DOCSLIB.ORG

Identification of Gastrointestinal Microflora in Hawaiian Green Turtles

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Identification of Gastrointestinal Microflora in Hawaiian Green Turtles Identification of gastrointestinal microflora in Hawaiian green turtles (Chelonia mydas Linnaeus), and effects of glyphosate herbicide on their gastrointestinal bacteria Presented to the Faculty of the Tropical Conservation Biology and Environmental Science Program University of Hawai‘i at Hilo in partial fulfillment of the requirements for the degree of Masters of Science in Tropical Conservation Biology and Environmental Science May 2017 By Ronald P. Kittle, III Thesis Committee: Karla J. McDermid, Chairperson Lisa K. Muehlstein George H. Balazs Keywords: bacteria, Chelonia mydas, gastrointestinal microflora, glyphosate, herbicide toxicity, metagenomics Dedication I dedicate my Master’s research to my favorite science teachers in high school: Mrs. Kathy Teski, who showed me that chemistry is everywhere and is truly the “heart of science,” and Mrs. Holly Ruff, who bet me, while I was struggling with alternation of generations in AP Biology, that one day I would become a botanist—you were right! Both challenged me to think outside the box, and I can truly never repay you both for never giving up on me. I also dedicate my thesis to my sister Ruby, who paved the path for me and showed me that the pursuit of higher education is possible; and to my mother, Kimberly, who told me to follow my heart and supported me from afar. To all of my nieces and nephews, every step of the way you were all in my heart, even though I have been gone for many years and am thousands of miles away. I hope you love science too! Finally, to all LGBT scientists — take pride in science, and never stop being fabulous! ii Acknowledgements I express my deepest appreciation to my mentor at University of Hawaii at Hilo, Dr. Karla J. McDermid. Karla, you are like my mother in academia, and have watched me grow and develop from a “novice scientist” into the researcher I am today. I am so thankful for the guidance, knowledge, and memories you have given me throughout the years. It reminds me of the bond you had with your mentor, Izzie Abbott. To my committee members, Mr. George H. Balazs and Dr. Lisa K. Muehlstein, you both have been a pleasure to work with throughout this project and have expanded my skillsets. Thank you to Drs. Thierry Work, Bob Morris, and Jennifer Lynch, Ms. Shandell Brunson, Mr. Devon Franke, Ms. Olivia Hughes, and the rest of the team from NOAA National Marine Fisheries Service - PIFSC Marine Turtle Biology and Assessment Program for guidance during the necropsies; Ms. Anne Veillet from the UH-Hilo’s Core Genomics Facility, Dr. Scott Geib from the United States Department of Agriculture-Agricultural Research Service, and Mr. Donald Wong from University of British Columbia for guidance on DNA sequencing and Ion Torrent Platform; Mr. Casey Riegler for helping troubleshoot the Ion Torrent Platform from Thermo Fisher Scientific; Dr. Jonathan Awaya from UH-Hilo Biology Department; Mr. Erik Johnson and Ms. Tara Holitzki from the University of Hawaii at Hilo’s Analytical Lab for allowing me to utilize their supplies and lab space. iii TABLE OF CONTENTS Acknowledgements ...................................................................................................................... iii Glossary of Terms ........................................................................................................................ vi Executive Summary .......................................................................................................................1 Chapter 1: Review of Chelonia mydas Linnaeus digestion, microbiota, and glyphosate herbicide .........................................................................................................................................4 INTRODUCTION ........................................................................................................................4 FIGURES ...................................................................................................................................15 REFERENCES ...........................................................................................................................19 Chapter 2: Identification of gastrointestinal microflora in Hawaiian green turtles (Chelonia mydas Linnaeus)..........................................................................................................30 ABSTRACT ...............................................................................................................................30 INTRODUCTION ......................................................................................................................31 METHODS .................................................................................................................................32 RESULTS ...................................................................................................................................39 DISCUSSION ............................................................................................................................41 TABLES .....................................................................................................................................43 iv FIGURES ...................................................................................................................................53 REFERENCES ...........................................................................................................................62 Chapter 3: Glyphosate herbicide effects on gastrointestinal microflora of Hawaiian green turtles (Chelonia mydas Linnaeus) .............................................................................................66 ABSTRACT ...............................................................................................................................66 INTRODUCTION ......................................................................................................................68 METHODS .................................................................................................................................70 RESULTS ...................................................................................................................................73 DISCUSSION ............................................................................................................................74 FIGURES ...................................................................................................................................76 REFERENCES ...........................................................................................................................84 Appendix I: Turtle Necropsy Reports .......................................................................................90 Appendix II: Preliminary Collection Methods........................................................................104 v Glossary of Terms adapter: a short, chemically synthesized, double stranded DNA molecule which is used to link the ends of two other DNA molecule amplicon: product of polymerase chain reaction (PCR). barcode: a unique DNA sequence ligated to fragments within a sequencing library for downstream, in silico sorting and identification caecum: pouch or large tube-like structure in the lower abdominal cavity that receives undigested food material from the small intestine and is considered the first region of the large intestine cloaca: the common chamber into which the intestinal, urinary, and genital tracts discharge crop: pouch of the esophagus proximal to the stomach that functions for retention of food prior to entry into stomach digesta: material undergoing digestion emulsion PCR (emPCR): a reaction of DNA amplification in a water-in-oil emulsion. end repair: convert DNA with cohesive ends to blunt-ended 5’-phosphorylated DNA for use in blunt-end ligation reactions fibropapillomatosis (FP): a disease of sea turtles that results in the production of tumors, both external and internal that are considered benign, but may obstruct crucial functions, such as swimming, feeding, sight, and buoyancy. flow: the event of exposing the sequencing chip to one particular dNTP (T, A, C, or G) followed by a washing step vi hindgut fermentation: a digestive process seen in monogastric herbivores, animals with a simple, single-chambered stomach where cellulose is digested with the aid of symbiotic bacteria primarily in the large intestine and caecum ligation: the joining of two DNA strands or other molecules by a phosphate ester linkage metagenomics: is the use of DNA sequencing techniques to study DNA extracted directly from environmental samples operational taxonomic units (OTU): an operational definition used to classify groups of closely related individuals polymerase chain reaction (PCR): an in vitro technique for rapidly synthesizing large quantities of a given DNA segment that involves separating the DNA into its two complementary strands, using DNA polymerase to synthesize two-stranded DNA from each single strand, and repeating the process quantitative PCR (qPCR): a laboratory technique based on PCR that monitors the amplification of a targeted DNA molecule during the PCR, i.e. in real-time, and not at its end, as in conventional PCR vii Executive Summary Long-term conservation of the green turtle (Chelonia mydas Linnaeus), the largest marine herbivore in the Hawaiian archipelago, may depend on understanding their microflora. Using hindgut fermentation, green turtles rely on microbial degradation of cellulose and starch products from the
Load more

Recommended publications
  • 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.
    [Show full text]
  • Microbial Communities Mediating Algal Detritus Turnover Under Anaerobic Conditions
    Microbial communities mediating algal detritus turnover under anaerobic conditions Jessica M. Morrison1,*, Chelsea L. Murphy1,*, Kristina Baker1, Richard M. Zamor2, Steve J. Nikolai2, Shawn Wilder3, Mostafa S. Elshahed1 and Noha H. Youssef1 1 Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA 2 Grand River Dam Authority, Vinita, OK, USA 3 Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA * These authors contributed equally to this work. ABSTRACT Background. Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored. Results. Here, we characterized the microbial communities mediating the degradation of Chlorella vulgaris (Chlorophyta), Chara sp. strain IWP1 (Charophyceae), and kelp Ascophyllum nodosum (phylum Phaeophyceae), using sediments from an anaerobic spring (Zodlteone spring, OK; ZDT), sludge from a secondary digester in a local wastewater treatment plant (Stillwater, OK; WWT), and deeper anoxic layers from a seasonally stratified lake
    [Show full text]
  • Defluviitaleaceae Marie-Laure Fardeau, Anne Postec, Bernard Ollivier
    Defluviitaleaceae Marie-Laure Fardeau, Anne Postec, Bernard Ollivier To cite this version: Marie-Laure Fardeau, Anne Postec, Bernard Ollivier. Defluviitaleaceae. Bergey’s Manual of Systematics of Archaea and Bacteria (BMSAB), Hoboken, New Jersey : Wiley, [2015]-, 2017, 10.1002/9781118960608.fbm00280. hal-02884206 HAL Id: hal-02884206 https://hal.archives-ouvertes.fr/hal-02884206 Submitted on 20 Mar 2021 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. 1 Family Defluviitaleaceae 2 3 Marie-Laure Fardeau, Anne Postec and Bernard Ollivier 4 5 Aix Marseille Université, IRD, Université de Toulon, CNRS, Mediterranean Institute of 6 Oceanography (MIO), UM 110, 13288 Marseille cedex 9, France 7 8 Keywords: thermophilic, fermentative, anaerobic type of metabolism 9 10 11 Abstract : 12 The family Defluviitaleaceae belongs to the order Clostridiales. To date, it is currently 13 represented by only one genus containing two species and one species not validated. The 14 genus Defluviitalea was phylogenetically distantly to the genera Parasporobacterium, 15 Clostridium and Robinsoniella, pertaining to the family Lachnospiraceae with sequence 16 similartity of the 16S rRNA gene which approximates 87%. The delineation of the novel 17 family Defluviitaleaceae was primarily based on phylogenetic, metabolic and physiological 18 characteristics, with Defluviitalea as the type genus of the family.
    [Show full text]
  • Early Development of the Gut Microbiome and Immune-Mediated Childhood Disorders
    74 Early Development of the Gut Microbiome and Immune-Mediated Childhood Disorders Min Li, PhD1 Mei Wang, PhD1 Sharon M. Donovan, PhD, RD1 1 Department of Food Science and Human Nutrition, University of Address for correspondence Sharon M. Donovan, PhD, RD, Illinois, Urbana, Illinois Department of Food Science and Human Nutrition, University of Illinois, 339 Bevier Hall, 905 S. Goodwin Avenue, Urbana, IL 61801 Semin Reprod Med 2014;32:74–86 (e-mail: [email protected]). Abstract The human gastrointestinal tract inhabits a complex microbial ecosystem that plays a vital role in host health through its contributions to nutrient synthesis and digestion, protection from pathogens, and promoting maturation of host innate and adapt immune systems. The development of gut microbiota primarily occurs during infancy and is influenced by multiple factors, including prenatal exposure; gestational age; mode of delivery; feeding type; pre-, pro-, and antibiotic use; and host genetics. In genetically susceptible individuals, changes in the gut microbiota induced by environ- mental factors may contribute to the development of immune-related disorders in childhood, including atopic diseases, inflammatory bowel disease, irritable bowel syndrome, and necrotizing enterocolitis. Pre- and probiotics may be useful in the Keywords prevention and treatment of some immune-related diseases by modulating gut micro- ► microbiota biota and regulating host mucosal immune function. The review will discuss recent ► gastrointestinal findings on the environmental factors that influence development of gut microbiota ► allergy during infancy and its potential impact on some immune-related diseases in childhood. ► asthma The use of pre- and probiotics for prevention and intervention of several important ► immune diseases in early life will also be reviewed.
    [Show full text]
  • Expansion of and Reclassification Within the Family Lachnospiraceae
    University of Massachusetts Amherst ScholarWorks@UMass Amherst Doctoral Dissertations Dissertations and Theses November 2016 Expansion of and reclassification within the family Lachnospiraceae Kelly N. Haas University of Massachusetts Amherst Follow this and additional works at: https://scholarworks.umass.edu/dissertations_2 Part of the Biodiversity Commons, Bioinformatics Commons, Environmental Microbiology and Microbial Ecology Commons, Evolution Commons, Genomics Commons, Microbial Physiology Commons, Organismal Biological Physiology Commons, Other Ecology and Evolutionary Biology Commons, Other Microbiology Commons, and the Systems Biology Commons Recommended Citation Haas, Kelly N., "Expansion of and reclassification within the family Lachnospiraceae" (2016). Doctoral Dissertations. 843. https://doi.org/10.7275/9055799.0 https://scholarworks.umass.edu/dissertations_2/843 This Open Access Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. EXPANSION OF AND RECLASSIFICATION WITHIN THE FAMILY LACHNOSPIRACEAE A dissertation presented by KELLY NICOLE HAAS Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfilment of the requirements for the degree of DOCTOR OF PHILOSOPHY September 2016 Microbiology Department © Copyright by Kelly Nicole Haas 2016
    [Show full text]
  • Diet and Exercise Orthogonally Alter the Gut Microbiome and Reveal Independent Associations with Anxiety and Cognition
    Kang et al. Molecular Neurodegeneration 2014, 9:36 http://www.molecularneurodegeneration.com/content/9/1/36 RESEARCH ARTICLE Open Access Diet and exercise orthogonally alter the gut microbiome and reveal independent associations with anxiety and cognition Silvia S Kang1, Patricio R Jeraldo2, Aishe Kurti1, Margret E Berg Miller3,4, Marc D Cook3,4, Keith Whitlock3,4, Nigel Goldenfeld5,6, Jeffrey A Woods3,4, Bryan A White5, Nicholas Chia2* and John D Fryer1,7,8* Abstract Background: The ingestion of a high-fat diet (HFD) and the resulting obese state can exert a multitude of stressors on the individual including anxiety and cognitive dysfunction. Though many studies have shown that exercise can alleviate the negative consequences of a HFD using metabolic readouts such as insulin and glucose, a paucity of well-controlled rodent studies have been published on HFD and exercise interactions with regard to behavioral outcomes. This is a critical issue since some individuals assume that HFD-induced behavioral problems such as anxiety and cognitive dysfunction can simply be exercised away. To investigate this, we analyzed mice fed a normal diet (ND), ND with exercise, HFD diet, or HFD with exercise. Results: We found that mice on a HFD had robust anxiety phenotypes but this was not rescued by exercise. Conversely, exercise increased cognitive abilities but this was not impacted by the HFD. Given the importance of the gut microbiome in shaping the host state, we used 16S rRNA hypervariable tag sequencing to profile our cohorts and found that HFD massively reshaped the gut microbial community in agreement with numerous published studies.
    [Show full text]
  • Microbial Biogeography and Core Microbiota of the Rat Digestive Tract
    www.nature.com/scientificreports OPEN Microbial Biogeography and Core Microbiota of the Rat Digestive Tract Received: 07 November 2016 Dongyao Li1, Haiqin Chen1, Bingyong Mao1, Qin Yang1, Jianxin Zhao1, Zhennan Gu1, Accepted: 03 March 2017 Hao Zhang1, Yong Q. Chen1,2 & Wei Chen1,3 Published: 04 April 2017 As a long-standing biomedical model, rats have been frequently used in studies exploring the correlations between gastrointestinal (GI) bacterial biota and diseases. In the present study, luminal and mucosal samples taken along the longitudinal axis of the rat digestive tract were subjected to 16S rRNA gene sequencing-based analysis to determine the baseline microbial composition. Results showed that the community diversity increased from the upper to lower GI segments and that the stratification of microbial communities as well as shift of microbial metabolites were driven by biogeographic location. A greater proportion of lactate-producing bacteria (such as Lactobacillus, Turicibacter and Streptococcus) were found in the stomach and small intestine, while anaerobic Lachnospiraceae and Ruminococcaceae, fermenting carbohydrates and plant aromatic compounds, constituted the bulk of the large-intestinal core microbiota where topologically distinct co-occurrence networks were constructed for the adjacent luminal and mucosal compartments. When comparing the GI microbiota from different hosts, we found that the rat microbial biogeography might represent a new reference, distinct from other murine animals. Our study provides the first comprehensive characterization of the rat GI microbiota landscape for the research community, laying the foundation for better understanding and predicting the disease-related alterations in microbial communities. A large variety of symbiotic microorganisms coexist in the mammalian digestive tract, with their number around 10 times greater than the total number of mammalian somatic and germ cells1.
    [Show full text]
  • C G M 2 0 1 8 [0 4 on D Er Z O E K S R a Pp O
    Update of the bacterial the of bacterial Update intaxonomy the classification lists of COGEM CGM 2018 - 04 ONDERZOEKSRAPPORT report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly.
    [Show full text]
  • Microbial Micropatches Within Microbial Hotspots
    RESEARCH ARTICLE Microbial micropatches within microbial hotspots Lisa M. Dann1*, Jody C. McKerral2, Renee J. Smith1, Shanan S. Tobe1, James S. Paterson1, Justin R. Seymour3, Rod L. Oliver4, James G. Mitchell1 1 College of Science and Engineering at Flinders University, Adelaide, South Australia, Australia, 2 School of Computer Science, Engineering and Mathematics at Flinders University, Adelaide, South Australia, Australia, 3 Plant Functional Biology and Climate Change Cluster (C3) at University of Technology Sydney, Sydney, New South Wales, Australia, 4 CSIRO Land and Water Waite Research Institute, Adelaide, South Australia, Australia a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract a1111111111 The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have `hotspots' of high abun- dance, and `coldspots' of low abundance. Previously we showed that 300 μl abundance hot- OPEN ACCESS spots, coldspots and background regions were distinct at all taxonomic levels. Here we build Citation: Dann LM, McKerral JC, Smith RJ, Tobe on these results by showing taxonomic micropatches within these 300 μl microscale hot- SS, Paterson JS, Seymour JR, et al. (2018) spots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl Microbial micropatches within microbial hotspots. subsamples was driven by heightened abundance of specific genera. The micropatches PLoS ONE 13(5): e0197224. https://doi.org/ were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, 10.1371/journal.pone.0197224 Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas Editor: Luis Angel Maldonado Manjarrez, and Bacteroides being responsible for a shift in the most dominant genera in individual hot- Universidad Nacional Autonoma de Mexico Facultad de Quimica, MEXICO spot subsamples, representing up to 80.6% and 47.3% average abundance, respectively.
    [Show full text]
  • Bacterial Ecology of Abattoir Wastewater Treated by an Anaerobic Digestor
    b r a z i l i a n j o u r n a l o f m i c r o b i o l o g y 4 7 (2 0 1 6) 73–84 h ttp://www.bjmicrobiol.com.br/ Environmental Microbiology Bacterial ecology of abattoir wastewater treated by an anaerobic digestor a,b a,c a b Linda Jabari , Hana Gannoun , Eltaief Khelifi , Jean-Luc Cayol , d a b,∗ Jean-Jacques Godon , Moktar Hamdi , Marie-Laure Fardeau a Université de Carthage, Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie (INSAT), 2 Boulevard de la terre, B.P. 676, 1080 Tunis, Tunisia b Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MOI, UM 110, 13288 Marseille cedex 9, France c Université Tunis El Manar, Institut Supérieur des Sciences Biologiques Appliquées de Tunis (ISSBAT) 9, avenue Zouhaïer Essafi, 1006 Tunis, Tunisia d INRA U050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Étangs, F-11100 Narbonne, France a r a t i c l e i n f o b s t r a c t Article history: Wastewater from an anaerobic treatment plant at a slaughterhouse was analysed to deter- Received 19 September 2014 mine the bacterial biodiversity present. Molecular analysis of the anaerobic sludge obtained Accepted 6 July 2015 from the treatment plant showed significant diversity, as 27 different phyla were identified. Firmicutes, Proteobacteria, Bacteroidetes, Thermotogae, Euryarchaeota (methanogens), and msbl6 Associate Editor: Welington Luiz de (candidate division) were the dominant phyla of the anaerobic treatment plant and repre- Araújo sented 21.7%, 18.5%, 11.5%, 9.4%, 8.9%, and 8.8% of the total bacteria identified, respectively.
    [Show full text]
  • Rett Syndrome and Other Neurodevelopmental Disorders Share Common Changes in Gut Microbial Community: a Descriptive Review
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by AIR Universita degli studi di Milano International Journal of Molecular Sciences Review Rett Syndrome and Other Neurodevelopmental Disorders Share Common Changes in Gut Microbial Community: A Descriptive Review Elisa Borghi 1,* and Aglaia Vignoli 1,2,* 1 Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy 2 Child Neuropsychiatry Unit, ASST Santi Paolo Carlo Hospital, 20142 Milan, Italy * Correspondence: [email protected] (E.B.); [email protected] (A.V.); Tel.: +39-02-503-23287 (E.B.); +39-02-8184-4201 (A.V.) Received: 13 July 2019; Accepted: 24 August 2019; Published: 26 August 2019 Abstract: In this narrative review, we summarize recent pieces of evidence of the role of microbiota alterations in Rett syndrome (RTT). Neurological problems are prominent features of the syndrome, but the pathogenic mechanisms modulating its severity are still poorly understood. Gut microbiota was recently demonstrated to be altered both in animal models and humans with different neurodevelopmental disorders and/or epilepsy. By investigating gut microbiota in RTT cohorts, a less rich microbial community was identified which was associated with alterations of fecal microbial short-chain fatty acids. These changes were positively correlated with severe clinical outcomes. Indeed, microbial metabolites can play a crucial role both locally and systemically, having dynamic effects on host metabolism and gene expression in many organs. Similar alterations were found in patients with autism and down syndrome as well, suggesting a potential common pathway of gut microbiota involvement in neurodevelopmental disorders.
    [Show full text]
  • Gastrointestinal Microbiota Community Composition Has Significant Effects on Systemic Immune Responses
    © 2013 Kyle M. Schachtschneider GASTROINTESTINAL MICROBIOTA COMMUNITY COMPOSITION HAS SIGNIFICANT EFFECTS ON SYSTEMIC IMMUNE RESPONSES BY KYLE M SCHACHTSCHNEIDER DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Animal Sciences in the Graduate College of the University of Illinois at Urbana‐Champaign, 2013 Urbana, Illinois Doctoral Committee: Professor Lawrence B. Schook, Chair Professor Bryan White Associate Professor Kelly Swanson Doctor of Veterinary Medicine Sherrie Clark ABSTRACT This study explored the utility of an oral microbial inoculum as a therapeutic tool to affect systemic immune responses. Colonization of the gastrointestinal (GI) tract is initiated during birth and continually seeded from the individual’s environment. Gastrointestinal microorganisms for a mutualistic relationship with the host, playing a central role in developing and modulating host immune responses. Animal studies have demonstrated the impact of GI microbiota on the development of GI and systemic immune systems; however, the full spectrum of action of early gastrointestinal tract stimulation and subsequent modulation of systemic immune responses is poorly understood. Human trials have shown the successful use of probiotics and fecal transplantations to treat GI disorders. In addition, patients receiving fecal transplants have also reported improvements in systemic disorders such as multiple sclerosis. These results, in addition to increased incidence of allergic and autoimmune diseases associated with reduced GI microbial diversity has increased interest in the effect of early life GI colonization on the development of the systemic immune system. In order to address this issue, we sought to determine the effects of early life colonization on microbiome composition and systemic immune responses.
    [Show full text]