DOCSLIB.ORG

Holdemania Massiliensis Sp. Nov

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Holdemania Massiliensis Sp. Nov Standards in Genomic Sciences (2013) 9:395-409 DOI:10.4056/sig s.4628316 Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov. Ajay Kumar Mishra1, Jean-Christophe Lagier1, Anne Pfleiderer1, Thi Thien Nguyen1, Aurelia Caputo1, Didier Raou lt1,2 and Pierre-Edouard Fournier1* 1URMITE, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Faculté de Médecine, Marseille, France* 2King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia *Correspondence: Pierre-Edouard Fournier ([email protected]) Keywords: Holdemania massiliensis, genome, culturomics, taxono-g enomics. Hol deman ia mass il ie ns is st rain AP2T sp. nov. is the type strain of H. mass il iens is sp. nov., a new species within the genus Holdemania. This strain, whose g enome is described here, was isolated from the fecal flora of a 21-year-old French Caucasian female suffering from severe restrictive anorexia nervosa. H. massil iens is is a Gram-positive, anaerobic bacillus. Here we describe the features of this org anism, tog ether with the complete genome sequence and an- notation. The 3,795,625 bp-long genome (one chromosome but no plasmid) contains 3,461 protein-coding and 49 RNA genes, including 3 rRNA g enes. Introduction Holdemania massiliensis strain AP2T (= CSUR P195 The genus Holdemania (Willems et al. 1997) was = DSM 26143) is the type strain of H. massiliensis created in 1997 on the basis of 16S rDNA gene se- sp. nov. This bacterium is a Gram-positive, non- quence, biochemical tests, fatty acid and cell wall spore-forming, indole negative, anaerobic and murein analysis [28]. To date, this genus includes non-motile bacillus that was isolated from the a single species, H. filiformis, which was isolated stool of a 21-year-old woman suffering from ano- from feces of healthy humans [29]. rexia as part of a “culturomics” study aiming to individually cultivate all species within human Classification and features feces [1-3]. A stool sample was collected from a 21-year-old The current prokaryotic species classification, French Caucasian female suffering from severe known as polyphasic taxonomy, is based on a restrictive anorexia nervosa, who had been hospi- combination of genomic and phenotypic proper- talized for recurrent weight loss and aggravation ties [4]. The number of sequenced genomes is in- of her general state. She had an eight year history creasing exponentially and in parallel with the de- of mental anorexia. The patient gave an informed creasing cost of sequencing. To date, more than and signed consent. Both this study and the assent 6,000 bacterial genomes have been published and procedure were approved by the Ethics Commit- approximately 25,000 genomes project are antici- tee of the Institut Fédératif de Recherche IFR48, pated to be completed in a near future [5]. We re- Faculty of Medicine, Marseille, France and the cently proposed to integrate genomic information agreement of the ethics committee of the IFR48 in the taxonomic framework and description of (Marseille, France) was obtained under reference new bacterial species [6-27]. 09-022. Several other new bacterial species were Here we present a summary classification and a isolated from diverse stool samples using micro- set of features for H. massiliensis sp. nov. strain bial culturomics [6-27]. The fecal specimen from AP2T (= CSUR P195 = DSM 26143), together with the patient was preserved at -80°C immediately the description of the complete genomic sequenc- after collection. Strain AP2T (Table 1) was isolated ing and annotation. These characteristics support in November 2011 after preincubation in an an- the circumscription of the species H. massiliensis. aerobic blood culture bottle with the addition of The Genomic Standards Consortium Holdemania massiliensis sp. nov. 5ml of thioglycolate, and inoculation in Columbia [29] (Figure 1). This value was lower than the agar (BioMerieux, Marcy l’Etoile, France). 98.7% 16S rRNA gene sequence threshold rec- This strain exhibited a 97% nucleotide sequence ommended by Stackebrandt and Ebers to deline- similarity with H. filiformis [28], and a range of 90- ate a new species without carrying out DNA-DNA 91% nucleotide sequence similarity to most close- hybridization [40]. ly related members of the genus Erysipelothrix Table 1. Classification and general features of Holdemania massiliensis strain AP2T according to the MIGS recommendations [30] MIGS ID Property Term Evidence codea Domain Bacteria TAS [31] Phylum Firmicutes TAS [32 -34 ] Class Erysipelotrichia TAS [35,36] Current classification Order Erysipelotrichales TAS [36,37] Family Erysipelotrichaceae TAS [38] Genus Holdemania TAS [28] Species Holdemania massiliensis IDA T Type strain AP2 IDA Gram stain positive IDA Cell shape Bacillus IDA Motility Not motile IDA Sporulation Non-sporulating IDA Temperature range Mesophile IDA Optimum temperature 37°C IDA MIGS-6.3 Salinity Unknown IDA MIGS-22 Oxygen requirement Anaerobic IDA Carbon source Unknown NAS Energ y source Unknown NAS MIGS-6 Habitat Human g ut IDA MIGS-15 Biotic relationship Free living IDA MIGS-14 Pathogenicity Unknown NAS Biosafety level 2 Isolation Human feces MIGS-4 Geog raphic location France IDA MIGS-5 Sample collection time November 2011 IDA MIGS-4.1 Latitude 43.296482 IDA MIGS-4.1 Long itude 5.36978 IDA MIGS-4.3 Depth Surface IDA MIGS-4.4 Altitude 0 m above sea level IDA Evidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). The- se evidence codes are from the Gene Ontology project [39]. If the evidence is IDA, then the property was directly observed for a live isolate by one of the authors or an expert mentioned in the acknowledge- ments. 396 Standards in Genomic Sciences Mishra et al. Figure 1. Phylogenetic tree highlig hting the position of Holdemania massiliensis strain AP2T relative to other type strains within the Erysipelotrichaceae family. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtaine d using the max imum-likelihood method within MEGA program. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Eggerthella lenta was use d as outg roup . The sca le ba r rep rese nts a 2% nucleotide sequence divergence. Different growth temperatures (25, 30, 37, 45°C) GENbag anaer and GENbag microaer systems, re- were tested. Growth occurred at 25 and 30°C after spectively (BioMérieux), and under aerobic condi- 72 hours of inoculation and the optimal growth tions with or without 5% CO2. The strain growth was observed at 37°C after 24 hours of inocula- was obtained only in anaerobic condition. The mo- tion. Colonies were 0.2 mm in diameter, light grey, tility test was negative. Cells grown on agar are -haemolysis on blood-enriched Columbia Gram-positive rods (Figure 2). The mean dimen- agar. Growth of the strain was tested under an- sions by electron microscopy were 0.57 µm in aerobicwith α and microaerophilic conditions using width and 1.75 µm in length (Figure 3). Figure 2. Gram staining of H. massil iens is strain AP2T http://standardsing enomics.org 397 Holdemania massiliensis sp. nov. Figure 3. Transmission electron microscopy of H. massiliensis strain AP2T, using a Morgani 268D (Philips) at an operating voltage of 60kV. The scale bar represents 500 nm. Strain AP2T exhibited a positive oxidase but no carried out as previously described [41] using a catalase activity. Using an API rapid 32A strip Microflex spectrometer (Bruker Daltonics, Leipzig, (Biomerieux), positive reactions were obtained for Germany). Twelve individual colonies were depos- -gala - -fucosidase and ited on a MTP 384 MALDI-TOF target plate pyroglutamic acid arylamidase. Substrate oxida- (Bruker). The twelve AP2T spectra were imported tionβ andctosidase, assimilation α glucosidase, was examined α using an API into the MALDI BioTyper software (version 2.0, 50CH strip (Biomerieux) at 37°C. Positive reac- Bruker) and analyzed by standard pattern match- tions were observed for glycerol, D-ribose, D- ing (with default parameter settings) against the galactose, D-glucose, D-fructose, D-mannose, ino- main spectra of 4,706 bacteria. A score enabled sitol, D-mannitol, D-sorbitol, N-acetyl- the presumptive identification and discrimination glucosamine, amygdalin, arbutin, esculin, salicin, of the tested species from those in a database: a D-cellobiose, D-maltose, D-lactose, D-saccharose, score > 2 with a validated species enabled the D-melezitose, gentiobiose, D-tagatose and identification at the species level; and a score < 1.7 postassium gluconate. H. massiliensis is suscepti- did not enable any identification. For strain AP2T, ble to amoxicillin, metronidazole, vancomycin, no significant score was obtained, suggesting that clindamycin and imipenem. The phenotypic char- our isolate was not a member of any known spe- acteristics that differentiate H. massiliensis from cies (Figures 4 and 5). We added the spectrum other species are summarized in Table 2. from strain AP2T to our database (Figure 4). Matrix-assisted laser-desorption/ionization time- of-flight (MALDI-TOF) MS protein analysis was 398 Standards in Genomic Sciences Mishra et al. Table 2. Differential characteristics
Load more

Recommended publications
  • Sex Differences in Colonization of Gut Microbiota from a Man with Short
    www.nature.com/scientificreports OPEN Sex differences in colonization of gut microbiota from a man with short-term vegetarian and inulin- Received: 28 June 2016 Accepted: 11 October 2016 supplemented diet in germ-free Published: 31 October 2016 mice Jing-jing Wang1, Jing Wang2, Xiao-yan Pang2, Li-ping Zhao2, Ling Tian1,* & Xing-peng Wang1,* Gnotobiotic mouse model is generally used to evaluate the efficacy of gut microbiota. Sex differences of gut microbiota are acknowledged, yet the effect of recipient’s gender on the bacterial colonization remains unclear. Here we inoculated male and female germ-free C57BL/6J mice with fecal bacteria from a man with short-term vegetarian and inulin-supplemented diet. We sequenced bacterial 16S rRNA genes V3-V4 region from donor’s feces and recipient’s colonic content. Shannon diversity index showed female recipients have higher bacteria diversity than males. Weighted UniFrac principal coordinates analysis revealed the overall structures of male recipient’s gut microbiota were significantly separated from those of females, and closer to the donor. Redundancy analysis identified 46 operational taxonomic units (OTUs) differed between the sexes. The relative abundance of 13 OTUs were higher in males, such as Parabacteroides distasonis and Blautia faecis, while 33 OTUs were overrepresented in females, including Clostridium groups and Escherichia fergusonii/Shigella sonnei. Moreover, the interactions of these differential OTUs were sexually distinct. These findings demonstrated that the intestine of male and female mice preferred to accommodate microbiota differently. Therefore, it is necessary to designate the gender of gnotobiotic mice for complete evaluation of modulatory effects of gut microbiota from human feces upon diseases.
    [Show full text]
  • Supplemental Table 1: Taxa by Symptom Taxonomy Browser Https
    Supplemental table 1: Taxa by Symptom Taxonomy Browser https://www.ncbi.nlm.nih.gov/taxonomy ↑= Enriched (X) = study number ↓= Decreased Taxa reference Phylum Class Order Family Genus Species Actinobacteria Actinobacteria Bifidobacteriales Bifidobacteriaceae Bifidobacterium Bifidobacterium infantis Actinomyces Coriobacteriia Coriobacteriales Coriobacteriaceae Eggerthella Eggerthella lenta Bacteriodetes Bacteriodia Bacteriodales Bacteroidaceae Bacteroides Bacteroides fragilis Muribaculaceae Prevotellaceae Prevotella Rikenellaceae Acetobacteroides Alistipes Rikenella Tannerellaceae Parabacteroides Porphyromonadaceae Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus Enterococcaceae Enterococcus Dehalobacterium Streptococcaceae Streptococcus Streptococcus anginosus Lactococcus Clostridia Clostridiales Clostridiaceae Clostridium Clostridium histolyticum Hungatella Peptostreptococcaceae Intestinibacter Terrisporobacter Lachnospiraceae Anaerostipes Coprococcus Dorea Lachnospira Roseburia Lachnoclostridium Taxa reference Phylum Class Order Family Genus Species Tyzzerella Oscillospiraceae Oscillibacter Ruminococcaceae Faecalibacterium Ruminococcus Caproiciproducens Oscillospira Anaerotruncus Erysipelotrichia Erysipelotrichales Erysipelotrichaceae Holdemania Coprobacillus Negativicutes Acidaminococcales Acidaminococcaceae Vellionellales Vellonellaceae Veillonella Dialister Tissierellia Tissierellales Peptoniphilaceae Anaerococcus Proteobacteria Betaproteobacteria Betaproteobacteriales Burkholderiales Burkholderiaceae Sutterellaceae
    [Show full text]
  • Functional Comparison of Bacteria from the Human Gut and Closely
    Functional comparison of bacteria from the human gut and closely related non-gut bacteria reveals the importance of conjugation and a paucity of motility and chemotaxis functions in the gut environment Dragana Dobrijevic, Anne-Laure Abraham, Alexandre Jamet, Emmanuelle Maguin, Maarten van de Guchte To cite this version: Dragana Dobrijevic, Anne-Laure Abraham, Alexandre Jamet, Emmanuelle Maguin, Maarten van de Guchte. Functional comparison of bacteria from the human gut and closely related non-gut bacte- ria reveals the importance of conjugation and a paucity of motility and chemotaxis functions in the gut environment. PLoS ONE, Public Library of Science, 2016, 11 (7), pp.e0159030. 10.1371/jour- nal.pone.0159030. hal-01353535 HAL Id: hal-01353535 https://hal.archives-ouvertes.fr/hal-01353535 Submitted on 11 Aug 2016 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. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals
    [Show full text]
  • Computational Methods for the Identification and Quantification Of
    Computational methods for the identification and quantification of microbial organisms in metagenomes Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) am Fachbereich Mathematik und Informatik der Freien Universit¨atBerlin von Martin Michael Serenus Lindner Berlin August 2014 Betreuer: PD Dr. Bernhard Renard Erstgutachter: PD Dr. Bernhard Renard Zweitgutachter: Jun.-Prof. Dr. Tobias Marschall Tag der Disputation: 15. Oktober 2014 ii Abstract Metagenomics allows analyzing genomic material taken directly from the environ- ment. In contrast to classical genomics, no purification of single organisms is per- formed and therefore the extracted genomic material reflects the composition of the original microbial community. The possible applications of metagenomics are mani- fold and the field has become increasingly popular due to the recent improvements in sequencing technologies. One of the most fundamental challenges in metagenomics is the identification and quantification of organisms in a sample, called taxonomic profiling. In this work, we present approaches to the following current problems in taxo- nomic profiling: First, differentiation between closely related organisms in metage- nomic samples is still challenging. Second, the identification of novel organisms in metagenomic samples poses problems to current taxonomic profiling methods, especially when there is no suitable reference genome available. The contribution of this thesis comprises three major projects. First, we introduce the Genome Abundance Similarity Correction (GASiC) algorithm, a method that allows differentiating between and quantifying highly similar microbial organisms in a metagenomic sample. The method first estimates the similarities between the available reference genomes with a simulation approach. Based on the similarities, GASiC corrects the observed abundances of each reference genome using a non- negative lasso approach.
    [Show full text]
  • Draft Genome and Description of Merdibacter Massiliensis Gen.Nov., Sp
    www.nature.com/scientificreports OPEN Draft genome and description of Merdibacter massiliensis gen.nov., sp. nov., a new bacterium genus Received: 21 November 2018 Accepted: 9 May 2019 isolated from the human ileum Published: xx xx xxxx Hussein Anani1, Rita Abou Abdallah1, Nisrine Chelkha2, Anthony Fontanini2, Davide Ricaboni2, Morgane Mailhe2, Didier Raoult2,3 & Pierre-Edouard Fournier 1 We used phenotypic, genomic and phylogenetic information following the taxono-genomics approach to demonstrate that strain Marseille–P3254, isolated from an ileal sample of a 76-year old woman who underwent upper and lower digestive tract endoscopy for esophagitis and colonic polyp, is representative of a novel bacterial genus within the family Erysipelotrichaceae in the phylum Firmicutes. It is an anaerobic Gram-negative bacterium without catalase and oxidase activities. The genome of strain Marseille–P3254 is 2,468,496-bp long with a 40.1% G + C content. This new bacterium is most closely related to Eubacterium dolichum, with which it shares 90.7% 16S rRNA sequence similarity. In addition, genomic comparison using the digital DNA–DNA hybridization and OrthoANI analyses between the novel organism and the E. dolichum type strain revealed identities of 25.2 and 68.91%, respectively. The major fatty acids were C16: 0, C18: 1n9 and C18: 0. Based on these data, we propose the creation of the new genus Merdibacter gen. nov., with strain Marseille-P3254T (=CSUR P3254 = DSM 103534) being the type strain of the new species Merdibacter massiliensis gen. nov., sp. nov. A thorough knowledge of the gut microbiota composition appears essential to understand many aspects of health and diseases in humans.
    [Show full text]
  • Microbiota-Directed Fibre Activates Both Targeted and Secondary
    ARTICLE https://doi.org/10.1038/s41467-020-19585-0 OPEN Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut ✉ Leszek Michalak 1, John Christian Gaby1 , Leidy Lagos2, Sabina Leanti La Rosa 1, Torgeir R. Hvidsten 1, Catherine Tétard-Jones3, William G. T. Willats3, Nicolas Terrapon 4,5, Vincent Lombard4,5, Bernard Henrissat 4,5,6, Johannes Dröge7, Magnus Øverlie Arntzen 1, Live Heldal Hagen 1, ✉ ✉ Margareth Øverland2, Phillip B. Pope 1,2,8 & Bjørge Westereng 1,8 1234567890():,; Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. Here, we test the accuracy of AcGGM within the complex endogenous gut microbiome of pigs, wherein we resolve 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially express AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifests a “butterfly effect”, whereby numerous metabolic changes and interdependent cross-feeding pathways occur in neighboring non-mannanolytic populations that produce short-chain fatty acids. Our findings show how intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large. 1 Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway.
    [Show full text]
  • Collinsella Massiliensis Sp
    Standards in Genomic Sciences (2014) 9:1144-1158 DOI:10.4056/sigs.5399696 Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov. Roshan Padmanabhan1†, Gregory Dubourg1†, Jean-Christophe lagier1, Thi-Thien Ngu- yen1, Carine Couderc1, Morgane Rossi-Tamisier1, Aurelia Caputo1, Didier Raoult1,2 and Pierre-Edouard Fournier1* 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France 2 King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia *Correspondence: Pierre-Edouard Fournier ([email protected]) †Both authors participated equally to this work Key words: Collinsella massiliensis, genome, culturomics, taxono-genomics Collinsella massiliensis strain GD3T is the type strain of Collinsella massiliensis sp. nov., a new species within the genus Collinsella. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old French Caucasoid woman who had been admitted to intensive care unit for Guillain-Barré syndrome. Collinsella massiliensis is a Gram-positive, obligate anaerobic, non motile and non sporulating bacillus. Here, we describe the features of this organism, together with the complete genome sequence and annotation. The genome is 2,319,586 bp long (1 chromosome, no plasmid), exhibits a G+C content of 65.8% and contains 2,003 protein-coding and 54 RNA genes, including 1 rRNA operon. Introduction Collinsella massiliensis strain GD3T (= CSUR P902 In 1999, Kageyama et al. reclassified = DSM 26110) is the type strain of C. massiliensis Eubacterium aerofaciens into a new genus sp. nov.
    [Show full text]
  • Read Full Text (PDF)
    Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut Downloaded from: https://research.chalmers.se, 2021-10-02 23:09 UTC Citation for the original published paper (version of record): Michalak, L., Gaby, J., Lagos, L. et al (2020) Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut Nature Communications, 11(1) http://dx.doi.org/10.1038/s41467-020-19585-0 N.B. When citing this work, cite the original published paper. research.chalmers.se offers the possibility of retrieving research publications produced at Chalmers University of Technology. It covers all kind of research output: articles, dissertations, conference papers, reports etc. since 2004. research.chalmers.se is administrated and maintained by Chalmers Library (article starts on next page) ARTICLE https://doi.org/10.1038/s41467-020-19585-0 OPEN Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut ✉ Leszek Michalak 1, John Christian Gaby1 , Leidy Lagos2, Sabina Leanti La Rosa 1, Torgeir R. Hvidsten 1, Catherine Tétard-Jones3, William G. T. Willats3, Nicolas Terrapon 4,5, Vincent Lombard4,5, Bernard Henrissat 4,5,6, Johannes Dröge7, Magnus Øverlie Arntzen 1, Live Heldal Hagen 1, ✉ ✉ Margareth Øverland2, Phillip B. Pope 1,2,8 & Bjørge Westereng 1,8 1234567890():,; Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals.
    [Show full text]
  • Relationships Between Diet-Related Changes in the Gut Microbiome and Cognitive Flexibility
    Relationships Between Diet-Related Changes in the Gut Microbiome and Cognitive Flexibility Magnusson, K. R., Hauck, L., Jeffrey, B. M., Elias, V., Humphrey, A., Nath, R., Perrone, A., & Bermudez, L. E. (2015). Relationships Between Diet-Related Changes in the Gut Microbiome and Cognitive Flexibility. [Article in Press]. Neuroscience. Elsevier Accepted Manuscript http://cdss.library.oregonstate.edu/sa-termsofuse *Manuscript (Clear Copy) Click here to view linked References 1 2 3 4 Title: RELATIONSHIPS BETWEEN DIET-RELATED CHANGES IN THE GUT MICROBIOME 5 AND COGNITIVE FLEXIBILITY 6 7 Authors: K.R. Magnusson 1, 2, L. Hauck1, B.M. Jeffrey1, V. Elias 1,2, A. Humphrey1, R. Nath3, A. 8 1, 2 1 9 Perrone , and L.E. Bermudez 10 11 Affiliations: 1 Dept Biomedical Sciences, College of Veterinary Medicine 12 2 Linus Pauling Institute 13 3 Dept of Human Development and Family Sciences, School of Social and 14 Behavioral Health Sciences 15 Oregon State University, Corvallis, OR 97331 U.S.A. 16 17 18 Email addresses: Magnusson: [email protected] 19 Hauck: [email protected] 20 Jeffrey: [email protected] 21 Elias: [email protected] 22 Humphrey: [email protected] 23 Nath: [email protected] 24 Perrone: [email protected] 25 Bermudez: [email protected] 26 27 28 Corresponding Author: Dr. Kathy Magnusson 29 307 Linus Pauling Science Center 30 Oregon State University 31 Corvallis, OR 97331 U.S.A. 32 Phone: 541-737-6923 33 Fax: 541-737-5077 34 Email: [email protected] 35 36 37 38 39 40 41
    [Show full text]
  • Dakotella Fusiforme Gen. Nov., Sp. Nov., Isolated from Healthy Human Feces
    Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces Sudeep Ghimire, Supapit Wongkuna and Joy Scaria Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States of America ABSTRACT A Gram-positive, non-motile, rod-shaped facultative anaerobic bacterial strain SG502T was isolated from healthy human fecal samples in Brookings, SD, USA. The comparison of the 16S rRNA gene placed the strain within the family Erysipelotrichaceae. Within this family, Clostridium innocuum ATCC 14501T, Longicatena caecimuris strain PG- 426-CC-2, Eubacterium dolichum DSM 3991T and E. tortuosum DSM 3987T (=ATCC 25548T) were its closest taxa with 95.28%, 94.17%, 93.25%, and 92.75% 16S rRNA sequence identities respectively. The strain SG502T placed itself close to C. innocuum in the 16S rRNA phylogeny. The members of genus Clostridium within family Erysipelotrichaceae was proposed to be reassigned to genus Erysipelatoclostridium to resolve the misclassification of genus Clostridium. Therefore, C. innocuum was also classified into this genus temporarily with the need to reclassify it in the future because of its difference in genomic properties. Similarly, genome sequencing of the strain and comparison with its 16S phylogenetic members and proposed members of the genus Erysipelatoclostridium, SG502T warranted a separate genus even though its 16S rRNA similarity was >95% when comapred to C. innocuum. The strain was 71.8% similar at ANI, 19.8% [17.4–22.2%] at dDDH and 69.65% similar at AAI to its closest neighbor C. innocuum. The genome size was nearly 2,683,792 bp with 32.88 mol% G+C content, Submitted 19 November 2019 which is about half the size of C.
    [Show full text]
  • Gut Microbiome-Related Effects of Berberine and Probiotics on Type 2 Diabetes (The PREMOTE Study)
    ARTICLE https://doi.org/10.1038/s41467-020-18414-8 OPEN Gut microbiome-related effects of berberine and probiotics on type 2 diabetes (the PREMOTE study) Yifei Zhang 1,19, Yanyun Gu1,19, Huahui Ren2,19, Shujie Wang 1,19, Huanzi Zhong 2,19, Xinjie Zhao3, Jing Ma4, Xuejiang Gu5, Yaoming Xue6, Shan Huang7, Jialin Yang8, Li Chen9, Gang Chen10, Shen Qu11, Jun Liang12, Li Qin13, Qin Huang14, Yongde Peng15,QiLi3, Xiaolin Wang3, Ping Kong2, Guixue Hou 2, Mengyu Gao2, Zhun Shi2, Xuelin Li1, Yixuan Qiu1, Yuanqiang Zou2, Huanming Yang2,16, Jian Wang2,16, ✉ ✉ Guowang Xu3, Shenghan Lai17, Junhua Li 2,18 , Guang Ning1 & Weiqing Wang1 1234567890():,; Human gut microbiome is a promising target for managing type 2 diabetes (T2D). Measures altering gut microbiota like oral intake of probiotics or berberine (BBR), a bacteriostatic agent, merit metabolic homoeostasis. We hence conducted a randomized, double-blind, placebo- controlled trial with newly diagnosed T2D patients from 20 centres in China. Four-hundred- nine eligible participants were enroled, randomly assigned (1:1:1:1) and completed a 12-week treatment of either BBR-alone, probiotics+BBR, probiotics-alone, or placebo, after a one-week run-in of gentamycin pretreatment. The changes in glycated haemoglobin, as the primary outcome, in the probiotics+BBR (least-squares mean [95% CI], −1.04[−1.19, −0.89]%) and BBR-alone group (−0.99[−1.16, −0.83]%) were significantly greater than that in the placebo and probiotics-alone groups (−0.59[−0.75, −0.44]%, −0.53[−0.68, −0.37]%, P < 0.001). BBR treatment induced more gastrointestinal side effects.
    [Show full text]
  • | Hai Lui a Un Acut out on to a Man Uniti
    |HAI LUI AUN ACUTUS010058578B2 OUT ON TO A MAN UNITI (12 ) United States Patent (10 ) Patent No. : US 10 ,058 , 578 B2 Honda et al. (45 ) Date of Patent: * Aug. 28 , 2018 (54 ) HUMAN - DERIVED BACTERIA THAT 6 ,551 , 632 B2 4 / 2003 Borody INDUCE PROLIFERATION OR 6 ,645 ,530 B1 11/ 2003 Borody 7 ,629 , 330 B2 12 / 2009 Wang et al. ACCUMULATION OF REGULATORY T 7 , 749 , 494 B27 / 2010 Renaud et al. CELLS 8 , 906 ,668 B2 * 12 /2014 Henn A61K 38 / 13 @( 71 ) Applicants : The University of Tokyo, Bunkyo -ku 435 / 243 ( JP ) ; School Corporation , Azabu 9 ,011 ,834 B1 4 / 2015 McKenzie et al . 9 ,028 , 841 B2 * 5 /2015 Henn . .. A61K 38 / 13 Veterinary Medicine Educational 424 / 203 . 1 Institution , Sagamihara - shi, Kanagawa 9 , 180 , 147 B2 11/ 2015 McKenzie et al. ( JP ) 9 , 415 ,079 B2 * 8 / 2016 Honda . .. .. .. .. A61K 45 / 06 9 ,421 , 230 B2 * 8 / 2016 Honda . .. .. .. .. .. .. .. A61K 45 / 06 @(72 ) Inventors : Kenya Honda , Tokyo ( JP ) ; Koji 9 ,433 ,652 B2 * 9 / 2016 Honda .. .. .. .. .. A61K 45 /06 Atarashi, Tokyo ( JP ) ; Takeshi Tanoue, 9 , 446 , 080 B2 9 /2016 McKenzie et al. Tokyo (JP ) ; Masahira Hattori , Tokyo 9 ,533 ,014 B2 * 1 / 2017 Henn .. .. A61K 38 / 13 9 , 585, 921 B2 3 / 2017 McKenzie et al . ( JP ) ; Hidetoshi Morita , Sagamihara 9 , 603, 878 B2 3 / 2017 Berry et al. ( JP ) 9 ,610 , 307 B2 * 4 / 2017 Berry . .. .. .. A61K 9 /0031 @(73 ) Assignees : The University of Tokyo , Tokyo ( JP ) ; 9 ,642 , 881 B2 * 5 / 2017 Honda . .. .. .. .. .. .. · A61K 35 / 74 9 ,642 , 882 B2 * 5 / 2017 Honda .
    [Show full text]