Bootstrap Values 1 0 0.1 Co Bin71 00388

Total Page:16

File Type:pdf, Size:1020Kb

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 - Bacteroidetes WP 005505390.1 - Grimontia hollisae - 3d WP 014208491.1 - Mycobacterium rhodesiae - 3d WP 027856531.1 - Marinobacterium jannaschii - 3d WP 011516268.1 - Cupriavidus metallidurans - 3d WP 011154013.1 - Ralstonia eutropha - 3d WP 008526412.1 - Halorhabdus tiamatea - 3d Co bin234 01979 - Anaerolineales S2 bin4 00755 - Anaerolineales WP 012548375.1 - Dictyoglomus thermophilum - 3d S6 bin1 00232 - Actinobacteria S2 bin32 00308 - Anaerolineales Co bin311 02097 - Anaerolineales WP 013559391.1 - Anaerolinea thermophila - 3d Co bin215 00793 - Dehalococcoidia S5 bin34 00411 - Dehalococcoidia Co bin88 00762 - Dehalococcoidia S8 bin32 00434 - Dehalococcoidia Co bin215 00438 - Dehalococcoidia S4 bin46 01100 - Dehalococcoidia Co bin12 00383 - Dehalococcoidia S7 bin29 01189 - Dehalococcoidia S7 bin23 00754 - Dehalococcoidia S8 bin17 00239 - Dehalococcoidia S5 bin21 00309 - Dehalococcoidia S4 bin35 00850 - Dehalococcoidia S7 bin20 00333 - Dehalococcoidia Co bin136 00284 - Dehalococcoidia WP 024821667.1 - Aminobacterium mobile - 3d WP 014163745.1 - Thermovirga lienii - 3d S3 bin5 03435 - Deltaproteobacteria WP 007191859.1 - Thiocapsa marina - 3d WP 007042613.1 - Thiorhodococcus drewsii - 3d WP 012971066.1 - Allochromatium vinosum - 3d WP 020504162.1 - Lamprocystis purpurea - 3d WP 011686721.1 - Solibacter usitatus - 3d WP 015724758.1 - Desulfobulbus propionicus - 3d WP 014808238.1 - Desulfomonile tiedjei - 3d WP 020876264.1 - Desulfococcus multivorans - 3d WP 011699561.1 - Syntrophobacter fumaroxidans - 3d WP 014434113.1 - Caldilinea aerophila - 3d WP 014551946.1 - Geobacter sulfurreducens - 3d WP 027388897.1 - Chrysiogenes arsenatis - 3d WP 013506608.1 - Desulfurispirillum indicum - 3d WP 015941206.1 - Chloroflexus aggregans - 3d WP 015221229.1 - Cyanobacterium aponinum - 3d WP 016514321.1 - Microcystis aeruginosa - 3d WP 011378516.1 - Synechococcus elongatus - 3d WP 006562473.1 - Oscillochloris trichoides - 3d WP 012119893.1 - Roseiflexus castenholzii - 3d WP 012167698.1 - Acaryochloris marina - 3d WP 006276675.1 - Cylindrospermopsis raciborskii - 3d WP 011321324.1 - Anabaena variabilis - 3d WP 016860165.1 - Fischerella muscicola - 3d Co bin136 00892 - Dehalococcoidia Co bin209 00923 - Dehalococcoidia S6 bin31 00658 - Dehalococcoidia Co bin183 01472 - Dehalococcoidia S4 bin46 00331 - Dehalococcoidia Co bin88 00186 - Dehalococcoidia Co bin71 00388 - Dehalococcoidia S7 bin29 00166 - Dehalococcoidia S8 bin4 00017 - Dehalococcoidia Co bin183 01095 - Dehalococcoidia S6 bin7 01035 - Deltaproteobacteria S3 bin34 01651 - Deltaproteobacteria S3 bin7 02951 - Deltaproteobacteria S6 bin7 04194 - Deltaproteobacteria Co bin201 00293 - Candidatus Latescibacteria Co bin247 00818 - Candidatus Cloacimonetes S3 bin15 00128 - Candidatus Zixibacteria WP 006930005.1 - Caldithrix abyssi - 3c WP 012309762.1 - Korarchaeum cryptofilum - 3c WP 012376486.1 - Opitutus terrae - 3c Co bin112 02088 - Unknown-5 S4 bin49 02754 - Deltaproteobacteria Co bin30 01094 - Planctomycetes S2 bin52 00693 - Candidatus Aminicenantes S3 bin39 02345 - Candidatus Cloacimonetes Co bin60 01113 - Candidatus Aminicenantes S2 bin26 00090 - Candidate Division WOR-3 S7 bin19 00750 - Candidate Division WOR-3 S2 bin48 02101 - Candidate Division WOR-3 S2 bin11 00086 - Unknown-4 S3 bin2 02233 - Unknown-4 Co bin187 00371 - Candidatus Marinimicrobia S2 bin10 01839 - Candidatus Fermentibacteria S3 bin16 01324 - Candidate Division WOR-3 Co bin148 00250 - Dehalococcoidia S8 bin32 01560 - Dehalococcoidia Co bin217 00408 - Dehalococcoidia S2 bin33 00709 - Dehalococcoidia S4 bin35 00842 - Dehalococcoidia S5 bin21 00317 - Dehalococcoidia S7 bin20 00325 - Dehalococcoidia Co bin140 00262 - Anaerolineales WP 015935331.1 - Anaeromyxobacter dehalogenans - 3c Co bin304 00829 - Planctomycetes WP 022775381.1 - Symbiobacter mobilis - 3c Co bin173 01386 - Dehalococcoidia S2 bin49 00563 - Candidatus Coatesbacteria S2 bin40 00311 - Candidatus Sumerlaeota S2 bin18 01918 - Fermentibacteria Co bin217 00325 - Dehalococcoidia S2 bin33 00557 - Dehalococcoidia S2 bin27 00492 - Dehalococcoidia S4 bin35 00837 - Dehalococcoidia S5 bin21 00322 - Dehalococcoidia S7 bin20 00320 - Dehalococcoidia S7 bin23 00037 - Dehalococcoidia S8 bin17 00447 - Dehalococcoidia S2 bin20 03877 - Anaerolineales S2 bin45 01198 - Anaerolineales S5 bin24 00172 - Anaerolineales S2 bin12 01074 - Anaerolineales Co bin259 00044 - Anaerolineales S2 bin7 00082 - Anaerolineales Co bin140 00082 - Anaerolineales S3 bin31 02337 - Planctomycetes S6 bin26 02629 - Planctomycetes S3 bin31 01121 - Planctomycetes S6 bin26 00948 - Planctomycetes S7 bin5 01277 - Planctomycetes S8 bin31 00947 - Candidatus Bathyarchaeota Co bin208 00751 - Candidatus Bathyarchaeota Co bin56 01536 - Candidatus Bathyarchaeota Co bin105 01024 - Candidatus Heimdallarchaeota Co bin117 01450 - Thermoplasmata S5 bin8 01455 - Thermoplasmata Co bin180 00016 - Dehalococcoidia Co bin266 00410 - Dehalococcoidia Co bin215 00530 - Dehalococcoidia S5 bin44 00278 - Dehalococcoidia Co bin202 00559 - Dehalococcoidia S8 bin32 00876 - Dehalococcoidia Co bin245 00532 - Deltaproteobacteria S2 bin29 00234 - Candidatus Aerophobetes WP 020448391.1 - Methanomassiliicoccus intestinalis - 3c WP 019177457.1 - Methanomassiliicoccus luminyensis - 3c WP 012302733.1 - Desulforudis audaxviator - 3c WP 015739967.1 - Ammonifex degensii - 3c WP 015617925.1 - Desulfotomaculum gibsoniae - 3c S2 bin17 01432 - Krumholzibacteriota Co bin125 00099 - Bacteroidetes Co bin11 01870 - Bacteroidetes S2 bin39 01832 - Candidatus Aminicenantes Co bin232 02054 - Bacteroidetes S3 bin26 01477 - Bacteroidetes Co bin109 00796 - Methanomicrobia Co bin186 00291 - Planctomycetes Co bin39 01452 - Planctomycetes WP 010878869.1 - Archaeoglobus fulgidus - 3c WP 012965352.1 - Ferroglobus placidus - 3c WP 013637988.1 - Desulfurobacterium thermolithotrophum - 3c WP 013908379.1 - Thermodesulfatator indicus - 3c WP 022853555.1 - Thermodesulfatator atlanticus - 3c WP 015722755.1 - Desulfobulbus propionicus - 3c WP 013756665.1 - Thermodesulfobium narugense - 3c WP 012545782.1 - Thermodesulfovibrio yellowstonii - 3c WP 028840908.1 - Thermodesulfobacterium hveragerdense - 3c Co bin41 02897 - Candidatus Heimdallarchaeota WP 015233716.1 - Natronobacterium gregoryi - 3c Co bin80 00286 - Deltaproteobacteria S6 bin7 01210 - Deltaproteobacteria WP 011700738.1 - Syntrophobacter fumaroxidans - 3c WP 015903075.1 - Desulfobacterium autotrophicum - 3c WP 015724435.1 - Desulfobulbus propionicus - 3c S2 bin41 01673 - Deltaproteobacteria WP 011188256.1 - Desulfotalea psychrophila - 3c WP 027368703.1 - Desulfovibrio africanus - 3c WP 010936390.1 - Dehalococcoides mccartyi - 3c Co bin256 01032 - Planctomycetes S6 bin7 02495 - Deltaproteobacteria S2 bin42 02118 - Planctomycetes S7 bin38 01167 - Planctomycetes WP 013218178.1 - Dehalogenimonas lykanthroporepellens - 3c S2 bin30 01314 - Candidatus Aminicenantes Co bin259 01087 - Anaerolineales S8 bin11 02253 - Anaerolineales WP 012956704.1 - Methanobrevibacter ruminantium - 3c WP 013296307.1 - Methanothermobacter marburgensis - 3c WP 011170767.1 - Methanococcus maripaludis - 3c WP 011171638.1 - Methanococcus maripaludis - 3c Co bin157 01061 - Candidatus Thorarchaeota S7 bin1 00484 - Candidatus Thorarchaeota S5 bin18 01459 - Thorarchaeota Co bin157 00883 - Candidatus Thorarchaeota Co bin7 00067 - Candidatus Lokiarchaeota S2 bin16 00638 - Candidatus Lokiarchaeota S5 bin29 01482 - Candidatus Lokiarchaeota Co bin147 00733 - Candidatus Lokiarchaeota Co bin249 01159 - Candidatus Lokiarchaeota S3 bin39 02335 - Candidatus Cloacimonetes S2 bin8 01198 - Candidatus Bathyarchaeota S8 bin31 01959 - Candidatus Bathyarchaeota S2 bin18 01492 - Fermentibacteria WP 027358538.1 - Desulforegula conservatrix - 3c WP 014551809.1 - Geobacter sulfurreducens - 3c Co bin69 00226 - Unknown Asgard group S2 bin4 00947 - Anaerolineales S3 bin21 03248 - Anaerolineales WP 013638061.1 - Desulfurobacterium thermolithotrophum - 3a WP 013537869.1 - Thermovibrio ammonificans - 3a WP 022846160.1 - Desulfurobacterium
Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Identification of a Novel Cobamide Remodeling Enzyme in the Beneficial Human Gut Bacterium Akkermansia Muciniphila
    bioRxiv preprint doi: https://doi.org/10.1101/2020.09.02.280537; this version posted September 3, 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-NC 4.0 International license. 1 Identification of a novel cobamide remodeling enzyme in the beneficial human gut bacterium 2 Akkermansia muciniphila 3 4 Kenny C. Moka, Olga M. Sokolovskayaa, Alexa M. Nicolasa, Zachary F. Hallberga, Adam 5 Deutschbauerb, Hans K. Carlsonb, and Michiko E. Tagaa# 6 7 aDepartment of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 8 9 bEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National 10 Laboratory, Berkeley, CA 11 12 #Correspondence to [email protected] 13 14 Running title: Cobamide remodeling in a beneficial gut bacterium 15 16 Abstract word count: 233 17 18 Text word count: 6,114 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.02.280537; this version posted September 3, 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-NC 4.0 International license. 19 Abstract 20 21 The beneficial human gut bacterium Akkermansia muciniphila provides metabolites to other 22 members of the gut microbiota by breaking down host mucin, but most of its other metabolic 23 functions have not been investigated. A. muciniphila is known to use cobamides, the vitamin B12 24 family of cofactors with structural diversity in the lower ligand, though the specific cobamides it 25 can use have not been examined.
    [Show full text]
  • Homeschool Record Keeping Pdf
    Homeschool record keeping pdf Continue Bacteria time range: 4100-0Ma (2) Had. Archaic proterozoic fan. Sodium - The recent E. coli Escherichia has increased 15,000 times. TaxonomyDomen: BacteriaErenberg 1828 sensu Woese, Candler and Wheelis 1990 Thermomicrobials Diedermicos (Gram negative) Atidobachacteria, Akifiki, Armatimenadeths, Bacteroids, Caldizerica, Chlamydia, Chlorobi, Chrysiogenets, Cyanobacteria, Otreabibakters, Deinococus-Termus, Dictionoglomi, Elusimitrobia, Elusimorobia, Gemmaimonedet, Kiritimatiellae, Lentisfaer, Nitrospira, Planktonite, Proteobactery, Thermodesulfobacteria, Thermotoghe, Verru Candidate Blades, Absconditabacteria, Acetothermia, Egiribacteria, Aerofonet, Aninicanates, Atribacteria, Berkelbacteria, Kalesakaantes, Calditiceota , Cloacimonetes, Coprothermobacterota, Dadabacteria, Dependent, Dormibacteraeota, Dojkabacteria, Fervidibacteria, Fermentibacteria, Gracilibacteria, Hydrogenedents, Ignavibacteria, Katanobacteria , Kryptonia, Latescibacteria, Marinimicrobia, Melenabacteria, Superphilo Microgenomathes, Modribacteria, Nitrospina, Omnitromics, Superphilo Parkcoubacteria, Peregrinibacteria, Poribacteria, Pyropristinus, Rokubacteria, Saharibacteria, Tectomcrobia, Virtacteria, Cicibacteria microorganisms measuring several micrometers (usually from 0.5 to 5 mm in length) and various forms, including spheres (coconuts), bars (bacilli), curved threads (vibrions) and helical (spirots). Bacteria are prokaryotic cells, so unlike eukaryotic cells (animals, plants, fungi, etc.), they do not have a specific nucleus
    [Show full text]
  • Thammenomicrobia
    bioRxiv preprint doi: https://doi.org/10.1101/146886; this version posted June 7, 2017. 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-NC-ND 4.0 International license. 1 Title: 2 Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate- 3 reducing benthic microbial populations 4 5 6 Authors: 7 Zainab Abdulrahman Beiruti1, Srijak Bhatnagar2, Halina E. Tegetmeyer1,3, Jeanine S. Geelhoed1,4, 8 Marc Strous1, 3, 5, S. Emil Ruff1, 5, † 9 10 Affiliations: 11 1 Max Planck Institute for Marine Microbiology, Bremen, Germany 12 2 UC Davis Genome Center, Davis, CA, USA 13 3 Institute for Genome Research and Systems Biology, Center for Biotechnology, University of 14 Bielefeld, Bielefeld, Germany 15 4 NIOZ Royal Netherlands Institute for Sea Research, Yerseke, The Netherlands 16 5 Department of Geoscience, University of Calgary, Calgary, Canada 17 18 Correspondence: 19 S. Emil Ruff 20 Department of Geoscience, University of Calgary 21 2500 University Drive NW 22 Calgary, AB, Canada T2N 1N4 23 Email: [email protected] 24 25 Running title: Ecophysiology of benthic microbial populations 26 27 Subject category: Microbial ecology and functional diversity of natural habitats 28 29 Keywords: continuous culture, sulfate reduction, fermentation, heterotrophy, metagenomics, 30 transcriptomics, candidate phylum, stability, pulse disturbance, ecogenomics, syntrophy 31 32 Conflict of interest 33 The authors declare no conflict of interest. 1 bioRxiv preprint doi: https://doi.org/10.1101/146886; this version posted June 7, 2017.
    [Show full text]
  • Genomic Insights Into Members of the Candidate Phylum Hyd24-12 Common in Mesophilic Anaerobic Digesters
    The ISME Journal (2016) 10, 2352–2364 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 OPEN www.nature.com/ismej ORIGINAL ARTICLE Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters Rasmus Hansen Kirkegaard1, Morten Simonsen Dueholm1, Simon Jon McIlroy, Marta Nierychlo, Søren Michael Karst, Mads Albertsen and Per Halkjær Nielsen Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark Members of the candidate phylum Hyd24-12 are globally distributed, but no genomic information or knowledge about their morphology, physiology or ecology is available. In this study, members of the Hyd24-12 lineage were shown to be present and abundant in full-scale mesophilic anaerobic digesters at Danish wastewater treatment facilities. In some samples, a member of the Hyd24-12 lineage was one of the most abundant genus-level bacterial taxa, accounting for up to 8% of the bacterial biomass. Three closely related and near-complete genomes were retrieved using metagenome sequencing of full-scale anaerobic digesters. Genome annotation and metabolic reconstruction showed that they are Gram-negative bacteria likely involved in acidogenesis, producing acetate and hydrogen from fermentation of sugars, and may play a role in the cycling of sulphur in the digesters. Fluorescence in situ hybridization revealed single rod-shaped cells dispersed within the flocs. The genomic information forms a foundation for a more detailed understanding of their role in anaerobic digestion and provides the first insight into a hitherto undescribed branch in the tree of life. The ISME Journal (2016) 10, 2352–2364; doi:10.1038/ismej.2016.43; published online 8 April 2016 Introduction synergistic interactions of members of the commu- nity, a reductionist approach to understand the Production of methane by anaerobic digestion (AD) ecology of the system is not possible (Kaeberlein is widely used to convert organic waste into biogas et al., 2002; Fuhrman et al., 2015).
    [Show full text]
  • Illinois Cooperation Pape ... 1 Copy.Pdf
    Delft University of Technology Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome Mei, Ran; Nobu, Masaru K.; Narihiro, Takashi; Kuroda, Kyohei; Muñoz Sierra, Julian; Wu, Zhuoying; Ye, Lin; Lee, Patrick K.H.; Lee, Po Heng; van Lier, Jules B. DOI 10.1016/j.watres.2017.07.050 Publication date 2017 Document Version Accepted author manuscript Published in Water Research Citation (APA) Mei, R., Nobu, M. K., Narihiro, T., Kuroda, K., Muñoz Sierra, J., Wu, Z., Ye, L., Lee, P. K. H., Lee, P. H., van Lier, J. B., McInerney, M. J., Kamagata, Y., & Liu, W. T. (2017). Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome. Water Research, 124, 77- 84. https://doi.org/10.1016/j.watres.2017.07.050 Important note To cite this publication, please use the final published version (if applicable). Please check the document version above. Copyright Other than for strictly personal use, it is not permitted to download, forward or distribute the text or part of it, without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license such as Creative Commons. Takedown policy Please contact us and provide details if you believe this document breaches copyrights. We will remove access to the work immediately and investigate your claim. This work is downloaded from Delft University of Technology. For technical reasons the number of authors shown on this cover page is limited to a maximum of 10. © 2017 Manuscript version made available under CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/ Postprint of Water Research Volume 124, 1 November 2017, Pages 77-84 Link to formal publication (Elsevier): https://doi.org/10.1016/j.watres.2017.07.050 1 Operation-driven Heterogeneity and Overlooked Feed-associated Populations in Global 2 Anaerobic Digester Microbiome 3 4 Ran Meia, Masaru K.
    [Show full text]
  • Novel Microorganisms and Their Function in Anaerobic Digesters
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by VBN Aalborg Universitet Novel Microorganisms and Their Function on Anaerobic Digesters Kirkegaard, Rasmus Hansen DOI (link to publication from Publisher): 10.5278/vbn.phd.engsci.00180 Publication date: 2016 Document Version Publisher's PDF, also known as Version of record Link to publication from Aalborg University Citation for published version (APA): Kirkegaard, R. H. (2016). Novel Microorganisms and Their Function on Anaerobic Digesters. Aalborg Universitetsforlag. Ph.d.-serien for Det Teknisk-Naturvidenskabelige Fakultet, Aalborg Universitet https://doi.org/10.5278/vbn.phd.engsci.00180 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. ? Users may download and print one copy of any publication from the public portal for the purpose of private study or research. ? You may not further distribute the material or use it for any profit-making activity or commercial gain ? You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us at [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from vbn.aau.dk on: December 25, 2020 NOVEL MICROORGANISMS AND THEIR FUNCTION IN ANAEROBIC DIGESTERS AND THEIR FUNCTION IN MICROORGANISMS NOVEL NOVEL MICROORGANISMS AND THEIR FUNCTION IN ANAEROBIC DIGESTERS BY RASMUS H.
    [Show full text]