New Mesh Headings for 2021 Listed in Alphabetical Order with Heading, Scope Note, Annotation (AN), and Tree Locations
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Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
The Shiga Toxin Producing Escherichia Coli
microorganisms Review An Overview of the Elusive Passenger in the Gastrointestinal Tract of Cattle: The Shiga Toxin Producing Escherichia coli Panagiotis Sapountzis 1,* , Audrey Segura 1,2 , Mickaël Desvaux 1 and Evelyne Forano 1 1 Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France; [email protected] (A.S.); [email protected] (M.D.); [email protected] (E.F.) 2 Chr. Hansen Animal Health & Nutrition, 2970 Hørsholm, Denmark * Correspondence: [email protected] Received: 22 May 2020; Accepted: 7 June 2020; Published: 10 June 2020 Abstract: For approximately 10,000 years, cattle have been our major source of meat and dairy. However, cattle are also a major reservoir for dangerous foodborne pathogens that belong to the Shiga toxin-producing Escherichia coli (STEC) group. Even though STEC infections in humans are rare, they are often lethal, as treatment options are limited. In cattle, STEC infections are typically asymptomatic and STEC is able to survive and persist in the cattle GIT by escaping the immune defenses of the host. Interactions with members of the native gut microbiota can favor or inhibit its persistence in cattle, but research in this direction is still in its infancy. Diet, temperature and season but also industrialized animal husbandry practices have a profound effect on STEC prevalence and the native gut microbiota composition. Thus, exploring the native cattle gut microbiota in depth, its interactions with STEC and the factors that affect them could offer viable solutions against STEC carriage in cattle. Keywords: cattle; STEC colonization; microbiota; bacterial interactions 1. Introduction The domestication of cattle, approximately 10,000 years ago [1], brought a stable supply of protein to the human diet, which was instrumental for the building of our societies. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Suppl Table 2
Table S2. Large subunit rRNA gene sequences of Bacteria and Eukarya from V5. ["n" indicates information not specified in the NCBI GenBank database.] Accession number Q length Q start Q end e-value %-ident %-sim GI number Domain Phylum Family Genus / Species JQ997197 529 30 519 3E-165 89% 89% 48728139 Bacteria Actinobacteria Frankiaceae uncultured Frankia sp. JQ997198 732 17 128 2E-35 93% 93% 48728167 Bacteria Actinobacteria Frankiaceae uncultured Frankia sp. JQ997196 521 26 506 4E-95 81% 81% 48728178 Bacteria Actinobacteria Frankiaceae uncultured Frankia sp. JQ997274 369 8 54 4E-14 100% 100% 289551862 Bacteria Actinobacteria Mycobacteriaceae Mycobacterium abscessus JQ999637 486 5 321 7E-62 82% 82% 269314044 Bacteria Actinobacteria Mycobacteriaceae Mycobacterium immunoGenum JQ999638 554 17 509 0 92% 92% 44368 Bacteria Actinobacteria Mycobacteriaceae Mycobacterium kansasii JQ999639 552 18 455 0 93% 93% 196174916 Bacteria Actinobacteria Mycobacteriaceae Mycobacterium sHottsii JQ997284 598 5 598 0 90% 90% 2414571 Bacteria Actinobacteria Propionibacteriaceae Propionibacterium freudenreicHii JQ999640 567 14 560 8E-152 85% 85% 6714990 Bacteria Actinobacteria THermomonosporaceae Actinoallomurus spadix JQ997287 501 8 306 4E-119 93% 93% 5901576 Bacteria Actinobacteria THermomonosporaceae THermomonospora cHromoGena JQ999641 332 26 295 8E-115 95% 95% 291045144 Bacteria Actinobacteria Bifidobacteriaceae Bifidobacterium bifidum JQ999642 349 19 255 5E-82 90% 90% 30313593 Bacteria Bacteroidetes Bacteroidaceae Bacteroides caccae JQ997308 588 20 582 0 90% -
Exploring Bacteria Diversity in Commercialized Table Olive Biofilms
www.nature.com/scientificreports OPEN Exploring bacteria diversity in commercialized table olive bioflms by metataxonomic and compositional data analysis Antonio Benítez‑Cabello1, Verónica Romero‑Gil2, Eduardo Medina‑Pradas1, Antonio Garrido‑Fernández1 & Francisco Noé Arroyo‑López1* In this work, a total of 72 samples of non-thermally treated commercial table olives were obtained from diferent markets of the world. Then, prokaryotic diversity in olive bioflms was investigated by metataxonomic analysis. A total of 660 diferent OTUs were obtained, belonging to Archaea (2.12%) and Bacteria domains (97.88%). From these, 41 OTUs with a proportion of sequences ≥ 0.01% were studied by compositional data analysis. Only two genera were found in all samples, Lactobacillus, which was the predominant bacteria in the bioflm consortium (median 54.99%), and Pediococcus (26.09%). Celerinatantimonas, Leuconostoc, Alkalibacterium, Pseudomonas, Marinilactibacillus, Weissella, and the family Enterobacteriaceae were also present in at least 80% of samples. Regarding foodborne pathogens, only Enterobacteriaceae, Vibrio, and Staphylococcus were detected in at least 91.66%, 75.00%, and 54.10% of samples, respectively, but their median values were always below 0.15%. Compositional data analysis allowed discriminating between lye treated and natural olive samples, as well as between olives packaged in glass, PET and plastic bags. Leuconostoc, Celerinatantimonas, and Alkalibacterium were the bacteria genera with a higher discriminant power among samples. These results expand our knowledge of the bacteria diversity in olive bioflms, providing information about the sanitary and hygienic status of this ready‑to‑eat fermented vegetable. Te world’s olive grove consists of more than 10 million hectares, of which over 1 million are destined to table olives, which constitute the most important fermented vegetable in the Mediterranean countries, with also noticeable productions in South America, USA and Australia. -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge; -
Oral Microbiome Shifts from Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: a Longitudinal Study
fmicb-09-02009 August 27, 2018 Time: 17:19 # 1 ORIGINAL RESEARCH published: 28 August 2018 doi: 10.3389/fmicb.2018.02009 Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study He Xu1†, Jing Tian1†, Wenjing Hao1, Qian Zhang2, Qiong Zhou1, Weihua Shi1, Man Qin1*, Xuesong He3* and Feng Chen2* 1 Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China, 2 Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China, 3 The Forsyth Institute, Cambridge, MA, United States As one of the most prevalent human infectious diseases, dental caries results from dysbiosis of the oral microbiota driven by multiple factors. However, most of caries studies were cross-sectional and mainly focused on the differences in the oral microbiota Edited by: Giovanna Batoni, between caries-free (CF) and caries-affected (CA) populations, while little is known Università degli Studi di Pisa, Italy about the dynamic shift in microbial composition, and particularly the change in species Reviewed by: association pattern during disease transition. Here, we reported a longitudinal study Rainer Haak, of a 12-month follow-up of a cohort of 3-year-old children. Oral examinations and Leipzig University, Germany Xuedong Zhou, supragingival plaque collections were carried out at the beginning and every subsequent Sichuan University, China 6 months, for a total of three time points. All the children were CF at enrollment. Children *Correspondence: who developed caries at 6-month follow-up but had not received any dental treatment Man Qin [email protected]; until the end of the study were incorporated into the CA group. -
The Microbiome of the Footrot Lesion in Merino Sheep Is Characterized by a Persistent Bacterial Dysbiosis T ⁎ Andrew S
Veterinary Microbiology 236 (2019) 108378 Contents lists available at ScienceDirect Veterinary Microbiology journal homepage: www.elsevier.com/locate/vetmic The microbiome of the footrot lesion in Merino sheep is characterized by a persistent bacterial dysbiosis T ⁎ Andrew S. McPherson, Om P. Dhungyel, Richard J. Whittington Farm Animal Health, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, 425 Werombi Rd, Camden, New South Wales, 2570, Australia ARTICLE INFO ABSTRACT Keywords: Footrot is prevalent in most sheep-producing countries; the disease compromises sheep health and welfare and Footrot has a considerable economic impact. The disease is the result of interactions between the essential causative Merino agent, Dichelobacter nodosus, and the bacterial community of the foot, with the pasture environment and host Sheep resistance influencing disease expression. The Merino, which is the main wool sheep breed in Australia, is Microbiome particularly susceptible to footrot. We characterised the bacterial communities on the feet of healthy and footrot- Dichelobacter nodosus affected Merino sheep across a 10-month period via sequencing and analysis of the V3-V4 regions of the bacterial 16S ribosomal RNA gene. Distinct bacterial communities were associated with the feet of healthy and footrot- affected sheep. Infection with D. nodosus appeared to trigger a shift in the composition of the bacterial com- munity from predominantly Gram-positive, aerobic taxa to predominantly Gram-negative, anaerobic taxa. A total of 15 bacterial genera were preferentially abundant on the feet of footrot-affected sheep, several of which have previously been implicated in footrot and other mixed bacterial diseases of the epidermis of ruminants. -
Type of the Paper (Article
Supplementary Materials S1 Clinical details recorded, Sampling, DNA Extraction of Microbial DNA, 16S rRNA gene sequencing, Bioinformatic pipeline, Quantitative Polymerase Chain Reaction Clinical details recorded In addition to the microbial specimen, the following clinical features were also recorded for each patient: age, gender, infection type (primary or secondary, meaning initial or revision treatment), pain, tenderness to percussion, sinus tract and size of the periapical radiolucency, to determine the correlation between these features and microbial findings (Table 1). Prevalence of all clinical signs and symptoms (except periapical lesion size) were recorded on a binary scale [0 = absent, 1 = present], while the size of the radiolucency was measured in millimetres by two endodontic specialists on two- dimensional periapical radiographs (Planmeca Romexis, Coventry, UK). Sampling After anaesthesia, the tooth to be treated was isolated with a rubber dam (UnoDent, Essex, UK), and field decontamination was carried out before and after access opening, according to an established protocol, and shown to eliminate contaminating DNA (Data not shown). An access cavity was cut with a sterile bur under sterile saline irrigation (0.9% NaCl, Mölnlycke Health Care, Göteborg, Sweden), with contamination control samples taken. Root canal patency was assessed with a sterile K-file (Dentsply-Sirona, Ballaigues, Switzerland). For non-culture-based analysis, clinical samples were collected by inserting two paper points size 15 (Dentsply Sirona, USA) into the root canal. Each paper point was retained in the canal for 1 min with careful agitation, then was transferred to −80ºC storage immediately before further analysis. Cases of secondary endodontic treatment were sampled using the same protocol, with the exception that specimens were collected after removal of the coronal gutta-percha with Gates Glidden drills (Dentsply-Sirona, Switzerland). -
Lichens As Natural Sources of Biotechnologically Relevant Bacteria Marcelino T
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by HAL-Rennes 1 Lichens as natural sources of biotechnologically relevant bacteria Marcelino T. Suzuki, Delphine Parrot, Gabriele Berg, Martin Grube, Sophie Tomasi To cite this version: Marcelino T. Suzuki, Delphine Parrot, Gabriele Berg, Martin Grube, Sophie Tomasi. Lichens as natural sources of biotechnologically relevant bacteria. Applied Microbiology and Biotech- nology, Springer Verlag, 2016, 100 (2), pp.583-595. <10.1007/s00253-015-7114-z>. <hal- 01227960> HAL Id: hal-01227960 http://hal.upmc.fr/hal-01227960 Submitted on 12 Nov 2015 HAL is a multi-disciplinary open access L'archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destin´eeau d´ep^otet `ala diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publi´esou non, lished or not. The documents may come from ´emanant des ´etablissements d'enseignement et de teaching and research institutions in France or recherche fran¸caisou ´etrangers,des laboratoires abroad, or from public or private research centers. publics ou priv´es. Invited Mini Review Lichens as natural sources of biotechnologically relevant Bacteria Marcelino T. SUZUKI1*, Delphine PARROT2, Gabriele BERG3, Martin GRUBE4, Sophie TOMASI2 1Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologie Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls/Mer, France 2UMR CNRS 6226, Institut des Sciences chimiques de Rennes, Equipe PNSCM “Produits Naturels – Synthèses – Chimie Médicinale”, UFR Sciences Pharmaceutiques et Biologiques, Univ. Rennes 1, Université Européenne de Bretagne, 2 Avenue du Pr. Léon Bernard, F-35043 Rennes, France 3Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria. -
Laboratory Cultivation of Widespread and Previously Uncultured Soil Bacteria Shayne J
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Dec. 2003, p. 7210–7215 Vol. 69, No. 12 0099-2240/03/$08.00ϩ0 DOI: 10.1128/AEM.69.12.7210–7215.2003 Copyright © 2003, American Society for Microbiology. All Rights Reserved. Laboratory Cultivation of Widespread and Previously Uncultured Soil Bacteria Shayne J. Joseph,1 Philip Hugenholtz,2 Parveen Sangwan,1 1 1 Catherine A. Osborne, and Peter H. Janssen * Downloaded from Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia,1 and Department of Environmental Science, Policy and Management, Division of Ecosystem Sciences, University of California Berkeley, Berkeley, California 94720-31102 Received 17 June 2003/Accepted 16 September 2003 Most soil bacteria belong to family-level phylogenetic groups with few or no known cultivated representa- tives. We cultured a collection of 350 isolates from soil by using simple solid media in petri dishes. These isolates were assigned to 60 family-level groupings in nine bacterial phyla on the basis of a comparative http://aem.asm.org/ analysis of their 16S rRNA genes. Ninety-three (27%) of the isolates belonged to 20 as-yet-unnamed family-level groupings, many from poorly studied bacterial classes and phyla. They included members of subdivisions 1, 2, 3, and 4 of the phylum Acidobacteria, subdivision 3 of the phylum Verrucomicrobia, subdivision 1 of the phylum Gemmatimonadetes, and subclasses Acidimicrobidae and Rubrobacteridae of the phylum Actinobacteria. In addi- tion, members of 10 new family-level groupings of subclass Actinobacteridae of the phylum Actinobacteria and classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria of the phylum Proteobacteria were obtained. The high degree of phylogenetic novelty and the number of isolates affiliated with so-called uncul- turable groups show that simple cultivation methods can still be developed further to obtain laboratory cultures of many phylogenetically novel soil bacteria.