Publications

4713

Abstract Xi.phi.ne.ma.to.bac'ter. Gr. neut. n. Xiphinema, ‐atos the genus name of the host organism; N.L. masc. n. bacter the equivalent of Gr. neut. n. baktron a rod; N.L. masc. n. Xiphinematobacter the rod‐shaped microbe associated with Xiphinema . Full‐grown cells are rod‐shaped with rounded ends, 0.7–1.0 × 2.1–3.2 μm ; however, cells in the J 1 (first juvenile) stage of nematode development have a wrinkled, pleomorphic shape. The longer entities usually consist of a mother cell from which a daughter cell is budding, giving rise to serial pairs typical of this bacterial genus. In thin sections cells have two or three membranes consisting of, from inside to outside, a cytoplasmic membrane, an electron‐dense outer membrane, and, in many individuals, a vacuolar membrane which is probably derived from the host cell membrane and which often shows discontinuities. No peptidoglycan layer is evident ; however, a periplasmic hexagonally arrayed monolayer of 10 nm protein units is sometimes present. Gram‐stain‐negative, nonmotile, and nonsporulating. DNA is often condensed at cell poles . Bacteria live as obligate cytoplasmic symbionts with maternal transmission in nematodes of the Xiphinema americanum group ( Nematoda, Longidoridae ), in which they are presumed to induce thelytokous ( mother‐to‐daughter ) parthenogenesis . DNA G + C content ( mol %): not determined. Type species : “ Candidatus Xiphinematobacter brevicolli ” Vandekerckhove, Willems, Gillis and Coomans 2000, 2203. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Xiphinematobacter is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Verrucomicrobiota / Terrimicrobiia / Terrimicrobiales / Chthoniobacteraceae / Candidatus Xiphinematobacter Candidatus Xiphinematobacter could not be recovered in GTDB ** . * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Cla.vi.chla.my'di.a. L. n. clava a knotty branch, rough stick, cudgel, club; N.L. fem. n. Chlamydia taxonomic name of a bacterial genus; N.L. fem. n. Clavichlamydia a club Chlamydia (the morphology of the bacteria includes the characteristic head‐and‐tail cells that have been described earlier from salmonid fish suffering from epitheliocystis). Pleomorphic or elongated , nonmotile , obligate intracellular bacteria , up to 2 μ m in length . Cells show a developmental cycle with morphologically distinct stages and thrive inside a host vacuole . Organisms were found within gill lesions of fish and are differentiated from all other chlamydiae by the morphology of the proposed elementary bodies , which show a characteristic head‐and‐tail form (Figure 1). Members have not yet been obtained in cell culture. Type species : “ Candidatus Clavichlamydia salmonicola ” corrig. Karlsen, Nylund, Watanabe, Helvik, Nylund and Plarre 2008. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Clavichlamydia is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Chlamydiota / Chlamydiia / Chlamydiales / Chlamydiaceae / Candidatus Clavichlamydia The genus Candidatus Clavichlamydia can also be recovered in the Genome Taxonomy Database (GTDB) as g__Clavichlamydia (version v220) ** . GTDB classification: d__Bacteria / p__Chlamydiota / c__Chlamydiia / o__Chlamydiales / f__Chlamydiaceae / g__Clavichlamydia * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract A.my.co.la.top'sis. N.L. fem. n. Amycolata genus belonging to the order Actinomycetales ; Gr. fem. n. opsis aspect, appearance; N.L. fem. n. Amycolatopsis that which appears similar to Amycolata . Aerobic to facultatively anaerobic , Gram‐stain‐positive , non‐acid‐fast , nonmotile , catalase‐positive actinomycetes that form branching substrate hyphae which fragment into squarish and rod‐shaped elements . When formed , aerial hyphae may be sterile or differentiate into chains of smooth‐walled , squarish to ellipsoidal spore‐like structures . Chemo‐organotrophic to facultatively autotrophic. Grows on a broad range of organic and synthetic media. Mesophilic or thermophilic. Whole‐organism hydrolysates are rich in meso ‐2 , 6‐diaminopimelic acid , arabinose , and galactose . The peptidoglycan is of the A1γ type. Muramic acid moieties are N ‐acetylated. The diagnostic phospholipid is phosphatidylethanolamine ( with or without phosphatidylmethylethanolamine ) or phosphatidylmethylethanolamine with variable occurrence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidylinositol mannosides; contains complex mixtures of saturated and branched chain fatty acids . Does not contain mycolic acids. The phylogenetic position of Amycolatopsis , as determined by 16S rRNA gene sequence analysis, is in the family Pseudonocardiaceae . Common in arid soils but has also been isolated from activated sludge, equine placentas, and from clinical and plant material. DNA G + C content ( mol %): 66–75 ( T m ; HPLC). Type species : Amycolatopsis orientalis (Pittenger and Brigham 1956) Lechevalier, Prauser, Labeda and Ruan 1986, 35 VP . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Amycolatopsis is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Bacillati / Actinomycetota / Actinomycetes / Pseudonocardiales / Pseudonocardiaceae / Amycolatopsis The genus Amycolatopsis can also be recovered in the Genome Taxonomy Database (GTDB) as g__Amycolatopsis (version v220) ** . GTDB classification: d__Bacteria / p__Actinomycetota / c__Actinomycetes / o__Mycobacteriales / f__Pseudonocardiaceae / g__Amycolatopsis * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Paracaedibacter is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Pseudomonadota / Alphaproteobacteria / Holosporales / Candidatus Paracaedibacteraceae / Candidatus Paracaedibacter Candidatus Paracaedibacter could not be recovered in GTDB ** . * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776