DOCSLIB.ORG

Supplementary Data TMAO Microbiome R1

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplementary Data TMAO Microbiome R1 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Gut Content for Supplementary Data Tables Tables Page Annotation guide for taxonomic features. 1 Supplementary Data 1a. Microbial associations with TMAO, and intakes 7 of choline and red meat. Supplementary Data 1b. Microbial associations with TMAO in 8 15 sensitivity analysis models. Supplementary Data 2a. Associations of intakes of choline and red meat, 21 or other TMAO precursors with TMAO levels, stratified by TMAO- associated abundant species, in full models and additionally adjusted for other TMAO precursors or TMAO predicting species. Supplementary Data 2b. Associations of intakes of choline and red meat, 34 or other TMAO precursors with TMAO levels, stratified by TMAO- producer status, additionally adjusted for other TMAO precursors. Supplementary Data 2c. Associations of intakes of choline and red meat, 37 or other TMAO precursors with TMAO levels, stratified by TMAO- producer status, in 6 different sensitivity analysis models. Supplementary Data 2d. Associations of intakes of red meat with HDLC 39 and HBA1c levels, stratified by TMAO-producer status or TMAO- associated abundant species. Supplementary Data 3a. Association of DNA gene clusters within 40 TMAO-associated species with plasma TMAO levels, and intakes of choline and red meat. Supplementary Data 3b. Association of transcriptions of gene clusters 46 (RNA/DNA ratio) within TMAO-associated species with plasma TMAO levels, and intakes of choline and red meat. Supplementary Data 4a. Association of DNA enzyme within TMAO- 62 associated species with plasma TMAO levels, and intakes of choline and red meat. Supplementary Data 4b. Association of transcriptions of enzymes 64 (RNA/DNA ratio) within TMAO-associated species with plasma TMAO levels, and intakes of choline and red meat. Supplementary Data 5a. Association of functional pathways 75 (metagenomics) within TMAO-associated species with plasma TMAO levels, and intakes of choline and red meat. Supplementary Data 5b. Association of transcriptions of pathways 77 (RNA/DNA ratio) within TMAO-associated species with plasma TMAO levels, and intakes of choline and red meat. Li J, et al. Gut 2021;0:1–10. doi: 10.1136/gutjnl-2020-322473 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Gut Annotation Annotation guide for taxonomic features. Taxonomic label Taxonomic type Kingdom Phylum Class Order Family Genus Species Strain gcf_000173975 strain bacteria firmicutes clostridia clostridiales eubacteriaceae eubacterium eubacterium_hallii gcf_000173975 eubacterium_hallii species bacteria firmicutes clostridia clostridiales eubacteriaceae eubacterium eubacterium_hallii gcf_000210575 strain bacteria bacteroidetes bacteroidia bacteroidales rikenellaceae alistipes alistipes_shahii gcf_000210575 alistipes_shahii species bacteria bacteroidetes bacteroidia bacteroidales rikenellaceae alistipes alistipes_shahii eggerthella_unclassified species bacteria actinobacteria actinobacteria coriobacteriales coriobacteriaceae eggerthella eggerthella_unclassified clostridium_clostridioforme species bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_clostridioforme gcf_000225345 strain bacteria firmicutes clostridia clostridiales lachnospiraceae roseburia roseburia_hominis gcf_000225345 roseburia_hominis species bacteria firmicutes clostridia clostridiales lachnospiraceae roseburia roseburia_hominis gcf_000155435 strain bacteria firmicutes clostridia clostridiales clostridiales_noname clostridiales_noname clostridiales_bacterium_1_7_47faa gcf_000155435 clostridiales_bacterium_1_7_47faa species bacteria firmicutes clostridia clostridiales clostridiales_noname clostridiales_noname clostridiales_bacterium_1_7_47faa gcf_000233455 strain bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_citroniae gcf_000233455 clostridium_citroniae species bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_citroniae gcf_000242195 strain bacteria firmicutes erysipelotrichia erysipelotrichales erysipelotrichaceae erysipelotrichaceae_noname erysipelotrichaceae_bacterium_21_3 gcf_000242195 erysipelotrichaceae_bacterium_21_3 species bacteria firmicutes erysipelotrichia erysipelotrichales erysipelotrichaceae erysipelotrichaceae_noname erysipelotrichaceae_bacterium_21_3 gcf_000156035 strain bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_nexile gcf_000156035 clostridium_nexile species bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_nexile sutterellaceae_unclassified genus bacteria proteobacteria betaproteobacteria burkholderiales sutterellaceae sutterellaceae_unclassified gcf_000156655 strain bacteria firmicutes erysipelotrichia erysipelotrichales erysipelotrichaceae erysipelotrichaceae_noname eubacterium_biforme gcf_000156655 eubacterium_biforme species bacteria firmicutes erysipelotrichia erysipelotrichales erysipelotrichaceae erysipelotrichaceae_noname eubacterium_biforme clostridium_clostridioforme_unclassified strain bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_clostridioforme clostridium_clostridioforme_unclassified eggerthella genus bacteria actinobacteria actinobacteria coriobacteriales coriobacteriaceae eggerthella burkholderiales order bacteria proteobacteria betaproteobacteria burkholderiales gcf_000166035 strain bacteria firmicutes clostridia clostridiales ruminococcaceae faecalibacterium faecalibacterium_prausnitzii gcf_000166035 betaproteobacteria class bacteria proteobacteria betaproteobacteria sutterellaceae family bacteria proteobacteria betaproteobacteria burkholderiales sutterellaceae clostridium_hathewayi species bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_hathewayi bacteroides_uniformis species bacteria bacteroidetes bacteroidia bacteroidales bacteroidaceae bacteroides bacteroides_uniformis gcf_000158075 strain bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_asparagiforme gcf_000158075 clostridium_asparagiforme species bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_asparagiforme gcf_000218405 strain bacteria firmicutes clostridia clostridiales lachnospiraceae lachnospiraceae_noname lachnospiraceae_bacterium_3_1_57faa_ct1 gcf_000218405 lachnospiraceae_bacterium_3_1_57faa_ct1 species bacteria firmicutes clostridia clostridiales lachnospiraceae lachnospiraceae_noname lachnospiraceae_bacterium_3_1_57faa_ct1 clostridium_hathewayi_unclassified strain bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_hathewayi clostridium_hathewayi_unclassified clostridium_symbiosum_unclassified strain bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_symbiosum clostridium_symbiosum_unclassified clostridium_symbiosum species bacteria firmicutes clostridia clostridiales clostridiaceae clostridium clostridium_symbiosum gcf_000172175 strain bacteria bacteroidetes bacteroidia bacteroidales bacteroidaceae bacteroides bacteroides_intestinalis gcf_000172175 bacteroides_intestinalis species bacteria bacteroidetes bacteroidia bacteroidales bacteroidaceae bacteroides bacteroides_intestinalis clostridiales_noname genus bacteria firmicutes clostridia clostridiales clostridiales_noname clostridiales_noname lactococcus_lactis_unclassified strain bacteria firmicutes bacilli lactobacillales streptococcaceae lactococcus lactococcus_lactis lactococcus_lactis_unclassified lactococcus_lactis species bacteria firmicutes bacilli lactobacillales streptococcaceae lactococcus lactococcus_lactis lactococcus genus bacteria firmicutes bacilli lactobacillales streptococcaceae lactococcus bacteroides_uniformis_unclassified strain bacteria bacteroidetes bacteroidia bacteroidales bacteroidaceae bacteroides bacteroides_uniformis bacteroides_uniformis_unclassified dorea_formicigenerans_unclassified strain bacteria firmicutes clostridia clostridiales lachnospiraceae dorea dorea_formicigenerans dorea_formicigenerans_unclassified dorea_formicigenerans species bacteria firmicutes clostridia clostridiales lachnospiraceae dorea dorea_formicigenerans bacteroides_vulgatus_unclassified strain bacteria bacteroidetes bacteroidia bacteroidales bacteroidaceae bacteroides bacteroides_vulgatus bacteroides_vulgatus_unclassified clostridiaceae family bacteria firmicutes clostridia clostridiales clostridiaceae clostridium genus bacteria firmicutes clostridia clostridiales clostridiaceae clostridium gcf_000188175 strain bacteria firmicutes negativicutes selenomonadales acidaminococcaceae phascolarctobacterium phascolarctobacterium_succinatutens gcf_000188175 phascolarctobacterium_succinatutens species bacteria firmicutes negativicutes selenomonadales acidaminococcaceae phascolarctobacterium phascolarctobacterium_succinatutens phascolarctobacterium genus bacteria firmicutes negativicutes selenomonadales acidaminococcaceae phascolarctobacterium anaerostipes genus bacteria firmicutes clostridia clostridiales lachnospiraceae anaerostipes parabacteroides_goldsteinii_unclassified strain bacteria bacteroidetes bacteroidia bacteroidales porphyromonadaceae parabacteroides parabacteroides_goldsteinii
Load more

Recommended publications
  • The World of Cyclic Dinucleotides in Bacterial Behavior
    molecules Review The World of Cyclic Dinucleotides in Bacterial Behavior Aline Dias da Purificação, Nathalia Marins de Azevedo, Gabriel Guarany de Araujo , Robson Francisco de Souza and Cristiane Rodrigues Guzzo * Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 01000-000, Brazil * Correspondence: [email protected] or [email protected]; Tel.: +55-11-3091-7298 Received: 27 December 2019; Accepted: 17 March 2020; Published: 25 May 2020 Abstract: The regulation of multiple bacterial phenotypes was found to depend on different cyclic dinucleotides (CDNs) that constitute intracellular signaling second messenger systems. Most notably, c-di-GMP, along with proteins related to its synthesis, sensing, and degradation, was identified as playing a central role in the switching from biofilm to planktonic modes of growth. Recently, this research topic has been under expansion, with the discoveries of new CDNs, novel classes of CDN receptors, and the numerous functions regulated by these molecules. In this review, we comprehensively describe the three main bacterial enzymes involved in the synthesis of c-di-GMP, c-di-AMP, and cGAMP focusing on description of their three-dimensional structures and their structural similarities with other protein families, as well as the essential residues for catalysis. The diversity of CDN receptors is described in detail along with the residues important for the interaction with the ligand. Interestingly, genomic data strongly suggest that there is a tendency for bacterial cells to use both c-di-AMP and c-di-GMP signaling networks simultaneously, raising the question of whether there is crosstalk between different signaling systems. In summary, the large amount of sequence and structural data available allows a broad view of the complexity and the importance of these CDNs in the regulation of different bacterial behaviors.
    [Show full text]
  • Microbial Community Structure Dynamics in Ohio River Sediments During Reductive Dechlorination of Pcbs
    University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS Andres Enrique Nunez University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Nunez, Andres Enrique, "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS" (2008). University of Kentucky Doctoral Dissertations. 679. https://uknowledge.uky.edu/gradschool_diss/679 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Andres Enrique Nunez The Graduate School University of Kentucky 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Andres Enrique Nunez Director: Dr. Elisa M. D’Angelo Lexington, KY 2008 Copyright © Andres Enrique Nunez 2008 ABSTRACT OF DISSERTATION MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon.
    [Show full text]
  • Curr.Opin.Chem. Biol., 15, 587-594
    Available online at www.sciencedirect.com Bacterial replicases and related polymerases Charles S McHenry Bacterial replicases are complex, tripartite replicative replication that are conserved among all life forms are machines. They contain a polymerase, Pol III, a b2 processivity illustrated in Figure 1. factor and a DnaX complex ATPase that loads b2 onto DNA and chaperones Pol III onto the newly loaded b2. Many Structure and function of a, the catalytic bacteria encode both a full length t and a shorter g form of subunit DnaX by a variety of mechanisms. The polymerase catalytic Like all polymerases, Pol III a contains palm, thumb and subunit of Pol III, a, contains a PHP domain that not only binds fingers domains, in the shape of a cupped right hand 2+ to prototypical e Mg -dependent exonuclease, but also Figure 2. However, apo-enzyme structures of the full 2+ contains a second Zn -dependent proofreading length Thermus aquaticus (Taq) and a truncated version of exonuclease, at least in some bacteria. Replication of the E. coli (Eco) a subunit revealed a big surprise: the palm chromosomes of low GC Gram-positive bacteria require two domain has the basic fold of the X family of DNA Pol IIIs, one of which, DnaE, appears to extend RNA primers a polymerases, which includes the slow, non-processive only short distance before handing the product off to the major Pol bs [1 ,2 ]. replicase, PolC. Other bacteria encode a second Pol III (ImuC) that apparently replaces Pol V, required for induced A ternary complex of a dideoxy-terminated primer-tem- mutagenesis in E.
    [Show full text]
  • Two-Step Synthesis and Hydrolysis of Cyclic Di-AMP in Mycobacterium Tuberculosis
    Two-Step Synthesis and Hydrolysis of Cyclic di-AMP in Mycobacterium tuberculosis Kasi Manikandan1, Varatharajan Sabareesh2¤, Nirpendra Singh3, Kashyap Saigal1, Undine Mechold4, Krishna Murari Sinha1* 1 Institute of Molecular Medicine, New Delhi, India, 2 Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology, Delhi and IGIB Extension Centre (Naraina), New Delhi, India, 3 Central Instrument Facility, University of Delhi South Campus, New Delhi, India, 4 Institut Pasteur, CNRS UMR 3528, Unite´ de Biochimie des Interactions macromole´culaires, Paris, France Abstract Cyclic di-AMP is a recently discovered signaling molecule which regulates various aspects of bacterial physiology and virulence. Here we report the characterization of c-di-AMP synthesizing and hydrolyzing proteins from Mycobacterium tuberculosis. Recombinant Rv3586 (MtbDisA) can synthesize c-di-AMP from ATP through the diadenylate cyclase activity. Detailed biochemical characterization of the protein revealed that the diadenylate cyclase (DAC) activity is allosterically regulated by ATP. We have identified the intermediates of the DAC reaction and propose a two-step synthesis of c-di-AMP from ATP/ADP. MtbDisA also possesses ATPase activity which is suppressed in the presence of the DAC activity. Investigations by liquid chromatography -electrospray ionization mass spectrometry have detected multimeric forms of c- di-AMP which have implications for the regulation of c-di-AMP cellular concentration and various pathways regulated by the dinucleotide. We have identified Rv2837c (MtbPDE) to have c-di-AMP specific phosphodiesterase activity. It hydrolyzes c-di- AMP to 59-AMP in two steps. First, it linearizes c-di-AMP into pApA which is further hydrolyzed to 59-AMP.
    [Show full text]
  • Development of a Phage Display Library for Discovery of Antigenic Brucella Peptides Jeffrey Williams Iowa State University
    Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2018 Development of a phage display library for discovery of antigenic Brucella peptides Jeffrey Williams Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Microbiology Commons Recommended Citation Williams, Jeffrey, "Development of a phage display library for discovery of antigenic Brucella peptides" (2018). Graduate Theses and Dissertations. 16896. https://lib.dr.iastate.edu/etd/16896 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]. Development of a phage display library for discovery of antigenic Brucella peptides by Jeffrey Williams A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Microbiology Program of Study Committee: Bryan H. Bellaire, Major Professor Steven Olsen Steven Carlson The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this thesis. The Graduate College will ensure this thesis is globally accessible and will not permit alterations after a degree is conferred. Iowa State University
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]
  • Characterization of the Scavenger Cell Proteome in Mouse and Rat Liver
    Biol. Chem. 2021; 402(9): 1073–1085 Martha Paluschinski, Cheng Jun Jin, Natalia Qvartskhava, Boris Görg, Marianne Wammers, Judith Lang, Karl Lang, Gereon Poschmann, Kai Stühler and Dieter Häussinger* Characterization of the scavenger cell proteome in mouse and rat liver + https://doi.org/10.1515/hsz-2021-0123 The data suggest that the population of perivenous GS Received January 25, 2021; accepted July 4, 2021; scavenger cells is heterogeneous and not uniform as previ- published online July 30, 2021 ously suggested which may reflect a functional heterogeneity, possibly relevant for liver regeneration. Abstract: The structural-functional organization of ammonia and glutamine metabolism in the liver acinus involves highly Keywords: glutaminase; glutamine synthetase; liver specialized hepatocyte subpopulations like glutamine syn- zonation; proteomics; scavenger cells. thetase (GS) expressing perivenous hepatocytes (scavenger cells). However, this cell population has not yet been char- acterized extensively regarding expression of other genes and Introduction potential subpopulations. This was investigated in the present study by proteome profiling of periportal GS-negative and There is a sophisticated structural-functional organization in perivenous GS-expressing hepatocytes from mouse and rat. the liver acinus with regard to ammonium and glutamine Apart from established markers of GS+ hepatocytes such as metabolism (Frieg et al. 2021; Gebhardt and Mecke 1983; glutamate/aspartate transporter II (GLT1) or ammonium Häussinger 1983, 1990). Periportal hepatocytes express en- transporter Rh type B (RhBG), we identified novel scavenger zymes required for urea synthesis such as the rate-controlling cell-specific proteins like basal transcription factor 3 (BTF3) enzyme carbamoylphosphate synthetase 1 (CPS1) and liver- and heat-shock protein 25 (HSP25).
    [Show full text]
  • Generate Metabolic Map Poster
    Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_001591825Cyc: Bacillus vietnamensis NBRC 101237 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari sn-glycerol phosphate phosphate pro phosphate phosphate phosphate thiamine molybdate D-xylose D-ribose glutathione 3-phosphate D-mannitol L-cystine L-djenkolate lanthionine α,β-trehalose phosphate phosphate [+ 3 more] α,α-trehalose predicted predicted ABC ABC FliY ThiT XylF RbsB RS10935 UgpC TreP PutP RS10200 PstB PstB RS10385 RS03335 RS20030 RS19075 transporter transporter of molybdate of phosphate α,β-trehalose 6-phosphate L-cystine D-xylose D-ribose sn-glycerol D-mannitol phosphate phosphate thiamine glutathione α α phosphate phosphate phosphate phosphate L-djenkolate 3-phosphate , -trehalose 6-phosphate pro 1-phosphate lanthionine molybdate phosphate [+ 3 more] Metabolic Regulator Amino Acid Degradation Amine and Polyamine Biosynthesis Macromolecule Modification tRNA-uridine 2-thiolation Degradation ATP biosynthesis a mature peptidoglycan a nascent β an N-terminal-
    [Show full text]
  • Diadenylate Cyclase Evaluation of Ssdaca (SSU98 1483) in Streptococcus Suis Serotype 2
    Diadenylate cyclase evaluation of ssDacA (SSU98_1483) in Streptococcus suis serotype 2 B. Du and J.H. Sun Shanghai Key Laboratory of Veterinary Biotechnology, Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China Corresponding author: J.H. Sun E-mail: [email protected] Genet. Mol. Res. 14 (2): 6917-6924 (2015) Received December 19, 2014 Accepted February 19, 2015 Published June 18, 2015 DOI http://dx.doi.org/10.4238/2015.June.18.34 ABSTRACT. Cyclic diadenosine monophosphate is a recently identified signaling molecule. It has been shown to play important roles in bacterial pathogenesis. SSU98_1483 (ssDacA), which is an ortholog of Listeria monocytogenes DacA, is a putative diadenylate cyclase in Streptococcus suis serotype 2. In this study, we determined the enzymatic activity of ssDacA in vitro using high-performance liquid chromatography and mass spectrometry. Our results showed that ssDacA was a diadenylate cyclase that converts ATP into cyclic diadenosine monophosphate in vitro. The diadenylate cyclase activity of ssDacA was dependent on divalent metal ions such as Mg2+, Mn2+, or Co2+, and it is more active under basic pH than under acidic pH. The conserved RHR motif in ssDacA was essential for its enzymatic activity, and mutation in this motif abolished the diadenylate cyclase activity of ssDacA. These results indicate that ssDacA is a diadenylate cyclase, which synthesizes cyclic diadenosine monophosphate in Streptococcus suis serotype 2. Key words: Cyclic diadenosine monophosphate; Diadenylate cyclase; DacA; Streptococcus suis serotype 2 Genetics and Molecular Research 14 (2): 6917-6924 (2015) ©FUNPEC-RP www.funpecrp.com.br B.
    [Show full text]
  • Role of Actinobacteria and Coriobacteriia in the Antidepressant Effects of Ketamine in an Inflammation Model of Depression
    Pharmacology, Biochemistry and Behavior 176 (2019) 93–100 Contents lists available at ScienceDirect Pharmacology, Biochemistry and Behavior journal homepage: www.elsevier.com/locate/pharmbiochembeh Role of Actinobacteria and Coriobacteriia in the antidepressant effects of ketamine in an inflammation model of depression T Niannian Huanga,1, Dongyu Huaa,1, Gaofeng Zhana, Shan Lia, Bin Zhub, Riyue Jiangb, Ling Yangb, ⁎ ⁎ Jiangjiang Bia, Hui Xua, Kenji Hashimotoc, Ailin Luoa, , Chun Yanga, a Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China b Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China c Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan ARTICLE INFO ABSTRACT Keywords: Ketamine, an N-methyl-D-aspartic acid receptor (NMDAR) antagonist, elicits rapid-acting and sustained anti- Ketamine depressant effects in treatment-resistant depressed patients. Accumulating evidence suggests that gut microbiota Depression via the gut-brain axis play a role in the pathogenesis of depression, thereby contributing to the antidepressant Lipopolysaccharide actions of certain compounds. Here we investigated the role of gut microbiota in the antidepressant effects of Gut microbiota ketamine in lipopolysaccharide (LPS)-induced inflammation model of depression. Ketamine (10 mg/kg) sig- nificantly attenuated the increased immobility time in forced swimming test (FST), which was associated with the improvements in α-diversity, consisting of Shannon, Simpson and Chao 1 indices. In addition to α-diversity, β-diversity, such as principal coordinates analysis (PCoA), and linear discriminant analysis (LDA) coupled with effect size measurements (LEfSe), showed a differential profile after ketamine treatment.
    [Show full text]
  • The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
    Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota.
    [Show full text]
  • Diversity and Composition of the Skin, Blood and Gut Microbiome in Rosacea—A Systematic Review of the Literature
    microorganisms Review Diversity and Composition of the Skin, Blood and Gut Microbiome in Rosacea—A Systematic Review of the Literature Klaudia Tutka, Magdalena Zychowska˙ and Adam Reich * Department of Dermatology, Institute of Medical Sciences, Medical College of Rzeszow University, 35-055 Rzeszow, Poland; [email protected] (K.T.); [email protected] (M.Z.)˙ * Correspondence: [email protected]; Tel.: +48-605076722 Received: 30 August 2020; Accepted: 6 November 2020; Published: 8 November 2020 Abstract: Rosacea is a chronic inflammatory skin disorder of a not fully understood pathophysiology. Microbial factors, although not precisely characterized, are speculated to contribute to the development of the condition. The aim of the current review was to summarize the rosacea-associated alterations in the skin, blood, and gut microbiome, investigated using culture-independent, metagenomic techniques. A systematic review of the PubMed, Web of Science, and Scopus databases was performed, according to PRISMA (preferred reporting items for systematic review and meta-analyses) guidelines. Nine out of 185 papers were eligible for analysis. Skin microbiome was investigated in six studies, and in a total number of 115 rosacea patients. Blood microbiome was the subject of one piece of research, conducted in 10 patients with rosacea, and gut microbiome was studied in two papers, and in a total of 23 rosacea subjects. Although all of the studies showed significant alterations in the composition of the skin, blood, or gut microbiome in rosacea, the results were highly inconsistent, or even, in some cases, contradictory. Major limitations included the low number of participants, and different study populations (mainly Asians). Further studies are needed in order to reliably analyze the composition of microbiota in rosacea, and the potential application of microbiome modifications for the treatment of this dermatosis.
    [Show full text]