DOCSLIB.ORG

6S Bacterial Rrna Microbiome Analyses of the Lung Identifies a Unique Bacterial Species Associated with a Specific T-53 Mutation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
6S Bacterial Rrna Microbiome Analyses of the Lung Identifies a Unique Bacterial Species Associated with a Specific T-53 Mutation Species-specific 16S Bacterial rRNA Microbiome Analyses of the Lung Identifies a Unique Bacterial Species Associated with a Specific T-53 Mutation Garth D. Ehrlich, Ph.D., F.A.A.A.S Executive Director, Center for Genomic Sciences Executive Director, Center for Advanced Microbial Processing Professor of Microbiology and Immunology Drexel University College of Medicine Director, Meta-Omics Shared Resource Sidney Kimmel Cancer Center PacBio Users Group Meeting, St. Louis, MO, September 19, 2018. Thanks and acknowledgements The Lab Team The Bioinformatic Team Jarek Krol, PhD Azad Ahmed, MD Josh Earl, ABD Josh Mell, PhD Steven Lang, BS Bhaswati Sen, PhD Carol Hope, BS Archana Bhat, MS Rachael Ehrlich, MS Objectives of Pan-Domain Technology • Broad-based identification of Bacteria and Fungi – no a priori guessing of what to test for within these domains – No culture necessary • Mixed populations of microbes (polymicrobial assemblages) • Quantitative • High resolution genotyping • Identify emerging agents not previously seen • Costs effective, high throughput 16S Microbiome Analyses • Revolutionized community-based microbial studies – Revealed unprecedented levels of complexity • Natural systems - soils water • Organismal systems – Holobiont – Metazoans and their microbiota – Plants and their microbiota The Problem with NextGen Microbiome analyses Lack of specificity – good for global analyses of diversity • Short read-lengths – – Genus-level taxonomic characterization at best – Sometime only family level • High error rates – Single-pass sequencing make error correction very difficult – Vastly increases numbers of OTU’s The problem of false OTUs They create differences S1 0 error S1 w errors where there are none 400 OTUs 500 OTUs They amplify any real S2 0 error 0/400 100/500 differences 400 OTUs S2 w errors 100/500 200/600 500 OTUs S3 0 errors 200/500 300/600 400 OTUs S3 w errors 300/600 400/700 500 OTUs S1 and S2 are biological replicates S3 is different from S1 and S2 Current technical methods fail to provide the necessary taxonomic details to follow up associative studies How Circular Consensus Sequencing Works Multiple pass CCS Analysis Algorithm 1) Bin amplimers via barcodes 2) Filter out all amplimers that are not sequenced for ≥ 5 passes (circular sequencing), and do not have ≥ 90% PacBio quality scores 3) Filter out any reads aligning partially to the human genome 4) Remove all reads of > 1500bp (<1% of remaining reads) as likely chimerics 5) Remove all reads not having both forward and reverse primers, and trim primers 6) Correct for strandedness so that all reads are on the same strain 7) Remove any remaining reads which have > 10 expected errors calculated from PHRED scores (< 5% of remaining reads) 8) Use only reads with < 1expected error (so as to not inflate the number of OTU’s clusters formed at the level of 97% sequence identity 9) Use the OTU’s from (8) to map back all of the reads that passed filters 2-7 to provide the final counts for each taxon. Note with this approach essentially all of the surviving reads map back to one of the high-fidelity OTU’s Goals of Microbiome Data Processing • Minimize numbers of operational taxonomic units (OTUs) = species so as not to artificially inflate the diversity • This is critical for comparisons among specimens – for if each specimen has its own set of false OTUs it produces a greatly exaggerated picture of differences Expected Error vs. Average Error The Uclust pipeline recommends using the “Expected Error” Score rather than the average error: Q scores in read Avg. Q Expected number of errors 140 x Q35 + 10 x Q2 33 6.4 ! 150 x Q25 25 0.5 We can see that average quality is actually a poor representation of the probable number of errors in a sequence. Filtering • Phred Quality – Highest quality score in PacBio sequences is 42 where Quality is equal to -10*log10P, where P is equal to the proBaBility the Base is wrong. Our longest sequence was trimmed to 1500bp, therefore: – The *Best* expected error we can get is 10^(- 4.2)*1500 ~= 0.00946 (or about .01) Filtering applied to controls • Perfect (i.e. single OTU) clustering of positive controls happened only at an Expected Error (EE) level of one or less. • This suggests that we should filter to EE ≤ 1 for OTU clustering and classification, or expect that we will have spurious OTUs based on error profile, rather than true biological sequences BEI Mock Community (22 species) BEI Mock Community • Network of all BEI strain’s16s alignment Some results and graphs: BEI dataset Multiple expected error filtering and how it affects the number (and ‘correctness’) of the OTU’s Number of OTUs in BEI 500 472 450 400 350 300 250 210 200 150 NUMBER OF OTU'S NUMBER 80 100 50 65 19 19 19 19 20 22 25 36 50 0 0 0.01 0.25 0.5 0.75 1 2 3 4 5 6 7 8 9 10 EXPECTED ERROR BEI Mock Community • Initial Results – Able to resolve 19 out of 21 – No False Positives 100% species-level identity from mock community analysis Species %identity Streptococcus mutans UA159 100.00% Streptococcus agalactiae 2603V/R 100.00% Lactobacillus gasseri ATCC 33323 100.00% Enterococcus faecalis OG1RF 100.00% Actinomyces odontolyticus 100.00% Streptococcus pneumoniae TIGR4 99.90% Acinetobacter baumannii ATCC 17978 99.90% Neisseria meningitidis MC58 99.80% Listeria monocytogenes strain EGD 99.80% Bacillus cereus ATCC 10987 99.80% Staphylococcus epidermidis ATCC 12228 99.70% Rhodobacter sphaeroides 2.4.1 chromosome 1 99.70% Pseudomonas aeruginosa PAO1 99.70% Escherichia coli str. K-12 substr. MG1655 99.70% Clostridium beijerinckii NCIMB 8052 99.70% Propionibacterium acnes KPA171202 99.60% Helicobacter pylori 26695 99.40% Deinococcus radiodurans 99.20% Bacteroides vulgatus ATCC 8482 98.90% No species level confidence • Database had taxonomic classification up to species level • Command to assign taxonomy only gave confidences up to the genus level • We wanted the confidence values for the species levels as well • Spoof the database Shift taxonomy so Domain is now Phylum etc. • Command to assign taxonomy so program thinks of the species level as genus • Confidence of ‘g’ is actually species confidence Species-level confidence OTUId Genus genus_conf species species_con OTU_10;size=2442; ListeriA 0.987 ListeriA_monocytogenes 0.767 OTU_11;size=4118; BActeroidAceAe 0.9931 BActeroides_vulgAtus 0.9301 OTUId genus genus_conf species OTU_12;size=3798; StAphylococcus 0.9843 StAphylococcus_epidermidis 0.767 OTU_10;size=2442; ListeriA 0.978 ListeriA_monocytogenes OTU_13;size=597; RhodobActer 0.9684 RhodobActer_sphAeroides 0.6177 OTU_11;size=4118; BActeroidAceAe 0.9883 BActeroides_vulgAtus OTU_14;size=2281; ShigellA 0.7125 ShigellA_flexneri 0.4684 OTU_12;size=3798; StAphylococcus 0.9729 StAphylococcus_epidermidis OTU_15;size=417; PseudomonAs 0.9684 PseudomonAs_Aeruginosa 0.9128 OTU_13;size=597; RhodobActer 0.9678 RhodobActer_sphAeroides OTU_16;size=294; Deinococcus 0.9936 Deinococcus_rAdiodurAns 0.9301 OTU_14;size=2281; ShigellA 0.6849 ShigellA_flexneri OTU_15;size=417; PseudomonAs 0.9678 PseudomonAs_Aeruginosa OTU_17;size=238; Streptococcus 0.9887 Streptococcus_pneumoniAe 0.4684 OTU_16;size=294; Deinococcus 0.9891 Deinococcus_rAdiodurAns OTU_17;size=238; Streptococcus 0.9814 Streptococcus_pneumoniAe OTU_18;size=2227; Clostridium 0.9824 Clostridium_beijerinckii 0.319 OTU_18;size=2227; Clostridium 0.9746 Clostridium_beijerinckii OTU_19;size=101; Actinomyces 0.9878 Actinomyces_odontolyticus 0.9214 OTU_19;size=101; Actinomyces 0.9797 Actinomyces_odontolyticus OTU_1;size=5193; HelicobActerAceAe 0.9887 HelicobActer_pylori OTU_1;size=5193; HelicobActerAceAe 0.9934 HelicobActer_pylori 0.9128 OTU_2;size=2845; Streptococcus 0.9797 Streptococcus_AgAlActiAe OTU_3;size=2582; LActobAcillus 0.9879 LActobAcillus_gAsseri OTU_2;size=2845; Streptococcus 0.9878 Streptococcus_AgAlActiAe 0.9387 OTU_4;size=2658; NeisseriA 0.9678 NeisseriA_meningitidis OTU_3;size=2582; LActobAcillus 0.9922 LActobAcillus_gAsseri 0.767 OTU_5;size=1755; PropionibActerium 0.9865 PropionibActerium_Acnes OTU_6;size=1983; Streptococcus 0.9865 Streptococcus_mutAns OTU_4;size=2658; NeisseriA 0.9684 NeisseriA_meningitidis 0.9128 OTU_7;size=1812; AcinetobActer 0.9695 AcinetobActer_bAumAnnii OTU_8;size=1901; BAcillus 0.9746 BAcillus_AnthrAcis OTU_5;size=1755; PropionibActerium 0.9913 PropionibActerium_Acnes 0.956 OTU_9;size=886; Enterococcus 0.9712 Enterococcus_fAecalis OTU_6;size=1983; Streptococcus 0.9913 Streptococcus_mutAns 0.9474 OTU_7;size=1812; AcinetobActer 0.9824 AcinetobActer_bAumAnnii 0.9214 OTU_8;size=1901; BAcillus 0.9852 BAcillus_AnthrAcis 0.4684 OTU_9;size=886; Enterococcus 0.9835 Enterococcus_fAecalis 0.9214 CAMI Mock Community Sequencing OTU • 250 OTU found (232 mapped to unique species) out of 243 unique NCBI OTU (Or, How Did We Do?) – 6.9% (16/232) LabeLLed with incorrect species name (after correcting with reference OTU*) – 93.1% (216/232) Correct identification of OTU to species LeveL – 88.9% (216/243) Correct identification and classification to species LeveL out of entire expected OTU number in community – 2.2% (5/232) instances of the incorrect genus (onLy 2 of which had more than a singLe read mapping to it) – 93.4% (227/243) Correct identification and classification to genus LeveL of entire community – 66 correct unique Species identified from OTU pipeLine not present in predicted reference sequences – 27 missing/incorrect*16s genes predicted from species, genome assembLies 16 weremissing/incorrect assigned taxonomy from the generaNCBI. OTU Instances where a predicted 16s gene’s taxonomy matched the taxonomic assignment
Load more

Recommended publications
  • Bacterial Ecology of Abattoir Wastewater Treated by an Anaerobic
    Bacterial ecology of abattoir wastewater treated by an anaerobic digestor Linda Jabari, Hana Gannoun, Eltaief Khelifi, Jean-Luc Cayol, Jean-Jacques Godon, Moktar Hamdi, Marie-Laure Fardeau To cite this version: Linda Jabari, Hana Gannoun, Eltaief Khelifi, Jean-Luc Cayol, Jean-Jacques Godon, et al.. Bacterial ecology of abattoir wastewater treated by an anaerobic digestor. Brazilian Journal of Microbiology, Sociedade Brasileira de Microbiologia, 2016, 47 (1), pp.73-84. 10.1016/j.bjm.2015.11.029. hal- 02633155 HAL Id: hal-02633155 https://hal.inrae.fr/hal-02633155 Submitted on 27 May 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. 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.
    [Show full text]
  • A Metagenomic Β-Glucuronidase Uncovers a Core Adaptive Function of the Human Intestinal Microbiome
    A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome Karine Gloux, Olivier Berteau, Hanane El oumami, Fabienne Béguet, Marion Leclerc, and Joël Doré1 Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1319 Micalis, F-78352 Jouy en Josas, France Edited by Todd R. Klaenhammer, North Carolina State University, Raleigh, NC, and approved June 1, 2010 (received for review February 4, 2010) In the human gastrointestinal tract, bacterial β-D-glucuronidases (BG; XIVa), major reservoirs of BG-positive bacteria (11), are dys- E.C. 3.2.1.31) are involved both in xenobiotic metabolism and in some biosis markers in Crohn’s disease (12–15) and in intestinal carci- of the beneficial effects of dietary compounds. Despite their biolog- nogenesis (16). Nevertheless, the relative contribution of bacterial ical significance, investigations are hampered by the fact that only strains to the global intestinal BG activity remains unclear, and a few BGs have so far been studied. A functional metagenomic the molecular bases are essentially unknown. approach was therefore performed on intestinal metagenomic In the human digestive tract, bacterial BGs are known to be libraries using chromogenic glucuronides as probes. Using this strat- distributed among the Enterobacteriaceae family in some Firmi- egy, 19 positive metagenomic clones were identified but only one cutes genera (Lactobacillus, Streptococcus, Clostridium, Rumino- exhibited strong β-D-glucuronidase activity when subcloned into an coccus, Roseburia, and Faecalibacterium) and in a specific species expression vector. The cloned gene encoded a β-D-glucuronidase of Actinobacteria (Bifidobacterium dentium) (11, 17, 18). On (called H11G11-BG) that had distant amino acid sequence homolo- the basis of their sequence, BGs are highly homologous to gies and an additional C terminus domain compared with known β-galactosidases and only a few of them have been investigated β fi -D-glucuronidases.
    [Show full text]
  • UCC Library and UCC Researchers Have Made This Item Openly Available
    UCC Library and UCC researchers have made this item openly available. Please let us know how this has helped you. Thanks! Title Dairybiota: analysing the microbiota of the dairy chain using next generation sequencing Author(s) Doyle, Conor J. Publication date 2017 Original citation Doyle, C. 2017. Dairybiota: analysing the microbiota of the dairy chain using next generation sequencing. PhD Thesis, University College Cork. Type of publication Doctoral thesis Rights © 2017, Conor Doyle. http://creativecommons.org/licenses/by-nc-nd/3.0/ Embargo information No embargo required Item downloaded http://hdl.handle.net/10468/5524 from Downloaded on 2021-10-09T03:33:35Z Dairybiota: analysing the microbiota of the dairy chain using next generation sequencing A thesis presented to the National University of Ireland for the degree of Doctor of Philosophy By Conor Doyle B.Sc Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland 2017 Research supervisors: Dr. Paul Cotter and Professor Paul O’Toole i “And all this science, I don’t understand. It’s just my job five days a week” Rocket man “No number of sightings of white swans can prove the theory that all swans are white. The sighting of just one black one may disprove it.” Karl Popper ii Table of Contents Declaration .........................................................................................................................................x Abstract ..............................................................................................................................................xi
    [Show full text]
  • Germinants and Their Receptors in Clostridia
    JB Accepted Manuscript Posted Online 18 July 2016 J. Bacteriol. doi:10.1128/JB.00405-16 Copyright © 2016, American Society for Microbiology. All Rights Reserved. 1 Germinants and their receptors in clostridia 2 Disha Bhattacharjee*, Kathleen N. McAllister* and Joseph A. Sorg1 3 4 Downloaded from 5 Department of Biology, Texas A&M University, College Station, TX 77843 6 7 Running Title: Germination in Clostridia http://jb.asm.org/ 8 9 *These authors contributed equally to this work 10 1Corresponding Author on September 12, 2018 by guest 11 ph: 979-845-6299 12 email: [email protected] 13 14 Abstract 15 Many anaerobic, spore-forming clostridial species are pathogenic and some are industrially 16 useful. Though many are strict anaerobes, the bacteria persist in aerobic and growth-limiting 17 conditions as multilayered, metabolically dormant spores. For many pathogens, the spore-form is Downloaded from 18 what most commonly transmits the organism between hosts. After the spores are introduced into 19 the host, certain proteins (germinant receptors) recognize specific signals (germinants), inducing 20 spores to germinate and subsequently outgrow into metabolically active cells. Upon germination 21 of the spore into the metabolically-active vegetative form, the resulting bacteria can colonize the 22 host and cause disease due to the secretion of toxins from the cell. Spores are resistant to many http://jb.asm.org/ 23 environmental stressors, which make them challenging to remove from clinical environments. 24 Identifying the conditions and the mechanisms of germination in toxin-producing species could 25 help develop affordable remedies for some infections by inhibiting germination of the spore on September 12, 2018 by guest 26 form.
    [Show full text]
  • Wo 2010/096550 A2
    (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 26 August 2010 (26.08.2010) WO 2010/096550 A2 (51) International Patent Classification: (74) Agents: SALIWANCHIK, David, R. et al; Saliwanchik, C12N 1/20 (2006.01) A61K 35/74 (2006.01) Lloyd & Saliwanchik, P.O. Box 142950, Gainesville, FL A23C 9/123 (2006.01) C12R 1/225 (2006.01) 32614-2950 (US). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/US2010/024575 kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, (22) International Filing Date: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, 18 February 2010 (18.02.2010) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (25) Filing Language: English HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, (26) Publication Language: English ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (30) Priority Data: NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, 61/153,5 16 18 February 2009 (18.02.2009) US SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 61/297,480 22 January 2010 (22.01 .2010) US TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (71) Applicant (for all designated States except US): UNI¬ (84) Designated States (unless otherwise indicated, for every VERSITY OF FLORIDA RESEARCH FOUNDA¬ kind of regional protection available): ARIPO (BW, GH, TION, INC.
    [Show full text]
  • Characterization of Antibiotic Resistance Genes in the Species of the Rumen Microbiota
    ARTICLE https://doi.org/10.1038/s41467-019-13118-0 OPEN Characterization of antibiotic resistance genes in the species of the rumen microbiota Yasmin Neves Vieira Sabino1, Mateus Ferreira Santana1, Linda Boniface Oyama2, Fernanda Godoy Santos2, Ana Júlia Silva Moreira1, Sharon Ann Huws2* & Hilário Cuquetto Mantovani 1* Infections caused by multidrug resistant bacteria represent a therapeutic challenge both in clinical settings and in livestock production, but the prevalence of antibiotic resistance genes 1234567890():,; among the species of bacteria that colonize the gastrointestinal tract of ruminants is not well characterized. Here, we investigate the resistome of 435 ruminal microbial genomes in silico and confirm representative phenotypes in vitro. We find a high abundance of genes encoding tetracycline resistance and evidence that the tet(W) gene is under positive selective pres- sure. Our findings reveal that tet(W) is located in a novel integrative and conjugative element in several ruminal bacterial genomes. Analyses of rumen microbial metatranscriptomes confirm the expression of the most abundant antibiotic resistance genes. Our data provide insight into antibiotic resistange gene profiles of the main species of ruminal bacteria and reveal the potential role of mobile genetic elements in shaping the resistome of the rumen microbiome, with implications for human and animal health. 1 Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. 2 Institute for Global Food Security, School of Biological
    [Show full text]
  • ( 12 ) United States Patent
    US009956282B2 (12 ) United States Patent ( 10 ) Patent No. : US 9 ,956 , 282 B2 Cook et al. (45 ) Date of Patent: May 1 , 2018 ( 54 ) BACTERIAL COMPOSITIONS AND (58 ) Field of Classification Search METHODS OF USE THEREOF FOR None TREATMENT OF IMMUNE SYSTEM See application file for complete search history . DISORDERS ( 56 ) References Cited (71 ) Applicant : Seres Therapeutics , Inc. , Cambridge , U . S . PATENT DOCUMENTS MA (US ) 3 ,009 , 864 A 11 / 1961 Gordon - Aldterton et al . 3 , 228 , 838 A 1 / 1966 Rinfret (72 ) Inventors : David N . Cook , Brooklyn , NY (US ) ; 3 ,608 ,030 A 11/ 1971 Grant David Arthur Berry , Brookline, MA 4 ,077 , 227 A 3 / 1978 Larson 4 ,205 , 132 A 5 / 1980 Sandine (US ) ; Geoffrey von Maltzahn , Boston , 4 ,655 , 047 A 4 / 1987 Temple MA (US ) ; Matthew R . Henn , 4 ,689 ,226 A 8 / 1987 Nurmi Somerville , MA (US ) ; Han Zhang , 4 ,839 , 281 A 6 / 1989 Gorbach et al. Oakton , VA (US ); Brian Goodman , 5 , 196 , 205 A 3 / 1993 Borody 5 , 425 , 951 A 6 / 1995 Goodrich Boston , MA (US ) 5 ,436 , 002 A 7 / 1995 Payne 5 ,443 , 826 A 8 / 1995 Borody ( 73 ) Assignee : Seres Therapeutics , Inc. , Cambridge , 5 ,599 ,795 A 2 / 1997 McCann 5 . 648 , 206 A 7 / 1997 Goodrich MA (US ) 5 , 951 , 977 A 9 / 1999 Nisbet et al. 5 , 965 , 128 A 10 / 1999 Doyle et al. ( * ) Notice : Subject to any disclaimer , the term of this 6 ,589 , 771 B1 7 /2003 Marshall patent is extended or adjusted under 35 6 , 645 , 530 B1 . 11 /2003 Borody U .
    [Show full text]
  • Molecular Characterization of Bacterial Populations of Different Soils
    Brazilian Journal of Microbiology (2006) 37:439-447 ISSN 1517-8382 MOLECULAR CHARACTERIZATION OF BACTERIAL POPULATIONS OF DIFFERENT SOILS Rodrigo Matheus Pereira; Érico Leandro da Silveira; Denilson César Scaquitto; Eliamar Aparecida Nascimbém Pedrinho; Silvana Pompéia Val-Moraes; Ester Wickert; Lúcia Maria Carareto-Alves; Eliana Gertrudes de Macedo Lemos* Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal (SP), Brazil Submitted: January 01, 2006; Returned to authors for corrections: April 17, 2006; Approved: October 13, 2006 ABSTRACT Until recently, few studies were carried out in Brazil about diversity of bacterial soil communities. Aiming to characterize the bacterial population in the soil through 16S rRNA analysis, two types of soil have been analyzed: one of them characterized by intensive use where tomato, beans and corn were cultivated (CS); the other analyzed soil was under forest (FS), unchanged by man; both located in Guaíra, São Paulo State, Brazil. Using specific primers, 16S rRNA genes from metagenomic DNA in both soils were amplified by PCR, amplicons were cloned and 139 clones from two libraries were partially sequenced. The use of 16S rRNA analysis allowed identification of several bacterial populations in the soil belonging to the following phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria Verrucomicrobia in addition to the others that were not classified, beyond Archaea domain. Differences between FS and CS libraries were observed in size phyla. A larger number of phyla and, consequently, a greater bacterial diversity were found in the under-forest soil. These data were confirmed by the analyses of genetic diversity that have been carried out. The characterization of bacterial communities of soil has made its contribution by providing facts for further studies on the dynamics of bacterial populations in different soil conditions in Brazil.
    [Show full text]
  • WO 2014/135633 Al 12 September 2014 (12.09.2014) P O P C T
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2014/135633 Al 12 September 2014 (12.09.2014) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12N 9/04 (2006.01) C12P 7/16 (2006.01) kind of national protection available): AE, AG, AL, AM, C12N 9/88 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (21) Number: International Application DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/EP2014/054334 HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (22) International Filing Date: KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 6 March 2014 (06.03.2014) 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, (25) Filing Language: English SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, (26) Publication Language: English TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 13 158012.8 6 March 2013 (06.03.2013) EP (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (71) Applicants: CLARIANT PRODUKTE (DEUTSCH- GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, LAND) GMBH [DE/DE]; Briiningstrasse 50, 65929 UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, Frankfurt am Main (DE).
    [Show full text]
  • Outline Release 7 7C
    Garrity, et. al., March 6, 2007 Taxonomic Outline of the Bacteria and Archaea, Release 7.7 March 6, 2007. Part 7 – The Bacteria: Phylum “Firmicutes”: Class “Clostridia” George M. Garrity, Timothy G. Lilburn, James R. Cole, Scott H. Harrison, Jean Euzéby, and Brian J. Tindall F Phylum Firmicutes AL N4Lid DOI: 10.1601/nm.3874 Class "Clostridia" N4Lid DOI: 10.1601/nm.3875 71 Order Clostridiales AL Prévot 1953. N4Lid DOI: 10.1601/nm.3876 Family Clostridiaceae AL Pribram 1933. N4Lid DOI: 10.1601/nm.3877 Genus Clostridium AL Prazmowski 1880. GOLD ID: Gi00163. GCAT ID: 000971_GCAT. Entrez genome id: 80. Sequenced strain: BC1 is from a non-type strain. Genome sequencing is incomplete. Number of genomes of this species sequenced 6 (GOLD) 6 (NCBI). N4Lid DOI: 10.1601/nm.3878 Clostridium butyricum AL Prazmowski 1880. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 19398. High-quality 16S rRNA sequence S000436450 (RDP), M59085 (Genbank). N4Lid DOI: 10.1601/nm.3879 Clostridium aceticum VP (ex Wieringa 1940) Gottschalk and Braun 1981. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 35044. High-quality 16S rRNA sequence S000016027 (RDP), Y18183 (Genbank). N4Lid DOI: 10.1601/nm.3881 Clostridium acetireducens VP Örlygsson et al. 1996. Source of type material recommended for DOE sponsored genome sequencing by the JGI: DSM 10703. High-quality 16S rRNA sequence S000004716 (RDP), X79862 (Genbank). N4Lid DOI: 10.1601/nm.3882 Clostridium acetobutylicum AL McCoy et al. 1926. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 824.
    [Show full text]
  • Depression and Microbiome—Study on the Relation and Contiguity Between Dogs and Humans
    applied sciences Article Depression and Microbiome—Study on the Relation and Contiguity between Dogs and Humans Elisabetta Mondo 1,*, Alessandra De Cesare 1, Gerardo Manfreda 2, Claudia Sala 3 , Giuseppe Cascio 1, Pier Attilio Accorsi 1, Giovanna Marliani 1 and Massimo Cocchi 1 1 Department of Veterinary Medical Science, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, Italy; [email protected] (A.D.C.); [email protected] (G.C.); [email protected] (P.A.A.); [email protected] (G.M.); [email protected] (M.C.) 2 Department of Agricultural and Food Sciences, University of Bologna, Via del Florio 2, 40064 Ozzano Emilia, Italy; [email protected] 3 Department of Physics and Astronomy, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-051-209-7329 Received: 22 November 2019; Accepted: 7 January 2020; Published: 13 January 2020 Abstract: Behavioral studies demonstrate that not only humans, but all other animals including dogs, can suffer from depression. A quantitative molecular evaluation of fatty acids in human and animal platelets has already evidenced similarities between people suffering from depression and German Shepherds, suggesting that domestication has led dogs to be similar to humans. In order to verify whether humans and dogs suffering from similar pathologies also share similar microorganisms at the intestinal level, in this study the gut-microbiota composition of 12 German Shepherds was compared to that of 15 dogs belonging to mixed breeds which do not suffer from depression. Moreover, the relation between the microbiota of the German Shepherd’s group and that of patients with depression has been investigated.
    [Show full text]
  • Updates on the Sporulation Process in Clostridium Species
    Updates on the sporulation process in Clostridium species Talukdar, P. K., Olguín-Araneda, V., Alnoman, M., Paredes-Sabja, D., & Sarker, M. R. (2015). Updates on the sporulation process in Clostridium species. Research in Microbiology, 166(4), 225-235. doi:10.1016/j.resmic.2014.12.001 10.1016/j.resmic.2014.12.001 Elsevier Accepted Manuscript http://cdss.library.oregonstate.edu/sa-termsofuse *Manuscript 1 Review article for publication in special issue: Genetics of toxigenic Clostridia 2 3 Updates on the sporulation process in Clostridium species 4 5 Prabhat K. Talukdar1, 2, Valeria Olguín-Araneda3, Maryam Alnoman1, 2, Daniel Paredes-Sabja1, 3, 6 Mahfuzur R. Sarker1, 2. 7 8 1Department of Biomedical Sciences, College of Veterinary Medicine and 2Department of 9 Microbiology, College of Science, Oregon State University, Corvallis, OR. U.S.A; 3Laboratorio 10 de Mecanismos de Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de 11 Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile. 12 13 14 Running Title: Clostridium spore formation. 15 16 17 Key Words: Clostridium, spores, sporulation, Spo0A, sigma factors 18 19 20 Corresponding author: Dr. Mahfuzur Sarker, Department of Biomedical Sciences, College of 21 Veterinary Medicine, Oregon State University, 216 Dryden Hall, Corvallis, OR 97331. Tel: 541- 22 737-6918; Fax: 541-737-2730; e-mail: [email protected] 23 1 24 25 Abstract 26 Sporulation is an important strategy for certain bacterial species within the phylum Firmicutes to 27 survive longer periods of time in adverse conditions. All spore-forming bacteria have two phases 28 in their life; the vegetative form, where they can maintain all metabolic activities and replicate to 29 increase numbers, and the spore form, where no metabolic activities exist.
    [Show full text]