| 1. |
- Murray, Alison E., et al.
(författare)
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Roadmap for naming uncultivated Archaea and Bacteria
- 2020
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Ingår i: Nature Microbiology. - : NATURE PUBLISHING GROUP. - 2058-5276. ; 5:8, s. 987-994
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Tidskriftsartikel (refereegranskat)abstract
- The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity. In this Consensus Statement, the authors discuss the issue of naming uncultivated prokaryotic microorganisms, which currently do not have a formal nomenclature system due to a lack of type material or cultured representatives, and propose two recommendations including the recognition of DNA sequences as type material.
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| 2. |
- Haefele, A., et al.
(författare)
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Validation of ground-based microwave radiometers at 22 GHz for stratospheric and mesospheric water vapor
- 2009
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Ingår i: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 114:23
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Tidskriftsartikel (refereegranskat)abstract
- We present a detailed intercomparison of five ground-based 22 GHz microwave radiometers for stratospheric and mesospheric water vapor. Four of these instruments are members of the Network for the Detection of Atmospheric Composition Change (NDACC). The global measurements of middle atmospheric water vapor of the Microwave Limb Sounder (MLS) onboard the Aura satellite serve as reference and allow intercomparison of the ground-based systems that are located between 45 degrees S and 57 degrees N. The retrievals of water vapor profiles from the ground-based radiation measurements have been made consistent to a large extent: for the required temperature profiles, we used the global temperature measurements of MLS and we agreed on one common set of spectroscopic parameters. The agreement with the reference measurements is better than +/- 8% in the altitude range from 0.01 to 3 hPa. Strong correlation is found between the ground-based and the reference data in the mesosphere with respect to seasonal cycle and planetary waves. In the stratosphere the measurements are generally more noisy and become sensitive to instrumental instabilities toward lower levels (pressures greater than 3 hPa). We further present a compilation of a NDACC data set based on the retrieval parameters described herein but using a temperature climatology derived from the MLS record. This makes the ground-based measurements independent of additional information and allows extension of the data set for years in a homogeneous manner.
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| 3. |
- Huber, Birgit, et al.
(författare)
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Ochrobactrum pituitosum sp. nov., isolated from an industrial environment.
- 2010
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 60:Pt 2, s. 321-6
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Tidskriftsartikel (refereegranskat)abstract
- Strain CCUG 50899, a Gram-negative, rod-shaped, non-spore-forming, motile bacterium isolated from industrial environment in Sweden and tentatively assigned to the species Ochrobactrum anthropi, was studied in order to clarify its taxonomic status. 16S rRNA gene sequence similarities placed the strain in the genus Ochrobactrum, sharing highest similarity with the type strains of Ochrobactrum rhizosphaerae (99.3 %), Ochrobactrum thiophenivorans (98.7 %), Ochrobactrum pseudogrignonense (98.6 %) and Ochrobactrum grignonense (98.5 %). The fatty acid profile of [O. anthropi] CCUG 50899 (major fatty acids C(18 : 1)omega7c and C(19 : 0) cyclo omega8c and presence of C(18 : 1) 2-OH), the polar lipid profile (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, two unknown aminolipids and an unknown phospholipid), the presence of the quinone system ubiquinone Q-10 and a polyamine pattern with the major compounds putrescine and spermidine and moderate amounts of sym-homospermidine supported its affiliation to the genus Ochrobactrum. DNA-DNA reassociation experiments with the type strains of its closest relatives O. rhizosphaerae, O. pseudogrignonense, O. thiophenivorans and O. grignonense demonstrated that [O. anthropi] CCUG 50899 should be placed in a novel species, which is distinguishable from related species by a set of biochemical traits. Based on these data, reclassification of [O. anthropi] CCUG 50899 as the type strain of a novel species appears to be justified. Hence, we describe a novel species to accommodate this strain, for which we propose the name Ochrobactrum pituitosum sp. nov. The type strain is CCUG 50899(T) (=DSM 22207(T)).
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| 4. |
- Kämpfer, Peter, et al.
(författare)
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A revision of Massilia La Scola et al. 2000, with an emended description of the genus, and the inclusion of all species of the genus Naxibacter as new combinations and a proposal of Massilia consociata sp. nov.
- 2011
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 61:7, s. 1528-1533
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Tidskriftsartikel (refereegranskat)abstract
- A Gram-negative, rod-shaped, non-spore-forming bacterium originating from a human clinical specimen was studied for its taxonomic position. 16S rRNA gene sequence similarity studies clearly allocated this strain (CCUG 58010T) to the Betaproteobacteria, closely related to members of both genera Massilia and Naxibacter. Naxibacter varians was shown to be the most closely related species on the basis of 16S rRNA gene sequence similarity (97,5%), followed by Massilia niastensis (96.8%) and Massilia aerilata (96.4%). Similarities to all other Naxibacter and Massilia species were in a range of 93.9 - 96.2%. Chemotaxonomic data (major ubiquinone: Q-8; major polar lipids: phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, and major fatty acids: summed feature 3 (C16:1omega7c/2-OH and/or iso-C15:0 2-OH), C16:0, C18:1omega7c, C12:0 and with C10:0 3-OH as hydroxylated fatty acid) supported the affiliation of the isolate to these genera, which are sharing these chemotaxonomic traits. DNA-DNA hybridization of strain CCUG 58010T with the type strain of N. varians CCUG 35299T resulted in values of 39.2% (reciprocal, 50%) and physiological and biochemical tests allowed also a phenotypic differentiation of the isolate from the most closely related species. There is currently no justification for a division of Massilia and Naxibacter and for this reason a proposal is made to transfer all Naxibacter species to the genus Massilia, as Massilia alkalitolerans comb. nov., Massilia varians comb. nov., Massilia haematophila comb. nov, and Massilia suwonensis comb. nov. Strain CCUG 58010T represents a novel species, for which the name Massilia consociata sp. nov. is proposed, with the type strain CCUG 58010T (= CCM 7792T).
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| 5. |
- Kämpfer, Peter, et al.
(författare)
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Corynebacterium lubricantis sp. nov., isolated from a coolant lubricant.
- 2009
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 59:5, s. 1112-1115
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Tidskriftsartikel (refereegranskat)abstract
- Three Gram-positive, rod-shaped, oxidase-negative, non-spore-forming, non-motile bacteria (KSS-3Se(T), KSS-4Se and KSS-10Se) were isolated from a coolant lubricant. 16S rRNA gene sequence analyses revealed almost identical sequences, with only a few (<10 positions) differences for these three isolates. Comparisons showed the highest similarities to Corynebacterium pilosum NCTC 11862(T) (97.6 % similarity with strain KSS-3Se(T)). Similarities with other established Corynebacterium species were lower than 97.0 %. Chemotaxonomic data studied for strain KSS-3Se(T) [polar lipids - major compounds phosphatidylglycerol and an unknown glycolipid, moderate amounts of phosphatidylinositol and diphosphatidylglycerol; polyamines (small amounts) - major compounds spermidine and spermine; quinones - significant amounts of menaquinones MK-9(H(2)), MK-8(H(2)) and MK-7(H(2)); and major fatty acids - tuberculostearic acid (10-methyl C(18 : 0)), C(16 : 0) and C(18 : 1)omega9c] were congruent with those reported for Corynebacterium. The strain showed differences in phenotype from C. pilosum. DNA-DNA hybridizations between KSS-3Se(T) and C. pilosum DSM 20521(T) yielded a relatedness of 22.9 % (20.4 % in the reciprocal assay). From these results, it is evident that the organisms represent a novel species, for which the name Corynebacterium lubricantis sp. nov. is proposed (type strain KSS-3Se(T) =DSM 45231(T) =CCUG 56567(T) =CCM 7546(T)).
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| 6. |
- Kämpfer, Peter, et al.
(författare)
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Deinococcus aquatilis sp. nov., isolated from water.
- 2008
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 58:12, s. 2803-2806
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Tidskriftsartikel (refereegranskat)abstract
- A pale-pink strain (CCUG 53370(T)) from water was investigated by a polyphasic taxonomic approach. The cells stained Gram-positive and were rod-shaped and non-spore-forming. Analyses using the 16S rRNA gene sequence of the isolate showed that the organism belongs to the genus Deinococcus, with the highest sequence similarities to the type strains of Deinococcus ficus (94.4 %), Deinococcus navajonensis (94.3 %) and Deinococcus mumbaiensis (94.3 %). Chemotaxonomic data revealed that CCUG 53370(T) contains exclusively menaquinone MK-8 as the respiratory quinone and a complex polar lipid profile consisting of different unidentified glycolipids and polar lipids, two unknown phospholipids and three unknown phosphoglycolipids. As in other deinococci, one of these phosphoglycolipids was predominant in the profile, and it was identified in Deinococcus radiodurans as 2'-O-(1,2-diacyl-sn-glycero-3-phospho)-3'-O-(alpha-galactosyl)-N-D-glyceroyl alkylamine. Predominant fatty acids were C(16 : 1)omega7c, C(17 : 1)omega8c and C(17 : 1)omega9c. Biochemical and chemotaxonomic properties demonstrate that strain CCUG 53370(T) represents a novel species, for which the name Deinococcus aquatilis sp. nov. is proposed. The type strain is CCUG 53370(T) (=CCM 7524(T)).
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| 7. |
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| 8. |
- Kämpfer, Peter, et al.
(författare)
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Hydrotalea flava gen. nov., sp. nov., a new species of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov.
- 2011
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 61:3, s. 518-523
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Tidskriftsartikel (refereegranskat)abstract
- Three orange pigmented bacterial isolates (strain CCUG 51397T, CCUG 53736 and CCUG 53920) isolated from water of different locations in Southern Sweden were studied for their taxonomic position in a polyphasic approach. Comparative analysis of 16S rRNA gene sequences showed that these bacteria had <93% similarity to all described species of the genera Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas, and Chitinophaga. The three organisms grouped most closely to Sediminibacterium salmoneum, but showed only 92.5% similarity to the only species of this genus. The fatty acid profile showed high amounts of iso 15:0, iso 17:0 3-OH and iso 15:1G and minor amounts of iso 15:0 3-OH, iso 16:0 3-OH and other fatty acids, allowing the differentiation of the genus from the other genera. Biochemical test patterns differed also from that of Sediminibacterium salmoneum and the other genera. On the basis of these data, it is proposed that the strains are representative of a novel genus, for which the name Hydrotalea gen. nov. is proposed. The type strain for Hydrotalea flava sp. nov. is CCUG 51397T = CCM 7760T. A formal allocation of the genera Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas, and Chitinophaga to the family Chitinophagaceae fam. nov. is proposed .
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| 9. |
- Kämpfer, Peter, et al.
(författare)
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Janibacter anophelis sp. nov., isolated from the midgut of Anopheles arabiensis
- 2006
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Ingår i: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 56:2, s. 389-392
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Tidskriftsartikel (refereegranskat)abstract
- A Gram-positive, aerobic, non-motile strain, H2.16BT, isolated from the midgut of the mosquito Anopheles arabiensis was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity studies, strain H2.16BT was shown to belong to the genus Janibacter, being most closely related to Janibacter melonis (98.3%), Janibacter terrae (98.5%) and Janibacter limosus (98.5%). Chemotaxonomic data (meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall and major fatty acids of iso-C16:0, C17:1omega8c and C17:0)) supported the allocation of the strain to the genus Janibacter. The results of DNA-DNA hybridization and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain H2.16BT from closely related species. Thus, H2.16BT represents a novel species of the genus Janibacter, for which the name Janibacter anophelis sp. nov. is proposed. The type strain is H2.16BT (=CCUG 49715T=CIP 108728T).
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| 10. |
- Kämpfer, Peter, et al.
(författare)
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Luteibacter anthropi sp. nov., isolated from human blood, and reclassification of Dyella yeojuensis Kim et al. 2006 as Luteibacter yeojuensis comb. nov.
- 2009
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 59:11, s. 2884-2887
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Tidskriftsartikel (refereegranskat)abstract
- A yellow-pigmented bacterium was isolated from blood of a 3-year-old boy in Göteborg, Sweden. Comparative analysis of 16S rRNA gene sequences showed that this bacterium is most closely related to Luteibacter rhizovicinus LJ96(T) and Dyella yeojuensis R2A16-10(T), with sequence similarity of 98.3 % to both. Strain CCUG 25036(T) is clearly different from L. rhizovicinus CCUG 50033(T) and also from D. yeojuensis DSM 17673(T) in that DNA-DNA hybridization revealed relatedness of 33.7 and 29.8 %, respectively. Strain CCUG 25036(T) is further distinguished from L. rhizovicinus CCUG 50033(T) and D. yeojuensis DSM 17673(T) by being able to use d-mannose, d-mannitol and gluconate as sole carbon sources and by lacking the ability to use maltose or sucrose as sole carbon sources. The name Luteibacter anthropi sp. nov. is proposed for this novel species, with the type strain CCUG 25036(T) (=CCM 7598(T)). The proposal is also made to reclassify Dyella yeojuensis as Luteibacter yeojuensis comb. nov., with the type strain R2A16-10(T) (=DSM 17673(T) =KACC 11405(T)).
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