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1 Immunopathogenesis Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, US Department of Health and Human Services, Bethesda, MD 20892, USA
2 Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Hamilton, MT 59840, USA
3 Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD 20892, USA
Correspondence
David E. Greenberg
degreenberg{at}niaid.nih.gov
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ABSTRACT |
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7c) and C16 : 0. The DNA base composition was 59.1 mol% G+C. The very weak production of acetic acid from ethanol, the ability to use methanol, the yellow pigmentation and high optimum temperature for growth distinguished this organism from other acetic acid bacteria. The unique phylogenetic and phenotypic characteristics suggest that the bacterium should be classified within a separate genus, for which the name Granulibacter bethesdensis gen. nov., sp. nov. is proposed. The type strain is CGDNIH1T (=ATCC BAA-1260T=DSM 17861T).
The GenBank/EMBL/DDBJ accession number for the 16S rRNA, ITS and recA gene sequences of strain CGDNIH1T are AY788950, DQ340304 and DQ340305, respectively.
A percentage similarity table of the ITS region and a phylogenetic tree based on RecA protein analysis are available as supplementary material in IJSEM Online.
These authors contributed equally to this work. 
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TOPABSTRACTMAIN TEXTREFERENCES |
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; Lisdiyanti et al., 2002; Yamashita et al., 2004; Jojima et al., 2004; Loganathan & Nair, 2004; Yukphan et al., 2005).
Chronic granulomatous disease (CGD) is a rare inherited disease of the phagocyte NADPH oxidase system, which leads to defective production of superoxide and hydrogen peroxide (Segal et al., 2000). Patients suffer from recurrent life-threatening infections with catalase-producing organisms and also develop tissue granulomas (Winkelstein et al., 2000). Organisms typically associated with CGD infection include members of the genera Staphylococcus, Serratia, Burkholderia, Nocardia and Aspergillus (Dorman et al., 2002; Guide et al., 2003; Speert et al., 1994). In August 2003, a novel Gram-negative rod was isolated from cervical and supraclavicular lymph nodes of a CGD patient (patient 1). This organism was subsequently isolated from the same patient three more times throughout 2005. A similar Gram-negative rod was isolated from two other CGD patients in December 2005 (patient 2) and in January 2006 (patient 3). Phenotypic and genotypic analyses are consistent with this being a previously undescribed bacterium in the group of acetic acid bacteria. Whole genome sequencing of the first isolate from patient 1 was performed and the sequence was deposited in the GenBank/EMBL/DDBJ databases as accession number CP000394. In this paper, we give a detailed description of the characteristics of these isolates and propose that they represent a new genus and species, Granulibacter bethesdensis gen. nov., sp. nov.
Lymph nodes from patient 1 were ground and inoculated onto various media. On initial isolation from patient 1, colonies were visible after 4–6 days of incubation on buffered charcoal yeast extract (BCYE) agar, Sabouraud dextrose agar, inhibitory mould agar and Middlebrook 7H11 agar, in either ambient air at 30 °C or 7 % CO2 at 35 °C. The isolate from patient 2 grew after 8 days in a commercial broth used for the isolation of mycobacteria (BD Bactec MGIT 960; Becton Dickinson). The isolate from patient 3 grew after 5 days on BCYE agar. Details of patient history and data on histology and pathogenicity in mice are discussed elsewhere (Greenberg et al., 2006).
For the characterization of the novel organism, we took a polyphasic taxonomic approach, using phenotypic data in the form of biochemical tests and a multilocus DNA sequence analysis for phylogenetic reconstruction. For the multilocus approach, we focused on (i) the 16S rRNA gene, (ii) the internal transcribed spacer (ITS) region and (3) the RecA protein. The first two loci have been used extensively in the phylogenetic analysis of the Acetobacteraceae (Tanasupawat et al., 2004; Ruiz et al., 2000; Lisdiyanti et al., 2000, 2002), whereas the RecA protein has been described as a model molecule for systematic studies between related species of the Alphaproteobacteria, generally producing results congruent with those obtained from 16S rRNA gene data (Eisen, 1995).
Phenotypic identification was initially attempted with commercial biochemical kits and supplementary phenotypic tests routinely used in clinical microbiology. Kits included API 20 NE (bioMérieux) and RapID NH (Remel), neither of which yielded an identification. Supplementary phenotypic characterization included tests for oxidase, catalase, oxidative–fermentative medium with either glucose, lactose, mannitol, sucrose, maltose or xylose (OF medium King; Remel), lysine- and ornithine decarboxylases (Remel), arginine dihydrolase (Remel), urease (Rapid Urea Slant; Hardy Diagnostics) and motility (Motility Test Medium; Hardy Diagnostics). Growth on methanol as a sole carbon source was performed on medium 569 (Sievers & Swings, 2005). Additional tests used for the acetic acid bacteria (Table 1) as well as morphological and physiological characterizations were carried out as described by Asai et al. (1964) and Shimwell et al. (1960).
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) containing (g l–1): glucose, 50.0; CaCO3, 12.5; autolysed yeast, 5.0; and agar, 15.0. Colonies on this medium were convex, entire and smooth and produced a yellow, non-diffusible pigment. The organism grew at a temperature range of 25–37 °C within 4 days, with an optimum temperature of 35–37 °C. There was no growth at 42 °C. The optimum pH range for growth was 5.0–6.5. The organism was able to grow at pH 3.5.
Cells of the novel organism were Gram-negative, coccobacillus to rod-shaped and non-motile. The bacterium was obligately aerobic, catalase-positive and oxidase-negative. Lysine- and ornithine decarboxylases and arginine dihydrolase were all negative. Urease was positive for the isolates from patients 1 and 2, but was weak or negative for the isolate from patient 3; there was weak acid production from glucose, but no acid production from lactose, mannitol, sucrose, maltose or xylose. The bacterium grew on glutamate and mannitol agars. It oxidized lactate and acetate to carbon dioxide and water, but the activity of the latter was weak. For tests for ketogenic activity on glycerol (dihydroxyacetone production), 1 g glucose l–1 was added to the glycerol medium because the organism failed to grow on the medium described by Shimwell et al. (1960). The bacterium did not produce dihydroxyacetone from glycerol. The organism grew on methanol as a sole carbon source. It generated acetic acid poorly on ethanol-CaCO3 agar (with 2 % CaCO3) (Asai et al., 1964). Acetic acid production was more evident on modified ethanol-CaCO3 agar plates containing lower concentrations of CaCO3. The results of these and additional biochemical tests are summarized in Table 1
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Cellular fatty acid analysis was performed as described by Weyant et al. (1996). The major fatty acids were a straight-chain unsaturated acid (C18 : 17c) and C16 : 0, which accounted for 50 and 17 % of the total cellular fatty acids, respectively. Other fatty acids identified were C19 : 0cyc11–12 (10 %) and smaller amounts of 2-OH C14 : 0, sum of 3-OH C14 : 0 and/or i-C16 : 1I, 3-OH C16 : 0, C17 : 0, C17 : 16c, C18 : 0, 2-OH C18 : 1, 2-OH C16 : 0, C16 : 17c and 3-OH C18 : 0.
DNA–DNA relatedness was determined by using the hybridization method described by Brenner et al. (1982). Purified DNA of the first isolate from patient 1 (type strain) and the isolates from patient 2 and patient 3 were prepared from lysed protoplasts based on a protocol described by Loeffelholz & Scholl (1989). In brief, bacteria grown in SOC broth were incubated for 2 h at 37 °C with 2 mg lysozyme ml–1 in 0.05 M TE buffer (pH 8.0), followed by overnight incubation at 56 °C with proteinase K (50 µg ml–1), SDS (0.5 %) and NaCl (0.1 M). Nucleic acids were purified by the phenol/chloroform/isoamyl alcohol (25 : 24 : 1, by vol.) method and treated with RNase, followed by three washes with chloroform/isoamyl alcohol (24 : 1, v/v) and sodium acetate precipitation. Subsequent isolates from patient 1 were undistinguishable from the first isolate by PFGE and repetitive sequence-based PCR (data not shown) and therefore were not assayed for DNA–DNA relatedness. DNA was labelled with [32P]dCTP by using a nick translation kit (Gibco). All reactions were performed in duplicate at 63 °C. The relative binding ratio (RBR) [(percentage of heterologous DNA bound to hydroxyapatite/percentage of homologous DNA bound to hydroxyapatite)x100] was calculated by using methods described by Brenner et al. (1983). Labelled DNA from the isolate from patient 1 showed 97 and 93 % DNA–DNA relatedness to the isolates from patients 2 and 3, respectively. When the DNA from the isolate from patient 3 was labelled, the DNA–DNA relatedness values were 90 and 92 % to the isolates of patients 1 and 2, respectively. By using the accepted interpretive criteria (an RBR greater than 70 %) (Brenner et al., 1983; Wayne et al., 1987), the DNA–DNA hybridization results confirmed that the three isolates represent a single species.
DNA was isolated using a NucliSens kit (bioMérieux). The 16S rRNA genes of the isolates from the three patients were PCR-amplified and sequenced using a MicroSeq Full Gene 16S rRNA Bacterial Isolation sequencing kit (Applied Biosystems), according to the manufacturer's protocol. Sequences were analysed using a 3100 Genetic Analyzer (Applied Biosystems). The Lasergene program (version 5.51; DNASTAR) was used for sequence assembly and alignment. The 16S rRNA gene sequences of the patients' isolates were compared with 16S rRNA gene sequences available in the GenBank/EMBL/DDBJ databases. The isolates from the three patients had identical 16S rRNA gene sequences.
Preliminary whole genome sequencing for Granulibacter bethesdensis (patient 1, first isolate) was performed using methods that have been used for several other bacteria (DelVecchio et al., 2002; Kapatral et al., 2002; Ivanova et al., 2003; D. E. Greenberg and others, unpublished results). The 16S rRNA gene, ITS region and the RecA protein-encoding gene were collected by BLAST searching of the preliminary genome assembly. Nucleotide and deduced amino acid sequences for targeted genes were analysed initially with MacVector version 6.0/7.0 software package (Oxford Molecular). DNA sequences were first aligned with the CLUSTAL W program in the lasergene software package (DNASTAR). Alignments for the 16S rRNA gene, ITS region and RecA sequences were performed following standard procedures provided by the manufacturer (DNASTAR). The alignments were transferred into the MacClade program (Maddison & Maddison, 2003) for removal of insertions/deletions (indels), sequence errors, equalizing sequence lengths and manual correction of the alignments. MacClade output files were opened in PAUP (Swofford, 2002) with an ‘include all’ line command. For the 16S rRNA gene, ITS region and RecA protein, maximum-likelihood neighbour-joining trees were created with a paraphyletic outgroup. The robustness of clade designations was tested with a full heuristic search and 1000 bootstrap replicates. The nucleotide sequence for the ITS region of Rhodospirillium rubrum was obtained from the Rhodospirillium rubrum genome project of the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/).
During genome sequencing, three homologous 16S–23S rRNA gene loci were discovered. The 16S rRNA gene was 1482 bases in length and was identical at all three loci. BLAST searches indicated that the 16S rRNA gene sequence was most similar to sequences of other organisms in the family Acetobacteraceae. Because 16S rRNA gene sequences are of varying lengths in the database, CLUSTAL W alignments were used to identify a conserved, common, internal 1381 bp region, among multiple representatives of the Acetobacteraceae. This region spanned positions 33–1413 of the 16S rRNA gene of our bacterium. Eighteen 16S rRNA gene sequences of representative taxa or type strains within and related to the family Acetobacteraceae were collected from NCBI and the resulting phylogenetic tree is shown in Fig. 1. Multiple iterations of 16S rRNA gene analyses were performed with many different species and strains of Acetobacteraceae with no strains similar to our bacterium detected (data not shown). Phylogenetic groupings of representatives of the genera Acetobacter, Gluconobacter, Saccharibacter, Swaminathania, Neoasaia, Gluconacetobacter, Acidomonas, Asaia and Kozakia, as shown in Fig. 1 are similar to what has previously been published (Jojima et al., 2004; Loganathan & Nair, 2004; Tanasupawat et al., 2004; Yukphan et al., 2004a, b, 2005) (Fig. 1). The 16S rRNA gene sequence of strain CGDNIH1T grouped within the family Acetobacteraceae, whereas the branch length and positioning indicated that it warrants separate genus-level status (Fig. 1). Percentage similarity values for the novel bacterium compared with representative members of the Acetobacteraceae ranged from 95.4 % with Gluconacetobacter liquefaciens to 86.0 % with Stella humosa (Table 2).
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) and on the ITS alone (Yukphan et al., 2004a, b). The ITS sequence of the novel bacterium was 776 bases in length and was identical at all three ribosomal loci. Given the variant lengths of ITS sequences in the database, we chose a conserved internal 734 bp region from the ITS sequence, spanning base positions 36–769, for further phylogenetic analysis. Similar regions from 14 representative taxa (including eight type strains), with a focus on the acetic acid bacteria, were collected from GenBank for analysis. The resulting phylogenetic tree is shown in Fig. 2. The grouping and associations seen in Fig. 2 for the Acetobacter, Gluconobacter and Gluconacetobacter species are compatible with previously published results for the ITS regions of these species (Loganathan & Nair, 2004; Tanasupawat et al., 2004; Yukphan et al., 2004a, b, 2005). In addition, the ITS sequence of strain CGDNIH1T demonstrated distances from these species that were apparent in our genus-level analysis (Fig. 1). Our results confirm that the ITS region in the Acetobacteraceae is well-suited to comparative analysis with the 16S rRNA gene, as demonstrated previously by Tanasupawat et al. (2004) and Yukphan et al. (2004a, b). Branch length (substitutions per site) and branching pattern support our contention that the novel organism warrants a separate genus placement within the Acetobacteraceae. Percentage similarity values of the ITS region of the novel isolate ranged from 55.3 % with Gluconobacter albidus to 42.9 % with Rhodospirillium rubrum. The percentage similarity table of the ITS region is available as Supplementary Table S1 in IJSEM Online.
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). The recA gene sequences are the only protein-encoding gene sequences that are publicly available in databases for organisms in the genera Acetobacter, Gluconobacter and Gluconacetobacter. Whereas a protein-encoding locus such as recA is subject to different functional selective pressures than the 16S rRNA gene or ITS sequences (Liiv et al., 1998), recA is considered to be a conserved gene and is suitable for multilocus phylogenetic analyses (Eisen, 1995). The recA gene of the novel isolate is 1053 bases in length and translates into 351 amino acids. Most recA genes or proteins of members of the Acetobacteraceae available in the database are partial sequences; therefore, we chose to focus on 152 amino acids encoded in 456 conserved nucleotides, spanning residues 407–863 in the recA gene of the novel organism. The results for 12 RecA sequences, including those for six type strains, with a focus again on the acetic acid bacteria, were similar to those seen for the ITS and 16S rRNA gene regions. Branching pattern and length again suggested separate genus-level status for the novel organism within the family Acetobacteraceae (a phylogenetic tree based on the RecA protein analysis is available as Supplementary Fig. S1 in IJSEM Online). Sequence similarities for the recA gene of our organism ranged from 80.6 % with Acetobacter estunensis to 71.4 % for Rhodobacter sphaeroides (data not shown), while RecA protein similarities ranged from 90.8 % with Acetobacter orleanensis to 75.0 % with Rhodobacter sphaeroides (data not shown).
Acetic acid bacteria have been isolated from fruits, fermented foods, plants, soil and water, and are important in the food and biotechnology industry (Seearunruangchai et al., 2004; Sokollek et al., 1998). Based on 16S rRNA gene sequence analysis, these bacteria are associated with a group of acidophilic bacteria in the Alphaproteobacteria (Sievers et al., 1995). The novel organism shows unique phenotypic characteristics compared with isolates belonging to the nine described genera of acetic acid bacteria, and therefore clearly represents a new taxon. Like Acidomonas methanolica, the novel bacterium is a facultative methylotroph that is able to use methanol as a sole carbon source. However, it is distinguished from Acidomonas methanolica in that it generates acetic acid poorly on ethanol-CaCO3 agar (with 2 % CaCO3), oxidizes lactate and grows on glutamate and mannitol agar, and forms colonies that are yellow-pigmented. Whereas the optimum temperature for growth of most acetic acid bacteria is 
30 °C, the novel organism prefers higher temperatures (35–37 °C). The fatty acid profile was roughly in agreement with those reported for other genera in the acetic acid bacteria, with the predominant fatty acid being C18 : 17c (Franke et al., 1999); however, the novel bacterium contained relatively high amounts of the cyclopropane fatty acid C19 : 0cyc11–12.
Multilocus sequence analysis is a widely accepted method for identifying and analysing novel genera and species or differentiating strains or isolates (Garcia-Martinez et al., 1999; Owen, 2004; Ludwig et al., 1998; Zeigler, 2003). Because of the distinctiveness of the novel organism, we undertook a multilocus sequence analysis in an effort to definitively determine the phylogenetic position of this organism. Our analyses of the 16S, ITS and RecA sequences broadly support previously published findings for members of the Acetobacteraceae (Tanasupawat et al., 2004; Yamada et al., 2000; Cleenwerck et al., 2002), while establishing a separate lineage for our organism. Our results confirm that the isolate represents a member of the Acetobacteraceae, yet is distinct enough to warrant separate genus-level designation. The name Granulibacter bethesdensis gen. nov., sp. nov. is proposed.
Description of Granulibacter gen. nov.
Granulibacter (Gra.nu.li.bac'ter. L. neut. n. granulum grain; N.L. masc. n. bacter from Gr. n. baktron rod; N.L. masc. n. Granulibacter a rod that causes granules or granuloma formation).
Cells are Gram-negative, non-motile and coccobacillus to rod-shaped. Strictly aerobic. Catalase-positive. Oxidase-negative. Urease variable. Produce a yellow pigment. Optimum temperature for growth is 35–37 °C. Optimum pH for growth is 5.0–6.5. Oxidize lactate and acetate to carbon dioxide and water, but the activity of the latter is weak. Produce little acetic acid from ethanol. Can use methanol as a sole carbon source. Prefer high glucose concentration for growth [e.g. 5 % (w/v) glucose]. Grow on glutamate agar and on mannitol agar. Ammoniacal nitrogen is assimilated on glucose medium. Do not produce dihydroxyacetone from glycerol. Acid is produced from glucose and ethanol and variably from glycerol (weak or negative reactions), but not from mannitol, sorbitol, dulcitol, lactose, sucrose, maltose or xylose. DNA base composition is 59.1 mol% G+C. The type species is Granulibacter bethesdensis.
Description of Granulibacter bethesdensis sp. nov.
Granulibacter bethesdensis (be.thes.den'sis. N.L. masc. adj. bethesdensis pertaining to Bethesda, MD, USA, where the type strain was isolated).
Characteristics are the same as those described for the genus. The type strain is strain CGDNIH1T (=ATCC BAA-1260T=DSM 17861T), which was isolated from lymph node cultures from a chronic granulomatous disease patient in Bethesda, MD, USA, in 2003.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTMAIN TEXTREFERENCES |
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Atlas, R. M. (1993). Handbook of Microbiological Media, 2nd edn. Boca Raton, FL: CRC Press.
Brenner, D. J., McWhorter, A. C., Leete Knutson, J. K. & Steigerwalt, A. G. (1982). Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds. J Clin Microbiol 15, 1133–1140.
Brenner, D. J., Hickman-Brenner, F. W., Lee, J. V. & 7 other authors (1983). Vibrio furnissii (formerly aerogenic biogroup of Vibrio fluvialis), a new species isolated from human feces and the environment. J Clin Microbiol 18, 816–824.
Cleenwerck, I., Vandemeulebroecke, K., Janssens, D. & Swings, J. (2002). Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microbiol 52, 1551–1558.[Abstract]
DelVecchio, V. G., Kapatral, V., Redkar, R. J. & 22 other authors (2002). The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc Natl Acad Sci U S A 99, 443–448.
Dorman, S. E., Guide, S. V., Conville, P. S., DeCarlo, E. S., Malech, H. L., Gallin, J. I., Witebsky, F. G. & Holland, S. M. (2002). Nocardia infection in chronic granulomatous disease. Clin Infect Dis 35, 390–394.[CrossRef][Medline]
Eisen, J. A. (1995). The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol 41, 1105–1123.[Medline]
Franke, I. H., Fegan, M., Hayward, C., Leonard, G., Stackebrandt, E. & Sly, L. I. (1999). Description of Gluconacetobacter sacchari sp. nov., a new species of acetic acid bacterium isolated from the leaf sheath of sugar cane and from the pink sugar-cane mealy bug. Int J Syst Bacteriol 49, 1681–1693.
Garcia-Martinez, J., Acinas, S. G., Anton, A. I. & Rodríguez-Valera, F. (1999). Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiol Methods 36, 54–64.
Greenberg, D. E., Ding, L., Zelazny, A. M. & 10 other authors (2006). A novel bacterium associated with lymphadenitis in a patient with chronic granulomatous disease. PloS Pathog 2, e28.[CrossRef][Medline]
Guide, S. V., Stock, F., Gill, V. J., Anderson, V. L., Malech, H. L., Gallin, J. I. & Holland, S. M. (2003). Reinfection, rather than persistent infection, in patients with chronic granulomatous disease. J Infect Dis 187, 845–853.[CrossRef][Medline]
Ivanova, N., Sorokin, A., Anderson, I. & 20 other authors (2003). Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423, 87–91.[CrossRef][Medline]
Jojima, Y., Mihara, Y., Suzuki, S., Yokozeki, K., Yamanaka, S. & Fudou, R. (2004). Saccharibacter floricola gen. nov., sp. nov., a novel osmophilic acetic acid bacterium isolated from pollen. Int J Syst Evol Microbiol 54, 2263–2267.
Kapatral, V., Anderson, I., Ivanova, N. & 22 other authors (2002). Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J Bacteriol 184, 2005–2018.
Liiv, A., Tenson, T., Margus, T. & Remme, J. (1998). Multiple functions of the transcribed spacers in ribosomal RNA operons. Biol Chem 379, 783–793.[Medline]
Lisdiyanti, P., Kawasaki, H., Seki, T., Yamada, Y., Uchimura, T. & Komagata, K. (2000). Systematic study of the genus Acetobacter with descriptions of Acetobacter indonesiensis sp. nov., Acetobacter tropicalis sp. nov., Acetobacter orleanensis (Henneberg 1906) comb. nov., Acetobacter lovaniensis (Frateur 1950) comb. nov., and Acetobacter estunensis (Carr 1958) comb. nov. J Gen Appl Microbiol 46, 147–165.
Lisdiyanti, P., Kawasaki, H., Widyastuti, Y., Saono, S., Seki, T., Yamada, Y., Uchimura, T. & Komagata, K. (2002). Kozakia baliensis gen. nov., sp. nov., a novel acetic acid bacterium in the 
-Proteobacteria. Int J Syst Evol Microbiol 52, 813–818.[Abstract]
Loeffelholz, M. J. & Scholl, D. R. (1989). Method for improved extraction of DNA from Nocardia asteroides. J Clin Microbiol 27, 1880–1881.
Loganathan, P. & Nair, S. (2004). Swaminathania salitolerans gen. nov., sp. nov., a salt-tolerant, nitrogen-fixing and phosphate-solubilizing bacterium from wild rice (Porteresia coarctata Tateoka). Int J Syst Evol Microbiol 54, 1185–1190.
Ludwig, W., Strunk, O., Klugbauer, S., Klugbauer, N., Weizenegger, M., Neumaier, J., Bachleitner, M. & Schleifer, K. H. (1998). Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19, 554–568.[CrossRef][Medline]
Maddison, D. R. & Maddison, W. P. (2003). MacClade 4: analysis of phylogeny and character evolution, version 4.06. Sunderland, MA: Sinauer Associates.
Owen, R. J. (2004). Bacterial taxonomics: finding the wood through the phylogenetic trees. In Genomics, Proteomics, and Clinical Bacteriology: Methods and Reviews, pp. 353–384. Edited by N. Woodford & A. P. Johnson. London, UK: Humana Press.
Ruiz, A., Poblet, M., Mas, A. & Guillamon, J. M. (2000). Identification of acetic acid bacteria by RFLP of PCR-amplified 16S rDNA and 16S-23S rDNA intergenic spacer. Int J Syst Evol Microbiol 50, 1981–1987.[Abstract]
Seearunruangchai, A., Tanasupawat, S., Keeratipibul, S., Thawai, C., Itoh, T. & Yamada, Y. (2004). Identification of acetic acid bacteria isolated from fruits collected in Thailand. J Gen Appl Microbiol 50, 47–53.
Segal, B. H., Leto, T. L., Gallin, J. I., Malech, H. L. & Holland, S. M. (2000). Genetic, biochemical, and clinical features of chronic granulomatous disease. Medicine 79, 170–200.[CrossRef][Medline]
Shimwell, J. L., Carr, J. G. & Rhodes, M. E. (1960). Differentiation of Acetomonas and Pseudomonas. J Gen Microbiol 23, 283–286.[Medline]
Sievers, M. & Swings, J. (2005). Genus V. Acidomonas Urakami, Tamaoka, Suzuki and Komagata 1989a, 54VP. In Bergey's Manual of Systematic Bacteriology, pp. 68–69. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
Sievers, M., Gaberthuel, C., Boesch, C., Ludwig, W. & Teuber, M. (1995). Phylogenetic position of Gluconobacter species as a coherent cluster separated from all Acetobacter species on the basis of 16S ribosomal RNA sequences. FEMS Microbiol Lett 126, 123–126.[CrossRef][Medline]
Sokollek, S. J., Hertel, C. & Hammes, W. P. (1998). Description of Acetobacter oboediens sp. nov. and Acetobacter pomorum sp. nov., two new species isolated from industrial vinegar fermentations. Int J Syst Bacteriol 48, 935–940.
Speert, D. P., Bond, M., Woodman, R. C. & Curnutte, J. T. (1994). Infection with Pseudomonas cepacia in chronic granulomatous disease: role of nonoxidative killing by neutrophils in host defense. J Infect Dis 170, 1524–1531.[Medline]
Swofford, D. L. (2002). PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), version 4. Sunderland, MA: Sinauer Associates.
Tanasupawat, S., Thawai, C., Yukphan, P., Moonmangmee, D., Itoh, T., Adachi, O. & Yamada, Y. (2004). Gluconobacter thailandicus sp. nov., an acetic acid bacterium in the alpha-Proteobacteria. J Gen Appl Microbiol 50, 159–167.
Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
Weyant, R. S., Moss, C. W., Weaver, R. E., Hollis, D. G., Jordan, J. G., Cook, E. C. & Daneshvar, M. I. (1996). Bacterial identification by cellular fatty analysis. In CDC's Identification of Unusual Pathogenic Gram-Negative and Facultatively Anaerobic Bacteria, 2nd edn. Baltimore: Williams & Wilkins.
Winkelstein, J. A., Marino, M. C., Johnston, R. B., Jr & 11 other authors (2000). Chronic granulomatous disease. Report on a national registry of 368 patients. Medicine 79, 155–169.[CrossRef][Medline]
Yamada, Y., Katsura, K., Kawasaki, H., Widyastuti, Y., Saono, S., Seki, T., Uchimura, T. & Komagata, K. (2000). Asaia bogorensis gen. nov., sp. nov., an unusual acetic acid bacterium in the -Proteobacteria. Int J Syst Evol Microbiol 50, 823–829.[Abstract]
Yamashita, S.-i., Uchimura, T. & Komagata, K. (2004). Emendation of the genus Acidomonas Urakami, Tamaoka, Suzuki and Komagata 1989. Int J Syst Evol Microbiol 54, 865–870.
Yukphan, P., Malimas, T., Takahashi, M., Potacharoen, W., Busabun, T., Tanasupawat, S., Nakagawa, Y., Tanticharoen, M. & Yamada, Y. (2004a). Re-identification of Gluconobacter strains based on restriction analysis of 16S-23S rDNA internal transcribed spacer regions. J Gen Appl Microbiol 50, 189–195.
Yukphan, P., Potacharoen, W., Nakagawa, Y., Tanticharoen, M. & Yamada, Y. (2004b). Identification of strains assigned to the genus Gluconobacter Asai 1935 based on the sequence and the restriction analyses of the 16S-23S rDNA internal transcribed spacer regions. J Gen Appl Microbiol 50, 9–15.
Yukphan, P., Malimas, T., Potacharoen, W., Tanasupawat, S., Tanticharoen, M. & Yamada, Y. (2005). Neoasaia chiangmaiensis gen. nov., sp. nov., a novel osmotolerant acetic acid bacterium in the alpha-Proteobacteria. J Gen Appl Microbiol 51, 301–311.
Zeigler, D. R. (2003). Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53, 1893–1900.
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 I. Cleenwerck, M. De Wachter, A. Gonzalez, L. De Vuyst, and P. De Vos Differentiation of species of the family Acetobacteraceae by AFLP DNA fingerprinting: Gluconacetobacter kombuchae is a later heterotypic synonym of Gluconacetobacter hansenii Int J Syst Evol Microbiol, July 1, 2009; 59(7): 1771 - 1786. [Abstract] [Full Text] [PDF]
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 D. E. Greenberg, S. F. Porcella, A. M. Zelazny, K. Virtaneva, D. E. Sturdevant, J. J. Kupko III, K. D. Barbian, A. Babar, D. W. Dorward, and S. M. Holland Genome Sequence Analysis of the Emerging Human Pathogenic Acetic Acid Bacterium Granulibacter bethesdensis J. Bacteriol., December 1, 2007; 189(23): 8727 - 8736. [Abstract] [Full Text] [PDF]
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I. Cleenwerck, N. Camu, K. Engelbeen, T. De Winter, K. Vandemeulebroecke, P. De Vos, and L. De Vuyst Acetobacter ghanensis sp. nov., a novel acetic acid bacterium isolated from traditional heap fermentations of Ghanaian cocoa beans Int J Syst Evol Microbiol, July 1, 2007; 57(7): 1647 - 1652. [Abstract] [Full Text] [PDF]
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D. Dutta and R. Gachhui Nitrogen-fixing and cellulose-producing Gluconacetobacter kombuchae sp. nov., isolated from Kombucha tea Int J Syst Evol Microbiol, February 1, 2007; 57(2): 353 - 357. [Abstract] [Full Text] [PDF]
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