Relationships Between Diet-Related Changes in the Gut Microbiome and Cognitive Flexibility
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Supplementary Information for Acute Infection of Mice with Clostridium
IMM-2013-2862, Sadighi Akha et al-Supplementary Information 1 Supplementary Information for Acute infection of mice with Clostridium difficile leads to eIF2α phosphorylation and pro-survival signalling as part of the mucosal inflammatory response Amir A. Sadighi Akha1, Casey M. Theriot2, John R. Erb-Downward1, Andrew J. McDermott3, Nicole R. Falkowski1, Heather M. Tyra4, D. Thomas Rutkowski4, Vincent B. Young2,3 and Gary B. Huffnagle1,3* IMM-2013-2862, Sadighi Akha et al-Supplementary Information 2 Supplementary Text Materials and Methods for Figures S1 and S2 DNA isolation, amplicon library preparation and 454 pyrosequencing- The DNeasy blood and tissue kit (Qiagen) was used to extract genomic DNA from the caecal and colonic contents obtained from untreated and C. difficile-infected mice. The extraction was performed according to the manufacturer’s instructions except for the following modifications: adding a bead-beating step using UltraClean fecal DNA bead tubes (Mo Bio Laboratories, Carlsbad, CA); doubling the amount of ATL buffer and the proteinase K used in the protocol; and decreasing by half the amount of the AE buffer used to elute the DNA. Subsequently, the V3, V4 and V5 hyper-variable regions of the 16S ribosomal RNA gene in each of the samples were targeted for amplification with the 357F and 929R primer sets [1]. Amplicons were purified with the Agencourt AMPure XP PCR purification system (Beckman Coulter, Indianapolis, IN), and quantified with the Quant- iT PicoGreen dsDNA kit (Life Technologies) to obtain an equal pool for pyrosequencing. They were then sequenced on a Roche 454 GS Junior Titanium platform according to the manufacturer’s specifications. -
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. -
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. -
Environment-Dependent Variation in Gut Microbiota of an Oviparous Lizard (Calotes Versicolor)
animals Article Environment-Dependent Variation in Gut Microbiota of an Oviparous Lizard (Calotes versicolor) Lin Zhang 1,2,*,† , Fang Yang 3,†, Ning Li 4 and Buddhi Dayananda 5 1 School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China 2 State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China 3 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China; [email protected] 4 College of Food Science, Nanjing Xiaozhuang University, Nanjing 211171, China; [email protected] 5 School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; [email protected] * Correspondence: [email protected] † These authors contributed equally to this work. Simple Summary: The different gut sections potentially provide different habitats for gut microbiota. We found that Bacteroidetes, Firmicutes, and Proteobacteria were the three primary phyla in gut micro- biota of C. versicolor. The relative abundance of dominant phyla Bacteroidetes and Firmicutes exhibited an increasing trend from the small intestine to the large intestine, and there was a higher abun- dance of genus Bacteroides (Class: Bacteroidia), Coprobacillus and Eubacterium (Class: Erysipelotrichia), Parabacteroides (Family: Porphyromonadaceae) and Ruminococcus (Family: Lachnospiraceae), and Family Odoribacteraceae and Rikenellaceae in the hindgut, and some metabolic pathways were higher in the hindgut. Our results reveal the variations of gut microbiota composition and metabolic pathways in Citation: Zhang, L.; Yang, F.; Li, N.; different parts of the lizards’ intestine. Dayananda, B. Environment- Dependent Variation in Gut Abstract: Vertebrates maintain complex symbiotic relationships with microbiota living within their Microbiota of an Oviparous Lizard gastrointestinal tracts which reflects the ecological and evolutionary relationship between hosts and (Calotes versicolor). -
Influence of External and Internal Environmental Factors on Intestinal Microbiota of Wild and Domestic Animals A
Influence of external and internal environmental factors on intestinal microbiota of wild and domestic of animals factors on intestinal microbiota Influence of external and internal environmental Influence of external and internal environmental factors on intestinal microbiota of wild and domestic animals A. Umanets Alexander Umanets Propositions 1. Intestinal microbiota and resistome composition of wild animals are mostly shaped by the animals’ diet and lifestyle. (this thesis) 2. When other environmental factors are controlled, genetics of the host lead to species- or breed specific microbiota patterns. (this thesis) 3. Identifying the response of microbial communities to factors that only have a minor contribution to overall microbiota variation faces the same problems as the discovery of exoplanets. 4. Observational studies in microbial ecology using cultivation- independent methods should be considered only as a guide for further investigations that employ controlled experimental conditions and mechanistic studies of cause-effect relationships. 5. Public fear of genetic engineering and artificial intelligence is not helped by insufficient public education and misleading images created through mass- and social media. 6. Principles of positive (Darwinian) and negative selection govern the repertoire of techniques used within martial arts. Propositions belonging to the thesis, entitled Influence of external and internal environmental factors on intestinal microbiota of wild and domestic animals Alexander Umanets Wageningen, 17 October -
Early-Life Gut Dysbiosis Linked to Juvenile Mortality in Ostriches Elin Videvall1,2* , Se Jin Song3,4, Hanna M
Videvall et al. Microbiome (2020) 8:147 https://doi.org/10.1186/s40168-020-00925-7 RESEARCH Open Access Early-life gut dysbiosis linked to juvenile mortality in ostriches Elin Videvall1,2* , Se Jin Song3,4, Hanna M. Bensch1, Maria Strandh1, Anel Engelbrecht5, Naomi Serfontein6, Olof Hellgren1, Adriaan Olivier7, Schalk Cloete5,8, Rob Knight3,4,9,10 and Charlie K. Cornwallis1 Abstract Background: Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbiosis, and if particular gut regions or specific time periods during ontogeny are more susceptible. We also know very little of this process in non-model organisms, despite an increasing realization of the general importance of gut microbiota for health. Methods: Here, we examine the changes that occur in the microbiome during dysbiosis in different parts of the gastrointestinal tract in a long-lived bird with high juvenile mortality, the ostrich (Struthio camelus). We evaluated the 16S rRNA gene composition of the ileum, cecum, and colon of 68 individuals that died of suspected enterocolitis during the first 3 months of life (diseased individuals), and of 50 healthy individuals that were euthanized as age-matched controls. We combined these data with longitudinal environmental and fecal sampling to identify potential sources of pathogenic bacteria and to unravel at which stage of development dysbiosis- associated bacteria emerge. Results: Diseased individuals had drastically lower microbial alpha diversity and differed substantially in their microbial beta diversity from control individuals in all three regions of the gastrointestinal tract. -
Insights Into the Role of Erysipelotrichaceae in the Human Host
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector OPINION published: 20 November 2015 doi: 10.3389/fcimb.2015.00084 Insights into the Role of Erysipelotrichaceae in the Human Host Nadeem O. Kaakoush * School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia Keywords: Erysipelotrichaceae, gastrointestinal, microbiota, metabolic disorders, inflammatory bowel diseases, colorectal cancer Understanding the human gut microbiota has garnered interest from researchers and clinicians to pharmaceutical companies looking at novel mechanisms to manipulate the microbiota for the benefit of the host. Studies on the gut microbiota can be loosely characterized into three areas that include investigating the microbiota’s role in the physiology of the healthy gut, in the establishment of gastrointestinal disease, and in extra-intestinal manifestations. With deep sequencing technologies now in routine use in the research environment, novel members of the gut microbiota are coming to light, and our understanding of this complex ecosystem and its relationship to the host is slowly improving. IMPORTANCE OF ERYSIPELOTRICHACEAE IN HUMANS Edited by: Reports documenting a potential role for the bacterial family Erysipelotrichaceae, which belongs D. Scott Merrell, to the Firmicutes phylum, in host physiology and/or disease are on the rise. However, more often Uniformed Services University of the than not, these organisms are mentioned in passing, despite the fact that members of this bacterial Health Sciences, USA family appear to be highly immunogenic and can potentially flourish post-treatment with broad Reviewed by: spectrum antibiotics (Zhao et al., 2013; Palm et al., 2014; Dinh et al., 2015). -
Downloaded from Genome Website
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.18.388454; this version posted November 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Characterization of the first cultured free-living representative of 2 Candidatus Izimaplasma uncovers its unique biology 3 Rikuan Zheng1,2,3,4, Rui Liu1,2,4, Yeqi Shan1,2,3,4, Ruining Cai1,2,3,4, Ge Liu1,2,4, Chaomin Sun1,2,4* 1 4 CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea 5 Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China 2 6 Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory 7 for Marine Science and Technology, Qingdao, China 3 8 College of Earth Science, University of Chinese Academy of Sciences, Beijing, 9 China 10 4Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China 11 12 * Corresponding author 13 Chaomin Sun Tel.: +86 532 82898857; fax: +86 532 82898857. 14 E-mail address: [email protected] 15 16 17 Key words: Candidatus Izimaplasma, uncultivation, biogeochemical cycling, 18 extracellular DNA, in situ, deep sea 19 Running title: Characterization of the first cultured Izimaplasma 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.18.388454; this version posted November 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 22 Abstract 23 Candidatus Izimaplasma, an intermediate in the reductive evolution from Firmicutes 24 to Mollicutes, was proposed to represent a novel class of free-living wall-less bacteria 25 within the phylum Tenericutes found in deep-sea methane seeps. -
Improved Diagnostics and Further Investigation of Condemnations and Outbreaks Associated with Erysipelothrix Spp Joseph Samuel Bender Iowa State University
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2010 Improved diagnostics and further investigation of condemnations and outbreaks associated with Erysipelothrix spp Joseph Samuel Bender Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Veterinary Microbiology and Immunobiology Commons Recommended Citation Bender, Joseph Samuel, "Improved diagnostics and further investigation of condemnations and outbreaks associated with Erysipelothrix spp" (2010). Graduate Theses and Dissertations. 11370. https://lib.dr.iastate.edu/etd/11370 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Improved diagnostics and further investigation of condemnations and outbreaks associated with Erysipelothrix spp by Joseph Samuel Bender A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Veterinary Preventive Medicine Program of Study Committee: Tanja Opriessnig, Major Professor Kent J. Schwartz Leo L. Timms Iowa State University Ames, Iowa 2010 Copyright © Joseph Samuel Bender, 2010. All rights reserved. ii TABLE OF CONTENTS CHAPTER 1. GENERAL INTRODUCTION Thesis Organization 1 Statement of Problem and Research Summary 1 Reference List 3 CHAPTER 2. LITERATURE REVIEW Introduction 4 Morphology, Growth, and Biological Characteristics 5 Epidemiology 6 Prevalence and Condemnations 7 Pathogenesis and Clinical Signs of Disease 9 Virulence Factors 11 Diagnosis 14 Characterization 19 Prevention and Biologics Development 21 Reference List 23 CHAPTER 3. -
Erysipelothrix Rhusiopathiae in Laying Hens
Erysipelothrix rhusiopathiae in Laying Hens Helena Eriksson Faculty of Veterinary Medicine and Animal Science Department of Clinical Sciences Uppsala Doctoral Thesis Swedish University of Agricultural Sciences Uppsala 2013 Acta Universitatis agriculturae Sueciae 2013:26 Cover: “Ruvande”. Sculpture by Hermine Keller. (photo: H. Keller) ISSN 1652-6880 ISBN (Printed copy) 978-91-576-7790-7 ISBN (Electronic copy) 978-91-576-7791-4 © 2013 Helena Eriksson, Uppsala Print: SLU Service/Repro, Uppsala 2013 Erysipelothrix rhusiopathiae in Laying Hens Abstract The bacterium Erysipelothrix rhusiopathiae can infect a wide range of mammals (including humans) and birds. Disease outbreaks (erysipelas) have been considered unusual in chickens internationally, but outbreaks with high mortality and egg production losses have been diagnosed in Swedish laying hen flocks every year since 1998. Different aspects of E. rhusiopathiae infection in chickens were examined in this thesis with the aim of preventing future outbreaks. These aspects included determining occurrence of the bacterium in different housing systems for laying hens and the potential of the poultry red mite (Dermanyssus gallinae) to carry it, characterization of isolates of the bacterium from different hosts using pulsed-field gel electrophoresis (PFGE), serotyping, antimicrobial susceptibility testing and 16S rRNA gene sequencing, and determining the incidence of E. rhusiopathiae in the environment on affected organic laying hen farms by the use of selective culture and PCR. The results showed an association between erysipelas outbreaks and housing system. Flocks in free-range systems appeared to be at a higher risk than flocks in indoor litter- based systems, while flocks in cages appeared to be at the lowest risk. -
Enrofloxacin Shifts Intestinal Microbiota and Metabolic Profiling and Hinders Recovery
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.13.201830; this version posted July 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Enrofloxacin shifts intestinal microbiota and metabolic profiling and hinders recovery 2 from Salmonella enterica subsp. enterica serovar Typhimurium infection in neonatal 3 chickens 4 5 Boheng Ma,a,b,c,& Xueran Mei,a,b,c,& Changwei Lei,a,b,c Cui Li,a,b,c Yufeng Gao,a,b,c Linghan 6 Kong,a,b,c Xiwen Zhai,a,b,c,d Hongning Wanga,b,c,# 7 8 a College of Life Sciences, Sichuan University, Chengdu, People’s Republic of China 9 b Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Chengdu, 10 People’s Republic of China 11 c Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 12 People’s Republic of China 13 d Sichuan Water Conservancy Vocational Collage, Chengdu, People’s Republic of China 14 15 Running head: Effects of enrofloxacin on chickens 16 17 # Address correspondence to Hongning Wang, [email protected] 18 & Both authors are identified as Co-First Author. 19 20 Word count: 211 words (Abstract); 4895 words (main text) 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.13.201830; this version posted July 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. -
The Gut Microbiota Profile According to Glycemic Control in Type 1
microorganisms Article The Gut Microbiota Profile According to Glycemic Control in Type 1 Diabetes Patients Treated with Personal Insulin Pumps Sandra Mrozinska 1,2 , Przemysław Kapusta 3 , Tomasz Gosiewski 4 , Agnieszka Sroka-Oleksiak 4, Agnieszka H. Ludwig-Słomczy ´nska 3 , Bartłomiej Matejko 1,2 , Beata Kiec-Wilk 1,2, Malgorzata Bulanda 4, Maciej T. Malecki 1,2, Pawel P. Wolkow 3 and Tomasz Klupa 1,2,* 1 Jagiellonian University Medical College, Faculty of Medicine, Department of Metabolic Diseases, 2 Jakubowskiego Street, 30-688 Krakow, Poland; [email protected] (S.M.); [email protected] (B.M.); [email protected] (B.K.-W.); [email protected] (M.T.M.) 2 University Hospital, Department of Metabolic Diseases, 2 Jakubowskiego Street, 30-688 Krakow, Poland 3 Jagiellonian University Medical College, Center for Medical Genomics OMICRON, 7c Kopernika Street, 31-034 Krakow, Poland; [email protected] (P.K.); [email protected] (A.H.L.-S.); [email protected] (P.P.W.) 4 Jagiellonian University Medical College, Faculty of Medicine, Department of Microbiology, 18 Czysta Street, 31-121 Krakow, Poland; [email protected] (T.G.); [email protected] (A.S.-O.); [email protected] (M.B.) * Correspondence: [email protected]; Tel.: +48-1240-029-50 Abstract: Recently, several studies explored associations between type 1 diabetes (T1DM) and micro- biota. The aim of our study was to assess the colonic microbiota structure according to the metabolic control in T1DM patients treated with insulin pumps. We studied 89 T1DM patients (50.6% women) at the median age of 25 (IQR, 22–29) years.