INTRODUCTION Many Vibrio Species Are Recognized As
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Genomics 98 (2011) 370–375
Genomics 98 (2011) 370–375 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae Hiromi Nishida a,⁎, Teruhiko Beppu b, Kenji Ueda b a Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan b Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan article info abstract Article history: The anaerobic thermophilic bacterial genus Dictyoglomus is characterized by the ability to produce useful Received 2 June 2011 enzymes such as amylase, mannanase, and xylanase. Despite the significance, the phylogenetic position of Accepted 1 August 2011 Dictyoglomus has not yet been clarified, since it exhibits ambiguous phylogenetic positions in a single gene Available online 7 August 2011 sequence comparison-based analysis. The number of substitutions at the diverging point of Dictyoglomus is insufficient to show the relationships in a single gene comparison-based analysis. Hence, we studied its Keywords: evolutionary trait based on whole-genome comparison. Both gene content and orthologous protein sequence Whole-genome comparison Dictyoglomus comparisons indicated that Dictyoglomus is most closely related to the phylum Thermotogae and it forms a Bacterial systematics monophyletic group with Coprothermobacter proteolyticus (a constituent of the phylum Firmicutes) and Coprothermobacter proteolyticus Thermotogae. Our findings indicate that C. proteolyticus does not belong to the phylum Firmicutes and that the Thermotogae phylum Dictyoglomi is not closely related to either the phylum Firmicutes or Synergistetes but to the phylum Thermotogae. © 2011 Elsevier Inc. -
Vibrio Species in an Urban Tropical Estuary: Antimicrobial Susceptibility, Interaction with Environmental Parameters, and Possible Public Health Outcomes
microorganisms Article Vibrio Species in an Urban Tropical Estuary: Antimicrobial Susceptibility, Interaction with Environmental Parameters, and Possible Public Health Outcomes Anna L. B. Canellas 1 , Isabelle R. Lopes 1 , Marianne P. Mello 2, Rodolfo Paranhos 2, Bruno F. R. de Oliveira 1 and Marinella S. Laport 1,* 1 Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; [email protected] (A.L.B.C.); [email protected] (I.R.L.); [email protected] (B.F.R.d.O.) 2 Departamento de Biologia Marinha, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941617, Brazil; [email protected] (M.P.M.); [email protected] (R.P.) * Correspondence: [email protected] Abstract: The genus Vibrio comprises pathogens ubiquitous to marine environments. This study evaluated the cultivable Vibrio community in the Guanabara Bay (GB), a recreational, yet heavily polluted estuary in Rio de Janeiro, Brazil. Over one year, 66 water samples from three locations along a pollution gradient were investigated. Isolates were identified by MALDI-TOF mass spectrometry, revealing 20 Vibrio species, including several potential pathogens. Antimicrobial susceptibility testing confirmed resistance to aminoglycosides, beta-lactams (including carbapenems and third-generation cephalosporins), fluoroquinolones, sulfonamides, and tetracyclines. Four strains were producers Citation: Canellas, A.L.B.; Lopes, of extended-spectrum beta-lactamases (ESBL), all of which carried beta-lactam and heavy metal I.R.; Mello, M.P.; Paranhos, R.; de resistance genes. The toxR gene was detected in all V. parahaemolyticus strains, although none carried Oliveira, B.F.R.; Laport, M.S. -
Evaluation of the Natural Prevalence of Vibrio Spp. in Uruguayan Mussels
XA0100969 EVALUATION OF THE NATURAL PREVALENCE OF VIBRIO SPR IN URUGUAYAN MUSSELS (MYTILUS SP.) AND THEIR CONTROL USING IRRADIATION C. LOPEZ Laboratorio de Tecnicas Nucleares, Facultad de Veterinaria, Universidad de la Republica, Uruguay Abstract The presence of potentially pathogenic bacteria belonging to the Vibrionacea, especially Vibrio cholerae, and of Salmonella spp., was examined in fresh Uruguayan mussels (Mytilus sp.) during two annual seasons. The radiation decimal reduction dose (Dio) of various toxigenic strains of Vibrio cholerae was determined to vary in vitro between 0.11 and 0.19 kGy. These results and those from the examination of natural Vibrio spp. contamination in mussles were used to conclude that 1.0 kGy would be enough to render Uruguayan mussels Vibrio-safe. Mussels irradiated in the shell at the optimal dose survived long enough to allow the eventual introduction of irradiation as an effective intervention measure without affecting local marketing practices, and making it possible to market the fresh mussels live, as required by Uruguayan legislation. INTRODUCTION The Vibrionaceae are a family of facultatively anaerobic, halophilic, Gram-negative rods, polarly flagellated, motile bacteria that comprises 28 species, of which 11 are potential human pathogens (De Paola, 1981). Most of the Vibrio spp. are marine microorganisms, hence their natural occurrence in many raw seafood. Among the most prevalent species of Vibrio is V. parahaemolyticus, a fast growing bacterium that resists high salt concentrations (Battisti, R. and Moretto, E., 1994). It is reported to be the main cause of gastroenteritis in Japan, where there is a large consumption of raw fish. Vibrio vulnificus, another pathogenic species of the Vibrionaceae, is a pleomorphic, short rod that requires high salt concentrations for growth. -
Genomic Signatures of Predatory Bacteria
The ISME Journal (2013) 7, 756–769 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE By their genes ye shall know them: genomic signatures of predatory bacteria Zohar Pasternak1, Shmuel Pietrokovski2, Or Rotem1, Uri Gophna3, Mor N Lurie-Weinberger3 and Edouard Jurkevitch1 1Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel; 2Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel and 3Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel Predatory bacteria are taxonomically disparate, exhibit diverse predatory strategies and are widely distributed in varied environments. To date, their predatory phenotypes cannot be discerned in genome sequence data thereby limiting our understanding of bacterial predation, and of its impact in nature. Here, we define the ‘predatome,’ that is, sets of protein families that reflect the phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria from across the phylogenetic and ecological landscapes were compared. Protein families discriminating between the two groups were identified and quantified, demonstrating that differences in the proteomes of predatory and non-predatory bacteria are large and significant. This analysis allows predictions to be made, as we show by confirming from genome data an over-looked bacterial predator. The predatome exhibits deficiencies in riboflavin and amino acids biosynthesis, suggesting that predators obtain them from their prey. In contrast, these genomes are highly enriched in adhesins, proteases and particular metabolic proteins, used for binding to, processing and consuming prey, respectively. -
Interactions Between the Human Pathogen Vibrio Parahaemolyticus and Common Marine Microalgae
Current Trends in Microbiology Vol. 12, 2018 Interactions between the human pathogen Vibrio parahaemolyticus and common marine microalgae Savannah L. Klein, Katherine E. Haney, Thomas M. Hornaday, India B. Gartmon and Charles R. Lovell* Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, 29208, USA. ABSTRACT KEYWORDS: Vibrio parahaemolyticus, tdh, trh, T3SS2, T6SS, microalgae. Vibrio parahaemolyticus is a gastrointestinal pathogen that is abundant in coastal marine environments. Elevated numbers of V. parahaemolyticus cells INTRODUCTION have been correlated with marine microalgae Vibrio parahaemolyticus, a common organism in blooms, particularly blooms of diatoms and coastal environments, is a significant and sometimes dinoflagellates, but the nature of the relationship pandemic human pathogen responsible for an between V. parahaemolyticus and microalgae is estimated 34,000 cases of seafood-associated unknown. We performed in vitro assays using 27 gastroenteritis per year in the United States [1]. Most environmental V. parahaemolyticus strains and cases of V. parahaemolyticus-induced gastroenteritis various phototrophs; a diatom, a dinoflagellate, are self-limiting and relatively mild, but infections unarmored and armored forms of a coccolithophore, can be deadly in immunocompromised individuals. and two species of cyanobacteria. The V. The common mode of transmission of this parahaemolyticus strains we employed contained bacterium to the human host is ingestion of raw or different combinations of virulence-correlated genes, undercooked shellfish, primarily oysters. In addition, the hemolysin genes tdh and trh, the Type III some strains of V. parahaemolyticus can infect Secretion System 2 (T3SS2) marker gene vscC2, wounds and some produce systemic infections, and the Type VI Secretion System (T6SS) marker while others are apparently non-pathogenic. -
BACTERIAL and PHAGE INTERACTIONS INFLUENCING Vibrio Parahaemolyticus ECOLOGY
University of New Hampshire University of New Hampshire Scholars' Repository Master's Theses and Capstones Student Scholarship Spring 2016 BACTERIAL AND PHAGE INTERACTIONS INFLUENCING Vibrio parahaemolyticus ECOLOGY Ashley L. Marcinkiewicz University of New Hampshire, Durham Follow this and additional works at: https://scholars.unh.edu/thesis Recommended Citation Marcinkiewicz, Ashley L., "BACTERIAL AND PHAGE INTERACTIONS INFLUENCING Vibrio parahaemolyticus ECOLOGY" (2016). Master's Theses and Capstones. 852. https://scholars.unh.edu/thesis/852 This Thesis is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Master's Theses and Capstones by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. BACTERIAL AND PHAGE INTERACTIONS INFLUENCING Vibrio parahaemolyticus ECOLOGY BY ASHLEY MARCINKIEWICZ Bachelor of Arts, Wells College, 2011 THESIS Submitted to the University of New Hampshire In Partial Fulfillment of The Requirements for the Degree of Master of Science in Microbiology May, 2016 This thesis has been examined and approved in partial fulfillment of the requirements for the degree of Masters of Science in Microbiology by: Thesis Director, Cheryl A. Whistler Associate Professor of Molecular, Cellular, and Biomedical Sciences Stephen H. Jones Research Associate Professor of Natural Resources and the Environment Jeffrey T. Foster Assistant Professor of Molecular, Cellular, and Biomedical Sciences On April 15th, 2016 Original approved signatures are on file with the University of New Hampshire Graduate School. iii TABLE OF CONTENTS ACKNOWLEDGEMENTS………………………………………………………... vi LIST OF TABLES………………………………………………………………… vii LIST OF FIGURES…….………………………………………………………….. viii ABSTRACT………………………………………………………………………. -
(Crisprs) in Pandemic and Non-Pandemic Vibrio Parahaemolyticus Isolates from Seafood Sources
microorganisms Article Characterization and Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Pandemic and Non-Pandemic Vibrio parahaemolyticus Isolates from Seafood Sources Nawaporn Jingjit 1, Sutima Preeprem 2, Komwit Surachat 3,4 and Pimonsri Mittraparp-arthorn 1,4,* 1 Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai 90110, Songkla, Thailand; [email protected] 2 Microbiology Program, Faculty of Science Technology and Agriculture, Yala Rajabhat University, Muang District, Yala 95000, Yala, Thailand; [email protected] 3 Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand; [email protected] 4 Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand * Correspondence: [email protected]; Tel.: +66-74-288-314 Abstract: Vibrio parahaemolyticus is one of the significant seafood-borne pathogens causing gastroen- teritis in humans. Clustered regularly interspaced short palindromic repeats (CRISPR) are commonly Citation: Jingjit, N.; Preeprem, S.; Surachat, K.; Mittraparp-arthorn, P. detected in the genomes of V. parahaemolyticus and the polymorphism of CRISPR patterns has been Characterization and Analysis of applied as a genetic marker for tracking its evolution. In this work, a total of 15 pandemic and Clustered Regularly Interspaced 36 non-pandemic V. parahaemolyticus isolates obtained from seafood between 2000 and 2012 were Short Palindromic Repeats (CRISPRs) characterized based on hemolytic activity, antimicrobial susceptibility, and CRISPR elements. The in Pandemic and Non-Pandemic results showed that 15/17 of the V. parahaemolyticus seafood isolates carrying the thermostable direct Vibrio parahaemolyticus Isolates from hemolysin gene (tdh+) were Kanagawa phenomenon (KP) positive. -
Whole-Body Microbiota of Sea Cucumber
J. Microbiol. Biotechnol. (2017), 27(10), 1753–1762 https://doi.org/10.4014/jmb.1707.07067 Research Article Review jmb Whole-Body Microbiota of Sea Cucumber (Apostichopus japonicus) from South Korea for Improved Seafood Management S Tae-Yoon Kim1,3, Jin-Jae Lee1,3, Bong-Soo Kim1,3*, and Sang Ho Choi2,3* 1Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea 2Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Republic of Korea 3Food-borne Pathogen Omics Research Center (FORC), Seoul National University, Seoul 08826, Republic of Korea Received: July 27, 2017 Revised: August 24, 2017 Sea cucumber (Apostichopus japonicus) is a popular seafood source in Asia, including South Accepted: August 28, 2017 Korea, and its consumption has recently increased with recognition of its medicinal First published online properties. However, because raw sea cucumber contains various microbes, its ingestion can August 31, 2017 cause foodborne illness. Therefore, analysis of the microbiota in the whole body of sea *Corresponding authors cucumber can extend our understanding of foodborne illness caused by microorganisms and B.S.K. help to better manage products. We collected 40 sea cucumbers from four different sites in Phone: +82-33-248-2093; Fax: +82-33-256-3420; August and November, which are known as the maximum production areas in Korea. The E-mail: [email protected] microbiota was analyzed by an Illumina MiSeq system, and bacterial amounts were quantified S.H.C. by real-time PCR. The diversity and bacterial amounts in sea cucumber were higher in August Phone: +82-2-880-4857; Fax: +82-2-873-5095; than in November. -
Cryptic Inoviruses Revealed As Pervasive in Bacteria and Archaea Across Earth’S Biomes
ARTICLES https://doi.org/10.1038/s41564-019-0510-x Corrected: Author Correction Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes Simon Roux 1*, Mart Krupovic 2, Rebecca A. Daly3, Adair L. Borges4, Stephen Nayfach1, Frederik Schulz 1, Allison Sharrar5, Paula B. Matheus Carnevali 5, Jan-Fang Cheng1, Natalia N. Ivanova 1, Joseph Bondy-Denomy4,6, Kelly C. Wrighton3, Tanja Woyke 1, Axel Visel 1, Nikos C. Kyrpides1 and Emiley A. Eloe-Fadrosh 1* Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach lever- aging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. -
Dynamics of Coral-Associated Bacterial Communities Acclimated To
www.nature.com/scientificreports OPEN Dynamics of coral-associated bacterial communities acclimated to temperature stress based on Received: 20 June 2017 Accepted: 13 October 2017 recent thermal history Published: xx xx xxxx Jia-Ho Shiu1,2,3, Shashank Keshavmurthy 2, Pei-Wen Chiang2, Hsing-Ju Chen2, Shueh-Ping Lou2, Ching-Hung Tseng4, Hernyi Justin Hsieh5, Chaolun Allen Chen2 & Sen-Lin Tang 1,2,6 Seasonal variation in temperature fuctuations may provide corals and their algal symbionts varying abilities to acclimate to changing temperatures. We hypothesized that diferent temperature ranges between seasons may promote temperature-tolerance of corals, which would increase stability of a bacterial community following thermal stress. Acropora muricata coral colonies were collected in summer and winter (water temperatures were 23.4–30.2 and 12.1–23.1 °C, respectively) from the Penghu Archipelago in Taiwan, then exposed to 6 temperature treatments (10–33 °C). Changes in coral-associated bacteria were determined after 12, 24, and 48 h. Based on 16S rRNA gene amplicons and Illumina sequencing, bacterial communities difered between seasons and treatments altered the dominant bacteria. Cold stress caused slower shifts in the bacterial community in winter than in summer, whereas a more rapid shift occurred under heat stress in both seasons. Results supported our hypothesis that bacterial community composition of corals in winter are more stable in cold temperatures but changed rapidly in hot temperatures, with opposite results for the bacterial communities in summer. We infer that the thermal tolerance ranges of coral-associated bacteria, with a stable community composition, are associated with their short-term (3 mo) seawater thermal history. -
S41598-020-68891-6.Pdf
www.nature.com/scientificreports OPEN Structure and co‑occurrence patterns of bacterial communities associated with white faeces disease outbreaks in Pacifc white‑leg shrimp Penaeus vannamei aquaculture Yustian Rovi Alfansah1,2,3*, Sonja Peters1, Jens Harder4, Christiane Hassenrück1,7 & Astrid Gärdes1,5,6,7 Bacterial diseases cause production failures in shrimp aquacultures. To understand environmental conditions and bacterial community dynamics contributing to white faeces disease (WFD) events, we analysed water quality and compared bacterial communities in water as well as in intestines and faeces of healthy and diseased shrimps, respectively, via 16S rRNA gene sequencing and qPCR of transmembrane regulatory protein (toxR), thermolabile haemolysin (tlh), and thermostable direct haemolysin genes of pathogenic Vibrio parahaemolyticus as a proxy for virulence. WFD occurred when pH decreased to 7.71–7.84, and Alteromonas, Pseudoalteromonas and Vibrio dominated the aquatic bacterial communities. The disease severity further correlated with increased proportions of Alteromonas, Photobacterium, Pseudoalteromonas and Vibrio in shrimp faeces. These opportunistic pathogenic bacteria constituted up to 60% and 80% of the sequences in samples from the early and advances stages of the disease outbreak, respectively, and exhibited a high degree of co-occurrence. Furthermore, toxR and tlh were detected in water at the disease event only. Notably, bacterial community resilience in water occurred when pH was adjusted to 8. Then WFD ceased without a mortality event. In conclusion, pH was a reliable indicator of the WFD outbreak risk. Dissolved oxygen and compositions of water and intestinal bacteria may also serve as indicators for better prevention of WFD events. Bacterial diseases are a major problem for Penaeus vannamei pond aquaculture in Asia and Latin America. -
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bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 3 4 5 Re-evaluating the salty divide: phylogenetic specificity of 6 transitions between marine and freshwater systems 7 8 9 10 Sara F. Pavera, Daniel J. Muratorea, Ryan J. Newtonb, Maureen L. Colemana# 11 a 12 Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA 13 b School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA 14 15 Running title: Marine-freshwater phylogenetic specificity 16 17 #Address correspondence to Maureen Coleman, [email protected] 18 bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 Abstract 20 Marine and freshwater microbial communities are phylogenetically distinct and transitions 21 between habitat types are thought to be infrequent. We compared the phylogenetic diversity of 22 marine and freshwater microorganisms and identified specific lineages exhibiting notably high or 23 low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA 24 gene tag-sequencing datasets. As expected, marine and freshwater microbial communities 25 differed in the relative abundance of major phyla and contained habitat-specific lineages; at the 26 same time, however, many shared taxa were observed in both environments. 27 Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between 28 marine and freshwater sample pairs.