Mucosal Prevalence and Interactions with the Epithelium Indicate Commensalism of Sutterella Spp
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Dehydrated Culture Media Description Packaging Ref
Product Catalogue 2016 © Liofilchem® s.r.l. Clinical and Industrial Microbiology Est. 1983 Dehydrated Culture Media Description Packaging Ref. A1 Medium APHA 500 g 610105 Basal liquid medium for fecal coliforms detection in water and food. 100 g 620105 TRITON X 100 supplement 5x5 mL 80046 Acetamide Agar 500 g 610312 Medium for differentiation of nonfermentative, Gram-negative bacteria, especially Pseudomonas aeruginosa, on the basis of acetamide utilization. Acetamide Broth 500 g 610313 Broth for the differentiation of nonfermentative, Gram-negative bacteria, especially Pseudomonas aeruginosa, on the basis of acetamide utilization. Aeromonas Agar Base 500 g 610048 Basal medium for selective isolation of Aeromonas spp. 100 g 620048 Ampicillin supplement 10 vials 81001 Alkaline Peptone Water APHA 500 g 610098 Liquid enrichment medium for Vibrio spp. isolation. 100 g 620098 Amies Transport Medium (with charcoal) 500 g 610152 Semi-solid medium for transport of clinical, environmental specimens and of 100 g 620152 microorganisms. 5 kg 6101525 Amies Transport Medium (w/o charcoal) 500 g 610191 Semi-solid medium for transport of clinical, environmental specimens and of 100 g 620191 microorganisms. 5 kg 6101915 Anaerobic Agar (Brewer) 500 g 610320 Medium for cultivating anaerobic microorganisms. Andrade Lactose Peptone Water 500 g 610118 Liquid medium for coliforms detection with andrade's indicator. 100 g 620118 Andrade Peptone Water 500 g 610119 Liquid enrichment medium with andrade's indicator. 100 g 620119 Antibiotic Agar No.1 E.P. 500 g 610314 Surface medium for the antibiotic assay by Agar-diffusion method. Antibiotic Broth No.3 U.S.P. 500 g 610316 Broth for turbidimetric assay of antibiotics. -
Shotgun Metagenomics of 361 Elderly Women Reveals Gut Microbiome
bioRxiv preprint doi: https://doi.org/10.1101/679985; this version posted June 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss Qi Wang1,2,3,4, *, Hui Zhao1,2,3,4, *, Qiang Sun2,5, *, Xiaoping Li3,4, *, Juanjuan Chen3,4, Zhefeng Wang6, Yanmei Ju2,3,4, Zhuye Jie3,4, Ruijin Guo3,4,7,8, Yuhu Liang2, Xiaohuan Sun3,4, Haotian Zheng3,4, Tao Zhang3,4, Liang Xiao3,4, Xun Xu3,4, Huanming Yang3,9, Songlin Peng6, †, Huijue Jia3,4,7,8, †. 1. School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China. 2. BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; 3. BGI-Shenzhen, Shenzhen 518083, China; 4. China National Genebank, Shenzhen 518120, China; 5. Department of Statistical Sciences, University of Toronto, Toronto, Canada; 6. Department of Spine Surgery, Shenzhen People's Hospital, Ji Nan University Second College of Medicine, 518020, Shenzhen, China. 7. Macau University of Science and Technology, Taipa, Macau 999078, China; 8. Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China; 9. James D. Watson Institute of Genome Sciences, 310058 Hangzhou, China; * These authors have contributed equally to this study †Corresponding authors: S.P., [email protected]; H.J., [email protected]; bioRxiv preprint doi: https://doi.org/10.1101/679985; this version posted June 23, 2019. -
(12) Patent Application Publication (10) Pub. No.: US 2011/0206654 A1 Hodin Et Al
US 2011 0206654A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2011/0206654 A1 Hodin et al. (43) Pub. Date: Aug. 25, 2011 (54) METHODS OF MODULATING Related U.S. Application Data GASTRONTESTINAL TRACTFLORA LEVELS WITH ALKALINE PHOSPHATASE (60) Provisional application No. 61/093,129, filed on Aug. 29, 2008. (75) Inventors: Richard A. Hodin, Newton, MA (US); Madhu S. Malo, Burlington, Publication Classification MA (US) (51) Int. Cl. (73) Assignee: THE GENERAL, HOSPITAL A638/46 (2006.01) CORPORATION, Boston, MA CI2N 9/16 (2006.01) (US) A6IPI/00 (2006.01) (21) Appl. No.: 13/060,863 (52) U.S. Cl. ........................................ 424/94.6; 435/196 (22) PCT Fled: Aug. 27, 2009 (57) ABSTRACT (86) PCT NO.: PCT/USO9/55216 This invention relates generally to a therapeutic use of alka S371 (c)(1), line phosphatase to modulate gastrointestinal tract flora levels (2), (4) Date: May 5, 2011 in Subject. C 7 e 4 ---. W. Mouse Stoo B Mac Brucella MacConkey Agar Plates Media Aerobic Condition) B D WT AP-KO n . 1 ^: O Š AP-KO Mouse Stool Brucella MacConkey Agar Plates Media (Anaerobic Condition) Patent Application Publication Aug. 25, 2011 Sheet 1 of 7 US 2011/0206654 A1 F.G. 1 W &ws s IAP-KOS ls S 4 S.Š 3 WT Mouse Stoo LB BH Mac Brucella MacConkey Agar Plates Media (Aerobic Condition) D 12 SS 9 : AP-KO Mouse Stool Brucella MacConkey Agar Plates Media (Anaerobic Condition) Patent Application Publication Aug. 25, 2011 Sheet 2 of 7 US 2011/0206654 A1 FIG 2 $2$3$?2 8?duesdødsweeg38),jojaquumN A. -
APPENDIX a Media and Reagents
APPENDIX A Media and Reagents Pauline K. w. Yu, M.S. The use of appropriate and dependable media is integral to the isolation and identification of microorganisms. Unfortunately, comparative data docu menting the relative efficacy or value of media designed for similar purposes are often lacking. Moreover, one cannot presume identity in composition of a given generic product which is manufactured by several companies because each may supplement the generic products with components, often of a proprietary nature and not specified in the product's labeling. Finally, the actual production of similar products may vary among manufacturers to a sufficient extent to affect their performance. For all of these reasons, therefore, product selection for the laboratory should not be strictly based on cost considerations and should certainly not be based on promotional materials. Evaluations that have been published in the scientific literature should be consulted when available. Alternatively, the prospective buyer should consult a recognized authority in the field. It is seldom necessary for the laboratory to prepare media using basic components since these are usually available combined in dehydrated form from commercial sources; however, knowledge of a medium's basic compo nents is helpful in understanding how the medium works and what might be wrong when it does not work. Hence, the components have been listed for each medium included in this chapter. All dehydrated media must be prepared exactly according to the manu facturers' directions. Any deviation from these directions may adversely affect or significantly alter a medium's performance. Containers of media should be dated on receipt and when opened, and the media should never be used beyond expiration dates specified by the manufacturers or recom mended by quality control programs. -
The Design and Application of a Molecular Profiling Strategy to Identify Polymicrobial Acute Sepsis Infections
University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2015-08-14 The Design and Application of a Molecular Profiling Strategy to Identify Polymicrobial Acute Sepsis Infections Faria Crowder, Monica Faria Crowder, M. (2015). The Design and Application of a Molecular Profiling Strategy to Identify Polymicrobial Acute Sepsis Infections (Unpublished doctoral thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/28047 http://hdl.handle.net/11023/2388 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY The Design and Application of a Molecular Profiling Strategy to Identify Polymicrobial Acute Sepsis Infections by Monica Martins Pereira Faria-Crowder A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPY GRADUATE PROGRAM IN MICROBIOLOGY, IMMUNOLOGY, AND INFECTIOUS DISEASES CALGARY, ALBERTA AUGUST 2015 © Monica Martins Pereira Faria-Crowder 2015 Abstract Sepsis is a term used to describe an array of clinical presentations ranging from mild body dysfunction to multiple organ failure. These clinical signs result from a systemic inflammatory response to microbes or microbial products present in sterile sites such as blood. Current clinical diagnostics rely on culture techniques to identify systemic infections. -
BD Industry Catalog
PRODUCT CATALOG INDUSTRIAL MICROBIOLOGY BD Diagnostics Diagnostic Systems Table of Contents Table of Contents 1. Dehydrated Culture Media and Ingredients 5. Stains & Reagents 1.1 Dehydrated Culture Media and Ingredients .................................................................3 5.1 Gram Stains (Kits) ......................................................................................................75 1.1.1 Dehydrated Culture Media ......................................................................................... 3 5.2 Stains and Indicators ..................................................................................................75 5 1.1.2 Additives ...................................................................................................................31 5.3. Reagents and Enzymes ..............................................................................................75 1.2 Media and Ingredients ...............................................................................................34 1 6. Identification and Quality Control Products 1.2.1 Enrichments and Enzymes .........................................................................................34 6.1 BBL™ Crystal™ Identification Systems ..........................................................................79 1.2.2 Meat Peptones and Media ........................................................................................35 6.2 BBL™ Dryslide™ ..........................................................................................................80 -
Supplementary Material
Supplementary Material SUPPLEMENTARY METHODS Definition of failure for prior clinical treatments According to the standard operating procedures of our outpatient clinic treatment, failures are defined by Mayo-score as follows: 1. Patients are non-responders to thiopurines after treament with azathioprine 2- 2.5mg/kg/day or 6-mercaptopurine 1-1.5mg/kg/day for at least 3-6 months despite 6-TGN levels > 235 pmol/8x108 red blood cells (RBC). 2. Primary lack of response to anti-TNF agents is determined within the first 12 weeks of therapy. 3. In patients with loss of response to anti-TNF agents, reduction in interval between doses, dose escalation or both (e.g. infliximab: up to 10mg/kg every 4 weeks, adalimumab: up to 40mg every week) is performed. If there is no response after reduction in interval and dose escalation patients are rated as secondary anti-TNF failures. Evaluation of different methods for preparation of faecal suspensions Because protocols for donor stool preparations differ between published faecal transplantation studies, prior to treating patients we assessed the quantitative and qualitative difference in the bacterial content between native stool and three different stool preparations: (A) 30 g of fresh stool were mixed with 450 ml of 0.9% sterile saline solution to an almost homogeneous suspension, (B) the suspension prepared from (A) was filtered several times through an increasing number of gauze pads to remove small particles, (C) the suspension prepared from (A) was centrifuged at 1912xg (3000 rpm) and the supernatant was used for further analysis. Native stool and each of the preparations were plated on five different solid culture media. -
Long-Read Metagenomics Retrieves Complete Single-Contig Bacterial Genomes from Canine Feces
Cuscó et al. BMC Genomics (2021) 22:330 https://doi.org/10.1186/s12864-021-07607-0 RESEARCH Open Access Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces Anna Cuscó1*, Daniel Pérez2, Joaquim Viñes1,2, Norma Fàbregas1 and Olga Francino2 Abstract Background: Long-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the mobile genetic elements, which are usually missed with short-reads. We applied long-read metagenomics with Nanopore sequencing to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample. Results: We used nanopore long-read metagenomics and frameshift aware correction on a canine fecal sample and retrieved eight single-contig HQ MAGs, which were > 90% complete with < 5% contamination, and contained most ribosomal genes and tRNAs. At the technical level, we demonstrated that a high-molecular-weight DNA extraction improved the metagenomics assembly contiguity, the recovery of the rRNA operons, and the retrieval of longer and circular contigs that are potential HQ MAGs. These HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Catenibacterium, Blautia, and Enterococcus genera. Linking our results to previous gastrointestinal microbiome reports (metagenome or 16S rRNA-based), we found that some bacterial species on the gastrointestinal tract seem to be more canid-specific –Succinivibrio, Prevotellamassilia, Phascolarctobacterium, Blautia_A sp900541345–, whereas others are more broadly distributed among animal and human microbiomes –Sutterella, Catenibacterium, Enterococcus, and Blautia sp003287895. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. -
Prepared Culture Media
PREPARED CULTURE MEDIA 030220SG PREPARED CULTURE MEDIA Made in the USA AnaeroGRO™ DuoPak A 02 Bovine Blood Agar, 5%, with Esculin 13 AnaeroGRO™ DuoPak B 02 Bovine Blood Agar, 5%, with Esculin/ AnaeroGRO™ BBE Agar 03 MacConkey Biplate 13 AnaeroGRO™ BBE/PEA 03 Bovine Selective Strep Agar 13 AnaeroGRO™ Brucella Agar 03 Brucella Agar with 5% Sheep Blood, Hemin, AnaeroGRO™ Campylobacter and Vitamin K 13 Selective Agar 03 Brucella Broth with 15% Glycerol 13 AnaeroGRO™ CCFA 03 Brucella with H and K/LKV Biplate 14 AnaeroGRO™ Egg Yolk Agar, Modifi ed 03 Buffered Peptone Water 14 AnaeroGRO™ LKV Agar 03 Buffered Peptone Water with 1% AnaeroGRO™ PEA 03 Tween® 20 14 AnaeroGRO™ MultiPak A 04 Buffered NaCl Peptone EP, USP 14 AnaeroGRO™ MultiPak B 04 Butterfi eld’s Phosphate Buffer 14 AnaeroGRO™ Chopped Meat Broth 05 Campy Cefex Agar, Modifi ed 14 AnaeroGRO™ Chopped Meat Campy CVA Agar 14 Carbohydrate Broth 05 Campy FDA Agar 14 AnaeroGRO™ Chopped Meat Campy, Blood Free, Karmali Agar 14 Glucose Broth 05 Cetrimide Select Agar, USP 14 AnaeroGRO™ Thioglycollate with Hemin and CET/MAC/VJ Triplate 14 Vitamin K (H and K), without Indicator 05 CGB Agar for Cryptococcus 14 Anaerobic PEA 08 Chocolate Agar 15 Baird-Parker Agar 08 Chocolate/Martin Lewis with Barney Miller Medium 08 Lincomycin Biplate 15 BBE Agar 08 CompactDry™ SL 16 BBE Agar/PEA Agar 08 CompactDry™ LS 16 BBE/LKV Biplate 09 CompactDry™ TC 17 BCSA 09 CompactDry™ EC 17 BCYE Agar 09 CompactDry™ YMR 17 BCYE Selective Agar with CAV 09 CompactDry™ ETB 17 BCYE Selective Agar with CCVC 09 CompactDry™ YM 17 -
Shifts in the Fecal Microbiota Associated with Adenomatous Polyps
Published OnlineFirst September 26, 2016; DOI: 10.1158/1055-9965.EPI-16-0337 Research Article Cancer Epidemiology, Biomarkers Shifts in the Fecal Microbiota Associated with & Prevention Adenomatous Polyps Vanessa L. Hale1,2, Jun Chen3, Stephen Johnson3, Sean C. Harrington2, Tracy C. Yab4, Thomas C. Smyrk5, Heidi Nelson1, Lisa A. Boardman4, Brooke R. Druliner4, Theodore R. Levin6, Douglas K. Rex7, Dennis J. Ahnen8, Peter Lance9, David A. Ahlquist4, and Nicholas Chia1,2,10,11 Abstract Background: Adenomatous polyps are the most common production, as well as starch, sucrose, lipid, and phenylpropa- precursor to colorectal cancer, the second leading cause of cancer- noid metabolism. related death in the United States. We sought to learn more about Conclusions: These data hint that increased sugar, protein, and early events of carcinogenesis by investigating shifts in the gut lipid metabolism along with increased bile acid production could microbiota of patients with adenomas. promote a colonic environment that supports the growth of bile- Methods: We analyzed 16S rRNA gene sequences from the tolerant microbes such as Bilophilia and Desulfovibrio. In turn, these fecal microbiota of patients with adenomas (n ¼ 233) and microbes may produce genotoxic or inflammatory metabolites without (n ¼ 547). such as H2S and secondary bile acids, which could play a role in Results: Multiple taxa were significantly more abundant in catalyzing adenoma development and eventually colorectal patients with adenomas, including Bilophila, Desulfovibrio, cancer. proinflammatory bacteria in the genus Mogibacterium,and Impact: This study suggests a plausible biological mechanism multiple Bacteroidetes species. Patients without adenomas had to explain the links between shifts in the microbiota and colo- greater abundances of Veillonella, Firmicutes (Order Clostridia), rectal cancer. -
Protection of the Human Gut Microbiome From
Protection of the Human Gut Microbiome From Antibiotics Jean de Gunzburg, Amine Ghozlane, Annie Ducher, Emmanuelle Le Chatelier, Xavier Duval, Etienne Ruppé, Laurence Armand-Lefevre, Frédérique Sablier-Gallis, Charles Burdet, Loubna Alavoine, et al. To cite this version: Jean de Gunzburg, Amine Ghozlane, Annie Ducher, Emmanuelle Le Chatelier, Xavier Duval, et al.. Protection of the Human Gut Microbiome From Antibiotics. Journal of Infectious Diseases, Oxford University Press (OUP), 2018, 217 (4), pp.628-636. 10.1093/infdis/jix604. pasteur-02552147 HAL Id: pasteur-02552147 https://hal-pasteur.archives-ouvertes.fr/pasteur-02552147 Submitted on 23 Apr 2020 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. Distributed under a Creative Commons Attribution - NonCommercial - NoDerivatives| 4.0 International License The Journal of Infectious Diseases MAJOR ARTICLE Protection of the Human Gut Microbiome From Antibiotics Jean de Gunzburg,1,a Amine Ghozlane,2,a Annie Ducher,1,a Emmanuelle Le Chatelier,2,a Xavier Duval,3,4,5 Etienne Ruppé,2,b Laurence Armand-Lefevre,3,4,5 -
Microbiology for Specialty
MEDICAL UNIVERSITY – PLOVDIV FACULTY OF MEDICINE SYLLABUS IN MICROBIOLOGY Approved by the Section Council on 31.01.2020/Proceedings №1 Confirmed by the Faculty Council on 08.07.2020/ Proceedings №5 MICROBIOLOGY SYLLABUS Final Hours by year Course Academic hour count exam and semester Total Lectures Seminars Credit ІV V Microbiology V 135 60 75 9.3 2/3 2/2 Course name: Microbiology Type of course according to the uniform state requirements: Compulsory Level of education: Master /M/ Forms of training: Regular Year of training: 2nd and 3rd year Duration of training: 1 year (2 semesters) Academic hours: 60 hours of lectures, 75 hours of exercises Technical equipment applied in the training: - multimedia - demonstration materials - lectures - handbooks Forms of evaluation: Semester exam Evaluation criteria: The final grade is multicomponent and includes the marks from the written final exam and the following components: - average mark from ongoing control (colloquium, tests) - mark from the oral final examination - mark from the practical final exam If one of the components of the final grade is poor 2, then the final grade is necessarily poor 2. Score assesment: For each component participating in the final evaluation, a significance coefficient (from 0 to 1) is determined, and the total sum of the coefficients must always be 1. The overall mark is obtained as the sum of the evaluation marks on a six-point scale from the various components multiplied by the respective coefficients of significance. Q final grade = K1 Q grade from current control + K2 Q grade from written exam + K3 Q grade from the oral exam K1 = 0.20; K2 = 0.50; K3 = 0.30 Annual exam: Yes State exam: No Lecturers: Habilitated lecturer from the Department of Microbiology and Immunology Prof.