic rearrangements across the replication axis play an important role in Streptococcus genetic shuffling. We further confirmed the genomic diversity among 95 clinical isolates using long-PCR analysis. Genomic diversity in S. mutans appears to occur frequently between insertion sequence (IS) elements and transposons, and these diversity regions consist of restriction/modification systems, antimicrobial peptide synthesis systems, and transporters. S. mutans may preferentially reject the phage infection by clustered regularly interspaced short palindromic repeats (CRISPRs). In particular, the CRISPR-2 region, which is highly divergent between strains, in NN2025 has long repeated spacer sequences corresponding to the streptococcal phage genome. Conclusion These observations suggest that S. mutans strains evolve through chromosomal shuffling and that phage infection is not needed for gene acquisition. In contrast, S. pyogenes tolerates phage infection for acquisition of virulence determinants for niche adaptation.
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Affiliation(s)
- Fumito Maruyama
- Division of Bacteriology, Department of Infectious Diseases Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.
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Human Microbiome Project--paving the way to a better understanding of ourselves and our microbes. Drug Discov Today 2009; 14:331-3. [PMID: 19340927 DOI: 10.1016/j.drudis.2009.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Alam SI, Dixit A, Tomar A, Singh L. Comparative genomic analysis of a neurotoxigenic Clostridium species using partial genome sequence: Phylogenetic analysis of a few conserved proteins involved in cellular processes and metabolism. Anaerobe 2009; 16:147-54. [PMID: 19527791 DOI: 10.1016/j.anaerobe.2009.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 04/27/2009] [Accepted: 06/03/2009] [Indexed: 11/18/2022]
Abstract
Clostridial organisms produce neurotoxins, which are generally regarded as the most potent toxic substances of biological origin and potential biological warfare agents. Clostridium tetani produces tetanus neurotoxin and is responsible for the fatal tetanus disease. In spite of the extensive immunization regimen, the disease is an important cause of death especially among neonates. Strains of C. tetani have not been genetically characterized except the complete genome sequencing of strain E88. The present study reports the genetic makeup and phylogenetic affiliations of an environmental strain of this bacterium with respect to C. tetani E88 and other clostridia. A shot gun library was constructed from the genomic DNA of C. tetani drde, isolated from decaying fish sample. Unique clones were sequenced and sequences compared with its closest relative C. tetani E88. A total of 275 clones were obtained and 32,457 bases of non-redundant sequence were generated. A total of 150 base changes were observed over the entire length of sequence obtained, including, additions, deletions and base substitutions. Of the total 120 ORFs detected, 48 exhibited closest similarity to E88 proteins of which three are hypothetical proteins. Eight of the ORFs exhibited similarity with hypothetical proteins from other organisms and 10 aligned with other proteins from unrelated organisms. There is an overall conservation of protein sequences among the two strains of C. tetani and. Selected ORFs involved in cellular processes and metabolism were subjected to phylogenetic analysis.
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Affiliation(s)
- Syed Imteyaz Alam
- Biotechnology Division, Defence Research & Development Establishment, Gwalior 474002, India.
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Abstract
Lateral gene transfer (LGT) and gene rearrangement are essential for shaping bacterial genomes during evolution. Separate attention has been focused on understanding the process of lateral gene transfer and the process of gene translocation. However, little is known about how gene translocation affects laterally transferred genes. Here we have examined gene translocations and lateral gene transfers in closely related genome pairs. The results reveal that translocated genes undergo elevated rates of evolution and gene translocation tends to take place preferentially in recently acquired genes. Translocated genes have a high probability to be truncated, suggesting that translocation followed by truncation/deletion might play an important role in the fast turnover of laterally transferred genes. Furthermore, more recently acquired genes have a higher proportion of genes on the leading strand, suggesting a strong strand bias of lateral gene transfer.
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Fournier PE, El Karkouri K, Leroy Q, Robert C, Giumelli B, Renesto P, Socolovschi C, Parola P, Audic S, Raoult D. Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction. BMC Genomics 2009; 10:166. [PMID: 19379498 PMCID: PMC2694212 DOI: 10.1186/1471-2164-10-166] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 04/20/2009] [Indexed: 11/13/2022] Open
Abstract
Background The Rickettsia genus includes 25 validated species, 17 of which are proven human pathogens. Among these, the pathogenicity varies greatly, from the highly virulent R. prowazekii, which causes epidemic typhus and kills its arthropod host, to the mild pathogen R. africae, the agent of African tick-bite fever, which does not affect the fitness of its tick vector. Results We evaluated the clonality of R. africae in 70 patients and 155 ticks, and determined its genome sequence, which comprises a circular chromosome of 1,278,540 bp including a tra operon and an unstable 12,377-bp plasmid. To study the genetic characteristics associated with virulence, we compared this species to R. prowazekii, R. rickettsii and R. conorii. R. africae and R. prowazekii have, respectively, the less and most decayed genomes. Eighteen genes are present only in R. africae including one with a putative protease domain upregulated at 37°C. Conclusion Based on these data, we speculate that a loss of regulatory genes causes an increase of virulence of rickettsial species in ticks and mammals. We also speculate that in Rickettsia species virulence is mostly associated with gene loss. The genome sequence was deposited in GenBank under accession number [GenBank: NZ_AAUY01000001].
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Affiliation(s)
- Pierre-Edouard Fournier
- Unité des rickettsies, IFR 48 CNRS UMR 6020, Faculté de médecine, Université de la Méditerranée, 27 Boulevard Jean Moulin, Marseille cedex 05, France.
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