Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring.

A cream-coloured, Gram-negative, aerobic, non-motile moderately thermophilic, rod-to-irregular-shaped bacterium, CC-GIMAT-2(T), was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on marine agar 2216. The 16S rRNA gene sequence analysis and subsequent comparisons showed that it was placed into the genus Ruegeria with 97.4 % similarity to Ruegeria lacuscaerulensis ITI-1157(T), and a lower sequence similarity to all other species of the genus Ruegeria. Reconstruction of phylogenetic trees indicated that strain CC-GIMAT-2(T) clustered within the genus Ruegeria. Robust tree topology for the genus Ruegeria including the new strain was only obtained by including all Rhodobacteraceae type strains but not if the analysis was limited to few selected taxa. The quinone system contained exclusively ubiquinone Q-10 and the fatty acid profile consisted mainly of C18 : 1ω7c, 11-methyl C18 : 1ω7c and C12 : 0 3-OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminolipid. Other lipids were detected in moderate to minor amounts. The characteristic feature of the polyamine pattern was the predominant triamine spermidine. On the basis of the 16S rRNA gene sequence analysis and of the chemotaxonomic and physiological data, strain CC-GIMAT-2(T) represents a novel species of the genus Ruegeria, for which the name Ruegeria intermedia sp. nov. is proposed. The type strain is CC-GIMAT-2(T) ( = CCUG 59209(T) = LMG 25539(T) = CCM 7758(T)).

Virgibacillus soli sp. nov., isolated from mountain soil.

A Gram-positive bacterium (strain CC-YMP-6(T)) was isolated from soil samples collected from Yang-Ming Mountain, Taiwan. On the basis of 16S rRNA gene sequence analysis, strain CC-YMP-6(T) clearly belonged to the genus Virgibacillus and was most closely related to the type strains of Virgibacillus halophilus (96.2 % similarity) and Virgibacillus kekensis (96.3 %). The predominant isoprenoid quinone was menaquinone MK-7 and the polar lipid profile was composed of the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid plus moderate amounts of two unidentified aminophospholipids and a phospholipid. The polyamine pattern comprised spermidine as the single major component with spermine and putrescine present in minor amounts. The major fatty acids of strain CC-YMP-6(T) were iso-C(15 : 0) and anteiso-C(15 : 0). The results of physiological and biochemical tests allowed the clear phenotypic differentiation of strain CC-YMP-6(T) from all recognized species of the genus Virgibacillus. Strain CC-YMP-6(T) is therefore considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus soli sp. nov. is proposed. The type strain is CC-YMP-6(T) (=DSM 22952(T)=CCM 7714(T)).

First Report of Pathogenic Bacterium Kalamiella piersonii Isolated from Urine of a Kidney Stone Patient: Draft Genome and Evidence for Role in Struvite Crystallization.

Uropathogenic bacteria are widely distributed in the environment and urinary tract infection is implicated in kidney stone disease. Here, we report on a urease negative bacterium Kalamiella piersonii (strain YU22) isolated from the urine of a struvite stone (MgNH4PO4·6H2O) patient. The closest species, K. piersonii IIIF1SW-P2T was reported from International Space Station samples. However, there are no earlier reports on its human association. Using whole genome and experimental analysis, its involvement in urinary tract colonization and struvite crystallization was explored. The strain YU22 showed many virulence factors that are needed for host cell invasion and colonization including cell adhesion factors, swimming and swarming motilities, biofilm and siderophore among others. In vitro infection studies in HEK-293T cells demonstrated the host cell attachment and killing. It was able to utilize amino acids as sole carbon source and showed growth in synthetic and healthy urine establishing metabolic adaptation to urinary tract. Increased pH and availability of ammonium ions from amino acid breakdown promoted struvite crystallization. The results from this study support the involvement of urease negative uropathogen in the struvite lithogenesis. Further studies on other isolates of K. peirsonii are warranted to assess its health risks.

Microbacterium agarici sp. nov., Microbacterium humi sp. nov. and Microbacterium pseudoresistens sp. nov., isolated from the base of the mushroom Agaricus blazei.

Three Gram-positive, rod-shaped bacteria (strains CC-SBCK-209( T), CC-12309(T) and CC-5209(T)) were isolated from the stalk of the edible mushroom Agaricus blazei grown in the laboratory. 16S rRNA gene sequence analysis indicated that all three isolates clearly belonged to the genus Microbacterium. Strains CC-SBCK-209( T) and CC-12309(T) were most related closely to the type strain of Microbacterium halotolerans (95.9 and 96.1 % 16S rRNA gene sequence similarity, respectively). These two novel strains shared 97.9 % 16S rRNA gene sequence similarity. Levels of similarity to the type strains of all other recognized Microbacterium species were lower than 95.5 %. The third strain (CC-5209( T)) showed the highest 16S rRNA gene sequence similarity to the type strain of Microbacterium resistens (97.6 %); levels of similarity to the type strains of all other recognized Microbacterium species were lower than 96 %. The quinone systems of strains CC-SBCK-209(T), CC-12309(T) and CC-5209(T) consisted of MK-11/MK-12, MK-11/MK-10 and MK-13 as major compounds, respectively. All three strains contained ornithine in their peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The polyamine pattern consisted of spermidine and spermine as predominant components. Fatty acid profiles (anteiso-C(15 : 0), iso-C(16 : 0) and anteiso-C(17 : 0 ) as major components) supported the affiliation of all three strains to the genus Microbacterium. The results of physiological and biochemical tests and DNA-DNA hybridization experiments allowed the clear phenotypic and genotypic differentiation of strains CC-SBCK-209(T) and CC-12309( T) from M. halotolerans and other closely related Microbacterium species. Strain CC-5209(T) could be differentiated clearly from M. resistens both genotypically and phenotypically. Based on these data, the novel strains are considered to represent three novel species of the genus Microbacterium. The names proposed for these organisms are Microbacterium agarici sp. nov. [type strain CC-SBCK-209( T) (=DSM 21798(T)=CCM 7686(T))], Microbacterium humi sp. nov. [type strain CC-12309(T) (=DSM 21799(T)=CCM 7687(T))] and Microbacterium pseudoresistens sp. nov. [type strain CC-5209(T) (=DSM 22185(T)=CCM 7688(T))].

Georgenia soli sp. nov., isolated from iron-ore-contaminated soil in India.

A Gram-positive actinobacterium (CC-NMPT-T3(T)) was isolated from iron-ore-contaminated soil near New Mangalore Port, Karnataka, India. Based on 16S rRNA gene sequence similarity studies, strain CC-NMPT-T3(T) belongs to the genus Georgenia and is most closely related to Georgenia muralis (98.6 %), Georgenia ruanii (97.4 %) and Georgenia thermotolerans (97.4 %). The peptidoglycan is of the type A4alpha l-Lys<--l-Glu. The predominant isoprenoid quinone is menaquinone MK-8(H(4)) and the polar lipid profile is composed of the predominant compound diphosphatidylglycerol, moderate amounts of a phosphatidylinositol-mannoside, phosphatidylinositol and minor amounts of another phosphatidylmannoside and phosphatidylglycerol. The major fatty acids of strain CC-NMPT-T3(T) are anteiso-C(15 : 0) and iso-C(15 : 0). The results of DNA-DNA hybridizations, and physiological and biochemical tests allowed a clear phenotypic differentiation of strain CC-NMPT-T3(T) from all other Georgenia species. Strain CC-NMPT-T3(T) represents a novel species, for which the name Georgenia soli sp. nov. is proposed. The type strain is CC-NMPT-T3(T) (=DSM 21838(T)=CCM 7658(T)).

Nutritional and biological qualities of the ripened beans of Canavalia maritima from the coastal sand dunes of India.

Raw and pressure-cooked ripened beans of Canavalia maritima were assessed for nutritional quality. The beans possess high protein, carbohydrate, fiber and energy contents. Potassium, magnesium, zinc and manganese of the raw and cooked beans meet NRC/NAS recommended pattern for infants. The essential amino acids (threonine, valine, isoleucine, leucine, tyrosine/phenylalanine and lysine) in raw and cooked ripened beans fulfill the FAO/WHO/UNU recommended pattern for adults. Oleic acid in raw beans and linolenic acid in cooked beans were highest and linoleic and arachidonic acids were confined to raw beans. Cooking lowered the total phenolics, while tannins were negligible and devoid of orthodihydric phenols and trypsin inhibitors. Hemagglutinating activity decreased up to 50% in cooked beans. Rats fed with a pressure-cooked bean diet showed significant elevation of all growth and nitrogen balance parameters (P<0.05) than the rats which received the raw bean diet. The low protein quality of beans warrants appropriate thermal processing to eliminate antinutritional factors.

Sphingobium rhizovicinum sp. nov., isolated from rhizosphere soil of Fortunella hindsii (Champ. ex Benth.) Swingle.

The taxonomic status of a pale-yellow-coloured bacterial isolate from rhizosphere soil of Fortunella hindsii (Champ. ex Benth.) Swingle was characterized using a polyphasic taxonomic approach. Comparative analysis of the 16S rRNA gene sequence showed that the isolate constituted a distinct branch within the genus Sphingobium. The generic assignment was confirmed by chemotaxonomic data, which revealed the presence of a fatty acid profile that was characteristic for the genus Sphingobium, consisting of straight-chain saturated and unsaturated as well as 2-OH fatty acids and the lack of 3-OH fatty acids, ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone, and a polar lipid pattern that consisted of the predominant compounds phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, sphingoglycolipid and an unknown glycolipid. Spermidine was the major polyamine component. The genotypic and phenotypic data (physiology and fatty acid and polar lipid profiles) showed that the isolate merits classification as representing a novel species of the genus Sphingobium, for which the name Sphingobium rhizovicinum sp. nov. is proposed. The type strain is CC-FH12-1T (=CCM 7491(T)=BCRC 17770T) [corrected]