Methods for General and Molecular Microbiology

Marzluf, George A.; Reddy, C. A.; Beveridge, Terrance; Schmidt, Thomas M.; Snyder, Larry; Breznak, John A.

doi:10.1128/9781555817497

Cited by 176 publications

(72 citation statements)

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“…Fatty acid profiles of the strain P51 T and related strains were shown in Table 2. The sole menaquinone of strain P51 T was MK-7, which was consistent with other members of the genus Echinicola (Kim et al 2011;Lee et al 2017;Nedashkovskaya et al 2007;Nedashkovskaya et al 2006;Srinivas et al 2012). The polar lipids included one phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, three unidentified aminolipids and one unknown lipid (Fig.…”

Section: Chemotaxonomic Characterizationsupporting

confidence: 83%

“…There were 5S rRNAs of 6, 16S rRNA of 2, 23S rRNAs of 2 and tRNAs of 43. According to the genome sequence, the DNA G + C content was 39.9 mol%, which was outside the range of existing species of genus Echinicola (Kim et al 2011;Liang et al 2016)(43.8-46.9 mol%). However, it was similar to that of unpublished species submitted in the NCBI, such as 39.8 mol% at Echinicola sp.…”

Section: Phylogenetic Analysis and Whole Genome Sequencingmentioning

confidence: 70%

“…In 2006, the genus Echinicola was first established (Nedashkovskaya et al 2006), which belonged to the family Cyclobacteriaceae in the phylum Bacteroidetes. Presently, the genus Echinicola comprises seven species, which were motile by gliding, rodshaped, heterotrophic, with non-diffusible carotenoid pigments, strictly aerobic bacteria with menaquinone-7 (MK-7) as major respiratory quinone, iso-C15:0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c) as major cellular fatty acids and the DNA G + C content ranging between 43.8 and 46.9 mol% (Jung et al 2017;Kim et al 2011;Lee et al 2017;Liang et al 2016;Nedashkovskaya et al 2007;Nedashkovskaya et al 2006;Srinivas et al 2012;Xing et al 2020). Species of the genus Echinicola were isolated from different marine habitats such as brackish water pond, coastal sediment and the sea urchin Strongylocentrotus intermedius (Lee et al 2017;Nedashkovskaya et al 2006;Srinivas et al 2012).…”

Section: Introductionmentioning

confidence: 99%

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Echinicola Salinicaeni sp. nov., A Novel Bacterium Isolated from Saltern

Han

Song

Yin

et al. 2021

Preprint

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A Gram-stain-negative, aerobiotic, pink, motile, rod-shaped bacterium, designated P51 T was isolated from saline silt samples in Yantai, China. The novel isolate was able to grow at 4–42 °C (optimum 33 °C), pH 4.0–9.0 (optimum 7.0) and with 0–11.0% NaCl (optimum 4.0%, w/v). It could grow at 4 °C, which was different from the neighbour strains. The draft genome consisted of 4111 genes with a total length of 5139782 bp and 39.9% G + C content. The 16S rRNA gene sequence analysis indicated that strain P51 T was a member of the genus Echinicola and most closely related to ‘ Echinicola shivajiensis ’ with pair-wise sequence similarity of 97.7%. Genome analysis identified genes encoding proteins relating to carbon source utilization such as glycoside hydrolases and glycosyl transferases; carotenoid biosynthesis pathway and β -lactam resistance pathway were observed. Strain P51 T shared average nucleotide identity value below 84.7%, average amino acid identity value between of 70.8 – 89.3%, digital DNA-DNA hybridization identity of between 17.9–28.2% with the closely related type strains within the genus Echinicola . The sole menaquinone was MK-7; the major fatty acids were iso-C 15:0 , summed feature 3(C 16:1 ω 7 c and/or C 16:1 ω 6 c ), summed feature 4 (anteiso-C 17:1 B and/or iso-C 17:1 I) and summed feature 9 (iso-C 17:1 ω 9 c and/or 10-methyl C 16:0 ); the polar lipids included one phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, three unidentified aminolipids and one unknown lipid. Based on phenotypic, chemotaxonomic, and phylogenetic analyses, strain P51 T represents a novel species of the genus Echinicola , for which the name Echinicola salinicaeni sp. nov. is proposed. The type strain is P51 T (KCTC 82513 T = MCCC 1K04413 T ).

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Section: Chemotaxonomic Characterizationsupporting

confidence: 83%

Section: Phylogenetic Analysis and Whole Genome Sequencingmentioning

confidence: 70%

Section: Introductionmentioning

confidence: 99%

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Echinicola Salinicaeni sp. nov., A Novel Bacterium Isolated from Saltern

Han

Song

Yin

et al. 2021

Preprint

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“…Cells are motile as determined by making a wet mount slide in which one drop of a 24 h culture incubating at 37 °C was added to a glass slide and then covered with a glass coverslip. Directional motility of the bacteria was observed using a phase contrast microscope [28]. Cells are also lecithinase-positive.…”

Section: Physiology and Chemotaxonomymentioning

confidence: 99%

Clostridium chrysemydis sp. nov., isolated from the faecal material of a painted turtle

Hunter

Lawson

Dowd

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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A strict anaerobic, Gram-stain-positive rod-shaped bacterium, designated PTT, was isolated from the faecal material of a painted turtle (Chrysemys picta). Based on a comparative 16S rRNA gene sequence analysis, the isolate was assigned to Clostridium sensu stricto with the highest sequence similarities to Clostridium moniliforme (97.4 %), Clostridium sardiniense (97.2 %) and the misclassified organism Eubacterium multiforme (97.1 %). The predominant cellular fatty acids of strain PTT were C14 : 0, C16 : 0 and an unidentified product with an equivalent chain length of 14.969. The G+C content determined from the genome was 28.8 mol%. The fermentation end products from glucose were acetate and butyrate with no alcohols detected and trace amounts of CO2 and H2 also detected; no respiratory quinones were detected. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, the isolate represents a novel species of the genus Clostridium for which the name Clostridium chrysemydis sp. nov. is proposed. The type strain is strain PTT (=CCUG 74180T=ATCC TSD-219T).

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“…Physicochemical factors (physical and chemical conditions) are abiotic factors that influence the environment. Hydrogen ion activity (pH), temperature, dissolved oxygen (DO), and ammonium (NH 4 -N) are examples of physicochemical factors [28]. Numerous previous investigations have established that the bacterial communities in freshwater is commonly strongly correlated with physicochemical factors, including temperature, pH, DO, and nutrients [24].…”

Section: Physicochemical and Deoxyribose Nucleic Acid Sequencing Factorsmentioning

confidence: 99%

Predicting Microbial Species in a River Based on Physicochemical Properties by Bio-Inspired Metaheuristic Optimized Machine Learning

Chou

Truong

et al. 2019

Sustainability

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The main goal of the analysis of microbial ecology is to understand the relationship between Earth’s microbial community and their functions in the environment. This paper presents a proof-of-concept research to develop a bioclimatic modeling approach that leverages artificial intelligence techniques to identify the microbial species in a river as a function of physicochemical parameters. Feature reduction and selection are both utilized in the data preprocessing owing to the scarce of available data points collected and missing values of physicochemical attributes from a river in Southeast China. A bio-inspired metaheuristic optimized machine learner, which supports the adjustment to the multiple-output prediction form, is used in bioclimatic modeling. The accuracy of prediction and applicability of the model can help microbiologists and ecologists in quantifying the predicted microbial species for further experimental planning with minimal expenditure, which is become one of the most serious issues when facing dramatic changes of environmental conditions caused by global warming. This work demonstrates a neoteric approach for potential use in predicting preliminary microbial structures in the environment.

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Methods for General and Molecular Microbiology

Cited by 176 publications

References 0 publications

Echinicola Salinicaeni sp. nov., A Novel Bacterium Isolated from Saltern

Echinicola Salinicaeni sp. nov., A Novel Bacterium Isolated from Saltern

Clostridium chrysemydis sp. nov., isolated from the faecal material of a painted turtle

Predicting Microbial Species in a River Based on Physicochemical Properties by Bio-Inspired Metaheuristic Optimized Machine Learning

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