DOCSLIB.ORG

The Cause of Death of a Child in the 18Th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Cause of Death of a Child in the 18Th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing International Journal of Molecular Sciences Article The Cause of Death of a Child in the 18th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing Valeria D’Argenio 1,2, Marielva Torino 3, Vincenza Precone 1, Giorgio Casaburi 1,†, Maria Valeria Esposito 1, Laura Iaffaldano 1, Umberto Malapelle 4, Giancarlo Troncone 4, Iolanda Coto 1,2, Paolina Cavalcanti 5, Gaetano De Rosa 6, Francesco Salvatore 1,7,* and Lucia Sacchetti 1,* 1 CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy; [email protected] (V.D.); [email protected] (V.P.); [email protected] (G.C.); [email protected] (M.V.E.); [email protected] (L.I.); [email protected] (I.C.) 2 Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, via Pansini 5, 80131 Naples, Italy 3 Department of Paleopathology, University of Naples Suor Orsola Benincasa, via Suor Orsola 10, 80125 Naples, Italy; [email protected] 4 Department of Public Health, University of Naples Federico II, Naples, via Pansini 5, 80131 Naples, Italy; [email protected] (U.M.); [email protected] (G.T.) 5 Microbiology Unit, Hospital of Cosenza, via San Martino, 87100 Cosenza, Italy; [email protected] 6 Department of Advanced Biomedical Sciences, University of Naples Federico II, via Pansini 5, 80131 Naples, Italy; [email protected] 7 IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico)-Fondazione SDN, via Gianturco 113, 80143 Naples, Italy * Correspondence: [email protected] (F.S.); [email protected] (L.S.); Tel.: +39-081-746-3648 (F.S.); +39-081-373-7827 (L.S.); Fax+39-081-746-3133 (F.S.); +39-081-373-7808 (L.S.) † Present address: Life Sciences Lab, University of Florida, Kennedy Space Center, Merritt Island, FL 32953, USA. Academic Editor: William Chi-shing Cho Received: 28 October 2016; Accepted: 3 January 2017; Published: 6 January 2017 Abstract: The history of medicine abounds in cases of mysterious deaths, especially by infectious diseases, which were probably unresolved because of the lack of knowledge and of appropriate technology. The aim of this study was to exploit contemporary technologies to try to identify the cause of death of a young boy who died from a putative “infection” at the end of the 18th century, and for whom an extraordinarily well-preserved minute bone fragment was available. After confirming the nature of the sample, we used laser microdissection to select the most “informative” area to be examined. Tissue genotyping indicated male gender, thereby confirming the notary’s report. 16S ribosomal RNA sequencing showed that Proteobacteria and Actinobacteria were more abundant than Firmicutes and Bacteroidetes, and that Pseudomonas was the most abundant bacterial genus in the Pseudomonadaceae family. These data suggest that the patient most likely died from Pseudomonas osteomyelitis. This case is an example of how new technological approaches, like laser microdissection and next-generation sequencing, can resolve ancient cases of uncertain etiopathology. Lastly, medical samples may contain a wealth of information that may not be accessible until more sophisticated technology becomes available. Therefore, one may envisage the possibility of systematically storing medical samples for evaluation by future generations. Keywords: metagenomics; human microbiome; cold case; next generation sequencing Int. J. Mol. Sci. 2017, 18, 109; doi:10.3390/ijms18010109 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2017, 18, 109 2 of 9 1. Introduction Int. J. Mol. Sci. 2017, 18, 109 2 of 10 Past cases of death from unknown causes, particularly those of famous personalities, are commonly1. Introduction referred to as “mysterious deaths”. In many instances, such cases can now be solved thanks toPast advances cases inof researchdeath from and unknown to the advent causes, of modernparticularly technologies those of famous [1,2]. Notably, personalities, identification are of causescommonly of death referred in ancientto as “mysterious “cold cases” deaths”. may In also many shed instances, light on such the cases evolution can now of be a diseasesolved [3]. Thisthanks article concernsto advances a young in research boy who and died to at the the ad endvent of theof 18thmodern century technolo fromgies a putative [1,2]. Notably, infection of a boneidentification wound (possibly of causes osteomyelitis). of death in ancient His parents“cold cases” feltthat may their also sonshed was light not on receivingthe evolution appropriate of a treatmentdisease because [3]. This his article condition concerns was a young not correctly boy who diagnosed. died at the Consequently,end of the 18th century they took from the a unusualputative step infection of a bone wound (possibly osteomyelitis). His parents felt that their son was not receiving of preserving a fragment of the affected bone for future analysis. Thus, the fragment was sealed by a appropriate treatment because his condition was not correctly diagnosed. Consequently, they took public notary in a small envelope (see the documentation in the Supplementary File 1 and Figure S1) the unusual step of preserving a fragment of the affected bone for future analysis. Thus, the untilfragment the study was described sealed inby thisa public paper. notary in a small envelope (see the documentation in the SupplementaryNext-generation File technology1 and Supplementary for high-throughput Figure S1) until sequencingthe study described of nucleic in this acidspaper. has been a breakthroughNext-generation in the field technology of metagenomics, for high-throughpu and hast producedsequencing aof wealth nucleic of acids data has about been various a environmentalbreakthrough niches in the in medicalfield of metagenomics, research, particularly and has in produced the field ofa wealth infectious of data diseases about [4 ,various5]. The aim of ourenvironmental study was toniches try to in identifymedical theresearch, cause particularly of death of in this the boyfield usingof infectious contemporary diseases [4,5]. technologies The and methods.aim of our study was to try to identify the cause of death of this boy using contemporary technologies and methods. 2. Results 2. Results Hematoxylin and eosin (H and E) stained sections of the specimen showed the features typical of Hematoxylin and eosin (H and E) stained sections of the specimen showed the features typical bone tissue and aggregates of granulocytes, which is indicative of an inflammatory reaction (Figure1A). of bone tissue and aggregates of granulocytes, which is indicative of an inflammatory reaction To minimize the risk of external contamination and obtain a sufficient quantity of DNA-rich material, (Figure 1A). To minimize the risk of external contamination and obtain a sufficient quantity of we isolatedDNA-rich a piecematerial, of the we infectedisolated a bone piece by of laser the infected microdissection bone by laser under microdissection sterile conditions. under sterile Figure 1B showsconditions. the pre-microdissected Figure 1B shows area,the pre-microdissect and Figure1Ced the area, post-microdissected and Figure 1C the area.post-microdissected Sex-determining regionarea. Y (SRY)Sex-determining analysis confirmed region Y (SRY) that analysis the DNA confirmed was from that a malethe DNA (Figure was1 fromD). a male (Figure 1D). Figure 1. Bone sample characterization. (A) Microscopy image (hematoxylin and eosin staining) Figure 1. Bone sample characterization. (A) Microscopy image (hematoxylin and eosin staining) showing the features typical of bone tissue and inflammatory infiltration; example of a laser showing the features typical of bone tissue and inflammatory infiltration; example of a laser captured captured microdissected area of the bone sample: (B) shows the pre-microdissected area × microdissected(40× resolution), area of(C the) the bone green sample: line encircles (B) shows the microdissected the pre-microdissected area; (D) areasex-determining (40 resolution); region( CY ) the greenamplification line encircles revealed the microdissected the sex of the area;patient: (D )lane sex-determining 1: ladder (100–1200 region bp); Y amplificationlane 2: sample; revealed lane 3: the sex ofnegative the patient: control; lane lanes 1: ladder4 and 5: (100–1200male controls; bp); lanes lane 6–8: 2: sample; uncharged lane slots. 3: negative control; lanes 4 and 5: male controls; lanes 6–8: uncharged slots. Int. J. Mol. Sci. 2017, 18, 109 3 of 9 Int. J. Mol. Sci. 2017, 18, 109 3 of 10 WeWe analyzed analyzed the the entire entire bacterial bacterial microbiome microbiome of the of bone the sample bone bysample a next-generation by a next-generation sequencing approach,sequencing as describedapproach, as under described Methods under (see Methods the Section (see the 4.5 ).Section A total 4.5). of A 7,357,569 total of 7,357,569 base pairs base (bp) correspondingpairs (bp) corresponding to 14,172 16S sequencesto 14,172 16S (mean sequence sequences (mean length, sequence 528.7 bp length, and average 528.7 qualitybp and scoreaverage 34.18) werequality generated. score 34.18) After were pre-quality generated. filtering After (see pre-quality Section 4.6filtering for details), (see Section 12,829 4.6 high for qualitydetails), sequences 12,829 werehigh considered quality sequences for subsequent were considered analysis. In for detail, subseq 243uent representative analysis. In operationaldetail, 243 taxonomicrepresentative units (OTUs)operational
Load more

Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • 1Gyd Lichtarge Lab 2006
    Pages 1–7 1gyd Evolutionary trace report by report maker January 18, 2010 4.3.3 DSSP 6 4.3.4 HSSP 6 4.3.5 LaTex 6 4.3.6 Muscle 6 4.3.7 Pymol 6 4.4 Note about ET Viewer 6 4.5 Citing this work 6 4.6 About report maker 7 4.7 Attachments 7 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1gyd): Title: Structure of cellvibrio cellulosa alpha-l-arabinanase Compound: Mol id: 1; molecule: arabinan endo-1,5-alpha-l- arabinosidase a; chain: b; synonym: alpha-l-arabinanase, abn a, endo-1,5-alpha-l- arabinanase a; ec: 3.2.1.99; engineered: yes Organism, scientific name: Cellvibrio Japonicus; 1gyd contains a single unique chain 1gydB (315 residues long). 2 CHAIN 1GYDB 2.1 P95470 overview CONTENTS From SwissProt, id P95470, 99% identical to 1gydB: 1 Introduction 1 Description: Endo-a1,5-arabinanase (EC 3.2.1.99). Organism, scientific name: Cellvibrio japonicus. 2 Chain 1gydB 1 Taxonomy: Bacteria; Proteobacteria; Gammaproteobacteria; Pseu- 2.1 P95470 overview 1 domonadales; Pseudomonadaceae; Cellvibrio. 2.2 Multiple sequence alignment for 1gydB 1 2.3 Residue ranking in 1gydB 1 2.2 Multiple sequence alignment for 1gydB 2.4 Top ranking residues in 1gydB and their position on For the chain 1gydB, the alignment 1gydB.msf (attached) with 99 the structure 2 sequences was used. The alignment was downloaded from the HSSP 2.4.1 Clustering of residues at 25% coverage. 2 database, and fragments shorter than 75% of the query as well as 2.4.2 Possible novel functional surfaces at 25% duplicate sequences were removed.
    [Show full text]
  • Genomic Encyclopedia of Sugar Utilization Pathways in The
    Rodionov et al. BMC Genomics 2010, 11:494 http://www.biomedcentral.com/1471-2164/11/494 RESEARCH ARTICLE Open Access Genomic encyclopedia of sugar utilization pathways in the Shewanella genus Dmitry A Rodionov1,2, Chen Yang1,3, Xiaoqing Li1, Irina A Rodionova1, Yanbing Wang4, Anna Y Obraztsova4,7, Olga P Zagnitko5, Ross Overbeek5, Margaret F Romine6, Samantha Reed6, James K Fredrickson6, Kenneth H Nealson4,7, Andrei L Osterman1,5* Abstract Background: Carbohydrates are a primary source of carbon and energy for many bacteria. Accurate projection of known carbohydrate catabolic pathways across diverse bacteria with complete genomes constitutes a substantial challenge due to frequent variations in components of these pathways. To address a practically and fundamentally important challenge of reconstruction of carbohydrate utilization machinery in any microorganism directly from its genomic sequence, we combined a subsystems-based comparative genomic approach with experimental validation of selected bioinformatic predictions by a combination of biochemical, genetic and physiological experiments. Results: We applied this integrated approach to systematically map carbohydrate utilization pathways in 19 genomes from the Shewanella genus. The obtained genomic encyclopedia of sugar utilization includes ~170 protein families (mostly metabolic enzymes, transporters and transcriptional regulators) spanning 17 distinct pathways with a mosaic distribution across Shewanella species providing insights into their ecophysiology and adaptive evolution. Phenotypic
    [Show full text]
  • Achromobacter Infections and Treatment Options
    AAC Accepted Manuscript Posted Online 17 August 2020 Antimicrob. Agents Chemother. doi:10.1128/AAC.01025-20 Copyright © 2020 American Society for Microbiology. All Rights Reserved. 1 Achromobacter Infections and Treatment Options 2 Burcu Isler 1 2,3 3 Timothy J. Kidd Downloaded from 4 Adam G. Stewart 1,4 5 Patrick Harris 1,2 6 1,4 David L. Paterson http://aac.asm.org/ 7 1. University of Queensland, Faculty of Medicine, UQ Center for Clinical Research, 8 Brisbane, Australia 9 2. Central Microbiology, Pathology Queensland, Royal Brisbane and Women’s Hospital, 10 Brisbane, Australia on August 18, 2020 at University of Queensland 11 3. University of Queensland, Faculty of Science, School of Chemistry and Molecular 12 Biosciences, Brisbane, Australia 13 4. Infectious Diseases Unit, Royal Brisbane and Women’s Hospital, Brisbane, Australia 14 15 Editorial correspondence can be sent to: 16 Professor David Paterson 17 Director 18 UQ Center for Clinical Research 19 Faculty of Medicine 20 The University of Queensland 1 21 Level 8, Building 71/918, UQCCR, RBWH Campus 22 Herston QLD 4029 AUSTRALIA 23 T: +61 7 3346 5500 Downloaded from 24 F: +61 7 3346 5509 25 E: [email protected] 26 http://aac.asm.org/ 27 28 29 on August 18, 2020 at University of Queensland 30 31 32 33 34 35 36 37 38 39 2 40 Abstract 41 Achromobacter is a genus of non-fermenting Gram negative bacteria under order 42 Burkholderiales. Although primarily isolated from respiratory tract of people with cystic Downloaded from 43 fibrosis, Achromobacter spp. can cause a broad range of infections in hosts with other 44 underlying conditions.
    [Show full text]
  • Plant-Derived Benzoxazinoids Act As Antibiotics and Shape Bacterial Communities
    Supplemental Material for: Plant-derived benzoxazinoids act as antibiotics and shape bacterial communities Niklas Schandry, Katharina Jandrasits, Ruben Garrido-Oter, Claude Becker Contents Supplemental Tables 2 Supplemental Table 1. Phylogenetic signal lambda . .2 Supplemental Table 2. Syncom strains . .3 Supplemental Table 3. PERMANOVA . .6 Supplemental Table 4. PERMANOVA comparing only two treatments . .7 Supplemental Table 5. ANOVA: Observed taxa . .8 Supplemental Table 6. Observed diversity means and pairwise comparisons . .9 Supplemental Table 7. ANOVA: Shannon Diversity . 11 Supplemental Table 8. Shannon diversity means and pairwise comparisons . 12 Supplemental Table 9. Correlation between change in relative abundance and change in growth . 14 Figures 15 Supplemental Figure 1 . 15 Supplemental Figure 2 . 16 Supplemental Figure 3 . 17 Supplemental Figure 4 . 18 1 Supplemental Tables Supplemental Table 1. Phylogenetic signal lambda Class Order Family lambda p.value All - All All All All 0.763 0.0004 * * Gram Negative - Proteobacteria All All All 0.817 0.0017 * * Alpha All All 0 0.9998 Alpha Rhizobiales All 0 1.0000 Alpha Rhizobiales Phyllobacteriacae 0 1.0000 Alpha Rhizobiales Rhizobiacaea 0.275 0.8837 Beta All All 1.034 0.0036 * * Beta Burkholderiales All 0.147 0.6171 Beta Burkholderiales Comamonadaceae 0 1.0000 Gamma All All 1 0.0000 * * Gamma Xanthomonadales All 1 0.0001 * * Gram Positive - Actinobacteria Actinomycetia Actinomycetales All 0 1.0000 Actinomycetia Actinomycetales Intrasporangiaceae 0.98 0.2730 Actinomycetia Actinomycetales Microbacteriaceae 1.054 0.3751 Actinomycetia Actinomycetales Nocardioidaceae 0 1.0000 Actinomycetia All All 0 1.0000 Gram Positive - All All All All 0.421 0.0325 * Gram Positive - Firmicutes Bacilli All All 0 1.0000 2 Supplemental Table 2.
    [Show full text]
  • Supplementary Fig. S2. Taxonomic Classification of Two Metagenomic Samples of the Gall-Inducing Mite Fragariocoptes Seti- Ger in Kraken2
    Supplementary Fig. S2. Taxonomic classification of two metagenomic samples of the gall-inducing mite Fragariocoptes seti- ger in Kraken2. There was a total of 708,046,814 and 82,009,061 classified reads in samples 1 and 2, respectively. OTUs (genera) were filtered based on a normalized abundance threshold of ≥0.0005% in either sample, resulting in 171 OTUs represented by 670,717,361 and 72,439,919 reads (sample 1 and 2, respectively). Data are given in Supplementary Table S3. Sample1 Sample2 0.000005 0.002990 Bacteria:Proteobacteria:Inhella Read % (log2) 0.000005 0.005342 Bacteria:Actinobacteria:Microbacteriaceae:Microterricola 10.00 0.000006 0.003983 Bacteria:Actinobacteria:Microbacteriaceae:Cryobacterium 5.00 0.000012 0.006576 Eukaryota:Ascomycota:Mycosphaerellaceae:Cercospora 0.00 0.000013 0.002947 Bacteria:Actinobacteria:Bifidobacteriaceae:Gardnerella 0.000017 0.003555 Eukaryota:Ascomycota:Chaetomiaceae:Thielavia -5.00 0.000014 0.004244 Bacteria:Firmicutes:Clostridiaceae:Clostridium -10.00 0.000010 0.001699 Bacteria:Proteobacteria:Caulobacteraceae:Phenylobacterium -15.00 0.000012 0.001183 Bacteria:Actinobacteria:Microbacteriaceae:Leifsonia 0.000009 0.001144 Bacteria:Proteobacteria:Desulfovibrionaceae:Desulfovibrio -20.00 0.000016 0.000777 Bacteria:Firmicutes:Leuconostocaceae:Weissella -25.00 0.000014 0.000761 Bacteria:Cyanobacteria:Oscillatoriaceae:Oscillatoria 0.000013 0.000683 Bacteria:Proteobacteria:Methylobacteriaceae:Microvirga Read % 0.000011 0.000578 Bacteria:Fusobacteria:Leptotrichiaceae:Leptotrichia 0.000009 0.000842 Bacteria:Firmicutes:Paenibacillaceae:Paenibacillus
    [Show full text]
  • A Taxonomic Framework for Emerging Groups of Ecologically
    Spring S, Scheuner C, Göker M, Klenk H-P. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Frontiers in Microbiology 2015, 6, 281. Copyright: Copyright © 2015 Spring, Scheuner, Göker and Klenk. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. DOI link to article: http://dx.doi.org/10.3389/fmicb.2015.00281 Date deposited: 07/03/2016 This work is licensed under a Creative Commons Attribution 4.0 International License Newcastle University ePrints - eprint.ncl.ac.uk ORIGINAL RESEARCH published: 09 April 2015 doi: 10.3389/fmicb.2015.00281 A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data Stefan Spring 1*, Carmen Scheuner 1, Markus Göker 1 and Hans-Peter Klenk 1, 2 1 Department Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 School of Biology, Newcastle University, Newcastle upon Tyne, UK Edited by: Marcelino T. Suzuki, Sorbonne Universities (UPMC) and In recent years a large number of isolates were obtained from saline environments that are Centre National de la Recherche phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, Scientifique, France which were originally identified in seawater samples using cultivation independent Reviewed by: Fabiano Thompson, methods and are characterized by high seasonal abundances in coastal environments.
    [Show full text]
  • Probiotic Properties of Alcaligenes Faecalis Isolated from Argyrosomus Regius in Experimental Peritonitis (Rat Model)
    Probiotics and Antimicrobial Proteins https://doi.org/10.1007/s12602-021-09767-7 Probiotic Properties of Alcaligenes faecalis Isolated from Argyrosomus regius in Experimental Peritonitis (Rat Model) A. I. Gutiérrez‑Falcón1 · A. M. Ramos‑Nuez2,3 · A. Espinosa de los Monteros y Zayas4 · D. F. Padilla Castillo1 · M. Isabel García‑Laorden2,3 · F. J. Chamizo‑López5 · F. Real Valcárcel1 · F. Artilles Campelo5 · A. Bordes Benítez5 · P. Nogueira Salgueiro6 · C. Domínguez Cabrera6 · J. C. Rivero‑Vera7 · J. M. González‑Martín8 · J. Martín Caballero9 · R. Frías‑Beneyto10 · Jesús Villar2,3 · J. L. Martín‑Barrasa1,3,11 Accepted: 3 March 2021 © The Author(s) 2021 Abstract A strain of Alcaligenes faecalis A12C (A. faecalis A12C) isolated from Argyrosomus regius is a probiotic in fsh. Previous experiments showed that A. faecalis A12C had inhibitory efects on the growth of multidrug-resistant bacteria. We aimed to confrm whether A. faecalis A12C is safe and has adequate intestinal colonization in experimental rats, and evaluate its efcacy in an animal model of peritonitis. We used 30 male rats, randomly divided into 6 groups (n = 5): three groups (HA7, HA15, HA30) received A. faecalis A12C in drinking water (6 × 108 CFU/mL) for 7 days, and three control groups received drinking water only. All groups were evaluated at 7, 15, and 30 days. Survival after A. faecalis A12C administration was 100% in all groups. Mild eosinophilia (1.5%, p < 0.01) and increased aspartate aminotransferase (86 IU/L, p < 0.05) were observed in HA7, followed by progressive normalization. No histological signs of organ injury were found. We observed signifcant E.
    [Show full text]
  • Pigmentiphaga Kullae Gen. Nov., Sp. Nov., a Novel Member of the Family
    International Journal of Systematic and Evolutionary Microbiology (2001), 51, 1867–1871 Printed in Great Britain Pigmentiphaga kullae gen. nov., sp. nov., a NOTE novel member of the family Alcaligenaceae with the ability to decolorize azo dyes aerobically 1 Institut fu$ r Mikrobiologie, Silke Blu$ mel,1 Barbara Mark,2 Hans-Ju$ rgen Busse,2,3 Peter Ka$ mpfer4 and Universita$ t Stuttgart, 1 Allmandring 31, D-70569 Andreas Stolz Stuttgart, Germany 2 Institut fu$ r Bakteriologie, Author for correspondence: Andreas Stolz. Tel: j49 711 6855489. Fax: j49 711 6855725. Mykologie und Hygiene, e-mail: andreas.stolz!po.uni-stuttgart.de Veterina$ rmedizinische Universita$ t Wien, Veterina$ rplatz 1, A-1210 Wien, Austria The taxonomic position of Pseudomonas strain K24, which was isolated previously after an aerobic enrichment with the azo compound 1-(4’- 3 Institut fu$ r Mikrobiologie und Genetik, Universita$ t carboxyphenylazo)-4-naphthol as the sole source of carbon and energy, was Wien, Dr Bohrgasse 9, investigated. The detection of a quinone system with ubiquinone Q-8 as the A-1030 Wien, Austria predominant compound and a polyamine pattern with putrescine and 2- 4 Institut fu$ r Angewandte hydroxyputrescine as the major polyamines present suggested that strain K24T Mikrobiologie, Justus- belongs to the β-subclass of the Proteobacteria. This was supported by Liebig-Universita$ t Giessen, Heinrich-Buff-Ring 26–32 sequencing the 16S rRNA gene, which demonstrated about 95–96% sequence (IFZ), D-35392 Giessen, similarity to different species of the genera Achromobacter, Alcaligenes and Germany Bordetella. This suggested that strain K24T is a member of the family Alcaligenaceae.
    [Show full text]
  • Alteration of the Gut Microbiota Associated with Childhood Obesity by 16S Rrna Gene Sequencing
    Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing Xiaowei Chen1,2, Haixiang Sun1, Fei Jiang1,2, Yan Shen1,2, Xin Li1, Xueju Hu1, Xiaobing Shen1,2 and Pingmin Wei1,2 1 Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China 2 Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China ABSTRACT Background. Obesity is a global epidemic in the industrialized and developing world, and many children suffer from obesity-related complications. Gut microbiota dysbiosis might have significant effect on the development of obesity. The microbiota continues to develop through childhood and thus childhood may be the prime time for microbiota interventions to realize health promotion or disease prevention. Therefore, it is crucial to understand the structure and function of pediatric gut microbiota. Methods. According to the inclusion criteria and exclusion criteria, twenty-three normal weight and twenty-eight obese children were recruited from Nanjing, China. Genomic DNA was extracted from fecal samples. The V4 region of the bacterial 16S rDNA was amplified by PCR, and sequencing was applied to analyze the gut microbiota diversity and composition using the Illumina HiSeq 2500 platform. Results. The number of operational taxonomic units (OTUs) showed a decrease in the diversity of gut microbiota with increasing body weight. The alpha diversity indices showed that the normal weight group had higher abundance and observed species than the obese group (Chao1: P < 0.001; observed species: P < 0.001; PD whole tree: P < 0.001; Shannon index: P D 0.008).
    [Show full text]
  • A Genomic Perspective on a New Bacterial Genus and Species from the Alcaligenaceae Family, Basilea Psittacipulmonis
    UC Irvine UC Irvine Previously Published Works Title A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis. Permalink https://escholarship.org/uc/item/0f60f7jm Journal BMC genomics, 15(1) ISSN 1471-2164 Authors Whiteson, Katrine L Hernandez, David Lazarevic, Vladimir et al. Publication Date 2014-03-01 DOI 10.1186/1471-2164-15-169 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Whiteson et al. BMC Genomics 2014, 15:169 http://www.biomedcentral.com/1471-2164/15/169 RESEARCH ARTICLE Open Access A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis Katrine L Whiteson1,5*, David Hernandez1, Vladimir Lazarevic1, Nadia Gaia1, Laurent Farinelli2, Patrice François1, Paola Pilo3, Joachim Frey3 and Jacques Schrenzel1,4 Abstract Background: A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The organism is described with a chemotaxonomic profile and the nearly complete genome sequence obtained through the assembly of short sequence reads. Results: Genome sequence analysis and characterization of respiratory quinones, fatty acids, polar lipids, and biochemical phenotype is presented here. Comparison of gene sequences revealed that the most similar species is Pelistega europaea, with BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene, and a similar GC content (~43%) as the organism isolated from the parakeet, DSM 24701 (40%). The closest full genome sequences are those of Bordetella spp.
    [Show full text]
  • Supplementary Material
    1 Supplementary Material 2 Changes amid constancy: flower and leaf microbiomes along land use gradients 3 and between bioregions 4 Paul Gaube*, Robert R. Junker, Alexander Keller 5 *Correspondence to Paul Gaube (email: [email protected]) 6 7 Supplementary Figures and Tables 8 Figures 9 Figure S1: Heatmap with relative abundance of Lactobacillales and Rhizobiales ASVs of each sample 10 related to tissue type. Differences in their occurrence on flowers and leaves (plant organs) were 11 statistically tested using t-test (p < 0.001***). 12 Figure S2A-D: Correlations between relative abundances of 25 most abundant bacterial genera and LUI 13 parameters. Correlations are based on linear Pearson correlation coefficients against each other and LUI 14 indices. Correlation coefficients are displayed by the scale color in the filled squares and indicate the 15 strength of the correlation (r) and whether it is positive (blue) or negative (red). P-values were adjusted 16 for multiple testing with Benjamini-Hochberg correction and only significant correlations are shown (p < 17 0.05). White boxes indicate non-significant correlations. A) Ranunculus acris flowers, B) Trifolium pratense 18 flowers, C) Ranunculus acris leaves (LRA), D) Trifolium pratense leaves (LTP). 19 20 Tables 21 Table S1: Taxonomic identification of the most abundant bacterial genera and their presence (average 22 in percent) on each tissue type. 23 Table S2: Taxonomic identification of ubiquitous bacteria found in 95 % of all samples, including their 24 average relative abundance on each tissue type. 25 Table S3: Bacterial Classes that differed significantly in relative abundance between bioregions for each 26 tissue type.
    [Show full text]