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Evaluation of the Bacterial Diversity in the Human Tongue Coating Based on Genus-Specific Primers for 16S Rrna Sequencing
Hindawi BioMed Research International Volume 2017, Article ID 8184160, 12 pages https://doi.org/10.1155/2017/8184160 Research Article Evaluation of the Bacterial Diversity in the Human Tongue Coating Based on Genus-Specific Primers for 16S rRNA Sequencing Beili Sun,1 Dongrui Zhou,2 Jing Tu,1 and Zuhong Lu1,2 1 State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China 2Key Laboratory of Child Development and Learning Science, Ministry of Education of China, Southeast University, Nanjing 210096, China Correspondence should be addressed to Zuhong Lu; [email protected] Received 25 February 2017; Revised 20 June 2017; Accepted 20 July 2017; Published 20 August 2017 Academic Editor: Koichiro Wada Copyright © 2017 Beili Sun et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The characteristics of tongue coating are very important symbols for disease diagnosis in traditional Chinese medicine (TCM) theory.Asahabitatoforalmicrobiota,bacteriaonthetonguedorsumhavebeenprovedtobethecauseofmanyoraldiseases.The high-throughput next-generation sequencing (NGS) platforms have been widely applied in the analysis of bacterial 16S rRNA gene. We developed a methodology based on genus-specific multiprimer amplification and ligation-based sequencing for microbiota analysis. In order to validate the efficiency of the approach, we thoroughly analyzed six tongue coating samples from lung cancer patients with different TCM types, and more than 600 genera of bacteria were detected by this platform. The results showed that ligation-based parallel sequencing combined with enzyme digestion and multiamplification could expand the effective length of sequencing reads and could be applied in the microbiota analysis. -
The Proteolytic Systems of Ruminal Microorganisms Rj Wallace
The proteolytic systems of ruminal microorganisms Rj Wallace To cite this version: Rj Wallace. The proteolytic systems of ruminal microorganisms. Annales de zootechnie, INRA/EDP Sciences, 1996, 45 (Suppl1), pp.301-308. hal-00889635 HAL Id: hal-00889635 https://hal.archives-ouvertes.fr/hal-00889635 Submitted on 1 Jan 1996 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. The proteolytic systems of ruminal microorganisms RJ Wallace Rowett Research Institute, Bucksburn, Aberdeen AB2 9SB, UK Protein breakdown in the rumen is generally the breakdown process and assesses the regarded as detrimental to the efficiency of relative importance of different species in the ruminant nutrition, certainly for animals on a light of population densities and the properties relatively high plane of nutrition. Peptides and of the mixed rumen population. amino acids arising from proteolysis are potential nutrients for the growth of rumen microorganisms, but they are also liable to be Proteolytic ruminal microorganisms degraded to ammonia and lost from the rumen. Proteolytic activity occurs in all three main The mixed rumen microbial population has a categories of rumen microorganisms. Bacteria proteolytic activity that is only moderate are mainly responsible for dietary protein compared with other proteolytic micro- breakdown, while ciliate protozoa break down organisms and the host’s own gastric and particulate feed protein of appropriate size and pancreatic secretions, but the length of time also bacterial protein. -
Phylogenetic Analysis of Butyrivibrio Strains Reveals Three Distinct Groups of Species Within the Clostvidium Subphylum of the Gram-Positive Bacteria
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1996, p. 195-199 Vol. 46, No. 1 0020-7713/96/$04.00+0 Copyright 0 1996, International Union of Microbiological Societies Phylogenetic Analysis of Butyrivibrio Strains Reveals Three Distinct Groups of Species within the Clostvidium Subphylum of the Gram-Positive Bacteria ANNE WILLEMS," MONICA AMAT-MARCO, AND MATTHEW D. COLLINS Department of Microbial Physiology, Institute of Food Research, Reading Laboratoy, Reading RG6 6BZ, United Kingdom The phylogenetic positions of 40 Butyrivibrio strains were determined by performing a comparative sequence analysis of the 165 rRNA genes of these organisms. We found that all of the strains which we studied belong to cluster XIVa (M. D. Collins, P. A. Lawson, A. Willems, J. J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J. A. E. Farrow, Int. J. Syst. Bacteriol. 442312-826, 1994) of the Clostridium subphylum of the gram-positive bacteria, which also includes several Clostridium, Coprococcus,Eubacterium, and Rumino- coccus species. We also found that the Butyrivibrio strains which we examined were genotypically heterogeneous and exhibited 12 distinct rRNA sequence types. The 12 rRNA sequence types formed three distinct lineages in cluster XIVa, which were separate from each other and from all other species belonging to this cluster. One lineage consisted of strains which exhibited a single rRNA type and corresponded to the species Butyrivibrio crossotus. The second lineage consisted of 12 strains designated Butyrivibrio Jibrisolvens which exhibited seven distinct rRNA sequence types. The type strain of B. Jibrisolvens was a member of this lineage, but its position was peripheral. The third lineage comprised 26 B. -
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Downloaded from British Journal of Nutrition (2014), 111, 1602–1610 doi:10.1017/S0007114513004200 q The Authors 2013 https://www.cambridge.org/core Selective proliferation of intestinal Barnesiella under fucosyllactose supplementation in mice Gisela A. Weiss1,2, Christophe Chassard3 and Thierry Hennet1* . IP address: 1Institute of Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland 170.106.33.14 2Clinical Chemistry and Biochemistry, University Children’s Hospital Zurich, Zurich, Switzerland 3 Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Switzerland (Submitted 29 May 2013 – Final revision received 14 November 2013 – Accepted 3 December 2013 – First published online 10 January 2014) , on 26 Sep 2021 at 14:57:53 Abstract The oligosaccharides 2-fucosyllactose and 3-fucosyllactose are major constituents of human breast milk but are not found in mouse milk. Milk oligosaccharides have a prebiotic action, thus affecting the colonisation of the infant intestine by microbiota. To determine the specific effect of fucosyllactose exposure on intestinal microbiota in mice, in the present study, we orally supplemented newborn mice with pure 2-fucosyllactose and 3-fucosyllactose. Exposure to 2-fucosyllactose and 3-fucosyllactose increased the levels of bacteria of the Porphyro- , subject to the Cambridge Core terms of use, available at monadaceae family in the intestinal gut, more precisely members of the genus Barnesiella as analysed by 16S pyrosequencing. The ability of Barnesiella to utilise fucosyllactose as energy source was confirmed in bacterial cultures. Whereas B. intestinihominis and B. viscericola did not grow on fucose alone, they proliferated in the presence of 2-fucosyllactose and 3-fucosyllactose following the secretion of linkage- specific fucosidase enzymes that liberated lactose. -
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 -
Naseribafrouei.Pdf (1.673Mb)
Correlation Between Gut Microbiota and Depression Ali Naseribafrouei Master degree in Applied Biotechnology HEDMARK UNIVERSITY COLLEGE 2013 Ali Naseribafrouei Page 1 Table of Contents Acknowledgment………………………………………………………………. 5 Abstracts……………………………………………………………………….. 6 Abbreviation………………………………………………………………………………..7 Introduction……………………………………………………………………..8 Definition…………...……………………………………………………………………………………………8 Signs and Symptoms…………………...………………………………….……………………………………..9 Etiology………...……………………………………………………………………………………………….10 Diagnosis...……………………………………………………………………………………………………...12 Management………...…………………………………………………………………………………………..13 Hypothalamic Pituitary Adrenal (HPA) System………..………………………………………………………14 Alterations of HPA system and Hypercortisolemia in depression……………….……………….………...…..14 Analysis of HPA system function………….…………………………………………………………………...15 Human Gut Microbiome…….…………………...……………………………………………………………..16 Human Gut Microbiome‘s contribution to health and disease……………………………………...………….21 Culture-independent analyzing methods……………………………….………………………………………22 16S rRNA gene as microbial molecular marker………………………...……………………………………..23 DNA Sequencing……………………………………….………………………………………………………24 BigDye Terminator………………...…………………………………………………………………………..26 Roche/454 GS FLS Titanium Sequencer…………………………….…………………………………………27 Deep Sequencing………………….……………………………………………………………………………28 Illumina Genome Analyzer………………………..………………………………………………………..….29 Applied Bio systems SOLiD………………………………………..………………………………………….30 Helicos Heliscope……………………………………………………..…………………...…………………..30 -
Genomic Characterization of the Uncultured Bacteroidales Family S24-7 Inhabiting the Guts of Homeothermic Animals Kate L
Ormerod et al. Microbiome (2016) 4:36 DOI 10.1186/s40168-016-0181-2 RESEARCH Open Access Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals Kate L. Ormerod1, David L. A. Wood1, Nancy Lachner1, Shaan L. Gellatly2, Joshua N. Daly1, Jeremy D. Parsons3, Cristiana G. O. Dal’Molin4, Robin W. Palfreyman4, Lars K. Nielsen4, Matthew A. Cooper5, Mark Morrison6, Philip M. Hansbro2 and Philip Hugenholtz1* Abstract Background: Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeothermic animals and are increasingly being recognized as a numerically predominant member of the gut microbiota; however, little is known about the nature of their interactions with the host. Results: Here, we provide the first whole genome exploration of this family, for which we propose the name “Candidatus Homeothermaceae,” using 30 population genomes extracted from fecal samples of four different animal hosts: human, mouse, koala, and guinea pig. We infer the core metabolism of “Ca. Homeothermaceae” to be that of fermentative or nanaerobic bacteria, resembling that of related Bacteroidales families. In addition, we describe three trophic guilds within the family, plant glycan (hemicellulose and pectin), host glycan, and α-glucan, each broadly defined by increased abundance of enzymes involved in the degradation of particular carbohydrates. Conclusions: “Ca. Homeothermaceae” representatives constitute a substantial component of the murine gut microbiota, as well as being present within the human gut, and this study provides important first insights into the nature of their residency. -
Systems Genetic Discovery of Host-Microbiome Interactions
bioRxiv preprint doi: https://doi.org/10.1101/349605; this version posted June 18, 2018. 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. 1 Systems genetic discovery of host-microbiome interactions 2 reveals mechanisms of microbial involvement in disease 3 4 5 Running Title: Host genomics, microbial abundance and disease. 6 7 Jason A. Bubier1, Vivek M. Philip1,2, Christopher Quince3, James Campbell4,5, Yanjiao Zhou1 8 Tatiana Vishnivetskaya2, Suman Duvvuru2, Rachel Hageman Blair6, Juliet Ndukum1, Kevin D. 9 Donohue7,8,Charles Phillips9, Carmen M. Foster4, David J. Mellert1, George Weinstock1, 10 Cymbeline T. Culiat2, Erich J. Baker10, Michael A. Langston9, Bruce O’Hara7,11, Anthony V. 11 Palumbo4, Mircea Podar4 and Elissa J. Chesler1,2,4 12 13 14 1The Jackson Laboratory 15 2Genome Science and Technology Program, University of Tennessee and Oak Ridge National 16 Laboratory 17 3School of Engineering, University of Glasgow, Glasgow G12 8LT, UK. 18 4Biosciences Division, Oak Ridge National Laboratory 19 5Department of Natural Sciences, Northwest Missouri State University, Maryville, MO 64468 20 6 Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 21 7Signal Solutions, LLC, Lexington, KY; 22 8 Electrical and Computer Engineering Department, University of Kentucky, Lexington, KY 23 9 Electrical Engineering and Computer Science, University of Tennessee 24 10School of Engineering & Computer Science, Baylor University, Waco, TX 76798 25 11 Department of Biology, University of Kentucky, Lexington, KY 26 27 Corresponding Author: 28 29 Elissa J. -
Isolation and Characterization of Superior Rumen Bacteria of Cattle (Bos Taurus) and Potential Application in Animal Feedstuff
Vol.2, No.4, 224-228 (2012) Open Journal of Animal Sciences http://dx.doi.org/10.4236/ojas.2012.24031 Isolation and characterization of superior rumen bacteria of cattle (Bos taurus) and potential application in animal feedstuff Krushna Chandra Das1,2, Wensheng Qin2* 1National Research Centre on Mithun, Indian Council of Agricultural Research, Medziphema, India 2Biorefining Research Institute, Department of Biology, Lakehead University, Thunder Bay, Canada; *Corresponding Author: [email protected] Received 16 August 2012; revised 20 September 2012; accepted 28 September 2012 ABSTRACT and they are able to utilize plant nutrients efficiently as source of energy. Microbes survive in the rumen under Rumen of cattle harbors many microorganisms different constraints which may be either natural or feed responsible for bioconversion of nutrients into a associated as some of the feeds contain a significant source of energy for the animals. In recent years amount of anti-nutritional factors [1]. Any contaminant many rumen microbes have been isolated and which cannot survive these constraints is eliminated. characterized by sequence analysis of 16S ri- Therefore, the microbes which harbor the rumen are bosomal RNA gene. Some of the microbes have unique and for better understanding of rumen environ- also been recommended as feed additives for ment, identification and molecular characterization of improving the overall growth or production of microbes are highly essential. Moreover, the rumen ma- animals. Rumen bacteria which have potential nipulation by improving the digestibility of plant nutrient application in animal feed stuffs were isolated is a priority area for improving the growth or production and characterized in this experiment. -
Symbiosis of Plants, Animals, and Microbes
9 Symbiosis of Plants, Animals, and Microbes james Wells and Vincent Varel CONTENTS C- Introduction ..................................................................................................... ... .. .......................... 185 Life on Eruth ... ........... ... ............................. .. .. ................................................................................ 186 Parasitism and Pathogenicity .... ..... ................................................................................................ 186 ;:--- Insects and Parasitism with Plants and Animals ........................................................................ 187 -.-- Microbes and ParasitismlPathogenicity with Plants and Animals ............................................ 188 Plant Microbial Parasites and Pathogens ......................................... ..................................... 188 Animal Microbial Parasites and Pathogens .............. .. .................................... .... ... ............... 188 Animals and Microsporidia ............................................. .. ................................................... 189 Animals and Zoonotic Bacterial Pathogens ......................................................................... 189 Commensalism and Mutualism .............................. ........ ..... .. ................................................ .. ....... 189 Commensalism and Mutualism among Plants and Animals ....... : ............................................. 190 Microbes and Mutualism/Commensalism -
1768 Amino Acid Metabolism in Intestinal Bacteria
[Frontiers in Bioscience 16, 1768-1786, January 1, 2011] Amino acid metabolism in intestinal bacteria: links between gut ecology and host health Zhao-Lai Dai1, Guoyao Wu2, 3, Wei-Yun Zhu1 1Zhao-lai Dai, Wei-yun Zhu, Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, Nanjing 210095, China, 2 Guoyao Wu, Department of Animal Science, Texas A and M University, College Station, TX 77843, USA, 3State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, China TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Diversity and abundance of the AA-fermenting bacteria in the digestive tract 4. AA metabolism in gut bacteria 4.1. Incorporation of AA into bacterial cells 4.2. Biosynthesis of AA 4.3. Catabolism of AA and production of important metabolites 4.4. Compartmental AA metabolism in gut bacteria 4.5. Metabolic interactions among gut bacteria and host 5. Functional aspects of the AA metabolism in gut bacteria 5.1. Adaptation and survival 5.2. Production of important molecules 6. Dietary modulations of the AA metabolism in gut bacteria 6.1. High protein diet 6.2. Non-digestible carbohydrates and availability of carbon source 6.3. Probiotics and synbiotics 6.4. Phytochemicals 7. Conclusions and perspectives 8. Acknowledgements 9. References 1. ABSTRACT 2. INTRODUCTION Bacteria in the gastrointestinal (GI) tract play an The digestive tract of humans and animals is important role in the metabolism of dietary substances in colonized by dense and highly complex community of the gut and extraintestinal tissues. Amino acids (AA) microorganisms composed mainly bacteria, whose total should be taken into consideration in the development of number can exceed 1014 cells (1). -
Fenollaria Massiliensis Gen. Nov., Sp. Nov., a New Genus of Anaerobic Bacterium
Standards in Genomic Sciences (2014) 9:704-717 DOI:10.4056/sig s.3957647 Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium Isabelle Pagnier, Olivier Croce, Catherine Robert, Didier Raoult and Bernard La Scola Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de médecine, Aix-Marseille Université, France *Corresponding author: ([email protected]) Keywords: Fenollaria massiliensis, genome Fenollaria massiliensis strain 9401234T, is the type strain of Fenollaria massiliensis g en. nov., sp. nov., a new species within a new genus Fenollaria. This strain, whose genome is described here, was isolated from an osteoarticular sample. F. massil iensis strain 9401234T is an obligate anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the com- plete genome sequence and annotation. The 1.71 Mbp long genome exhibits a G+C content of 34.46% and contains 1,667 protein-coding and 30 RNA genes, including 3 rRNA genes. Introduction Fenollaria massiliensis strain 9401234T (= CSUR teristics support the circumscription of a novel P127 = DSM 26367), is the type strain of genus, Fenollaria gen. nov., within the Clostridiales Fenollaria massiliensis sp. nov., and the first mem- Family XI Incertae sedis, with Fenollaria ber of the new genus Fenollaria gen. nov. This bac- massiliensis gen. nov., sp. nov, as the type species. terium is a Gram-negative, anaerobic, non spore- Clostridiales Family XI Incertae sedis was created forming, indole positive bacillus that was isolated in 2009 [13], and currently comprises 11 genera, from an osteoarticular sample, during a study pro- including Anaerococcus, Peptoniphilus and specting anaerobic isolates from deep samples [1].