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Appendix 1. New and Emended Taxa Described Since Publication of Volume One, Second Edition of the Systematics

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188 THE REVISED ROAD MAP TO THE MANUAL Appendix 1. New and emended taxa described since publication of Volume One, Second Edition of the Systematics Acrocarpospora corrugata (Williams and Sharples 1976) Tamura et Basonyms and synonyms1 al. 2000a, 1170VP Bacillus thermodenitrificans (ex Klaushofer and Hollaus 1970) Man- Actinocorallia aurantiaca (Lavrova and Preobrazhenskaya 1975) achini et al. 2000, 1336VP Zhang et al. 2001, 381VP Blastomonas ursincola (Yurkov et al. 1997) Hiraishi et al. 2000a, VP 1117VP Actinocorallia glomerata (Itoh et al. 1996) Zhang et al. 2001, 381 Actinocorallia libanotica (Meyer 1981) Zhang et al. 2001, 381VP Cellulophaga uliginosa (ZoBell and Upham 1944) Bowman 2000, VP 1867VP Actinocorallia longicatena (Itoh et al. 1996) Zhang et al. 2001, 381 Dehalospirillum Scholz-Muramatsu et al. 2002, 1915VP (Effective Actinomadura viridilutea (Agre and Guzeva 1975) Zhang et al. VP publication: Scholz-Muramatsu et al., 1995) 2001, 381 Dehalospirillum multivorans Scholz-Muramatsu et al. 2002, 1915VP Agreia pratensis (Behrendt et al. 2002) Schumann et al. 2003, VP (Effective publication: Scholz-Muramatsu et al., 1995) 2043 Desulfotomaculum auripigmentum Newman et al. 2000, 1415VP (Ef- Alcanivorax jadensis (Bruns and Berthe-Corti 1999) Ferna´ndez- VP fective publication: Newman et al., 1997) Martı´nez et al. 2003, 337 Enterococcus porcinusVP Teixeira et al. 2001 pro synon. Enterococcus Alistipes putredinis (Weinberg et al. 1937) Rautio et al. 2003b, VP villorum Vancanneyt et al. 2001b, 1742VP De Graef et al., 2003 1701 (Effective publication: Rautio et al., 2003a) Hongia koreensis Lee et al. 2000d, 197VP Anaerococcus hydrogenalis (Ezaki et al. 1990) Ezaki et al. 2001, VP Mycobacterium bovis subsp. caprae (Aranaz et al. 1999) Niemann 1526 et al. 2002, 435VP Anaerococcus lactolyticus (Li et al. 1992) Ezaki et al. 2001, 1527VP Natronobacterium nitratireducens Xin et al. 2001, 1828VP Anaerococcus octavius (Murdoch et al. 1997) Ezaki et al. 2001, Novosphingobium Takeuchi et al. 2001, 1415VP 1527VP Saccharococcus caldoxylosilyticus Ahmad et al. 2000, 522VP Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001, Saccharothrix violacea Lee et al. 2000e, 1320VP 1526VP Salibacillus marismortui (Arahal et al. 1999) Arahal et al. 2000, Anaerococcus tetradius (Ezaki et al. 1983) Ezaki et al. 2001, 1526VP 1503VP Anaerococcus vaginalis (Li et al. 1992) Ezaki et al. 2001, 1527VP Sinorhizobium adhaerens (Casida 1982) Willems et al. 2003, 1215 Anaplasma phagocytophilum (Foggie 1949) Dumler et al. 2001, (Request for an Opinion)VP 2158VP Sinorhizobium kummerowiae Wei et al. 2002, 2237VP Asanoa ferruginea (Kawamoto 1986) Lee and Hah 2002, 970VP Sinorhizobium morelense Wang et al. 2002, 1691VP Bacteriovorax starrii (Seidler et al. 1972) Baer et al. 2000, 223VP Sphingobium Takeuchi et al. 2001, 1415VP Bacteriovorax stolpii (Seidler et al. 1972) Baer et al. 2000, 223VP Sphingomonas alaskensis Vancanneyt et al. 2001a, 78VP Carnobacterium maltaromaticum (Miller et al. 1974) Mora et al. Sphingopyxis Takeuchi et al. 2001, 1415VP 2003, 677VP VP Streptococcus pasteurianus Poyart et al. 2002, 1253 Cellulomonas humilata (Gledhill and Casida 1969) Collins and Pas- VP Subtercola pratensis Behrendt et al. 2002, 1452 cual 2000, 662VP VP Vibrio viscosus Lunder et al. 2000, 447 Cellulosimicrobium cellulans (Metcalf and Brown 1957) Schumann et al. 2001, 1009VP VP New combinations Chlorobaculum tepidum (Wahlund et al. 1996) Imhoff 2003, 950 VP Acetobacter estunensis (Carr 1958) Lisdiyanti et al. 2001b, 263VP Chlorobium clathratiforme (Szafer 1911) Imhoff 2003, 948 (Effective publication: Lisdiyanti et al., 2000) Chlorobium luteolum (Schmidle 1901) Imhoff 2003, 948VP Acetobacter lovaniensis (Frateur 1950) Lisdiyanti et al. 2001b, 263 Chromohalobacter canadensis (Huval et al. 1996) Arahal et al. 2001a, (Effective publication: Lisdiyanti et al., 2000)VP 1447VP Acetobacter orleanensis (Henneberg 1906) Lisdiyanti et al. 2001b, Chromohalobacter israelensis (Huval et al. 1996) Arahal et al. 2001a, 263VP (Effective publication: Lisdiyanti et al., 2000) 1447VP Achromobacter denitrificans (Ru¨ger and Tan 1983) Coenye et al. Clostridium estertheticum subsp. laramiense (Kalchayanand et al. 2003b, 1829VP 1993) Spring et al. 2003, 1028VP Acidithiobacillus albertensis (Bryant et al. 1988) Kelly and Wood Clostridium stercorarium subsp. leptospartum (Toda et al. 1989) Far- 2000, 514VP deau et al. 2001, 1130VP Acidithiobacillus caldus (Hallberg and Lindstro¨m 1995) Kelly and Clostridium stercorarium subsp. thermolacticum (Le Ruyet et al. 1988) Wood 2000, 514VP) Fardeau et al. 2001, 1130VP Acidithiobacillus ferrooxidans (Temple and Colmer 1951) Kelly and Cobetia marina (Cobet et al. 1970) Arahal et al. 2002b, 1915VP VP Wood 2000, 513 (Effective publication: Arahal et al., 2002a) Acidithiobacillus thiooxidans (Waksman and Joffe 1922) Kelly and Comamonas aquatica (Hylemon et al. 1973) Wauters et al. 2003b, VP Wood 2000, 513 861VP Crossiella cryophila (Labeda and Lechevalier 1989) Labeda 2001, 1579VP 1. *Citations for emendations and for the original authorities for basonyms, syn- onyms, and new combinations do not appear in the bibliography unless cited Cryptosporangium minutisporangium (Ruan et al. 1986) Tamura and elsewhere in this book. Hatano 2001, 2123VP THE REVISED ROAD MAP TO THE MANUAL 189 Dendrosporobacter quercicolus (Stankewich et al. 1971) Stro¨mpl et Halothiobacillus hydrothermalis (Durand et al. 1997) Kelly and al. 2000, 105VP Wood 2000, 515VP Desulfobacula phenolica (Bak and Widdel 1988) Kuever et al. 2001, Halothiobacillus neapolitanus (Parker 1957) Kelly and Wood 2000, 175VP 515VP Desulfomicrobium macestii (Gogotova and Vainstein 1989) Hippe Hydrogenobacter hydrogenophilus (Kryukov et al. 1984) Sto¨hretal. et al. 2003, 1129VP 2001b, 1860VP Desulfosporosinus auripigmenti (Newman et al. 2000) Stackebrandt Hydrogenobaculum acidophilum (Shima and Suzuki 1993) Sto¨hr et et al. 2003, 1442VP al. 2001b, 1860VP Desulfovibrio piger (Moore et al. 1976) Loubinoux et al. 2002, Kitasatospora kifunensis (Nakagaito et al. 1993) Groth et al. 2003, VP 1307 2038VP Dorea formicigenerans (Holdeman and Moore 1974) Taras et al. Kribbella koreensis (Lee et al. 2000) Sohn et al. 2003, 1007VP VP 2002, 426 Lamprocystis purpurea (Eichler and Pfennig 1989) Imhoff 2001b, VP Ehrlichia ruminantium (Cowdry 1925) Dumler et al. 2001, 2158 1700VP VP Ensifer arboris (Nick et al. 1999) Young 2003, 2109 Lechevalieria aerocolonigenes (Labeda 1986) Labeda et al. 2001, VP Ensifer fredii (Scholla and Elkan 1984) Young 2003, 2109 1050VP VP Ensifer kostiensis (Nick et al. 1999) Young 2003, 2109 Lechevalieria flava (Gauze et al. 1974) Labeda et al. 2001, 1050VP VP Ensifer kummerowiae (Wei et al. 2002) Young 2003, 2109 Leifsonia aquatica (ex Leifson 1962) Evtushenko et al. 2000a, 377VP VP Ensifer medicae (Rome et al. 1996) Young 2003, 2109 Leifsonia cynodontis (Davis et al. 1984) Suzuki et al. 2000a, 1415VP VP Ensifer meliloti (Dangeard 1926) Young 2003, 2109 (Effective publication: Suzuki et al., 1999a) Ensifer saheli (de Lajudie et al. 1994) Young 2003, 2109VP VP Leifsonia xyli subsp. cynodontis (Davis et al. 1984) Evtushenko et Ensifer terangae (de Lajudie et al. 1994) Young 2003, 2109 VP VP al. 2000a, 378 Ensifer xinjiangensis (Chen et al. 1988) Young 2003, 2109 Leifsonia xyli subsp. xyli (Davis et al. 1984) Evtushenko et al. 2000a, Faecalibacterium prausnitzii (Hauduroy et al. 1937) Duncan et al. 378VP 2002b, 2145VP Lentzea violacea (Lee et al. 2000) Labeda et al. 2001, 1049VP Finegoldia magna (Prevot 1933) Murdoch and Shah 2000, 1415VP Lentzea waywayandensis (Labeda and Lyons 1989) Labeda et al. (Effective publication: Murdoch and Shah, 1999) 2001, 1049VP Gallibacterium anatis (Mutters et al. 1985) Christensen et al. 2003, Leuconostoc fructosum (Kodama 1956) Antunes et al. 2002, 654VP 285VP Marinibacillus marinus (Ru¨ger and Richter 1979) Yoon et al. Gallicola barnesae (Schiefer-Ullrich and Andreesen 1986) Ezaki et 2001e, 2092VP al. 2001, 1527VP Marinobacterium jannaschii (Bowditch et al. 1984) Satomi et al. Geobacillus caldoxylosilyticus (Ahmad et al. 2000) Fortina et al. 2002, 745VP 2001a, 2069VP Marinobacterium stanieri (Baumann et al. 1983) Satomi et al. 2002, Geobacillus kaustophilus (Priest et al. 1989) Nazina et al. 2001, 746VP 444VP Metallosphaera hakonensis (Takayanagi et al. 1996) Kurosawa et al. Geobacillus stearothermophilus (Donk 1920) Nazina et al. 2001, VP 443VP 2003, 1608 Methanocaldococcus fervens ( Jeanthon et al. 1999) Whitman 2002, Geobacillus thermocatenulatus (Golovacheva 1991) Nazina et al. VP 2001, 444VP 686 (Effective publication: Whitman, 2001a) Geobacillus thermodenitrificans (Manachini et al. 2000) Nazina et Methanocaldococcus infernus ( Jeanthon et al. 1998) Whitman 2002, VP al. 2001, 444VP 686 (Effective publication: Whitman, 2001a) Geobacillus thermoglucosidasius (Suzuki 1984) Nazina et al. 2001, Methanocaldococcus jannaschii ( Jones et al. 1984) Whitman 2002, VP 444VP 686 (Effective publication: Whitman, 2001a) Geobacillus thermoleovorans (Zarilla and Perry 1988) Nazina et al. Methanocaldococcus vulcanius ( Jeanthon et al. 1999) Whitman VP 2001, 444VP 2002, 686 (Effective publication: Whitman, 2001a) VP Gluconacetobacter intermedius (Boesch et al. 1998) Yamada 2000, Methanolobus oregonensis (Liu et al. 1990) Boone 2002, 686 (Ef- 2226VP fective publication: Boone, 2001c) Gluconacetobacter oboediens (Sokollek et al. 1998) Yamada 2000, Methanosalsum zhilinae (Mathrani et al. 1988) Boone and Baker VP 2226VP 2002, 686 (Effective publication: Boone and Baker,
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    Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E.
  • Targeting the Gut Microbiome in Allogeneic Hematopoietic Stem Cell Transplantation

    Targeting the Gut Microbiome in Allogeneic Hematopoietic Stem Cell Transplantation

    medRxiv preprint doi: https://doi.org/10.1101/2020.04.08.20058198; this version posted June 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Targeting the gut microbiome in allogeneic hematopoietic stem cell transplantation Marcel A. de Leeuw & Manuel X. Duval, GeneCreek List of Figures Contents 1 GM composition evolution across allo-HSCT . 2 I 2 Baseline GM composition and conditioning level . 3 NTRODUCTION 1 3 Top 10 variable importances estimated by the ran- dom survival forest models .............. 3 MATERIALS & METHODS 2 4 Biological safety level and aGvHD at onset . 3 DATA ANALYSIS .................. 2 5 Relative importance of regressors explaining the RESULTS 2 aGvHD status ...................... 3 OVERALL GM COMPOSITION EVOLUTION ACROSS 6 Co-exclusion by and co-occurrence with QPS species 4 ALLO-HSCT ................. 2 List of Tables CORRELATION BETWEEN CONDITIONING AND THE GM 2 BASELINE GM COMPOSITION AND SURVIVAL . 3 1 Prospective data sets used in the study . 1 AGVHD CASES, CONTROLS AND GM COMPOSITION 3 IMMUNO-MODULATING METABOLITES . 4 IN SILICO SCREENING OF THE ALLO-HSCT GM . 4 DISCUSSION 4 CONCLUSIONS 6 SUMMARY 6 DECLARATIONS 6 BIBLIOGRAPHY 7 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. Revised manuscript medRxiv preprint doi: https://doi.org/10.1101/2020.04.08.20058198; this version posted June 9, 2020.
  • (12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub

    (12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub

    US 2005O289672A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub. Date: Dec. 29, 2005 (54) BIOLOGICAL GENE TRANSFER SYSTEM Publication Classification FOR EUKARYOTC CELLS (75) Inventor: Richard A. Jefferson, Canberra (AU) (51) Int. Cl. ............................. A01H 1700; C12N 15/82 (52) U.S. Cl. .............................................................. 800,294 Correspondence Address: CAROL NOTTENBURG 81432ND AVE 5 SEATTLE, WA 98144 (US) (57) ABSTRACT (73) Assignee: CAMBIA Appl. No.: 10/954,147 This invention relates generally to technologies for the (21) transfer of nucleic acids molecules to eukaryotic cells. In Filed: Sep. 28, 2004 particular non-pathogenic Species of bacteria that interact (22) with plant cells are used to transfer nucleic acid Sequences. Related U.S. Application Data The bacteria for transforming plants usually contain binary vectors, Such as a plasmid with a Vir region of a Tiplasmid (60) Provisional application No. 60/583,426, filed on Jun. and a plasmid with a T region containing a DNA sequence 28, 2004. of interest. pEHA105 244981 bp M3REW M13Fw f1 origin accA W pEHA105::pWBE58 (Km, Ap) moaa. Patent Application Publication Dec. 29, 2005 Sheet 1 of 24 US 2005/0289672 A1 FIGURE 1A CLASS ALPHAPROTEOBACTERIA ORDER Rhizobiales family Rhizobiaceae bgenus Rhizobium (includes former Agrobacterium) bgenus Chelatobacter bgenus Sinorhizobium Dunclassified Rhizobiaceae family Bartonellaceae bgenus Bartonella Dunclassified Bartonellaceae family Brucellaceae