Enterococcus florum sp. nov., isolated from a cotton flower (Gossypium hirsutum L.)

Techo, Sujitra; Shiwa, Yuh; Tanaka, Naoto; Fujita, Nobuyuki; Miyashita, Mika; Shibata, Chiyo; Booncharoen, Auttaporn; Tanasupawat, Somboon

doi:10.1099/ijsem.0.003524

Cited by 12 publications

(5 citation statements)

References 23 publications

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“…To perform high-throughput sequencing, bacterial DNA isolated from feces was amplified with the universal direct 785F forward primer (5'-GGATTAGATACCCTGGTA) and reverse 1100R primer (5'-GGGTTGCGCTCGTTG) [20]. PCR was performed using a 5X ScreenMix-HS Master Mix (Evrogen, Russia) in the following regime: 94˚for 4 min followed by 37 cycles of 94˚for 30 s, 53˚for 30 s, and 72˚for 30 s with the final elongation at 72˚for 5 min.…”

Section: High-throughput Sequencingmentioning

confidence: 99%

Effect of long-term methylene blue treatment on the composition of mouse gut microbiome and its relationship with the cognitive abilities of mice

et al. 2020

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In recent years, methylene blue (MB) has attracted considerable interest as a potential drug for the treatment of methemoglobinemia and neurodegenerative diseases. MB is active against microorganisms from various taxonomic groups. However, no studies have yet been conducted on the effect of MB on the intestinal microbiome of model animals. The aim of this work was to study the effect of different concentrations of MB on the mouse gut microbiome and its relationship with the cognitive abilities of mice. We showed that a low MB concentration (15 mg/kg/day) did not cause significant changes in the microbiome composition. The Bacteroidetes/Firmicutes ratio decreased relative to the control on the 2nd and 3rd weeks. A slight decrease in the levels Actinobacteria was detected on the 3rd week of the experiment. Changes in the content of Delta, Gamma, and Epsilonproteobacteria have been also observed. We did not find significant alterations in the composition of intestinal microbiome, which could be an indication of the development of dysbiosis or other gut dysfunction. At the same time, a high concentration of MB (50 mg/kg/day) led to pronounced changes, primarily an increase in the levels of Delta, Gamma and Epsilonproteobacteria. Over 4 weeks of therapy, the treatment with high MB concentration has led to an increase in the median content of Proteobacteria to 7.49% vs. 1.61% in the control group. Finally, we found that MB at a concentration of 15 mg/kg/day improved the cognitive abilities of mice, while negative correlation between the content of Deferribacteres and cognitive parameters was revealed. Our data expand the understanding of the relationship between MB, cognitive abilities, and gut microbiome in respect to the antibacterial properties of MB.

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Section: High-throughput Sequencingmentioning

confidence: 99%

Effect of long-term methylene blue treatment on the composition of mouse gut microbiome and its relationship with the cognitive abilities of mice

et al. 2020

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“…PCR was performed on individual bacterial colonies using a ScreenMix-HS reaction mixture (Evrogen, Moscow, Russia) in an Eppendorf MasterCycler Personal cycler. Direct and reverse primers for bacterial DNA amplification were 785F (5 -GGATTAGATACCCTGGTA) and 1492R (5 -TACGGYTACCTTGTTACGACTT) [17], respectively. PCR was performed in the following regime: Denaturation at 94 • C for 4 min, 35 cycles of 94 • C for 30 s, 52 • C for 30 s, and 72 • C for 45 s, and final elongation at 72 • C for 10 min.…”

Section: Dna Barcodingmentioning

confidence: 99%

“…The microorganisms were collected from the enrichment broth medium by centrifugation at 10,000× g for 5 min. Bacterial DNA isolated from collected bacteria was amplified with the universal direct 785F forward primer (5 -GGATTAGATACCCTGGTA) and reverse 1100R primer (5 -GGGTTGCGCTCGTTG) [17]. PCR was performed using a ScreenMix-HS Master Mix (Evrogen, Moscow, Russia) in the following regime: 94 • C for 4 min followed by 37 cycles of 94 • C for 30 s, 53 • C for 30 s, and 72 • C for 30 s, with the final elongation at 72 • C for 5 min.…”

Section: High-throughput Sequencingmentioning

confidence: 99%

High-Throughput 16S rRNA Gene Sequencing of Butter Microbiota Reveals a Variety of Opportunistic Pathogens

Syromyatnikov

Kokina

Solodskikh

et al. 2020

Foods

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Microbial contamination of dairy products with a high fat content (e.g., butter) has been studied insufficiently. No studies using modern molecular methods to investigate microbial communities in butter have been conducted so far. In this work, we used high-throughput sequencing and Sanger sequencing of individual bacterial colonies to analyze microbial content of commercially available butter brands. A total of 21 samples of commercially available butter brands were analyzed. We identified a total of 94 amplicon sequence variants corresponding to different microbial taxa. The most abundant lactic acid bacteria in butter were Lactobacillus kefiri, Lactobacillus parakefiri, Lactococcus taiwanensis and Lactococcus raffinolactis. A large amount of Streptococcus spp. bacteria (87.9% of all identified bacteria) was found in one of the butter samples. Opportunistic pathogens such as Bacillus cereus group, Pseudomonas aeruginosa, Cronobacter spp., Escherichia coli, Listeria innocua, Citrobacter spp., Enterococcus spp., Klebsiella pneumonia were detected. The analyzed butter samples were most strongly contaminated with bacteria from the Bacillus cereus group, and to a lesser extent - with Cronobacter spp. and Enterococcus spp. The plating and Sanger sequencing of individual colonies revealed the presence of Enterobacter cloacae and Staphylococcus epidermidis. The Sanger sequencing also showed the presence of Cronobacter sakazakii in butter which can be dangerous for children under the age of 1 year. We demonstrated that butter is a good growth medium for opportunistic pathogenic bacteria. Our data indicate that despite the fact that butter is a dairy product with a long shelf life, it should be subjected to quality control for the presence of opportunistic bacteria.

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“…Digital DNA–DNA hybridization (dDDH) was also calculated using the blast + method of the Genome-to-Genome Distance Calculator version 2.1 [29]. The results were based on formula 2 [30].…”

Section: Genomic Featuresmentioning

confidence: 99%

Rhizobium dioscoreae sp. nov., a plant growth-promoting bacterium isolated from yam (Dioscorea species)

Ouyabe

Tanaka

Shiwa

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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This study investigated endophytic nitrogen-fixing bacteria isolated from two species of yam (water yam, Dioscorea alata L.; lesser yam, Dioscorea esculenta L.) grown in nutrient-poor alkaline soil conditions on Miyako Island, Okinawa, Japan. Two bacterial strains of the genus Rhizobium , S-93T and S-62, were isolated. The phylogenetic tree, based on the almost-complete 16S rRNA gene sequences (1476 bp for each strain), placed them in a distinct clade, with Rhizobium miluonense CCBAU 41251T, Rhizobium hainanense I66T, Rhizobium multihospitium HAMBI 2975T, Rhizobium freirei PRF 81T and Rhizobium tropici CIAT 899T being their closest species. Their bacterial fatty acid profile, with major components of C19 : 0 cyclo ω8c and summed feature 8, as well as other phenotypic characteristics and DNA G+C content (59.65 mol%) indicated that the novel strains belong to the genus Rhizobium . Pairwise average nucleotide identity analyses separated the novel strains from their most closely related species with similarity values of 90.5, 88.9, 88.5, 84.5 and 84.4 % for R. multihospitium HAMBI 2975T, R. tropici CIAT 899T, R. hainanense CCBAU 57015T, R. miluonense HAMBI 2971T and R. freirei PRF 81T, respectively; digital DNA–DNA hybridization values were in the range of 26–42 %. Considering the phenotypic characteristics as well as the genomic data, it is suggested that strains S-93T and S-62 represent a new species, for which the name Rhizobium dioscoreae is proposed. The type strain is S-93T (=NRIC 0988T=NBRC 114257T=DSM 110498T).

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Enterococcus florum sp. nov., isolated from a cotton flower (Gossypium hirsutum L.)

Cited by 12 publications

References 23 publications

Effect of long-term methylene blue treatment on the composition of mouse gut microbiome and its relationship with the cognitive abilities of mice

Effect of long-term methylene blue treatment on the composition of mouse gut microbiome and its relationship with the cognitive abilities of mice

High-Throughput 16S rRNA Gene Sequencing of Butter Microbiota Reveals a Variety of Opportunistic Pathogens

Rhizobium dioscoreae sp. nov., a plant growth-promoting bacterium isolated from yam (Dioscorea species)

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