DOCSLIB.ORG

Isolation, Identification and Genomic Analysis of Plesiomonas Shigelloides Isolated from Diseased Percocypris Pingi (Tchang, 1930)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

American Journal of Biochemistry and Biotechnology Original Research Paper Isolation, Identification and Genomic Analysis of Plesiomonas shigelloides Isolated from Diseased Percocypris pingi (Tchang, 1930) 1, 2, 3 Lei Pan, 4Shuiyi Liu, 1Xuwei Cheng, 1Yiting Tao, 5Tao Yang, 5Peipei Li, 1,2 Zhengxiang Wang, 3Dongguo Shao and 6Defeng Zhang 1School of Resources and Environmental Science, Hubei University, Wuhan 430062, People's Republic of China 2Hubei Key Laboratory of Regional Development and Environmental Response (Hubei University), Wuhan 430062, People's Republic of China 3State key Laboratory of Water Resources and Hydropower Engineering Science (Wuhan University), Wuhan, 430072, People's Republic of China 4Department of Medical Laboratory, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, People's Republic of China 5Wuhan Heyuan Green Biological Co., Ltd., Wuhan 430206, People's Republic of China 6Key Laboratory of Fishery Drug Development, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, People's Republic of China Article history Abstract: Recently, the outbreak of a serious infectious disease of Received: 25-10-2017 unknown etiology was noted in Percocypris pingi (Tchang, 1930) farms in Revised: 11-12-2017 Yunnan province. Due to currently limited information, we aimed to Accepted: 20-12-2017 identify the pathogen isolates, determine the susceptibility of the isolates, evaluate the pathogenicity and analyze the genome of the representative Corresponding Author: Defeng Zhang strain. Ten strains of Gram-negative rods were isolated from diseased P. Key Laboratory of Fishery Drug pingi and the isolates were identified as Plesiomonas shigelloides based Development, Ministry of on biochemical characteristics, 16S rRNA gene sequencing and species- Agriculture, Pearl River Fisheries specific PCR detection. The results of susceptibility analysis showed that Research Institute, Chinese two selected strains LS1 and LL2 were resistant to ampicillin, penicillin Academy of Fishery Sciences, G, trimethoprim/sulfamethoxazole, tetracycline, enrofloxacin, nalidixic Guangzhou, People's Republic of acid and enoxacin. A virulence assay indicated that the pathogen was China virulent to zebrafish. Genomic analysis revealed that the LS1 isolate was Email: [email protected] closely related to strain GN7, which was isolated from animal farms. To the best of our knowledge, this is the first report of P. shigelloides as a pathogen of P. pingi . This study will provide a rational framework for exploration of epidemiological analysis of P. shigelloides in fish diseases and would further benefit conservation of the species. Keywords: Plesiomonas shigelloides , Percocypris pingi (Tchang, 1930), Identification, Genomic Analysis Introduction emerging enteric pathogen that is linked to intestinal and extra-intestinal infections in humans (González-Rey et al ., Plesiomonas shigelloides is a Gram-negative, motile, 2011). It is recognized as a potential fish pathogen and has non-spore-forming, oxidase-positive and rod-shaped been isolated from red hybrid tilapia (Nadirah et al ., bacterium belonging to the Enterobacteriaceae family 2012). In China, P. shigelloides is the pathogen of grass (Brenner et al ., 2005). P. shigelloides is widely distributed carp ( Ctenopharyngodon idella ), sturgeon ( Huso in the aquatic environment even under cold climatic huso ×Acipenser ruthenus ), gibel carp ( Carassius auratus conditions (Salerno et al ., 2010). Thus far, P. shigelloides gibelio ), black carp ( Mylopharyngodon piceus ) and tilapia has been isolated from streams, lakes, estuarine waters, (Oreochromis niloticus ). mammals, crustaceans, mollusks, reptiles, amphibians and Percocypris pingi (Tchang, 1930), an endemic and fish (Alexander et al ., 2016). P. shigelloides is an commercially important species only found in the upper © 2017 Lei Pan, Shuiyi Liu, Xuwei Cheng, Yiting Tao, Tao Yang, Peipei Li, Zhengxiang Wang, Dongguo Shao and Defeng Zhang. This open access article is distributed under a Creative Commons Attribution (CC-BY) 3.0 license. Lei Pan et al . / American Journal of Biochemistry and Biotechnology 2017, 13 (4): 226.232 DOI: 10.3844/ajbbsp.2017.226.232 reaches of the Yangtze River in China, is a benthic fish Molecular Characterization that is typically found in rivers with torrential flow. The population of this fish decreased intensely due to Genomic DNA from ten isolates was extracted using overfishing, dam construction, habitat deterioration and the EasyPure Genomic DNA Kit (Transgen Biotech, water pollution, becoming endangered in the past Beijing, China) in accordance with the manufacturer’s decade. In May 2015, this species has been listed as instructions. A partial 16S rRNA gene sequence was Endangered (EN) in the Red List of China’s Vertebrates amplified as described previously (Zhang et al ., 2011). (Li et al ., 2016). Aquaculture may counteract this decline Briefly, universal PCR primers 27F (5′- and improve biodiversity by sustaining healthy fish AGAGTTTGATCMTGGCTCAG-3′) and 1492R (5′- populations (Pan et al ., 2016). Therefore, further TACGGMTACCTTGTTACGACTT-3′) were used for research is essential to maintain sufficient production of amplification of the 16S rRNA gene. In addition, primers P. pingi to meet fishing demands for conservation. PS23FW3 (5′-CTCCGAATACCGTAGAGTGCTATC Recently, artificial propagation of P. pingi has been C-3′) and PS23RV3 (5′- conducted in Sichuan and Yunnan provinces in China to CTCCCCTACCCAATAACACCTAAA-3′) were used restore their population and the hatchery-reared fish have for detection of the 23S rRNA gene of P. shigelloides been released into the river by several institutions (Li et al ., (González-Rey et al ., 2000). 2016). Unfortunately, bacterial diseases are one of the Biochemical Characteristics major obstacles to the expansion of P. pingi farming. In 2016, an outbreak caused by P. shigelloides occurred in Of the ten isolates, two (strains LS1 and LL2) were farmed P. pingi in China. However, the information identified based on biochemical characteristics, which were examined by API 20E system (bioMèrieux, Marcy about P. pingi disease is limited. In this study, we have l’Etoile, France) as reported previously (Krovacek et al ., described the isolation, identification and genomic 2000) and by API strips (Chen et al ., 2013). Hemolytic analysis of P. shigelloides from diseased P. pingi . The activity was assayed by spot inoculation of these strains aim of this study is to provide a theoretical foundation on 5% sheep erythrocytes in BHI agar and erythrocyte for further understanding of the epidemiology of P. lysis was recorded after 24 h of incubation at 37°C. shigelloides strains and ensure effective prevention and control measures. Pathogenicity Test In this study, zebrafish ( Danio rerio ) was used as the Materials and Methods target fish to evaluate the pathogenicity of strain LS1 (Saralahti and Rämet, 2015). The isolate LS1 was used Sample Collection for the experimental infection of healthy zebrafish to In August 2016, a disease outbreak in P. pingi (average assess their pathogenic potential. A total of 300 healthy body weight 45 gram) were obtained from a commercial zebrafish were randomly divided into seven groups (20 source, which were cultured in a recirculating system in per group) and then allowed to acclimatize at 28°C for 7 Lijiang city, Yunnan province, China. The culture water d prior to challenge. Challenge assays were performed in temperature was maintained at 24±1°C. In the early stage triplicate. Isolate LS1 was cultured in BHI broth of the disease, several fish began to show clinical signs overnight, centrifuged and collected. The bacteria were including anorexia, caudal fin and skin ulceration and resuspended in sterile PBS buffer at six different doses. ascites (accumulation of abdominal fluid). Four days later, Experimental groups were intraperitoneally inoculated mortalities started to occur in this farm. Moribund fish with 20 µL of cultured cells at doses of 3 ×10 8, 3 ×10 7, were sampled and kidney tissues were incubated on Brain 3×10 6 and 3 ×10 5 CFU/mL, respectively. The zebrafish in Heart Infusion (BHI, Difco Laboratories, Detroit, MI, the control group were injected with the same volume of USA) agar for bacterial isolation. PBS buffer. Clinical signs and mortality were recorded daily for 14 d. In addition, bacteria were isolated from Bacterial Isolation the moribund zebrafish and were detected by PCR assay Tissue samples were aseptically collected from the based on the 23S rRNA gene of P. shigelloides . The kidney of moribund P. pingi (N=10) and incubated on statistical analysis was calculated using SPSS software BHI agar. Plates were incubated at 28°C for 24 h. The (version 22.0) and the survival curve was performed by bacterial colonies were re-streaked on BHI agar to obtain Origin software (version 9.0). a pure culture. For long-term preservation the bacterial Antimicrobial Susceptibility Testing isolates were stored at -80°C in sterile BHI containing 15% glycerol. In this study, a total of ten strains were In order to select the antimicrobial agents for treatment isolated and two of them, were selected for further study. and define the antibiotic pattern of the isolates, antibiotic 227 Lei Pan et al . / American Journal of Biochemistry and Biotechnology 2017, 13 (4): 226.232 DOI: 10.3844/ajbbsp.2017.226.232 susceptibility of bacterial
Recommended publications
  • Resource Enhancement and Sustainable Aquaculture Practices in Southeast Asia 2014 (RESA)

    Resource Enhancement and Sustainable Aquaculture Practices in Southeast Asia 2014 (RESA)

    Challenges in Responsible Production of Aquatic Species Proceedings of the International Workshop on Resource Enhancement and Sustainable Aquaculture Practices in Southeast Asia 2014 (RESA) Maria Rowena R. Romana-Eguia Fe D. Parado-Estepa Nerissa D. Salayo Ma. Junemie Hazel Lebata-Ramos Editors Southeast Asian Fisheries Development Center AQUACULTURE DEPARTMENT Tigbauan, Iloilo, Philippines www.seafdec.org.ph Challenges in Responsible Production of Aquatic Species Proceedings of the International Workshop on Resource Enhancement and Sustainable Aquaculture Practices in Southeast Asia 2014 (RESA) August 2015 ISBN: 978-971-9931-04-1 Copyright © 2015 Southeast Asian Fisheries Development Center Aquaculture Department Tigbauan, Iloilo, Philippines ALL RIGHTS RESERVED No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without the permission in writing from the publisher. For inquiries SEAFDEC Aquaculture Department Tigbauan 5021, Iloilo, Philippines Tel (63-33) 330 7030; Fax (63-33) 330 7031 E-mail: [email protected] Website: www.seafdec.org.ph On the cover Logo design courtesy of Mr. Demy D. Catedral of SEAFDEC/AQD International Workshop on Resource Enhancement and Sustainable Aquaculture Practices in Southeast Asia (2014: Iloilo City, Philippines). Resource enhancement and sustainable aquaculture practices in Southeast Asia: challenges in responsible production of aquatic species : proceedings of the international workshop on resource enhancement and sustainable aquaculture practices in Southeast Asia 2014 (RESA) / Maria Rowena R. Romana-Eguia, Fe D. Parado-Estepa, Nerissa D. Salayo, Ma. Junemie Hazel L. Ramos, editors. -- Tigbauan, Iloilo, Philippines : Aquaculture Dept., Southeast Asian Fisheries Development Center, 2015, ©2015.
  • Identification of Human Enteric Pathogens in Gull Feces at Southwestern Lake Michigan Bathing Beaches

    Identification of Human Enteric Pathogens in Gull Feces at Southwestern Lake Michigan Bathing Beaches

    1006 Identification of human enteric pathogens in gull feces at Southwestern Lake Michigan bathing beaches Julie Kinzelman, Sandra L. McLellan, Ashley Amick, Justine Preedit, Caitlin O. Scopel, Ola Olapade, Steve Gradus, Ajaib Singh, and Gerald Sedmak Abstract: Ring-billed (Larus delawarensis Ord, 1815) and herring (Larus argentatus Pontoppidan, 1763) gulls are predom- inant species of shorebirds in coastal areas. Gulls contribute to the fecal indicator burden in beach sands, which, once transported to bathing waters, may result in water quality failures. The importance of these contamination sources must not be overlooked when considering the impact of poor bathing water quality on human health. This study examined the occurrence of human enteric pathogens in gull populations at Racine, Wisconsin. For 12 weeks in 2004 and 2005, and 7 weeks in 2006, 724 gull fecal samples were examined for pathogen occurrence on traditional selective media (BBL CHROMagar-Salmonella, Remel Campy-BAP, 7% horse blood agar) or through the use of novel isolation techniques (Campylobacter, EC FP5-funded CAMPYCHECK Project), and confirmed using polymerase chain reaction (PCR) for pathogens commonly harbored in gulls. An additional 226 gull fecal samples, collected in the same 12-week period in 2004, from a beach in Milwaukee, Wisconsin, were evaluated with standard microbiological methods and PCR. Five iso- lates of Salmonella (0.7%), 162 (22.7%) isolates of Campylobacter, 3 isolates of Aeromonas hydrophila group 2 (0.4%), and 28 isolates of Plesiomonas shigelloides (3.9%) were noted from the Racine beach. No occurrences of Salmonella and 3 isolates of Campylobacter (0.4%) were found at the Milwaukee beach.
  • Use of the Diagnostic Bacteriology Laboratory: a Practical Review for the Clinician

    Use of the Diagnostic Bacteriology Laboratory: a Practical Review for the Clinician

    148 Postgrad Med J 2001;77:148–156 REVIEWS Postgrad Med J: first published as 10.1136/pmj.77.905.148 on 1 March 2001. Downloaded from Use of the diagnostic bacteriology laboratory: a practical review for the clinician W J Steinbach, A K Shetty Lucile Salter Packard Children’s Hospital at EVective utilisation and understanding of the Stanford, Stanford Box 1: Gram stain technique University School of clinical bacteriology laboratory can greatly aid Medicine, 725 Welch in the diagnosis of infectious diseases. Al- (1) Air dry specimen and fix with Road, Palo Alto, though described more than a century ago, the methanol or heat. California, USA 94304, Gram stain remains the most frequently used (2) Add crystal violet stain. USA rapid diagnostic test, and in conjunction with W J Steinbach various biochemical tests is the cornerstone of (3) Rinse with water to wash unbound A K Shetty the clinical laboratory. First described by Dan- dye, add mordant (for example, iodine: 12 potassium iodide). Correspondence to: ish pathologist Christian Gram in 1884 and Dr Steinbach later slightly modified, the Gram stain easily (4) After waiting 30–60 seconds, rinse with [email protected] divides bacteria into two groups, Gram positive water. Submitted 27 March 2000 and Gram negative, on the basis of their cell (5) Add decolorising solvent (ethanol or Accepted 5 June 2000 wall and cell membrane permeability to acetone) to remove unbound dye. Growth on artificial medium Obligate intracellular (6) Counterstain with safranin. Chlamydia Legionella Gram positive bacteria stain blue Coxiella Ehrlichia Rickettsia (retained crystal violet).
  • Contagious Antibiotic Resistance: Plasmid Transfer Among Bacterial Residents Of

    Contagious Antibiotic Resistance: Plasmid Transfer Among Bacterial Residents Of

    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.09.375964; this version posted November 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Contagious Antibiotic Resistance: Plasmid Transfer Among Bacterial Residents of 2 the Zebrafish Gut. 3 4 Wesley Loftie-Eaton1,2, Angela Crabtree1, David Perry1, Jack Millstein1,2, Barrie 5 Robinson1,2, Larry Forney1,2 and Eva Top1,2 # 6 7 1Department of Biological Sciences, 2Institute for Bioinformatics and Evolutionary Studies 8 (IBEST), University of Idaho, PO Box 443051, Moscow, Idaho, USA. Phone: +1-208-885- 9 8858; E-mail: [email protected]; Fax: 208-885-7905 10 # Corresponding author: Department of Biological Sciences, Institute for Bioinformatics 11 and Evolutionary Studies (IBEST), University of Idaho, PO Box 443051, Moscow, Idaho, 12 USA. Phone: +1-208-885-5015; Email: [email protected]; Fax: 208-885-7905 13 14 15 Running title: Plasmid transfer in the zebrafish gut microbiome 16 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.09.375964; this version posted November 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 17 Abstract 18 By characterizing the trajectories of antibiotic resistance gene transfer in bacterial 19 communities such as the gut microbiome, we will better understand the factors that 20 influence this spread of resistance.
  • THESIS Submitted in Fulfilment of the Requirements for the Degree of MASTER of SCIENCE of Rhodes University

    THESIS Submitted in Fulfilment of the Requirements for the Degree of MASTER of SCIENCE of Rhodes University

    THE KARYOLOGY AND TAXONOMY OF THE SOUTHERN AFRICAN YELLOWFISH (PISCES: CYPRINIDAE) THESIS Submitted in Fulfilment of the Requirements for the Degree of MASTER OF SCIENCE of Rhodes University by LAWRENCE KEITH OELLERMANN December, 1988 ABSTRACT The southern African yellowfish (Barbus aeneus, ~ capensls, .!L. kimberleyensis, .!L. natalensis and ~ polylepis) are very similar, which limits the utility of traditional taxonomic methods. For this reason yellowfish similarities were explored using multivariate analysis and karyology. Meristic, morphometric and Truss (body shape) data were examined using multiple discriminant, principal component and cluster analyses. The morphological study disclosed that although the species were very similar two distinct groups occurred; .!L. aeneus-~ kimberleyensis and ~ capensis-~ polylepis-~ natalensis. Karyology showed that the yellowfish were hexaploid, ~ aeneus and IL... kimberleyensis having 148 chromosomes while the other three species had 150 chromosomes. Because the karyotypes of the species were variable the fundamental number for each species was taken as the median value for ten spreads. Median fundamental numbers were ~ aeneus ; 196, .!L. natalensis ; 200, ~ kimberleyensis ; 204, ~ polylepis ; 206 and ~ capensis ; 208. The lower chromosome number and higher fundamental number was considered the more apomorphic state for these species. Silver-staining of nucleoli showed that the yellowfish are probably undergoing the process of diploidization. Southern African Barbus and closely related species used for outgroup comparisons showed three levels of ploidy. The diploid species karyotyped were ~ anoplus (2N;48), IL... argenteus (2N;52), ~ trimaculatus (2N;42- 48), Labeo capensis (2N;48) and k umbratus (2N;48); the tetraploid species were B . serra (2N;102), ~ trevelyani (2N;±96), Pseudobarbus ~ (2N;96) and ~ burgi (2N;96); and the hexaploid species were ~ marequensis (2N;130-150) and Varicorhinus nelspruitensis (2N;130-148).
  • Pathogenesis of Providencia Rettgeri in Mice

    Pathogenesis of Providencia Rettgeri in Mice

    Journal of Babylon University/Pure and Applied Sciences/ No.(8)/ Vol.(21): 2013 Pathogenesis of Providencia rettgeri in mice Hayder S.Obayes College of Vet. Medicine Al-Qasim Green University Frias GAbd college of science Babylon university Abstract: Providencia rettgeri strains were isolated from urinary tract infections (UTIs) patients and identified according to morphological and biochemical tests, furthermore, the identification was confirmed using the Hi 25 Enterobacteriaceae system. The crude lipopolysaccharide (LPS) was extracted from P.rettgeri isolate by sonication with ethylene diamine tetraacetic acid (EDTA) and then with enzymic digestion, then partially purified by an ion exchange chromatography .It have been 7 revealed that the lethal dose 50% (LD50) of P.rettgeri was about 5.62 × 10 cell/mouse . The microscopic examination of stained tissue sections of organs obtained from mice injected with sub lethal doses of P.rettgeri and LPS, showed sever changes in kidney and bladder induced by bacterial suspension than LPS, while sever changes were shown in spleen ,liver , and intestine caused by LPS compared with control animals. In general, these histopathological changes included the congestion, hemorrhage, migration and infiltration of inflammatory cells, tissue necrosis and oedema but in spleen there were hypertrophy of white bulb and congestion of red bulb . Key words: Pathogenesis , LPS, Providencia, histopathogenesis,mice. اﻟﺧﻼﺻﺔ: ﻋزﻟـت ﺟرﺛوﻣـﺔ Providencia rettgeri ﻣـن اﻟﻣرﺿـﻰ اﻟﻣـﺻﺎﺑﯾن ﺑﺎﻟﺗﻬـﺎب اﻟﻣـﺳﺎﻟك اﻟﺑوﻟﯾـﺔ وﺷﺧـﺻت ﻋﻠـﻰ
  • PHD Dissertaiton by Zhen Tao.Pdf (3.618Mb)

    PHD Dissertaiton by Zhen Tao.Pdf (3.618Mb)

    Vibrios associated with marine samples from the Northern Gulf of Mexico: implications for human health by Zhen Tao A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama August 3, 2013 Keywords: recreational fishing, Vibrio vulnificus, public health Copyright 2013 by Zhen Tao Approved by Covadonga R. Arias, Chair, Full Professor of Fisheries and Allied Aquacultures Thomas A. McCaskey, Professor of Animal Science Calvin M. Johnson, Professor of Pathology Stephen A. Bullard, Assistant Professor of Fisheries and Allied Aquacultures Abstract In this dissertation, I investigated the distribution and prevalence of two human- pathogenic Vibrio species (V. vulnificus and V. parahaemolyticus) in non-shellfish samples including fish, bait shrimp, water, sand and crude oil material released by the Deepwater Horizon oil spill along the Northern Gulf of Mexico (GoM) coast. In my study, the Vibrio counts were enumerated in samples by using the most probable number procedure or by direct plate counting. In general, V. vulnificus isolates recovered from different samples were genotyped based on the polymorphism present in 16S rRNA or the vcg (virulence correlated gene) locus. Amplified fragment length polymorphism (AFLP) was used to resolve the genetic diversity within V. vulnificus population isolated from fish. PCR analysis was used to screen for virulence factor genes (trh and tdh) in V. parahaemolyticus isolates yielded from bait shrimp. A series of laboratory microcosm experiments and an allele-specific quantitative PCR (ASqPCR) technique were designed and utilized to reveal the relationship between two V. vulnificus 16S rRNA types and environmental factors (temperature and salinity).
  • International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/Ijsem.0.001485

    International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/Ijsem.0.001485

    International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/ijsem.0.001485 Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Mobolaji Adeolu,† Seema Alnajar,† Sohail Naushad and Radhey S. Gupta Correspondence Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Radhey S. Gupta L8N 3Z5, Canada [email protected] Understanding of the phylogeny and interrelationships of the genera within the order ‘Enterobacteriales’ has proven difficult using the 16S rRNA gene and other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses of the members of the order ‘Enterobacteriales’ which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins and four multilocus sequence analysis proteins, as well as examining the overall genome similarity amongst the members of this order. The results of these analyses all support the existence of seven distinct monophyletic groups of genera within the order ‘Enterobacteriales’. In parallel, our analyses of protein sequences from the ‘Enterobacteriales’ genomes have identified numerous molecular characteristics in the forms of conserved signature insertions/deletions, which are specifically shared by the members of the identified clades and independently support their monophyly and distinctness. Many of these groupings, either in part or in whole, have been recognized in previous evolutionary studies, but have not been consistently resolved as monophyletic entities in 16S rRNA gene trees. The work presented here represents the first comprehensive, genome- scale taxonomic analysis of the entirety of the order ‘Enterobacteriales’.
  • Aerobic Gram-Positive Bacteria

    Aerobic Gram-Positive Bacteria

    Aerobic Gram-Positive Bacteria Abiotrophia defectiva Corynebacterium xerosisB Micrococcus lylaeB Staphylococcus warneri Aerococcus sanguinicolaB Dermabacter hominisB Pediococcus acidilactici Staphylococcus xylosusB Aerococcus urinaeB Dermacoccus nishinomiyaensisB Pediococcus pentosaceusB Streptococcus agalactiae Aerococcus viridans Enterococcus avium Rothia dentocariosaB Streptococcus anginosus Alloiococcus otitisB Enterococcus casseliflavus Rothia mucilaginosa Streptococcus canisB Arthrobacter cumminsiiB Enterococcus durans Rothia aeriaB Streptococcus equiB Brevibacterium caseiB Enterococcus faecalis Staphylococcus auricularisB Streptococcus constellatus Corynebacterium accolensB Enterococcus faecium Staphylococcus aureus Streptococcus dysgalactiaeB Corynebacterium afermentans groupB Enterococcus gallinarum Staphylococcus capitis Streptococcus dysgalactiae ssp dysgalactiaeV Corynebacterium amycolatumB Enterococcus hiraeB Staphylococcus capraeB Streptococcus dysgalactiae spp equisimilisV Corynebacterium aurimucosum groupB Enterococcus mundtiiB Staphylococcus carnosusB Streptococcus gallolyticus ssp gallolyticusV Corynebacterium bovisB Enterococcus raffinosusB Staphylococcus cohniiB Streptococcus gallolyticusB Corynebacterium coyleaeB Facklamia hominisB Staphylococcus cohnii ssp cohniiV Streptococcus gordoniiB Corynebacterium diphtheriaeB Gardnerella vaginalis Staphylococcus cohnii ssp urealyticusV Streptococcus infantarius ssp coli (Str.lutetiensis)V Corynebacterium freneyiB Gemella haemolysans Staphylococcus delphiniB Streptococcus infantarius
  • Bacterial Flagellar Motor PL-Ring Disassembly Sub-Complexes Are

    Bacterial Flagellar Motor PL-Ring Disassembly Sub-Complexes Are

    bioRxiv preprint doi: https://doi.org/10.1101/786715; this version posted September 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Bacterial flagellar motor PL-ring disassembly 2 Sub-complexes are widespread and ancient 3 4 Mohammed Kaplan1, Michael J. Sweredoski1, João P.G.L.M. Rodrigues2, Elitza I. Tocheva1,3, Yi-Wei 5 Chang1,4, Davi R. Ortega1, Morgan Beeby1,5 and Grant J. Jensen1,6,7 6 1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 7 91125, USA 8 2Department of Structural Biology, Stanford University, Stanford, CA, USA 9 3Present address: Department of Microbiology and Immunology, Life Sciences Institute, The University 10 of British Columbia, Vancouver, BC V6T 1Z3, Canada 11 4Present address: Department of Biochemistry and Biophysics, Perelman School of Medicine, University 12 of Pennsylvania, Philadelphia, PA 19104, USA 13 5Present address: Department of Life Sciences, Imperial College London, South Kensington Campus, 14 London SW7 2AZ, UK 15 6Howard Hughes Medical Institute, 1200 E. California Boulevard, Pasadena, CA 91125, USA 16 7Corresponding author: [email protected] 17 18 19 20 21 22 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/786715; this version posted September 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
  • Minnows and Molecules: Resolving the Broad and Fine-Scale Evolutionary Patterns of Cypriniformes

    Minnows and Molecules: Resolving the Broad and Fine-Scale Evolutionary Patterns of Cypriniformes

    Minnows and molecules: resolving the broad and fine-scale evolutionary patterns of Cypriniformes by Carla Cristina Stout A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama May 7, 2017 Keywords: fish, phylogenomics, population genetics, Leuciscidae, sequence capture Approved by Jonathan W. Armbruster, Chair, Professor of Biological Sciences and Curator of Fishes Jason E. Bond, Professor and Department Chair of Biological Sciences Scott R. Santos, Professor of Biological Sciences Eric Peatman, Associate Professor of Fisheries, Aquaculture, and Aquatic Sciences Abstract Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world. Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. The goal of this dissertation is to provide robust support for relationships at various taxonomic levels within Cypriniformes. For the entire order, an anchored hybrid enrichment approach was used to resolve relationships. This resulted in a phylogeny that is largely congruent with previous multilocus phylogenies, but has much stronger support. For members of Leuciscidae, the relationships established using anchored hybrid enrichment were used to estimate divergence times in an attempt to make inferences about their biogeographic history. The predominant lineage of the leuciscids in North America were determined to have entered North America through Beringia ~37 million years ago while the ancestor of the Golden Shiner (Notemigonus crysoleucas) entered ~20–6 million years ago, likely from Europe. Within Leuciscidae, the shiner clade represents genera with much historical taxonomic turbidity. Targeted sequence capture was used to establish relationships in order to inform taxonomic revisions for the clade.
  • Kit Systems for Identifying Gram Negative Aerobic Bacilli: Report of the Welsh Standing Specialist Advisory Working Group in Microbiology

    Kit Systems for Identifying Gram Negative Aerobic Bacilli: Report of the Welsh Standing Specialist Advisory Working Group in Microbiology

    J Clin Pathol: first published as 10.1136/jcp.39.6.666 on 1 June 1986. Downloaded from J Clin Pathol 1986;39:666-671 Kit systems for identifying Gram negative aerobic bacilli: report of the Welsh Standing Specialist Advisory Working Group in Microbiology CHN BENNETT, DHM JOYNSON From the Department of Pathology, General Hospital, Neath, West Glamorgan, Wales SUMMARY Under the auspices of the Welsh Standing Specialist Advisory Working Group in Micro- biology (WMG) 10 clinical microbiology laboratories in Wales undertook a collaborative study to assess 10 commercial kits for the identification of aerobic Gram negative bacilli. In excess of 1000 such strains were examined in parallel with each kit system. Accuracy, reproducibility of accuracy, and reproducibility alone were assessed, together with the cost effectiveness of the kits used. A ranking order of kit performance based on the above variables was drawn up. Since the foundation of bacteriology as a science in' ditional substrates by Holmes et al,4 and a compre- the second half of the nineteenth century, the use of hensive review article by D'Amato et al.5 We could various substrate reactions as an aid to identification find no reference to the kind of large scale collabo- has been well exploited. This is particularly true of rative and comparative study that we propose. copyright. Enterobacteriaceae and other associated Gram nega- tive aerobic bacilli. Antigenic analysis apart, bio- Material and methods chemical reactions remain the primary means by which these organisms are identified. A detailed protocol was agreed by the WMG and the The past decade has witnessed the introduction kit manufacturers to: evaluate the accuracy and reproducibility of the systems; attempt to assess the from commercial sources of several miniaturised kit http://jcp.bmj.com/ identification systems designed to replace traditional cost effectiveness of the systems.