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Deciphering a Marine Bone Degrading Microbiome Reveals a Complex Community Effort
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.13.093005; this version posted November 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Deciphering a marine bone degrading microbiome reveals a complex community effort 2 3 Erik Borcherta,#, Antonio García-Moyanob, Sergio Sanchez-Carrilloc, Thomas G. Dahlgrenb,d, 4 Beate M. Slabya, Gro Elin Kjæreng Bjergab, Manuel Ferrerc, Sören Franzenburge and Ute 5 Hentschela,f 6 7 aGEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, 8 Kiel, Germany 9 bNORCE Norwegian Research Centre, Bergen, Norway 10 cCSIC, Institute of Catalysis, Madrid, Spain 11 dDepartment of Marine Sciences, University of Gothenburg, Gothenburg, Sweden 12 eIKMB, Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany 13 fChristian-Albrechts University of Kiel, Kiel, Germany 14 15 Running Head: Marine bone degrading microbiome 16 #Address correspondence to Erik Borchert, [email protected] 17 Abstract word count: 229 18 Text word count: 4908 (excluding Abstract, Importance, Materials and Methods) 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.13.093005; this version posted November 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 19 Abstract 20 The marine bone biome is a complex assemblage of macro- and microorganisms, however the 21 enzymatic repertoire to access bone-derived nutrients remains unknown. -
Zygote Gene Expression and Plasmodial Development in Didymium Iridis
DePaul University Via Sapientiae College of Science and Health Theses and Dissertations College of Science and Health Summer 8-25-2019 Zygote gene expression and plasmodial development in Didymium iridis Sean Schaefer DePaul University, [email protected] Follow this and additional works at: https://via.library.depaul.edu/csh_etd Part of the Biology Commons Recommended Citation Schaefer, Sean, "Zygote gene expression and plasmodial development in Didymium iridis" (2019). College of Science and Health Theses and Dissertations. 322. https://via.library.depaul.edu/csh_etd/322 This Thesis is brought to you for free and open access by the College of Science and Health at Via Sapientiae. It has been accepted for inclusion in College of Science and Health Theses and Dissertations by an authorized administrator of Via Sapientiae. For more information, please contact [email protected]. Zygote gene expression and plasmodial development in Didymium iridis A Thesis presented in Partial fulfillment of the Requirements for the Degree of Master of Biology By Sean Schaefer 2019 Advisor: Dr. Margaret Silliker Department of Biological Sciences College of Liberal Arts and Sciences DePaul University Chicago, IL Abstract: Didymium iridis is a cosmopolitan species of plasmodial slime mold consisting of two distinct life stages. Haploid amoebae and diploid plasmodia feed on microscopic organisms such as bacteria and fungi through phagocytosis. Sexually compatible haploid amoebae act as gametes which when fused embark on an irreversible developmental change resulting in a diploid zygote. The zygote can undergo closed mitosis resulting in a multinucleated plasmodium. Little is known about changes in gene expression during this developmental transition. Our principal goal in this study was to provide a comprehensive list of genes likely to be involved in plasmodial development. -
Systema Naturae 2000 (Phylum, 6 Nov 2017)
The Taxonomicon Systema Naturae 2000 Classification of Domain Bacteria (prokaryotes) down to Phylum Compiled by Drs. S.J. Brands Universal Taxonomic Services 6 Nov 2017 Systema Naturae 2000 - Domain Bacteria - Domain Bacteria Woese et al. 1990 1 Genus †Eoleptonema Schopf 1983, incertae sedis 2 Genus †Primaevifilum Schopf 1983, incertae sedis 3 Genus †Archaeotrichion Schopf 1968, incertae sedis 4 Genus †Siphonophycus Schopf 1968, incertae sedis 5 Genus Bactoderma Tepper and Korshunova 1973 (Approved Lists 1980), incertae sedis 6 Genus Stibiobacter Lyalikova 1974 (Approved Lists 1980), incertae sedis 7.1.1.1.1.1 Superphylum "Proteobacteria" Craig et al. 2010 1.1 Phylum "Alphaproteobacteria" 1.2.1 Phylum "Acidithiobacillia" 1.2.2.1 Phylum "Gammaproteobacteria" 1.2.2.2.1 Candidate phylum Muproteobacteria (RIF23) Anantharaman et al. 2016 1.2.2.2.2 Phylum "Betaproteobacteria" 2 Phylum "Zetaproteobacteria" 7.1.1.1.1.2 Phylum "Deltaproteobacteria_1" 7.1.1.1.2.1.1.1 Phylum "Deltaproteobacteria" [polyphyletic] 7.1.1.1.2.1.1.2.1 Phylum "Deltaproteobacteria_2" 7.1.1.1.2.1.1.2.2 Phylum "Deltaproteobacteria_3" 7.1.1.1.2.1.2 Candidate phylum Dadabacteria (CSP1-2) Hug et al. 2015 7.1.1.1.2.2.1 Candidate phylum "MBNT15" 7.1.1.1.2.2.2 Candidate phylum "Uncultured Bacterial Phylum 10 (UBP10)" Parks et al. 2017 7.1.1.2.1 Phylum "Nitrospirae_1" 7.1.1.2.2 Phylum Chrysiogenetes Garrity and Holt 2001 7.1.2.1.1 Phylum "Nitrospirae" Garrity and Holt 2001 [polyphyletic] 7.1.2.1.2.1.1 Candidate phylum Rokubacteria (CSP1-6) Hug et al. -
Libros Sobre Enfermedades Autoinmunes: Tratamientos, Tipos Y Diagnósticos- Profesor Dr
- LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS . AUTOR: PROFESOR DR. ENRIQUE BARMAIMON.- - Doctor en Medicina.- - Cátedras de: - Anestesiología - Cuidados Intensivos - Neuroanatomía - Neurofisiología - Psicofisiología - Neuropsicología. - 9 TOMOS - - TOMO VI - -AÑO 2020- 1ª Edición Virtual: (.2020. 1)- - MONTEVIDEO, URUGUAY. 1 - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - Queda terminantemente prohibido reproducir este libro en forma escrita y virtual, total o parcialmente, por cualquier medio, sin la autorización previa del autor. -Derechos reservados. 1ª Edición. Año 2020. Impresión [email protected]. - email: [email protected].; y [email protected]; -Montevideo, 15 de enero de 2020. - BIBLIOTECA VIRTUAL DE SALUD del S. M.U. del URUGUAY; y BIBLIOTECA DEL COLEGIO MÉDICO DEL URUGUAY. 0 0 0 0 0 0 0 0. 2 - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - TOMO V I - 3 - LIBROS SOBRE ENFERMEDADES AUTOINMUNES: TRATAMIENTOS, TIPOS Y DIAGNÓSTICOS- PROFESOR DR. ENRIQUE BARMAIMON- 9 TOMOS- AÑO 2020.1- TOMO VI- - ÍNDICE.- - TOMO I . - - ÍNDICE. - PRÓLOGO.- - INTRODUCCIÓN. - CAPÍTULO I: -1)- GENERALIDADES. -1.1)- DEFINICIÓN. -1.2)- CAUSAS Y FACTORES DE RIESGO. -1.2.1)- FACTORES EMOCIONALES. -1.2.2)- FACTORES AMBIENTALES. -1.2.3)- FACTORES GENÉTICOS. -1.3)- Enterarse aquí, como las 10 Tipos de semillas pueden mejorar la salud. - 1.4)- TIPOS DE TRATAMIENTO DE ENFERMEDADES AUTOINMUNES. -1.4.1)- Remedios Naturales. -1.4.1.1)- Mejorar la Dieta. -
Marine Sediments Illuminate Chlamydiae Diversity and Evolution
Supplementary Information for: Marine sediments illuminate Chlamydiae diversity and evolution Jennah E. Dharamshi1, Daniel Tamarit1†, Laura Eme1†, Courtney Stairs1, Joran Martijn1, Felix Homa1, Steffen L. Jørgensen2, Anja Spang1,3, Thijs J. G. Ettema1,4* 1 Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden 2 Department of Earth Science, Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway 3 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, NL-1790 AB Den Burg, The Netherlands 4 Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands. † These authors contributed equally * Correspondence to: Thijs J. G. Ettema, Email: [email protected] Supplementary Information Supplementary Discussions ............................................................................................................................ 3 1. Evolutionary relationships within the Chlamydiae phylum ............................................................................. 3 2. Insights into the evolution of pathogenicity in Chlamydiaceae ...................................................................... 8 3. Secretion systems and flagella in Chlamydiae .............................................................................................. 13 4. Phylogenetic diversity of chlamydial nucleotide transporters. .................................................................... -
Lists of Names of Prokaryotic Candidatus Taxa
NOTIFICATION LIST: CANDIDATUS LIST NO. 1 Oren et al., Int. J. Syst. Evol. Microbiol. DOI 10.1099/ijsem.0.003789 Lists of names of prokaryotic Candidatus taxa Aharon Oren1,*, George M. Garrity2,3, Charles T. Parker3, Maria Chuvochina4 and Martha E. Trujillo5 Abstract We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, pro- posed between the mid- 1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evo- lutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current propos- als to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes. Introduction of the category called Candidatus was first pro- morphology, basis of assignment as Candidatus, habitat, posed by Murray and Schleifer in 1994 [1]. The provisional metabolism and more. However, no such lists have yet been status Candidatus was intended for putative taxa of any rank published in the journal. that could not be described in sufficient details to warrant Currently, the nomenclature of Candidatus taxa is not covered establishment of a novel taxon, usually because of the absence by the rules of the Prokaryotic Code. -
Bootstrap Values 1 0 0.1 Co Bin71 00388
WP 026687097.1 - Azovibrio restrictus - 3d Bootstrap values WP 027457859.1 - Dechloromonas agitata - 3d 1 WP 013293541.1 - Gallionella capsiferriformans - 3d WP 004322153.1 - Thauera aminoaromatica - 3d WP 015765571.1 - Candidatus Accumulibacter phosphatis - 3d WP 013029742.1 - Sideroxydans lithotrophicus - 3d WP 009205622.1 - Sulfuricella denitrificans - 3d WP 011380994.1 - Nitrosospira multiformis - 3d WP 011385756.1 - Magnetospirillum magneticum - 3d WP 028994701.1 - Azonexus hydrophilus - 3d WP 020162845.1 - Methyloversatilis universalis - 3d WP 022771893.1 - Symbiobacter mobilis - 3d WP 011466117.1 - Rhodoferax ferrireducens - 3d WP 011493687.1 - Burkholderia xenovorans - 3d WP 012346489.1 - Leptothrix cholodnii - 3d WP 020393771.1 - Thiothrix disciformis - 3d WP 009849435.1 - Mariprofundus ferrooxydans - 3d WP 028864775.1 - Psychromonas aquimarina - 3d WP 010959484.1 - Methylococcus capsulatus - 3d WP 029133296.1 - Sedimenticola selenatireducens - 3d S2 bin22 01677 - Gammaproteobacteria WP 020504783.1 - Lamprocystis purpurea - 3d WP 007191642.1 - Thiocapsa marina - 3d WP 028451929.1 - Chitinilyticum aquatile - 3d WP 028455450.1 - Chitinilyticum litopenaei - 3d WP 012591738.1 - Methylocella silvestris - 3d WP 006931831.1 - Labrenzia aggregata - 3d WP 011394103.1 - Hahella chejuensis - 3d S3 bin32 00249 - Planctomycetes 0 S8 bin16 03139 - Planctomycetes S2 bin2 02316 - Bacteroidetes Co bin115 00413 - Candidatus Marinimicrobia S4 bin27 00978 - Bacteroidetes Co bin11 01875 - Bacteroidetes Co bin265 02371 - Bacteroidetes S2 bin54 01708 -
The Bright Side of Microbial Dark Matter: Lessons Learned
Available online at www.sciencedirect.com ScienceDirect The bright side of microbial dark matter: lessons learned from the uncultivated majority 1 2 1 Lindsey Solden , Karen Lloyd and Kelly Wrighton Microorganisms are the most diverse and abundant life forms The first realizations of just how diverse and unexplored on Earth. Yet, in many environments, only 0.1–1% of them have microorganisms are came from analyzing microbial small been cultivated greatly hindering our understanding of the subunit ribosomal RNA (SSU or 16S rRNA) gene sequences microbial world. However, today cultivation is no longer a directly from environmental samples [7]. These analyses requirement for gaining access to information from the revealed that less than half of the known microbial phyla uncultivated majority. New genomic information from contained a single cultivated representative. Phyla com- metagenomics and single cell genomics has provided insights posed exclusively of uncultured representatives are referred into microbial metabolic cooperation and dependence, to as Candidate Phyla (CP). Borrowing language from generating new avenues for cultivation efforts. Here we astronomy, microbiologists operationally define these CP summarize recent advances from uncultivated phyla and as microbial dark matter, because these organisms likely discuss how this knowledge has influenced our understanding account for a large portion of the Earth’s biomass and of the topology of the tree of life and metabolic diversity. biodiversity, yet their basic metabolic and ecological prop- erties are not known. This uncultivated majority represents Addresses 1 a grand challenge to the scientific community and until we Department of Microbiology, The Ohio State University, Columbus, OH solve the mysteries of the CP, our knowledge of the micro- 43210, USA 2 Department of Microbiology, University of Tennessee, Knoxville, TN bial world around us is profoundly skewed by what we have 37996, USA cultivated in the laboratory [8 ]. -
Biological Capacities Clearly Define a Major Subdivision in Domain Bacteria 4 5 Raphaël Méheust+,1,2, David Burstein+,1,3,8, Cindy J
bioRxiv preprint doi: https://doi.org/10.1101/335083; this version posted May 30, 2018. 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. 1 Research article 2 3 Biological capacities clearly define a major subdivision in Domain Bacteria 4 5 Raphaël Méheust+,1,2, David Burstein+,1,3,8, Cindy J. Castelle1,2,4 and Jillian F. Banfield1,2,4,5,6,7,*,# 6 7 1Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA 8 2Innovative Genomics Institute, Berkeley, CA, USA 9 3 California Institute for Quantitative Biosciences (QB3), University of California Berkeley, CA USA 10 4Chan Zuckerberg Biohub, San Francisco, CA, USA 11 5University of Melbourne, Melbourne, VIC, Australia 12 6Lawrence Berkeley National Laboratory, Berkeley, CA, USA 13 7Department of Environmental Science, Policy and Management, University of California, Berkeley, 14 Berkeley, CA, USA 15 8Present address: School of Molecular and Cell Biology and Biotechnology, George S. Wise Faculty of 16 Life Sciences, Tel Aviv University, Tel Aviv, Israel 17 +These authors contributed equally to this work 18 *Correspondence: [email protected] 19 #Lead Contact 20 21 Resume 22 Phylogenetic analyses separate candidate phyla radiation (CPR) bacteria from other bacteria, but 23 the degree to which their proteomes are distinct remains unclear. Here, we leveraged a proteome 24 database that includes sequences from thousands of uncultivated organisms to identify protein 25 families and examine their organismal distributions. We focused on widely distributed protein 26 families that co-occur in genomes, as they likely foundational for metabolism. -
Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome Natasha K
Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome Natasha K. Dudek,1 Christine L. Sun,2,3 David Burstein,4 Rose S. Kantor,5 Daniela S. Aliaga Goltsman,2,3 Elisabeth M. Bik,2,8 Brian C. Thomas,4 Jillian F. Banfield,4,6 and David A. Relman2,3,7,9, * 1Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA 2Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA 3Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA 4Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA 5Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA 6Earth and Environmental Science, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 7Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA 8Present address: uBiome, San Francisco, CA 94105, USA 9Lead Contact *Correspondence: [email protected] Summary The vast majority of bacterial diversity lies within phylum-level lineages called “candidate phyla,” which lack isolated representatives and are poorly understood. These bacteria are surprisingly abundant in the oral cavity of marine mammals. We employed a genome-resolved metagenomic approach to recover and characterize genomes and functional potential from microbes in the oral gingival sulcus of two bottlenose dolphins (Tursiops truncatus). We detected organisms from 24 known bacterial phyla and one archaeal phylum. We also recovered genomes from two deep-branching, previously uncharacterized phylum-level lineages (here named “Candidatus Delphibacteria” and “Candidatus Fertabacteria”). The Delphibacteria lineage is found in both managed and wild dolphins; its metabolic profile suggests a capacity for denitrification and a possible role in dolphin health. -
Biosynthetic Capacity, Metabolic Variety and Unusual Biology in the CPR and DPANN Radiations Cindy J
Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations Cindy J. Castelle 1,2, Christopher T. Brown 1, Karthik Anantharaman 1,5, Alexander J. Probst 1,6, Raven H. Huang3 and Jillian F. Banfield 1,2,4* 1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. 2Chan Zuckerberg Biohub, San Francisco, CA, USA. 3Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA. 4Department of Environmental Science, Policy, and Management, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. 5Department of Bacteriology, University of WisconsinMadison, Madison, WI, USA. 6Department of Chemistry, Biofilm Center, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany. *e-mail: [email protected] Abstract Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth’s environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. -
Downloaded All Cas9 Proteins from the Refseq Database [28] and Confirmed Whether They Were Genuine Cas9 Proteins Using the Same HMM Search Pipeline
UC Berkeley UC Berkeley Previously Published Works Title Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome. Permalink https://escholarship.org/uc/item/1w91s3vq Journal Current biology : CB, 27(24) ISSN 0960-9822 Authors Dudek, Natasha K Sun, Christine L Burstein, David et al. Publication Date 2017-12-01 DOI 10.1016/j.cub.2017.10.040 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome Natasha K. Dudek,1 Christine L. Sun,2,3 David Burstein,4 Rose S. Kantor,5 Daniela S. Aliaga Goltsman,2,3 Elisabeth M. Bik,2,8 Brian C. Thomas,4 Jillian F. Banfield,4,6 and David A. Relman2,3,7,9, * 1Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA 2Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA 3Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA 4Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA 5Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA 6Earth and Environmental Science, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 7Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA 8Present address: uBiome, San Francisco, CA 94105, USA 9Lead Contact *Correspondence: [email protected] Summary The vast majority of bacterial diversity lies within phylum-level lineages called “candidate phyla,” which lack isolated representatives and are poorly understood. These bacteria are surprisingly abundant in the oral cavity of marine mammals.