Systems-Wide Effects of Short-Term Feed Deprivation in Obese Mice
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Macellibacteroides Fermentans Gen. Nov., Sp. Nov., a Member of the Family Porphyromonadaceae Isolated from an Upflow Anaerobic Filter Treating Abattoir Wastewaters
International Journal of Systematic and Evolutionary Microbiology (2012), 62, 2522–2527 DOI 10.1099/ijs.0.032508-0 Macellibacteroides fermentans gen. nov., sp. nov., a member of the family Porphyromonadaceae isolated from an upflow anaerobic filter treating abattoir wastewaters Linda Jabari,1,2 Hana Gannoun,2 Jean-Luc Cayol,1 Abdeljabbar Hedi,1 Mitsuo Sakamoto,3 Enevold Falsen,4 Moriya Ohkuma,3 Moktar Hamdi,2 Guy Fauque,1 Bernard Ollivier1 and Marie-Laure Fardeau1 Correspondence 1Aix-Marseille Universite´ du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, Marie-Laure Fardeau 163 Avenue de Luminy, 13288 Marseille Cedex 9, France [email protected] 2Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Applique´es et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis Cedex, Tunisia 3Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 4CCUG, Culture Collection, Department of Clinical Bacteriology, University of Go¨teborg, 41346 Go¨teborg, Sweden A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic bacterium, which stained Gram-positive but showed the typical cell wall structure of Gram-negative bacteria, was isolated from an upflow anaerobic filter treating abattoir wastewaters in Tunisia. The strain, designated LIND7HT, grew at 20–45 6C (optimum 35–40 6C) and at pH 5.0–8.5 (optimum pH 6.5–7.5). It did not require NaCl for growth, but was able to grow in the presence of up to 2 % NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. -
Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis
International Journal of Molecular Sciences Review Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis David Johane Machate 1, Priscila Silva Figueiredo 2 , Gabriela Marcelino 2 , Rita de Cássia Avellaneda Guimarães 2,*, Priscila Aiko Hiane 2 , Danielle Bogo 2, Verônica Assalin Zorgetto Pinheiro 2, Lincoln Carlos Silva de Oliveira 3 and Arnildo Pott 1 1 Graduate Program in Biotechnology and Biodiversity in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] (D.J.M.); [email protected] (A.P.) 2 Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; pri.fi[email protected] (P.S.F.); [email protected] (G.M.); [email protected] (P.A.H.); [email protected] (D.B.); [email protected] (V.A.Z.P.) 3 Chemistry Institute, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-67-3345-7416 Received: 9 March 2020; Accepted: 27 March 2020; Published: 8 June 2020 Abstract: Long-term high-fat dietary intake plays a crucial role in the composition of gut microbiota in animal models and human subjects, which affect directly short-chain fatty acid (SCFA) production and host health. This review aims to highlight the interplay of fatty acid (FA) intake and gut microbiota composition and its interaction with hosts in health promotion and obesity prevention and its related metabolic dysbiosis. -
Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis Within the Prevalent Canine Oral Species Porphyromonas Cangingivalis
GBE Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis Ciaran O’Flynn1,*, Oliver Deusch1, Aaron E. Darling2, Jonathan A. Eisen3,4,5, Corrin Wallis1,IanJ.Davis1,and Stephen J. Harris1 1 The WALTHAM Centre for Pet Nutrition, Waltham-on-the-Wolds, United Kingdom Downloaded from 2The ithree Institute, University of Technology Sydney, Ultimo, New South Wales, Australia 3Department of Evolution and Ecology, University of California, Davis 4Department of Medical Microbiology and Immunology, University of California, Davis 5UC Davis Genome Center, University of California, Davis http://gbe.oxfordjournals.org/ *Corresponding author: E-mail: ciaran.ofl[email protected]. Accepted: November 6, 2015 Abstract Porphyromonads play an important role in human periodontal disease and recently have been shown to be highly prevalent in canine mouths. Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and at University of Technology, Sydney on January 17, 2016 plaque from dogs with early periodontitis. The ability of P. cangingivalis to flourish in the different environmental conditions char- acterized by these two states suggests a degree of metabolic flexibility. To characterize the genes responsible for this, the genomes of 32 isolates (including 18 newly sequenced and assembled) from 18 Porphyromonad species from dogs, humans, and other mammals were compared. Phylogenetic trees inferred using core genes largely matched previous findings; however, comparative genomic analysis identified several genes and pathways relating to heme synthesis that were present in P. cangingivalis but not in other Porphyromonads. Porphyromonas cangingivalis has a complete protoporphyrin IX synthesis pathway potentially allowing it to syn- thesize its own heme unlike pathogenic Porphyromonads such as Porphyromonas gingivalis that acquire heme predominantly from blood. -
A Survey of Carbon Fixation Pathways Through a Quantitative Lens
Journal of Experimental Botany, Vol. 63, No. 6, pp. 2325–2342, 2012 doi:10.1093/jxb/err417 Advance Access publication 26 December, 2011 REVIEW PAPER A survey of carbon fixation pathways through a quantitative lens Arren Bar-Even, Elad Noor and Ron Milo* Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel * To whom correspondence should be addressed. E-mail: [email protected] Received 15 August 2011; Revised 4 November 2011; Accepted 8 November 2011 Downloaded from Abstract While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it http://jxb.oxfordjournals.org/ has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures at Weizmann Institute of Science on July 3, 2016 of yet unknown carbon fixation pathways are suggested and discussed. -
Description of Gabonibacter Massiliensis Gen. Nov., Sp. Nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota
Curr Microbiol DOI 10.1007/s00284-016-1137-2 Description of Gabonibacter massiliensis gen. nov., sp. nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota 1,2 1 3,4 Gae¨l Mourembou • Jaishriram Rathored • Jean Bernard Lekana-Douki • 5 1 1 Ange´lique Ndjoyi-Mbiguino • Saber Khelaifia • Catherine Robert • 1 1,6 1 Nicholas Armstrong • Didier Raoult • Pierre-Edouard Fournier Received: 9 June 2016 / Accepted: 8 September 2016 Ó Springer Science+Business Media New York 2016 Abstract The identification of human-associated bacteria Gabonibacter gen. nov. and the new species G. mas- is very important to control infectious diseases. In recent siliensis gen. nov., sp. nov. years, we diversified culture conditions in a strategy named culturomics, and isolated more than 100 new bacterial Keywords Gabonibacter massiliensis Á Taxonogenomics Á species and/or genera. Using this strategy, strain GM7, a Culturomics Á Gabon Á Gut microbiota strictly anaerobic gram-negative bacterium was recently isolated from a stool specimen of a healthy Gabonese Abbreviations patient. It is a motile coccobacillus without catalase and CSUR Collection de Souches de l’Unite´ des oxidase activities. The genome of Gabonibacter mas- Rickettsies siliensis is 3,397,022 bp long with 2880 ORFs and a G?C DSM Deutsche Sammlung von content of 42.09 %. Of the predicted genes, 2,819 are Mikroorganismen protein-coding genes, and 61 are RNAs. Strain GM7 differs MALDI-TOF Matrix-assisted laser desorption/ from the closest genera within the family Porphyromon- MS ionization time-of-flight mass adaceae both genotypically and in shape and motility. -
Endosymbiont Diversity and Evolution Across Weevil Tree of Life
bioRxiv preprint doi: https://doi.org/10.1101/171181; this version posted August 1, 2017. 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 4.0 International license. Endosymbiont diversity and evolution across weevil tree of life Guanyang Zhang1#, Patrick Browne1,2#, Geng Zhen1#, Andrew Johnston4, Hinsby Cadillo-Quiroz5, and Nico Franz1 1 School of Life Sciences, Arizona State University, Tempe, Arizona, USA 2 Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark # These authors contributed equally to this work ABSTRACT As early as the time of Paul Buchner, a pioneer of endosymbionts research, it was shown that weevils host diverse bacterial endosymbionts, probably only second to the hemipteran insects. To date, there is no taxonomically broad survey of endosymbionts in weevils, which preclude any systematic understanding of the diversity and evolution of endosymbionts in this large group of insects, which comprise nearly 7% of described diversity of all insects. We gathered the largest known taxonomic sample of weevils representing four families and 17 subfamilies to perform a study of weevil endosymbionts. We found that the diversity of endosymbionts is exceedingly high, with as many as 44 distinct kinds of endosymbionts detected. We recovered an ancient origin of association of Nardonella with weevils, dating back to 124 MYA. We found repeated losses of this endosymbionts, but also cophylogeny with weevils. We also investigated patterns of coexistence and coexclusion. INTRODUCTION Weevils (Insecta: Coleoptera: Curculionoidea) host diverse bacterial endosymbionts. -
Research Article Review Jmb
J. Microbiol. Biotechnol. (2017), 27(0), 1–7 https://doi.org/10.4014/jmb.1707.07027 Research Article Review jmb Methods 20,546 sequences and all the archaeal datasets were normalized to 21,154 sequences by the “sub.sample” Bioinformatics Analysis command. The filtered sequences were classified against The raw read1 and read2 datasets was demultiplexed by the SILVA 16S reference database (Release 119) using a trimming the barcode sequences with no more than 1 naïve Bayesian classifier built in Mothur with an 80% mismatch. Then the sequences with the same ID were confidence score [5]. Sequences passing through all the picked from the remaining read1 and read2 datasets by a filtration were also clustered into OTUs at 6% dissimilarity self-written python script. Bases with average quality score level. Then a “classify.otu” function was utilized to assign lower than 25 over a 25 bases sliding window were the phylogenetic information to each OTU. excluded and sequences which contained any ambiguous base or had a final length shorter than 200 bases were Reference abandoned using Sickle [1]. The paired reads were assembled into contigs and any contigs with an ambiguous 1. Joshi NA, FJ. 2011. Sickle: A sliding-window, adaptive, base, more than 8 homopolymeric bases and fewer than 10 quality-based trimming tool for FastQ files (Version 1.33) bp overlaps were culled. After that, the contigs were [Software]. further trimmed to get rid of the contigs that have more 2. Schloss PD. 2010. The Effects of Alignment Quality, than 1 forward primer mismatch and 2 reverse primer Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies. -
Genetics of Human Gut Microbiome Composition
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.26.173724; this version posted June 28, 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. Genetics of human gut microbiome composition Authors: Alexander Kurilshikov1,†, Carolina Medina-Gomez2,3,†, Rodrigo Bacigalupe4,5,†, Djawad Radjabzadeh2,†, Jun Wang4,5,6,†, Ayse Demirkan1,7§, Caroline I. Le Roy8,§, Juan Antonio 5 Raygoza Garay9,10,§, Casey T. Finnicum11,§, Xingrong Liu12,§, Daria V. Zhernakova1,§, Marc Jan Bonder1,§, Tue H. Hansen13, Fabian Frost14, Malte C. Rühlemann15, Williams Turpin9,10, Jee- Young Moon16, Han-Na Kim17,18, Kreete Lüll19, Elad Barkan20, Shiraz A. Shah21, Myriam Fornage22,23, Joanna Szopinska-Tokov24, Zachary D. Wallen25, Dmitrii Borisevich13, Lars Agreus26, Anna Andreasson27, Corinna Bang15, Larbi Bedrani9, Jordana T. Bell8, Hans 10 Bisgaard21, Michael Boehnke28, Dorret I. Boomsma29, Robert D. Burk16,30,31, Annique Claringbould1, Kenneth Croitoru9,10, Gareth E. Davies11,29, Cornelia M. van Duijn32,33, Liesbeth Duijts3,34, Gwen Falony4,5, Jingyuan Fu1,35, Adriaan van der Graaf1, Torben Hansen13, Georg Homuth36, David A. Hughes37,38, Richard G. Ijzerman39, Matthew A. Jackson7,40, Vincent W.V. Jaddoe3,32, Marie Joossens4,5, Torben Jørgensen41, Daniel Keszthelyi42,43, Rob Knight44,45,46, 15 Markku Laakso47, Matthias Laudes48, Lenore J. Launer49, Wolfgang Lieb50, Aldons J. Lusis51,52, Ad A.M. Masclee42,43, Henriette A. Moll34, Zlatan Mujagic42,43, Qi Qibin16, Daphna Rothschild20, Hocheol Shin53,54, Søren J. Sørensen55, Claire J. -
MICRO-ORGANISMS and RUMINANT DIGESTION: STATE of KNOWLEDGE, TRENDS and FUTURE PROSPECTS Chris Mcsweeney1 and Rod Mackie2
BACKGROUND STUDY PAPER NO. 61 September 2012 E Organización Food and Organisation des Продовольственная и cельскохозяйственная de las Agriculture Nations Unies Naciones Unidas Organization pour организация para la of the l'alimentation Объединенных Alimentación y la United Nations et l'agriculture Наций Agricultura COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE MICRO-ORGANISMS AND RUMINANT DIGESTION: STATE OF KNOWLEDGE, TRENDS AND FUTURE PROSPECTS Chris McSweeney1 and Rod Mackie2 The content of this document is entirely the responsibility of the authors, and does not necessarily represent the views of the FAO or its Members. 1 Commonwealth Scientific and Industrial Research Organisation, Livestock Industries, 306 Carmody Road, St Lucia Qld 4067, Australia. 2 University of Illinois, Urbana, Illinois, United States of America. This document is printed in limited numbers to minimize the environmental impact of FAO's processes and contribute to climate neutrality. Delegates and observers are kindly requested to bring their copies to meetings and to avoid asking for additional copies. Most FAO meeting documents are available on the Internet at www.fao.org ME992 BACKGROUND STUDY PAPER NO.61 2 Table of Contents Pages I EXECUTIVE SUMMARY .............................................................................................. 5 II INTRODUCTION ............................................................................................................ 7 Scope of the Study ........................................................................................................... -
Xylella Fastidiosa Biologia I Epidemiologia
Xylella fastidiosa Biologia i epidemiologia Emili Montesinos Seguí Catedràtic de Producció Vegetal (Patologia Vegetal) Universitat de Girona [email protected] www.youtube.com/watch?v=sur5VzJslcM Xylella fastidiosa, un patogen que no és nou Newton B. Pierce (1890s, USA) Agrobacterium tumefaciens Chlamydiae Proteobacteria Bartonella bacilliformis Campylobacter coli Bartonella henselae CDC Chlamydophila psittaci Campylobacter fetus Bartonella quintana Bacteroides fragilis CDC Brucella melitensis Bacteroidetes Chlamydophila pneumoniae Campylobacter hyointestinalis Bacteroides thetaiotaomicron Campylobacter jejuni CDC Brucella melitensis biovar Abortus CDC Chlamydia trachomatis Capnocytophaga canimorus Campylobacter lari CDC Brucella melitensis biovar Canis Chryseobacterium meningosepticum Parachlamydia acanthamoebae Campylobacter upsaliensis CDC Brucella melitensis biovar Suis Helicobacter pylori Candidatus Liberibacter africanus CDC Candidatus Liberibacter asiaticus Borrelia burgdorferi Epsilon Borrelia hermsii CDC Anaplasma phagocytophilum Borrelia recurrentis Alpha CDC Ehrlichia canis Spirochetes Borrelia turicatae CDC Ehrlichia chaffeensis Eikenella corrodens Leptospira interrogans CDC Ehrlichia ewingii CDC CDC Neisseria gonorrhoeae Treponema pallidum Ehrlichia ruminantium CDC Neisseria meningitidis CDC Neorickettsia sennetsu Spirillum minus Orientia tsutsugamushi Fusobacterium necrophorum Beta Fusobacteria CDC Bordetella pertussis Rickettsia conorii Streptobacillus moniliformis Burkholderia cepacia Rickettsia -
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).