Bacteroides Gracilis, an Important Anaerobic Bacterial Pathogen CAROLINE C
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Development of the Equine Hindgut Microbiome in Semi-Feral and Domestic Conventionally-Managed Foals Meredith K
Tavenner et al. Animal Microbiome (2020) 2:43 Animal Microbiome https://doi.org/10.1186/s42523-020-00060-6 RESEARCH ARTICLE Open Access Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals Meredith K. Tavenner1, Sue M. McDonnell2 and Amy S. Biddle1* Abstract Background: Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management. Results: Gut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. -
Potential Role of Microbiome in Oncogenesis, Outcome Prediction
Oral Oncology 99 (2019) 104453 Contents lists available at ScienceDirect Oral Oncology journal homepage: www.elsevier.com/locate/oraloncology Review Potential role of microbiome in oncogenesis, outcome prediction and therapeutic targeting for head and neck cancer T ⁎ Ester Orlandia,b, , Nicola Alessandro Iacovellib, Vincenzo Tombolinic, Tiziana Rancatid, Antonella Polimenie, Loris De Ceccof, Riccardo Valdagnia,d,g, Francesca De Felicec a Department of Radiotherapy 1, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy b Department of Radiotherapy 2, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy c Department of Radiotherapy, Policlinico Umberto I, “Sapienza” University of Rome, Rome, Italy d Prostate Cancer Program, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy e Department of Oral and Maxillo Facial Sciences, Policlinico Umberto I, “Sapienza” University of Rome, Italy f Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy g Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy ARTICLE INFO ABSTRACT Keywords: In the last decade, human microbiome research is rapidly growing involving several fields of clinical medicine Head and neck cancer and population health. Although the microbiome seems to be linked to all sorts of diseases, cancer has the Biomarkers biggest potential to be investigated. Microbiome Following the publication of the National Institute of Health - Human Microbiome Project (NIH-HMP), the Microbiota link between Head and Neck Cancer (HNC) and microbiome seems to be a fast-moving field in research area. Oncogenesis However, robust evidence-based literature is still quite scarce. Nevertheless the relationship between oral mi- Radiotherapy Immunotherapy crobiome and HNC could have important consequences for prevention and early detection of this type of tumors. -
Annotations of the Otus with the Lowest P-Values for SR Samples at 0 and 4H Fermentation Time Points
Electronic Supplementary Material (ESI) for Food & Function. This journal is © The Royal Society of Chemistry 2016 Table S1. Taxonomic annotations: Annotations of the OTUs with the lowest p-values for SR samples at 0 and 4h fermentation time points. TAXA ID PHYLUM CLASS ORDER FAMILY GENUS SPECIES 4452633 Firmicutes Clostridia Clostridiales Clostridiaceae unclassified unclassified 191399 Firmicutes Clostridia Clostridiales Ruminococcaceae unclassified unclassified 4256470 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides 97otu97833 179291 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 192046 Firmicutes Clostridia Clostridiales unclassified unclassified unclassified 4315974 Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus 97otu66887 4343627 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides fragilis 760967 Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella 97otu12794 4475758 Firmicutes Clostridia Clostridiales Veillonellaceae Veillonella unclassified 566976 Bacteroidetes Gammapro Bacteroidales Bacteroidaceae Bacteroides unclassified teobacteria 328617 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides uniformis 16054 Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminococcus 97otu97520 SR: sun-dried raisins. Table S2. Taxonomic annotations: Annotations of the OTUs with the lowest p-values for SR samples at 0 and 8h fermentation time points. TAXA ID PHYLUM CLASS ORDER FAMILY GENUS SPECIES 194443 Firmicutes Clostridia Clostridiales -
Gut Microbiota Differs in Composition and Functionality Between Children
Diabetes Care Volume 41, November 2018 2385 Gut Microbiota Differs in Isabel Leiva-Gea,1 Lidia Sanchez-Alcoholado,´ 2 Composition and Functionality Beatriz Mart´ın-Tejedor,1 Daniel Castellano-Castillo,2,3 Between Children With Type 1 Isabel Moreno-Indias,2,3 Antonio Urda-Cardona,1 Diabetes and MODY2 and Healthy Francisco J. Tinahones,2,3 Jose´ Carlos Fernandez-Garc´ ´ıa,2,3 and Control Subjects: A Case-Control Mar´ıa Isabel Queipo-Ortuno~ 2,3 Study Diabetes Care 2018;41:2385–2395 | https://doi.org/10.2337/dc18-0253 OBJECTIVE Type 1 diabetes is associated with compositional differences in gut microbiota. To date, no microbiome studies have been performed in maturity-onset diabetes of the young 2 (MODY2), a monogenic cause of diabetes. Gut microbiota of type 1 diabetes, MODY2, and healthy control subjects was compared. PATHOPHYSIOLOGY/COMPLICATIONS RESEARCH DESIGN AND METHODS This was a case-control study in 15 children with type 1 diabetes, 15 children with MODY2, and 13 healthy children. Metabolic control and potential factors mod- ifying gut microbiota were controlled. Microbiome composition was determined by 16S rRNA pyrosequencing. 1Pediatric Endocrinology, Hospital Materno- Infantil, Malaga,´ Spain RESULTS 2Clinical Management Unit of Endocrinology and Compared with healthy control subjects, type 1 diabetes was associated with a Nutrition, Laboratory of the Biomedical Research significantly lower microbiota diversity, a significantly higher relative abundance of Institute of Malaga,´ Virgen de la Victoria Uni- Bacteroides Ruminococcus Veillonella Blautia Streptococcus versityHospital,Universidad de Malaga,M´ alaga,´ , , , , and genera, and a Spain lower relative abundance of Bifidobacterium, Roseburia, Faecalibacterium, and 3Centro de Investigacion´ BiomedicaenRed(CIBER)´ Lachnospira. -
3. Jedna Z Krvných Skupín Systému AB0; 4. Skr. Bukálny. B – Symbo
B – 1. symbol pre bel; 2. chem. značka prvku →bór; 3. jedna z krvných skupín systému AB0; 4. skr. bukálny. B – symbol pre hustotu magnetického toku. B. – skr. pre →Bacillus. B-ALP – skr. angl. bone alcalic phosphatase kostná alkalická fosfatáza. B-bunky – 1. syn. -bunky Langerhansových ostrovčekov; →pankreas; 2. syn. B-lymfocyty; →lymfocyty. B-komplex – multivitamínový prípravok vitamínov B. B-lymfocyty – [B podľa Fabriciovej burzy, imunol. orgánu vtákov] B bunky, druh lymfocytov, kt. sa zúčastňuje na humorálnej imunite (tvorbe protilátok) a niekt. ďalších imunitných funkciách. Povrchové molekuly sú CD 19,20. Receptorom pre antigén je membránový imunoglobulín. B-reťazec – jeden z polypeptidových reťazcov →inzulínu. B-vírus – 1. vírus →hepatitídy B.; 2. vírus zo skupiny Cercopithecine herpes virus 1. B-vlákna →nerv. b – skr. 1. pre barn; 2. skr. angl. born narodený; 3. skr. báza (genet. označenie dĺţky sekvencie nukleotidov, napr. 50 b = sekvencia 50 nukleotidov). b-vlna – pozit. kmit s vyskou amplitúdou v →elektroretinograme nasledujúci po vlne a, prejav komplexnej aktivity vrstvy bipolárnych buniek. – - – predpona označujúca 1. staršie označenie druhého atómu uhlíka v reťazci, na kt. sa pripája hlavná funkčná skupina, napr. kys. -hydroxymaslová správ. kys. 3-hydroxymaslová; 2. špecifická rotácia opticky aktívnej látky, napr. -D-glukóza; 3. orientácia exocyklického atómu al. skupiny, napr. cholest-5-en-3--ol; 4. plazmatický proteín, kt. migruje v elektroforéze v pruhu - lipoproteín; 5. člen série príbuzných chem. látok, najmä série stereoizomérov, izomérov, polymérov al. alotroických foriem, napr. -karotén; 6. -lúč. B2 – staršie označenie pre CD21. B4 – staršie označenie pre CD 19. B19 virus – ľudský parvovírus z čeľade Parvoviridae, značne rozšírený, vyvolávajúci obvykle inaparentné infekcie. -
Bacteroides Gingivalis, and Bacteroides Endodontalis in a New Genus, Porphyromonas H
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1988, p. 128-131 Vol. 38, No. 1 0020-7713/88/010128-04$02.00/0 Copyright 0 1988, International Union of Microbiological Societies Proposal for Reclassification of Bacteroides asaccharolyticus , Bacteroides gingivalis, and Bacteroides endodontalis in a New Genus, Porphyromonas H. N. SHAH1* AND M. D. COLLINS’ Department of Oral Microbiology, London Hospital Medical College, London El 2AD,l and Division of Microbiology, AFRC Institute of Food Research, Shinfeld, Reading RG2 9AT,= United Kingdom The asaccharolytic, pigmented Bacteroides, Bacteroides asaccharolyticus, Bacteroides gingivalis, and Bacte- roides endodontalis, form a group of relatively homogeneous species which differ markedly in biochemical and chemical properties from the type species of Bacteroides, Bacteroides fragilis (Castellani and Chalmers), such that they should not be retained within this genus. Therefore, we propose that Bacteroides asaccharolyticus (Holdeman and Moore) Finegold and Barnes, Bacteroides gingivalis Coykendhll, Kaczmarek and Slots, and Bacteroides endodontalis van Steenbergen, van Winkelhoff, Mayrand, Grenier and de Graaff be reclassified in a new genus, Porphyromonas, as Porphyromonas asaccharolytica comb. nov., Porphyromonas gingivalis comb. nov., and Porphyromonas endodontalis comb. nov., respectively. In Bergey ’s Manual of Determinative Bacteriology, 8th quite unrelated to the type species of the genus Bacteroides, ed. (12), the asaccharolytic, pigmented Bacteroides were Bacteroides fragilis. All of the asaccharolytic, pigmented regarded as a single homogeneous taxon, Bacteroides mela- bacteroides accumulate major levels of protoheme rather ninogenicus subsp. asaccharolyticus. As the clinical signif- than protoporphyrin when cells are cultured on blood agar icance of these microorganisms in oral cavities was recog- (3,25, 27). The three species are nonfermentative and utilize nized, extensive taxonomic studies were carried out. -
974-Form.Pdf
California Association for Medical Laboratory Technology Distance Learning Program ANAEROBIC BACTERIOLOGY FOR THE CLINICAL LABORATORY by James I. Mangels, MA, CLS, MT(ASCP) Consultant Microbiology Consulting Services Santa Rosa, CA Course Number: DL-974 3.0 CE/Contact Hour Level of Difficulty: Intermediate © California Association for Medical Laboratory Technology. Permission to reprint any part of these materials, other than for credit from CAMLT, must be obtained in writing from the CAMLT Executive Office. CAMLT is approved by the California Department of Health Services as a CA CLS Accrediting Agency (#0021) and this course is is approved by ASCLS for the P.A.C.E. ® Program (#519) 1895 Mowry Ave, Suite 112 Fremont, CA 94538-1766 Phone: 510-792-4441 FAX: 510-792-3045 Notification of Distance Learning Deadline All continuing education units required to renew your license must be earned no later than the expiration date printed on your license. If some of your units are made up of Distance Learning courses, please allow yourself enough time to retake the test in the event you do not pass on the first attempt. CAMLT urges you to earn your CE units early!. CAMLT Distance Learning Course # DL-974 1 © California Association for Medical Laboratory Technology Outline A. Introduction B. What are anaerobic bacteria? Concepts of anaerobic bacteriology C. Why do we need to identify anaerobes? D. Normal indigenous anaerobic flora; the incidence of anaerobes at various body sites E. Anaerobic infections; most common anaerobic infections F. Specimen collection and transport; acceptance and rejection criteria G. Processing of clinical specimens 1. Microscopic examination 2. -
Susceptibility and Resistance Data
toku-e logo For a complete list of references, please visit antibiotics.toku-e.com Levofloxacin Microorganism Genus, Species, and Strain (if shown) Concentration Range (μg/ml)Susceptibility and Aeromonas spp. 0.0625 Minimum Inhibitory Alcaligenes faecalis 0.39 - 25 Bacillus circulans Concentration0.25 - 8 (MIC) Data Bacillus subtilis (ATCC 6051) 6.25 Issue date 01/06/2020 Bacteroides capillosus ≤0.06 - >8 Bacteroides distasonis 0.5 - 128 Bacteroides eggerthii 4 Bacteroides fragilis 0.5 - 128 Bacteroides merdae 0.25 - >32 Bacteroides ovatus 0.25 - 256 Bacteroides thetaiotaomicron 1 - 256 Bacteroides uniformis 4 - 128 Bacteroides ureolyticus ≤0.06 - >8 Bacteroides vulgatus 1 - 256 Bifidobacterium adolescentis 0.25 - >32 Bifidobacterium bifidum 8 Bifidobacterium breve 0.25 - 8 Bifidobacterium longum 0.25 - 8 Bifidobacterium pseudolongum 8 Bifidobacterium sp. 0.25 - >32 Bilophila wadsworthia 0.25 - 16 Brevibacterium spp. 0.12 - 8 Brucella melitensis 0.5 Burkholderia cepacia 0.25 - 512 Campylobacter coli 0.015 - 128 Campylobacter concisus ≤0.06 - >8 Campylobacter gracilis ≤0.06 - >8 Campylobacter jejuni 0.015 - 128 Campylobacter mucosalis ≤0.06 - >8 Campylobacter rectus ≤0.06 - >8 Campylobacter showae ≤0.06 - >8 Campylobacter spp. 0.25 Campylobacter sputorum ≤0.06 - >8 Capnocytophaga ochracea ≤0.06 - >8 Capnocytophaga spp. 0.006 - 2 Chlamydia pneumonia 0.125 - 1 Chlamydia psittaci 0.5 Chlamydia trachomatis 0.12 - 1 Chlamydophila pneumonia 0.5 Citrobacter diversus 0.015 - 0.125 Citrobacter freundii ≤0.00625 - >64 Citrobacter koseri 0.015 - -
Halophilic Bacteroidetes As an Example on How Their Genomes Interact with the Environment
DOCTORAL THESIS 2020 PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez DOCTORAL THESIS 2020 Doctoral Programme of Environmental and Biomedical Microbiology PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez Thesis Supervisor: Ramon Rosselló Móra Thesis Supervisor: Rudolf Amann Thesis tutor: Elena I. García-Valdés Pukkits Doctor by the Universitat de les Illes Balears Publications resulted from this thesis Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Systematic and Applied Microbiology, 39(5), 281–296 Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Corrigendum to “Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov.” [Syst. Appl. Microbiol. 39 (5) (2016) 281–296]. Systematic and Applied Microbiology, 39, 491–492. Munoz, R., Amann, R., & Rosselló-Móra, R. (2019). Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics. Systematic and Applied Microbiology, 43(2), 126065. Dr. Ramon Rosselló Móra, of the Institut Mediterrani d’Estudis Avançats, Esporles and Dr. Rudolf Amann, of the Max-Planck-Institute für Marine Mikrobiologie, Bremen WE DECLARE: That the thesis titled Phylogenomics of Bacteroidetes; halophilic Bacteroidetes as an example on how their genomes interact with the environment, presented by Raúl Muñoz Jiménez to obtain a doctoral degree, has been completed under our supervision and meets the requirements to opt for an International Doctorate. For all intents and purposes, we hereby sign this document. -
Human Microbiota Reveals Novel Taxa and Extensive Sporulation Hilary P
OPEN LETTER doi:10.1038/nature17645 Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation Hilary P. Browne1*, Samuel C. Forster1,2,3*, Blessing O. Anonye1, Nitin Kumar1, B. Anne Neville1, Mark D. Stares1, David Goulding4 & Trevor D. Lawley1 Our intestinal microbiota harbours a diverse bacterial community original faecal sample and the cultured bacterial community shared required for our health, sustenance and wellbeing1,2. Intestinal an average of 93% of raw reads across the six donors. This overlap was colonization begins at birth and climaxes with the acquisition of 72% after de novo assembly (Extended Data Fig. 2). Comparison to a two dominant groups of strict anaerobic bacteria belonging to the comprehensive gene catalogue that was derived by culture-independent Firmicutes and Bacteroidetes phyla2. Culture-independent, genomic means from the intestinal microbiota of 318 individuals4 found that approaches have transformed our understanding of the role of the 39.4% of the genes in the larger database were represented in our cohort human microbiome in health and many diseases1. However, owing and 73.5% of the 741 computationally derived metagenomic species to the prevailing perception that our indigenous bacteria are largely identified through this analysis were also detectable in the cultured recalcitrant to culture, many of their functions and phenotypes samples. remain unknown3. Here we describe a novel workflow based on Together, these results demonstrate that a considerable proportion of targeted phenotypic culturing linked to large-scale whole-genome the bacteria within the faecal microbiota can be cultured with a single sequencing, phylogenetic analysis and computational modelling that growth medium. -
(12) United States Patent (10) Patent No.: US 8,501,463 B2 Cox Et Al
USOO85O1463B2 (12) United States Patent (10) Patent No.: US 8,501,463 B2 Cox et al. (45) Date of Patent: Aug. 6, 2013 (54) ANAEROBC PRODUCTION OF HYDROGEN (56) References Cited AND OTHER CHEMICAL PRODUCTS U.S. PATENT DOCUMENTS (75) Inventors: Marion E. Cox, Morgan Hill, CA (US); 5,350,685 A 9/1994 Taguchi et al. Laura M. Nondorf, Morgan Hill, CA 5,464,539 A 11/1995 Ueno et al. 6,090,266 A 7/2000 Roychowdhury (US); Steven M. Cox, Morgan Hill, CA 6,251,643 B1 6/2001 Hansen et al. (US) 6,299,774 B1 * 10/2001 Ainsworth et al. ........... 210,603 6,342,378 B1 1/2002 Zhang et al. (73) Assignee: Anaerobe Systems, Morgan Hill, CA 6,569,332 B2 * 5/2003 Ainsworth et al. ........... 210,603 2004/0050778 A1 3/2004 Noike et al. (US) 2004/O115782 A1 6/2004 Paterek (*) Notice: Subject to any disclaimer, the term of this FOREIGN PATENT DOCUMENTS patent is extended or adjusted under 35 WO WO-2006-119052 A2 11/2006 U.S.C. 154(b) by 1347 days. OTHER PUBLICATIONS (21) Appl. No.: 11/912,881 Liu et al., 2004. Effects of Culture and Medium Conditions on Hydro gen Production from Starch Using Anaerobic Bacteria. Journal of (22) PCT Fled: Apr. 27, 2006 Bioscience and Bioengineering, vol. 98, No. 4, pp. 251-256.* Zhang et al., Distributed Computer Control of Penicillin Fermenta (86) PCT NO.: PCT/US2OO6/O16332 tion Industrial Production. Proceedings of the IEEE International Conference on Industrial Technology, 1996, pp. 52-56.* S371 (c)(1), New Brunswick, an eppenforf Company, pp. -
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 ...........................................................................................................