Investigating the Interactions Between Cyanobacteria and Vibrio Parahaemolyticus
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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. -
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………………………………………………………………………. -
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. -
Luxr Solos in Photorhabdus Species
ORIGINAL RESEARCH ARTICLE published: 18 November 2014 CELLULAR AND INFECTION MICROBIOLOGY doi: 10.3389/fcimb.2014.00166 LuxR solos in Photorhabdus species Sophie Brameyer 1, Darko Kresovic 2, Helge B. Bode 2* and Ralf Heermann 1* 1 Bereich Mikrobiologie, Biozentrum, Ludwig-Maximilians-Universität München, München, Germany 2 Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany Edited by: Bacteria communicate via small diffusible molecules to mediate group-coordinated Vittorio Venturi, International Centre behavior, a process designated as quorum sensing. The basic molecular quorum sensing for Genetic Engineering and system of Gram-negative bacteria consists of a LuxI-type autoinducer synthase producing Biotechnology, Italy acyl-homoserine lactones (AHLs) as signaling molecules, and a LuxR-type receptor Reviewed by: Brian Ahmer, The Ohio State detecting the AHLs to control expression of specific genes. However, many proteobacteria University, USA possess one or more unpaired LuxR-type receptors that lack a cognate LuxI-like synthase, Eric Déziel, Institut National de la referred to as LuxR solos. The enteric and insect pathogenic bacteria of the genus Recherche Scientifique, Canada Photorhabdus harbor an extraordinarily high number of LuxR solos, more than any other *Correspondence: known bacteria, and all lack a LuxI-like synthase. Here, we focus on the presence Helge B. Bode, Fachbereich Biowissenschaften, Merck and the different types of LuxR solos in the three known Photorhabdus species Stiftungsprofessur für Molekulare using bioinformatics analyses. Generally, the N-terminal signal-binding domain (SBD) of Biotechnologie, Goethe-Universität LuxR-type receptors sensing AHLs have a motif of six conserved amino acids that is Frankfurt, Max-von-Laue-Str. -
Enterovibrio, Grimontia (Grimontia Hollisae, Formerly Vibrio Hollisae), Listonella, Photobacterium (Photobacterium Damselae
VIBRIOSIS (Non-Cholera Vibrio spp) Genera in the family Vibrionaceae currently include: Aliivibrio, Allomonas, Catenococcus, Enterovibrio, Grimontia (Grimontia hollisae, formerly Vibrio hollisae), Listonella, Photobacterium (Photobacterium damselae, formerly Vibrio damselae), Salinivibrio, and Vibrio species including V. cholerae non-O1/non-O139, V. parahaemolyticus, V. vulnificus, V. fluvialis, V. furnissii, and V. mimicus alginolyticus and V. metschnikovi. (Not all of these have been recognized to cause human illness.) REPORTING INFORMATION • Class B2: Report by the end of the business week in which the case or suspected case presents and/or a positive laboratory result to the local public health department where the patient resides. If patient residence is unknown, report to the local public health department in which the reporting health care provider or laboratory is located. • Reporting Form(s) and/or Mechanism: Ohio Confidential Reportable Disease form (HEA 3334, rev. 1/09), Positive Laboratory Findings for Reportable Disease form (HEA 3333, rev. 8/05), the local health department via the Ohio Disease Reporting System (ODRS) or telephone. • The Centers for Disease Control and Prevention (CDC) requests that states collect information on the Cholera and Other Vibrio Illness Surveillance Report (52.79 E revised 08/2007) (COVIS), available at http://www.cdc.gov/nationalsurveillance/PDFs/CDC5279_COVISvibriosis.pdf. Reporting sites should use the COVIS reporting form to assist in local disease investigation and traceback activities. Information collected from the form should be entered into ODRS and sent to the Ohio Department of Health (ODH). • Additional reporting information, with specifics regarding the key fields for ODRS Reporting can be located in Section 7. AGENTS Vibrio parahaemolyticus; Vibrio cholerae non-O1 (does not agglutinate in O group-1 sera), strains other than O139; Vibrio vulnificus and Photobacterium damselae (formerly Vibrio damselae) and Grimontia hollisae (formerly Vibrio hollisae), V. -
(COVIS) Overview
National Enteric Disease Surveillance: Cholera and Other Vibrio Illness Surveillance (COVIS) Surveillance System Overview: Cholera and Other Vibrio Illness Surveillance (COVIS) Background on infection with species from the family Vibrionaceae Infection with pathogenic species of the family Vibrionaceae can cause two distinct categories of infection: cholera and vibriosis, both of which are nationally notifiable. Cholera is, by definition, caused by infection with toxigenic Vibrio cholerae O1 or O139 and was first reported in the United States in 1832. Infection is characterized by acute, watery diarrhea. An average of 5-10 cases of cholera are reported annually in the United States; most are acquired during international travel, however, on average 1-2 per year are domestically acquired. An increase in the number of cholera cases reported in the United States has occurred when there are cholera outbreaks in the Western Hemisphere, such as Latin America in the 1990s and Haiti in 2010, with almost all attributable to exposures during international travel. CDC annually reports to the World Health Organization all confirmed cholera cases diagnosed in the United States. Vibriosis is caused by infection with any species of the family Vibrionaceae (excluding toxigenic Vibrio cholerae O1 and O139), with an estimated 80,000 cases and 300 deaths annually in the United States (1). The most common clinical manifestations are watery diarrhea, primary septicemia, wound infection, and otitis externa. Risk factors for illness include consumption of shellfish, -
Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes
RESEARCH ARTICLE Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes Rachel E. Diner,a,b,c Drishti Kaul,c Ariel Rabines,a,c Hong Zheng,c Joshua A. Steele,d John F. Griffith,d Andrew E. Allena,c aScripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA bDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA cMicrobial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, California, USA dSouthern California Coastal Water Research Project, Costa Mesa, California, USA ABSTRACT Interactions between vibrio bacteria and the planktonic community impact marine ecology and human health. Many coastal Vibrio spp. can infect humans, represent- ing a growing threat linked to increasing seawater temperatures. Interactions with eukaryo- tic organisms may provide attachment substrate and critical nutrients that facilitate the per- sistence, diversification, and spread of pathogenic Vibrio spp. However, vibrio interactions with planktonic organisms in an environmental context are poorly understood. We quanti- fied the pathogenic Vibrio species V. cholerae, V. parahaemolyticus,andV. vulnificus monthly for 1 year at five sites and observed high abundances, particularly during summer months, with species-specific temperature and salinity distributions. Using metabarcoding, we estab- lished a detailed profile of both prokaryotic and eukaryotic coastal microbial communities. We found that pathogenic Vibrio species were frequently associated with distinct eukaryo- tic amplicon sequence variants (ASVs), including diatoms and copepods. Shared environ- mental conditions, such as high temperatures and low salinities, were associated with both high concentrations of pathogenic vibrios and potential environmental reservoirs, which may influence vibrio infection risks linked to climate change and should be incorporated into predictive ecological models and experimental laboratory systems. -
Differential RNA-Seq of Vibrio Cholerae Identifies the Vqmr Small RNA As a Regulator of Biofilm Formation
Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation Kai Papenforta, Konrad U. Förstnerb, Jian-Ping Conga, Cynthia M. Sharmab, and Bonnie L. Basslera,c,1 aDepartment of Molecular Biology and cHoward Hughes Medical Institute, Princeton University, Princeton, NJ 08544; and bResearch Center for Infectious Diseases (ZINF), University of Würzburg, D-97080 Würzburg, Germany Contributed by Bonnie L. Bassler, January 6, 2015 (sent for review October 30, 2014; reviewed by Brian K. Hammer) Quorum sensing (QS) is a process of cell-to-cell communication ther diversified the possible uses of RNA-seq. One such that enables bacteria to transition between individual and collec- technology is called differential RNA sequencing (dRNA-seq), tive lifestyles. QS controls virulence and biofilm formation in Vib- in which enrichment of primary transcript termini can be com- rio cholerae, the causative agent of cholera disease. Differential bined with strand-specific generation of cDNA libraries to ach- V. cholerae RNA sequencing (RNA-seq) of wild-type and a locked ieve genome-wide identification of transcriptional start sites low-cell-density QS-mutant strain identified 7,240 transcriptional (TSSs) (10). ∼ start sites with 47% initiated in the antisense direction. A total of In this study, we applied dRNA-seq to the study of QS in 107 of the transcripts do not appear to encode proteins, suggest- V. cholerae. We performed dRNA-seq on wild-type V. cholerae ing they specify regulatory RNAs. We focused on one such tran- under conditions of low and high cell density. We performed script that we name VqmR. -
Phylogenetically Conserved Resource Partitioning in the Coastal Microbial Loop
OPEN The ISME Journal (2017) 11, 2781–2792 www.nature.com/ismej ORIGINAL ARTICLE Phylogenetically conserved resource partitioning in the coastal microbial loop Samuel Bryson1, Zhou Li2,3, Francisco Chavez4, Peter K Weber5, Jennifer Pett-Ridge5, Robert L Hettich2,3, Chongle Pan2,3, Xavier Mayali5 and Ryan S Mueller1 1Department of Microbiology, Oregon State University, Corvallis, OR, USA; 2Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, USA; 3Oak Ridge National Laboratory, Oak Ridge, TN, USA; 4Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA and 5Lawrence Livermore National Laboratory, Livermore, CA, USA Resource availability influences marine microbial community structure, suggesting that population- specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive.