A Systematic Review of the Effect of Bariatric Surgery
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Pneumonia Types
Pneumonia Jodi Grandominico , MD Assistant Professor of Clinical Medicine Department of Internal Medicine Division of General Medicine and Geriatrics The Ohio State University Wexner Medical Center Pneumonia types • CAP- limited or no contact with health care institutions or settings • HAP: hospital-acquired pneumonia – occurs 48 hours or more after admission • VAP: ventilator-associated pneumonia – develops more than 48 to 72 hours after endotracheal intubation • HCAP: healthcare-associated pneumonia – occurs in non-hospitalized patient with extensive healthcare contact 2005 IDSA/ATS HAP, VAP and HCAP Guidelines Am J Respir Crit Care Med 2005; 171:388–416 1 Objectives-CAP • Epidemiology • Review cases: ‒ Diagnostic techniques ‒ Risk stratification for site of care decisions ‒ Use of biomarkers ‒ Type and length of treatment • Prevention Pneumonia Sarah Tapyrik, MD Assistant Professor – Clinical Division of Pulmonary, Allergy, Critical Care and Sleep Medicine The Ohio State University Wexner Medical Center 2 Epidemiology American lung association epidemiology and statistics unit research and health education division. November 2015 3 Who is at Risk? • Children <5 yo • Immunosuppressed: • Adults >65 yo ‒ HIV • Comorbid conditions: ‒ Cancer ‒ CKD ‒ Splenectomy ‒ CHF • Cigarette Smokers ‒ DM • Alcoholics ‒ Chronic Liver Disease ‒ COPD Clinical Presentation • Fever • Elderly and • Chills Immunocompromised • Cough w/ purulent ‒ Confusion sputum ‒ Lethargy • Dyspnea ‒ Poor PO intake • Pleuritic pain ‒ Falls • Night sweats ‒ Decompensation of -
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. -
Identification of Glucose Non-Fermenting Gram Negative Rods
UK Standards for Microbiology Investigations Identification of Glucose Non-Fermenting Gram Negative Rods REVIEW UNDER Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 17 | Issue no: 2.2 | Issue date: 11.03.14 | Page: 1 of 24 © Crown copyright 2014 Identification of Glucose Non-Fermenting Gram Negative Rods Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website http://www.hpa.org.uk/SMI/Partnerships. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see http://www.hpa.org.uk/SMI/WorkingGroups). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: http://www.hpa.org.uk/SMI UK Standards for Microbiology Investigations are produced in association with: REVIEW UNDER Bacteriology – Identification | ID 17 | Issue no: 2.2 | Issue date: 11.03.14 | Page: 2 of 24 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Glucose Non-Fermenting Gram Negative Rods Contents ACKNOWLEDGMENTS .......................................................................................................... 2 AMENDMENT TABLE ............................................................................................................. 4 UK STANDARDS FOR MICROBIOLOGY INVESTIGATIONS: SCOPE AND PURPOSE ...... -
Supplementary Information
doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION METAGENOMIC AND FUNCTIONAL ANALYSIS OF HINDGUT MICROBIOTA OF A WOOD FEEDING HIGHER TERMITE TABLE OF CONTENTS MATERIALS AND METHODS 2 • Glycoside hydrolase catalytic domains and carbohydrate binding modules used in searches that are not represented by Pfam HMMs 5 SUPPLEMENTARY TABLES • Table S1. Non-parametric diversity estimators 8 • Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies 8 • Table S3. Summary of numbers glycosyl hydrolases (GHs) and carbon-binding modules (CBMs) discovered in the P3 luminal microbiota 9 • Table S4. Summary of glycosyl hydrolases, their binning information, and activity screening results 13 • Table S5. Comparison of abundance of glycosyl hydrolases in different single organism genomes and metagenome datasets 17 • Table S6. Comparison of abundance of glycosyl hydrolases in different single organism genomes (continued) 20 • Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 23 • Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families 24 • Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. 25 • Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. 29 • Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. 30 SUPPLEMENTARY FIGURES • Fig. S1. Phylogenetic identification of termite host species 38 • Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota 39 • Fig. S3. Phylogenetic diversity of P3 luminal microbiota within the phylum Spirocheates 40 • Fig. -
Infrastructure for a Phage Reference Database: Identification of Large-Scale Biases in The
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.01.442102; this version posted May 1, 2021. 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. 1 INfrastructure for a PHAge REference Database: Identification of large-scale biases in the 2 current collection of phage genomes 3 4 Ryan Cook1, Nathan Brown2, Tamsin Redgwell3, Branko Rihtman4, Megan Barnes2, Martha 5 Clokie2, Dov J. Stekel5, Jon Hobman5, Michael A. Jones1, Andrew Millard2* 6 7 1 School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington 8 Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK 9 2 Dept Genetics and Genome Biology, University of Leicester, University Road, Leicester, 10 Leicestershire, LE1 7RH, UK 11 3 COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte 12 Hospital, University of Copenhagen, Copenhagen, Denmark 13 4 University of Warwick, School of Life Sciences, Coventry, UK 14 5 School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, 15 Loughborough, Leicestershire, LE12 5RD, 16 17 Corresponding author: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.05.01.442102; this version posted May 1, 2021. 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. -
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. -
Effect of Ph and Temperature on Microbial Community Structure And
Calicioglu et al. Biotechnol Biofuels (2018) 11:275 https://doi.org/10.1186/s13068-018-1278-6 Biotechnology for Biofuels RESEARCH Open Access Efect of pH and temperature on microbial community structure and carboxylic acid yield during the acidogenic digestion of duckweed Ozgul Calicioglu1, Michael J. Shreve1, Tom L. Richard2 and Rachel A. Brennan1* Abstract Background: Duckweeds (Lemnaceae) are efcient aquatic plants for wastewater treatment due to their high nutri- ent-uptake capabilities and resilience to severe environmental conditions. Combined with their rapid growth rates, high starch, and low lignin contents, duckweeds have also gained popularity as a biofuel feedstock for thermochemi- cal conversion and alcohol fermentation. However, studies on the acidogenic anaerobic digestion of duckweed into carboxylic acids, another group of chemicals which are precursors of higher-value chemicals and biofuels, are lacking. In this study, a series of laboratory batch experiments were performed to determine the favorable operating condi- tions (i.e., temperature and pH) to maximize carboxylic acid production from wastewater-derived duckweed during acidogenic digestion. Batch reactors with 25 g/l solid loading were operated anaerobically for 21 days under meso- philic (35 °C) or thermophilic (55 °C) conditions at an acidic (5.3) or basic (9.2) pH. At the conclusion of the experiment, the dominant microbial communities under various operating conditions were assessed using high-throughput sequencing. Results: The highest duckweed–carboxylic acid conversion of 388 28 mg acetic acid equivalent per gram volatile solids was observed under mesophilic and basic conditions, with an± average production rate of 0.59 g/l/day. This result is comparable to those reported for acidogenic digestion of other organics such as food waste. -
Gut Microbiota and Inflammation
Nutrients 2011, 3, 637-682; doi:10.3390/nu3060637 OPEN ACCESS nutrients ISSN 2072-6643 www.mdpi.com/journal/nutrients Review Gut Microbiota and Inflammation Asa Hakansson and Goran Molin * Food Hygiene, Division of Applied Nutrition, Department of Food Technology, Engineering and Nutrition, Lund University, PO Box 124, SE-22100 Lund, Sweden; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +46-46-222-8327; Fax: +46-46-222-4532. Received: 15 April 2011; in revised form: 19 May 2011 / Accepted: 24 May 2011 / Published: 3 June 2011 Abstract: Systemic and local inflammation in relation to the resident microbiota of the human gastro-intestinal (GI) tract and administration of probiotics are the main themes of the present review. The dominating taxa of the human GI tract and their potential for aggravating or suppressing inflammation are described. The review focuses on human trials with probiotics and does not include in vitro studies and animal experimental models. The applications of probiotics considered are systemic immune-modulation, the metabolic syndrome, liver injury, inflammatory bowel disease, colorectal cancer and radiation-induced enteritis. When the major genomic differences between different types of probiotics are taken into account, it is to be expected that the human body can respond differently to the different species and strains of probiotics. This fact is often neglected in discussions of the outcome of clinical trials with probiotics. Keywords: probiotics; inflammation; gut microbiota 1. Inflammation Inflammation is a defence reaction of the body against injury. The word inflammation originates from the Latin word ―inflammatio‖ which means fire, and traditionally inflammation is characterised by redness, swelling, pain, heat and impaired body functions. -
WO 2018/064165 A2 (.Pdf)
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
Development of Bacterial Communities in Biological Soil Crusts Along
1 Development of bacterial communities in biological soil crusts along 2 a revegetation chronosequence in the Tengger Desert, northwest 3 China 4 5 Author names and affiliations: 6 Lichao Liu1, Yubing Liu1, 2 *, Peng Zhang1, Guang Song1, Rong Hui1, Zengru Wang1, Jin Wang1, 2 7 1Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese 8 Academy of Sciences, Lanzhou, 730000, China 9 2Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Northwest Institute 10 of Eco–Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China 11 12 * Corresponding author: Yubing Liu 13 Address: Donggang West Road 320, Lanzhou 730000, P. R. China. 14 Tel: +86 0931 4967202. 15 E-mail address: [email protected] 16 17 Abstract. Knowledge of structure and function of microbial communities in different 18 successional stages of biological soil crusts (BSCs) is still scarce for desert areas. In this study, 19 Illumina MiSeq sequencing was used to assess the composition changes of bacterial communities 20 in different ages of BSCs in the revegetation of Shapotou in the Tengger Desert. The most dominant 21 phyla of bacterial communities shifted with the changed types of BSCs in the successional stages, 22 from Firmicutes in mobile sand and physical crusts to Actinobacteria and Proteobacteria in BSCs, 23 and the most dominant genera shifted from Bacillus, Enterococcus and Lactococcus to 24 RB41_norank and JG34-KF-361_norank. Alpha diversity and quantitative real-time PCR analysis 25 indicated that bacteria richness and abundance reached their highest levels after 15 years of BSC 26 development. -
Escherichia Coli
log bio y: O ro p c e i n M A l c Clinical Microbiology: Open a c c i e n s i l s Delmas et al., Clin Microbiol 2015, 4:2 C Access ISSN: 2327-5073 DOI:10.4172/2327-5073.1000195 Commentary Open Access Escherichia coli: The Good, the Bad and the Ugly Julien Delmas*, Guillaume Dalmasso and Richard Bonnet Microbes, Intestine, Inflammation and Host Susceptibility, INSERM U1071, INRA USC2018, Université Clermont Auvergne, Clermont-Ferrand, France *Corresponding author: Julien Delmas, Microbes, Intestine, Inflammation and Host Susceptibility, INSERM U1071, INRA USC2018, Université Clermont Auvergne, Clermont-Ferrand, France, Tel: +334731779; E-mail; [email protected] Received date: March 11, 2015, Accepted date: April 21, 2015, Published date: Aptil 28, 2015 Copyright: © 2015 Delmas J, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract The species Escherichia coli comprises non-pathogenic commensal strains that form part of the normal flora of humans and virulent strains responsible for acute infections inside and outside the intestine. In addition to these pathotypes, various strains of E. coli are suspected of promoting the development or exacerbation of chronic diseases of the intestine such as Crohn’s disease and colorectal cancer. Description replicate within both intestinal epithelial cells and macrophages. These properties were used to define a new pathotype of E. coli designated Escherichia coli is a non-sporeforming, facultatively anaerobic adherent-invasive E. -
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