Phenotypic and Physiological Characterization Methods

Krieg, Noel R.; Padgett, Penelope J.

doi:10.1016/b978-0-12-387730-7.00003-6

Cited by 57 publications

(42 citation statements)

References 62 publications

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“…The formation of lactic acid isomers was determined enzymically using the dl-lactate test kit (Megazyme). Nitrate and nitrite reduction, Voges-Proskauer reaction, H 2 S production, indole production, urease production and hydrolysis of hippurate were performed as described by Krieg and Padgett [55]. Tolerance to tellurite and pyruvate utilization were determined as described by Miyashita et al [9].…”

Section: Proposal Of Lactobacillus Kosoimentioning

confidence: 99%

Proposal of Lactobacillus kosoi Chiou et al. 2018 as a later heterotypic synonym of Lactobacillus micheneri McFrederick et al. 2018, elevation of Lactobacillus plantarum subsp. argentoratensis to the species level as Lactobacillus argentoratensis sp. nov., and Lactobacillus zhaodongensis sp. nov., isolated from traditional Chinese pickle and the intestinal tract of a honey bee (Apis mellifera)

Liu

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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Lactobacillus kosoi Chiou et al. 2018 and Lactobacillus micheneri McFrederick et al. 2018 are closely related, and they share 100 % 16S rRNA gene sequence similarity, 99.6 % pheS gene sequence similarity, 100 % rpoA gene sequence similarity, 97.3 % average nucleotide identity (ANI) value and 76.6 % in silico DNA–DNA hybridization (isDDH) value, indicating that they represent the same species. Fatty acid methyl esters (FAME) analysis and phenotypic characterization also indicated that L. kosoi and L. micheneri are very similar. We propose L. kosoi Chiou et al. 2018 as a later heterotypic synonym of L. micheneri McFrederick et al. 2018. The taxonomic position of Lactobacillus plantarum subsp. argentoratensis in the L. plantarum group was re-examined using a polyphasic approach, including sequence analyses of 16S rRNA, pheS, rpoA and recA genes, average nucleotide identity analysis, in silico DNA–DNA hybridization, fatty acid methyl ester analysis and phenotypic characterization. Results of 16S rRNA gene sequence analysis indicated that L. plantarum subsp. argentoratensis was closely related to L. plantarum subsp. plantarum , L. pentosus and L. paraplantarum in the L. plantarum group, sharing 99.6–99.7 % 16S rRNA gene sequence similarities. Results of pheS, rpoA and recA gene sequence analyses indicated that L. plantarum subsp. argentoratensis was most closely related to L. plantarum subsp. plantarum , having 91.8 % pheS gene sequence similarity, 98.9 % rpoA gene sequence similarity and 93.1 % recA gene sequence similarity. L. plantarum subsp. argentoratensis DSM 16365T shared 95.6 % ANI value and 62.9 % isDDH value with L. plantarum subsp. plantarum ATCC 14917T. The low isDDH value confirmed that L. plantarum subsp. argentoratensis and L. plantarum subsp. plantarum represent two different species, rather than two different subspecies in the L. plantarum group. On the basis of the data from polyphasic characterization obtained in the present study and in previous studies, L. plantarum subsp. argentoratensis is elevated to the species level and represents a novel species of the genus Lactobacillus , for which the name Lactobacillus argentoratensis sp. nov. is proposed and the type strain is DKO 22T (=CIP 108320T=DSM 16365T=JCM 16169T). Two novel Gram-stain-positive bacterial strains, designated 1206-1T and F027-1-2, were isolated from traditional pickle in Heilongjiang Province, PR China, and from the intestinal tract of a honey bee (Apis mellifera) in Hubei Province, PR China, respectively. The two bacteria were characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, fatty acid methyl ester analysis, average nucleotide identity analysis, in silico DNA–DNA hybridization analysis and an analysis of phenotypic features. The results of 16S rRNA gene sequence analysis indicated that strains 1206-1T and F027-1-2 were distantly related to Lactobacillus sharpeae , Lactobacillus hulanensis , Lactobacillus songhuajiangensis , Lactobacillus pantheris , Lactobacillus thailandensis , Lactobacillus camelliae , Lactobacillus jixianensis , Lactobacillus nasuensis , Lactobacillus baoqingensis , Lactobacillus manihotivorans and Lactobacillus porcinae . Strain 1206-1T exhibited 94.2–96.4 % 16S rRNA gene sequence similarities, 69.5–83.3 % pheS gene sequence similarities and 73.1–90.3 % rpoA gene sequence similarities to type strains of phylogenetically related species. ANI and isDDH values between strain 1206-1T and the type strains of phylogenetically related species were 52.7–73.7 % and 21.1–30.1 %, respectively. On the basis of the data obtained in the present study, a novel species, Lactobacillus zhaodongensis sp. nov. is proposed and the type strain is 1206-1T (=CCM 8981T=CCTCC AB 2019200T=LMG 31620T).

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Section: Proposal Of Lactobacillus Kosoimentioning

confidence: 99%

Proposal of Lactobacillus kosoi Chiou et al. 2018 as a later heterotypic synonym of Lactobacillus micheneri McFrederick et al. 2018, elevation of Lactobacillus plantarum subsp. argentoratensis to the species level as Lactobacillus argentoratensis sp. nov., and Lactobacillus zhaodongensis sp. nov., isolated from traditional Chinese pickle and the intestinal tract of a honey bee (Apis mellifera)

Liu

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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“…Hydrolysis of casein, starch, gelatin, urea, CM-cellulose, tyrosine, lysine and ornithine, production of H 2 S and indole, and the Voges-Proskauer (VP) test were investigated according to previously described methods (Krieg & Padgett, 2011). Enzyme activities, carbon-source utilization and other physiological characteristics were determined with the API 50 CHE, API 20NE, and API ZYM systems (BioMerieux) according to the instructions of the manufacturer, but incubated at 25 8C.…”

Section: Flavobacterium Limnosediminis Jc2902 T (Jq928688)mentioning

confidence: 99%

Flavobacterium lutivivi sp. nov., isolated from activated sludge

Feng

Han

Nogi

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, strictly aerobic, yellow, rod-shaped bacterium, designated strain HQQ T , was isolated from a municipal wastewater treatment plant in Hebei Province, PR China. Comparative 16S rRNA gene sequence analyses showed that strain HQQ T is a member of the genus Flavobacterium and is closely related to 'Flavobacterium shanxiense' CCTCC AB 2014079 T (94.8 %) and Flavobacterium macrobrachii DSM 22219 T (94.7 %). Phylogenetic analysis showed that strain HQQ T clustered with Flavobacterium fontis JCM 18212 T and Flavobacterium squillarum KCTC 23915 T . The polar lipid profile of strain HQQ T revealed the presence of phosphatidylethanolamine, six unknown aminolipids, one unknown glycolipid and one unknown lipid and the only isoprenoid quinone was MK-6. The dominant fatty acids of strain HQQ T were iso-C 15 : 0 , C 15 : 0 and C 16 : 1 v7c. The DNA G+C content of strain HQQ T is 32 mol%. On the basis of the phylogenetic and phenotypic data, strain HQQ T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium lutivivi sp. nov. is proposed. The type strain is HQQ T (5CGMCC 1.15347 T 5KCTC 42935 T ).

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“…Aesculin hydrolysis was assessed on bile aesculin agar medium (CM0888; Oxoid). Degradation of substrates was assessed according to previously described procedures [starch (Wheater, 1955;Krieg &Padgett, 2011), andTweens 40, 60, and80 (Sierra, 1957)]. …”

Section: Strains Uc12mentioning

confidence: 99%

Rhodococcus pedocola sp. nov. and Rhodococcus humicola sp. nov., two antibiotic-producing actinomycetes isolated from soil

Nguyen

Kim

2016

International Journal of Systematic and Evolutionary Microbiology

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Two novel actinobacterial strains, UC12T and UC33 Both strains showed similar chemotaxonomic characteristics. The major fatty acids were C 16 : 0 , summed feature 3, C 18 : 1 !9c and C 18 : 0 10-methyl. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major quinone derived was MK-8(H 2 ). The cell-wall peptidoglycan contained meso-diaminopimelic acid, and galactose, glucose, arabinose and ribose were detected in whole cells. Mycolic acids were detected. The DNA G+C content of strains UC12 T and UC33 T was 72.7 mol% and 68.8 mol%,respectively. Both strains produced antibiotic(s) that inhibited bacterial pathogens but not fungi. Based on the physiological, biochemical and genotypic features and the DNA-DNA hybridization between the isolates and type strains of closely related species, we propose that these bacteria be classified as novel species of the genus Rhodococcus with the names Rhodococcus pedocola sp. nov. (type strain UC12 T =KACC 18499

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Phenotypic and Physiological Characterization Methods

Cited by 57 publications

References 62 publications

Flavobacterium lutivivi sp. nov., isolated from activated sludge

Rhodococcus pedocola sp. nov. and Rhodococcus humicola sp. nov., two antibiotic-producing actinomycetes isolated from soil

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