Evolution of a Global Regulator: Lrp in Four Orders of Γ-Proteobacteria Yvette Unoarumhi1,2, Robert M
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Bacterial Communities of the Upper Respiratory Tract of Turkeys
www.nature.com/scientificreports OPEN Bacterial communities of the upper respiratory tract of turkeys Olimpia Kursa1*, Grzegorz Tomczyk1, Anna Sawicka‑Durkalec1, Aleksandra Giza2 & Magdalena Słomiany‑Szwarc2 The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplifcation of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identifed in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Diferences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identifed, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey focks. Next-generation sequencing has resulted in a marked increase in culture-independent studies characterizing the microbiome of humans and animals1–6. Much of these works have been focused on the gut microbiome of humans and other production animals 7–11. -
Identification of Pasteurella Species and Morphologically Similar Organisms
UK Standards for Microbiology Investigations Identification of Pasteurella species and Morphologically Similar Organisms Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 1 of 28 © Crown copyright 2015 Identification of Pasteurella species and Morphologically Similar Organisms Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website https://www.gov.uk/uk- standards-for-microbiology-investigations-smi-quality-and-consistency-in-clinical- laboratories. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for-microbiology-investigations- steering-committee). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories UK Standards for Microbiology Investigations are produced in association with: Logos correct at time of publishing. Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 2 of 28 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Pasteurella species and Morphologically Similar Organisms Contents ACKNOWLEDGMENTS ......................................................................................................... -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
Original Article EP300 Regulates the Expression of Human Survivin Gene in Esophageal Squamous Cell Carcinoma
Int J Clin Exp Med 2016;9(6):10452-10460 www.ijcem.com /ISSN:1940-5901/IJCEM0023383 Original Article EP300 regulates the expression of human survivin gene in esophageal squamous cell carcinoma Xiaoya Yang, Zhu Li, Yintu Ma, Xuhua Yang, Jun Gao, Surui Liu, Gengyin Wang Department of Blood Transfusion, The Bethune International Peace Hospital of China PLA, Shijiazhuang 050082, Hebei, P. R. China Received January 6, 2016; Accepted March 21, 2016; Epub June 15, 2016; Published June 30, 2016 Abstract: Survivin is selectively up-regulated in various cancers including esophageal squamous cell carcinoma (ESCC). The underlying mechanism of survivin overexpression in cancers is needed to be further studied. In this study, we investigated the effect of EP300, a well known transcriptional coactivator, on survivin gene expression in human esophageal squamous cancer cell lines. We found that overexpression of EP300 was associated with strong repression of survivin expression at the mRNA and protein levels. Knockdown of EP300 increased the survivin ex- pression as indicated by western blotting and RT-PCR analysis. Furthermore, our results indicated that transcription- al repression mediated by EP300 regulates survivin expression levels via regulating the survivin promoter activity. Chromatin immunoprecipitation (ChIP) analysis revealed that EP300 was associated with survivin gene promoter. When EP300 was added to esophageal squamous cancer cells, increased EP300 association was observed at the survivin promoter. But the acetylation level of histone H3 at survivin promoter didn’t change after RNAi-depletion of endogenous EP300 or after overexpression of EP300. These findings establish a negative regulatory role for EP300 in survivin expression. Keywords: Survivin, EP300, transcription regulation, ESCC Introduction transcription factors and the basal transcrip- tion machinery, or by providing a scaffold for Survivin belongs to the inhibitor of apoptosis integrating a variety of different proteins [6]. -
D 3111 Suppl
The following supplement accompanies the article Fine-scale transition to lower bacterial diversity and altered community composition precedes shell disease in laboratory-reared juvenile American lobster Sarah G. Feinman, Andrea Unzueta Martínez, Jennifer L. Bowen, Michael F. Tlusty* *Corresponding author: [email protected] Diseases of Aquatic Organisms 124: 41–54 (2017) Figure S1. Principal coordinates analysis of bacterial communities on lobster shell samples taken on different days. Principal coordinates analysis of the weighted UniFrac metric comparing bacterial community composition of diseased lobster shell on different days of sampling. Diseased lobster shell includes samples collected from the site of disease (square), as well as 0.5 cm (circle), 1 cm (triangle), and 1.5 cm (diamond) away from the site of the disease, while colors depict different days of sampling. Note that by day four, two of the lobsters had molted, hence there are fewer red symbols 1 Figure S2. Rank relative abundance curve for the 200+ most abundant OTUs for each shell condition. The number of OTUs, their abundance, and their order varies for each bar graph based on the relative abundance of each OTU in that shell condition. Please note the difference in scale along the y-axis for each bar graph. Bars appear in color if the OTU is a part of the core microbiome of that shell condition or appear in black if the OTU is not a part of the core microbiome of that shell condition. Dotted lines indicate OTUs that are part of the “abundant microbiome,” i.e. those whose cumulative total is ~50%, as well as OTUs that are a part of the “rare microbiome,” i.e. -
The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. -
Distinct Bacterial Communities Associated with the Coral Model Aiptasia in Aposymbiotic and Symbiotic States with Symbiodinium
ORIGINAL RESEARCH published: 18 November 2016 doi: 10.3389/fmars.2016.00234 Distinct Bacterial Communities Associated with the Coral Model Aiptasia in Aposymbiotic and Symbiotic States with Symbiodinium Till Röthig †, Rúben M. Costa †, Fabia Simona, Sebastian Baumgarten, Ana F. Torres, Anand Radhakrishnan, Manuel Aranda and Christian R. Voolstra * Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia Coral reefs are in decline. The basic functional unit of coral reefs is the coral metaorganism or holobiont consisting of the cnidarian host animal, symbiotic algae of the genus Symbiodinium, and a specific consortium of bacteria (among others), but research is slow due to the difficulty of working with corals. Aiptasia has proven to be a tractable Edited by: model system to elucidate the intricacies of cnidarian-dinoflagellate symbioses, but Thomas Carl Bosch, characterization of the associated bacterial microbiome is required to provide a complete University of Kiel, Germany and integrated understanding of holobiont function. In this work, we characterize and Reviewed by: analyze the microbiome of aposymbiotic and symbiotic Aiptasia and show that bacterial Simon K. Davy, Victoria University of Wellington, associates are distinct in both conditions. We further show that key microbial associates New Zealand can be cultured without their cnidarian host. Our results suggest that bacteria play an Mathieu Pernice, University of Technology, Australia important role in the symbiosis of Aiptasia with Symbiodinium, a finding that underlines *Correspondence: the power of the Aiptasia model system where cnidarian hosts can be analyzed in Christian R. Voolstra aposymbiotic and symbiotic states. -
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. -
Thalassomonas Agarivorans Sp. Nov., a Marine Agarolytic Bacterium Isolated from Shallow Coastal Water of An-Ping Harbour, Taiwan
International Journal of Systematic and Evolutionary Microbiology (2006), 56, 1245–1250 DOI 10.1099/ijs.0.64130-0 Thalassomonas agarivorans sp. nov., a marine agarolytic bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the genus Thalassomonas Wen Dar Jean,1 Wung Yang Shieh2 and Tung Yen Liu2 Correspondence 1Center for General Education, Leader University, No. 188, Sec. 5, An-Chung Rd, Tainan, Wung Yang Shieh Taiwan [email protected] 2Institute of Oceanography, National Taiwan University, PO Box 23-13, Taipei, Taiwan A marine agarolytic bacterium, designated strain TMA1T, was isolated from a seawater sample collected in a shallow-water region of An-Ping Harbour, Taiwan. It was non-fermentative and Gram-negative. Cells grown in broth cultures were straight or curved rods, non-motile and non-flagellated. The isolate required NaCl for growth and exhibited optimal growth at 25 6C and 3 % NaCl. It grew aerobically and was incapable of anaerobic growth by fermenting glucose or other carbohydrates. Predominant cellular fatty acids were C16 : 0 (17?5 %), C17 : 1v8c (12?8 %), C17 : 0 (11?1 %), C15 : 0 iso 2-OH/C16 : 1v7c (8?6 %) and C13 : 0 (7?3 %). The DNA G+C content was 41?0 mol%. Phylogenetic, phenotypic and chemotaxonomic data accumulated in this study revealed that the isolate could be classified in a novel species of the genus Thalassomonas in the family Colwelliaceae. The name Thalassomonas agarivorans sp. nov. is proposed for the novel species, with TMA1T (=BCRC 17492T=JCM 13379T) as the type strain. Alteromonas-like bacteria in the class Gammaproteobacteria however, they are not exclusively autochthonous in the comprise a large group of marine, heterotrophic, polar- marine environment, since some reports have shown that flagellated, Gram-negative rods that are mainly non- they also occur in freshwater, sewage and soil (Agbo & Moss, fermentative aerobes. -
Pasteurellaceae: P. Multocida, Avibacterium Gallinarum, A
Pasteurellaceae: P. Multocida, Avibacterium gallinarum, A. paragallinarum All the members of the family Pasteurellaceae are gram negative coccobacilli. They are facultative anaerobes, and typically oxidase-positive (which sets them apart from members of the family Enterobacteriaceae). Morphology and Staining Members of the genera Avibacterium, and Pasteurella are gram-negative coccobacilli. Bipolarity, that is, the staining of only the tips of cells, may be demonstrable with polychrome stains (e.g., Wright’s stain). Cell structure Adhesins. Some and probably all members of the family Pasteurellaceae produce adhesins (and possibly more than one kind). A type 4 fimbria (adhesin) has been described for avian strains of P. Multocida. Capsule. The hyaluronic acid capsule of type A strains P. multocida serves as an adhesin. The hyaluronic acid is similar (if not identical) to host tissue components, and is thus poorly antigenic; they also bind complement components poorly (and is therefore antiphagocytic).The hyaluronic acid capsule also serves as an adhesin for respiratory tract epithelial cells as in the case of capsule type A strains of P. Multocida Exotoxin. Pasteurella produce a number of proteins with toxic activity. At least two of these are important in the pathogenesis of disease: RTX and Rho toxin Growth Characteristics Avibacterium and Pasteurella grow best in the presence of serum or blood. After overnight incubation (35–37 ◦C), colonies are up to 2 mm in diameter, clear to 1 grayish, and smooth or mucoid. All are gram-negative, nonmotile coccobacilli. They are facultative anaerobes, typically oxidase-positive. Variability P. multocida consists of 5 capsular serogroups (A, B, D, E, and F) and 16 somatic serotypes (1–16). -
Dddy Is a Bacterial Dimethylsulfoniopropionate Lyase Representing a New Cupin Enzyme Superfamily with Unknown Primary Function
bioRxiv preprint doi: https://doi.org/10.1101/161257; this version posted July 9, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. DddY is a bacterial dimethylsulfoniopropionate lyase representing a new cupin enzyme superfamily with unknown primary function Lei Lei, Uria Alcolombri & Dan S Tawfik Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel. * Correspondence to: [email protected] Abstract Dimethylsulfide (DMS) is released at rates of >107 tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms, release DMS via cleavage of dimethylsulfoniopropionate (DMSP). Different genes encoding proteins with DMSP lyase activity are known belonging to different superfamilies and exhibiting highly variable levels of DMSP lyase activity. DddY shows the highest activity among all reported bacterial lyases yet is poorly characterized. Here, we describe the characterization of recombinant DddY is from different marine bacteria. We found that DddY activity demands a transition metal ion cofactor. DddY also shares two sequence motifs with other bacterial lyases assigned as cupin-like enzymes, DddQ, DddL, DddK, and DddW. These cupin motif residues are essential for DddY activity, as for the other cupin DMSP lyases, and all these enzymes are characterized by a common metal- chelator inhibitor (TPEN). Analysis of all sequences carrying these cupin motifs defined a superfamily: Cupin-DLL (DMSP lyases and lyase-like). The DMSP lyase families are sporadically distributed suggesting that DMSP lyases evolved within this superfamily independently along multiple lineages. -
Simulation of Deepwater Horizon Oil Plume Reveals Substrate Specialization Within a Complex Community of Hydrocarbon Degraders
Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders Ping Hua, Eric A. Dubinskya,b, Alexander J. Probstc, Jian Wangd, Christian M. K. Sieberc,e, Lauren M. Toma, Piero R. Gardinalid, Jillian F. Banfieldc, Ronald M. Atlasf, and Gary L. Andersena,b,1 aEcology Department, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; bDepartment of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720; cDepartment of Earth and Planetary Science, University of California, Berkeley, CA 94720; dDepartment of Chemistry and Biochemistry, Florida International University, Miami, FL 33199; eDepartment of Energy, Joint Genome Institute, Walnut Creek, CA 94598; and fDepartment of Biology, University of Louisville, Louisville, KY 40292 Edited by Rita R. Colwell, University of Maryland, College Park, MD, and approved May 30, 2017 (received for review March 1, 2017) The Deepwater Horizon (DWH) accident released an estimated Many studies of the plume samples reported that the structure 4.1 million barrels of oil and 1010 mol of natural gas into the Gulf of the microbial communities shifted as time progressed (3–6, 11– of Mexico, forming deep-sea plumes of dispersed oil droplets and 16). Member(s) of the order Oceanospirillales dominated from dissolved gases that were largely degraded by bacteria. During the May to mid-June, after which their numbers rapidly declined and course of this 3-mo disaster a series of different bacterial taxa were species of Cycloclasticus and Colwellia dominated for the next enriched in succession within deep plumes, but the metabolic capa- several weeks (4, 5, 14).