scholarly journals Isolation, Characterization, and Molecular Identification of Indigenous Bacteria from Fermented Almonds (Prunus dulcis)

2020 ◽  
pp. 15-22
Author(s):  
Salwa Nurhasanah ◽  
Edy Fachrial ◽  
Nyoman Ehrich Lister
Keyword(s):  
Bacillus Subtilis ◽  
Bacillus Licheniformis ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Diffusion Method ◽  
Subtilis Strain ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Disk Diffusion Method ◽  
Indigenous Bacteria

Aims: This study aims to isolate and identify the indigenous bacteria of almonds fermentation. Methods: Characterization of the indigeneous bacteria are using gram staining, biochemical tests, 16SrRNA gene sequencing, and the antimicrobial activity against Escherichia coli bacteria. Results: Approximately 28 x 106 CFU / mL bacteria were obtained from almonds fermentations with 14 isolates from enrichment results. Three randomly selected isolates were gram-positive rod-shaped with a negative catalase and positive fermentation test. However, one isolate showed positive results on the motility test. The antimicrobial test results from the three randomly selected isolates using the disk diffusion method obtained inhibition zones of 7 mm, 6.7 mm, and 7 mm, respectively. Therefore, by using 16S rRNA gene sequencing, three different microorganisms were found, namely Bacillus subtilis strain IAM 12118, Bacillus Piscis strain 16MFT21, and Bacillus licheniformis strain BaDB27. Conclusion: It was found that Bacillus subtilis strain IAM 12118, Bacillus Piscis strain 16MFT21, and Bacillus licheniformis strain BaDB27 in almonds fermentation and also can be used as probiotic bacteria.

scholarly journals Live Bacillus subtilis natto Promotes Rumen Fermentation by Modulating Rumen Microbiota In Vitro

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1519
Author(s):  
Meinan Chang ◽  
Fengtao Ma ◽  
Jingya Wei ◽  
Junhao Liu ◽  
Xuemei Nan ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
16S Rrna ◽  
Rumen Fluid ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rumen Fermentation ◽  
Rrna Gene ◽  
Bacillus Subtilis Natto ◽  
Rrna Gene Sequencing

Previous studies have shown that Bacillus subtilis natto affects rumen fermentation and rumen microbial community structure, which are limited to detect a few microbial abundances using traditional methods. However, the regulation of B. subtilis natto on rumen microorganisms and the mechanisms of microbiota that affect rumen fermentation is still unclear. This study explored the effects of live and autoclaved B. subtilis natto on ruminal microbial composition and diversity in vitro using 16S rRNA gene sequencing and the underlying mechanisms. Rumen fluid was collected, allocated to thirty-six bottles, and divided into three treatments: CTR, blank control group without B. subtilis natto; LBS, CTR with 109 cfu of live B. subtilis natto; and ABS, CTR with 109 cfu of autoclaved B. subtilis natto. The rumen fluid was collected after 0, 6, 12, and 24 h of fermentation, and pH, ammonia nitrogen (NH3-N), microbial protein (MCP), and volatile fatty acids (VFAs) were determined. The diversity and composition of rumen microbiota were assessed by 16S rRNA gene sequencing. The results revealed LBS affected the concentrations of NH3-N, MCP, and VFAs (p < 0.05), especially after 12 h, which might be attributed to changes in 18 genera. Whereas ABS only enhanced pH and NH3-N concentration compared with the CTR group (p < 0.05), which might be associated with changes in six genera. Supplementation with live B. subtilis natto improved ruminal NH3-N and propionate concentrations, indicating that live bacteria were better than autoclaved ones. This study advances our understanding of B. subtilis natto in promoting ruminal fermentation, providing a new perspective for the precise utilization of B. subtilis natto in dairy rations.

scholarly journals Assessment of temperature and acid tolerance of Bacillus subtilis isolated from a Brazilian fruit juice-added soy beverage

Interação ◽  
2021 ◽  
Vol 21 (2) ◽  
pp. 38-48
Author(s):  
Renato Ventresqui Oliveira ◽  
Lívio da Silva Amaral ◽  
Cristiane Aparecida Milagres ◽  
Celso Tadeu Barbosa Santos ◽  
Afonso Pelli ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
High Temperature ◽  
Fruit Juice ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Viable Cell ◽  
Low Ph ◽  
Rrna Gene ◽  
Peptone Water ◽  
Rrna Gene Sequencing

Bacillus subtilis is a spore-forming bacterium and an important food contaminant. The aim of this study was to analyze the ability of B. subtilis spores to survive under conditions of low pH and high temperature. The package was purchased at a local supermarket, in Uberaba, Minas Gerais. A sample was collected, diluted and plated on Brain-Heart-Infusion agar (BHI). After incubation, suspected colonies of B. subtilis were transferred to BHI agar. Cell morphology, the presence of spores and Gram stain were examined, and the isolate was identified by 16S rRNA gene sequencing . The microscope evaluation indicated the presence of spores. The thermal tolerance of the spores was evaluated by the addition of 3x109spores/mL in test tubes containing peptone water. Heat treatments were carried out at 80 and 90°C at different incubation times (0, 10, 20, 30, 40, 50 and 60 min). After heating, the tubes were cooled and the number of viable spores was determined in BHI Agar. For the analysis of spore survival, D and Z values were calculated. Tolerance to acid conditions was evaluated using BHI broth with different pH values. After incubation, the bacterial concentration was determined by determining viable cell count on BHI Agar medium. The vegetative cells were transferred to the BHI broth and the pH was adjusted to different values (3, 4 or 5). Sampling were taken 8, 12 and 24 h after incubation. The samples were serially diluted in peptone water and spread in BHI Agar to determine the viable cell count . The 16S rRNA gene sequencing indicated high similarity (99.99%) with B. subtilis. D values were 17.01 min at 80°C and 13.42 min at 90°C. The Z-value was 97.13°C. B. subtilis was not able to grow at pH 3 and pH 4, but its survival was confirmed after the growth of colonies on BHI agar. At pH 5, B. subtilis grew after 24 h and the final pH changed to 7. Our results suggest that the spores of B. subtilis isolated from fruit juice-added soy beverage are tolerant to low pH and high temperature.

scholarly journals Vagococcus elongatus sp. nov., isolated from a swine-manure storage pit

2007 ◽  
Vol 57 (4) ◽  
pp. 751-754 ◽  
Author(s):  
Paul A. Lawson ◽  
Enevold Falsen ◽  
Michael A. Cotta ◽  
Terence R. Whitehead
Keyword(s):  
Novel Species ◽  
Molecular Genetic ◽  
Swine Manure ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Molecular Genetic Analysis ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Manure Storage ◽  
Rrna Gene Sequencing

A polyphasic taxonomic study was performed on an uncharacterized Gram-positive, catalase-negative, elongated coccus-shaped bacterium isolated from a swine-manure storage pit. The bacterium, designated strain PPC9T, was facultatively anaerobic and had a DNA G+C content of 44.5 mol%. Comparative 16S rRNA gene sequencing indicated that the bacterium represented a novel subline within the genus Vagococcus, close to but distinct from Vagococcus lutrae. Strain PPC9T was readily distinguished from the five recognized species of the genus Vagococcus by using biochemical tests and molecular genetic analysis. Based on phylogenetic and phenotypic evidence strain PPC9T is considered to represent a novel species of the genus Vagococcus, for which the name Vagococcus elongatus sp. nov. is proposed. The type strain is PPC9T (=CCUG 51432T=NRRL B-41357T).

scholarly journals Gemella asaccharolytica sp. nov., isolated from human clinical specimens

2010 ◽  
Vol 60 (5) ◽  
pp. 1023-1026 ◽  
Author(s):  
Nurver Ulger-Toprak ◽  
Paula H. Summanen ◽  
Chengxu Liu ◽  
Marie-Claire Rowlinson ◽  
Sydney M. Finegold
Keyword(s):  
Type Strain ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gram Stain ◽  
Biochemical Tests ◽  
Clinical Specimens ◽  
Sequencing Studies ◽  
Taxonomic Methods ◽  
Rrna Gene Sequencing

Three strains of an unidentified Gram-stain-variable, fastidious, catalase-negative, capnophilic, non-spore-forming, coccus-shaped bacterium from human wound specimens were characterized by phenotypic and molecular taxonomic methods. Initially, these strains were anaerobic; with repeated culture, they became aerotolerant. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains were genealogically homogeneous and constituted a novel subline within the genus Gemella. The unknown bacterium was readily distinguished from other Gemella species by biochemical tests. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from clinical specimens be classified as Gemella asaccharolytica sp. nov. The type strain is WAL 1945JT (=ATCC BAA-1630T =CCUG 57045T).

scholarly journals Chemotaxis Away from 4-Chloro-2-nitrophenol, 4-Nitrophenol, and 2,6-Dichloro-4-nitrophenol byBacillus subtilisPA-2

2015 ◽  
Vol 2015 ◽  
pp. 1-4 ◽  
Author(s):  
Pankaj Kumar Arora ◽  
Mi-Jeong Jeong ◽  
Hanhong Bae
Keyword(s):  
Bacillus Subtilis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
The 16S Rrna Gene ◽  
Drop Plate ◽  
Chemotactic Behavior

Bacterial strain PA-2 exhibits chemotaxis away from 4-chloro-2-nitrophenol, 4-nitrophenol, and 2,6-dichloro-4-nitrophenol. This strain was identified asBacillus subtilison the basis of the 16S rRNA gene sequencing. The drop plate assay and the chemical-in-plug method were used to demonstrate negative chemotactic behavior of strain PA-2. The growth studies showed that strain PA-2 did not utilize 4-chloro-2-nitrophenol, 4-nitrophenol, and 2,6-dichloro-4-nitrophenol as its sole sources of carbon and energy. This is the first report of negative chemotaxis of 4-chloro-2-nitrophenol, 4-nitrophenol, and 2,6-dichloro-4-nitrophenol by any bacterium.

scholarly journals Description of Gemella sanguinis sp. nov., Isolated from Human Clinical Specimens

1998 ◽  
Vol 36 (10) ◽  
pp. 3090-3093 ◽  
Author(s):  
Matthew D. Collins ◽  
Roger A. Hutson ◽  
Enevold Falsen ◽  
Berit Sjöden ◽  
Richard R. Facklam
Keyword(s):  
Type Strain ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Electrophoretic Analysis ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Clinical Specimens ◽  
Sequencing Studies ◽  
Taxonomic Methods ◽  
Rrna Gene Sequencing

Six strains of a hitherto undescribed gram-positive, catalase-negative, facultatively anaerobic coccus isolated from human sources were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains were genealogically identical and constitute a new subline within the genus Gemella. The unknown bacterium was readily distinguished from Gemella haemolysans,Gemella bergeriae, and Gemella morbillorum by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Gemella sanguinis sp. nov. The type strain is CCUG 37820T.

scholarly journals Molecular Identification of a Nocardiopsis dassonvillei Blood Isolate

1999 ◽  
Vol 37 (10) ◽  
pp. 3366-3368 ◽  
Author(s):  
Frédéric Beau ◽  
Claude Bollet ◽  
Thierry Coton ◽  
Eric Garnotel ◽  
Michel Drancourt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
Morphological Characteristics ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Pulmonary Infections ◽  
Biochemical Tests ◽  
Blood Isolate ◽  
Rrna Gene Sequencing

Nocardiopsis dassonvillei is an environmental aerobic actinomycete seldom isolated in cutaneous and pulmonary infections. We herein report the first N. dassonvillei blood isolate in a patient hospitalized for cholangitis. Although morphological characteristics and biochemical tests allowed a presumptive identification of this isolate, cell wall fatty acid chromatographic analysis confirmed identification at the genus level, and 16S rRNA gene sequencing achieved definite identification. This study illustrates the usefulness of 16S rRNA gene sequencing as a routine method for the identification of actinomycetes.

scholarly journals Bacillus Subtilis 29784 as a Feed Additive for Broilers Shifts the Intestinal Microbial Composition and Supports the Production of Hypoxanthine and Nicotinic Acid

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1335
Author(s):  
Pearl Choi ◽  
Lamya Rhayat ◽  
Eric Pinloche ◽  
Estelle Devillard ◽  
Ellen De Paepe ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Nicotinic Acid ◽  
16S Rrna Gene Sequencing ◽  
Intestinal Content ◽  
Feed Additive ◽  
Subtilis Strain ◽  
Rrna Gene ◽  
Microbial Composition

The probiotic Bacillus subtilis strain 29784 (Bs29784) has been shown to improve performance in broilers. In this study, we used a metabolomic and 16S rRNA gene sequencing approach to evaluate effects of Bs29874 in the broiler intestine. Nicotinic acid and hypoxanthine were key metabolites that were produced by the strain in vitro and were also found in vivo to be increased in small intestinal content of broilers fed Bs29784 as dietary additive. Both metabolites have well-described anti-inflammatory effects in the intestine. Furthermore, Bs29784 supplementation to the feed significantly altered the ileal microbiome of 13-day-old broilers, thereby increasing the abundance of genus Bacillus, while decreasing genera and OTUs belonging to the Lactobacillaceae and Enterobacteriacae families. Moreover, Bs29784 did not change the cecal microbial community structure, but specifically enriched members of the family Clostridiales VadinBB60, as well as the butyrate-producing families Ruminococcaceae and Lachnospiraceae. The abundance of various OTUs and genera belonging to these families was significantly associated with nicotinic acid levels in the cecum, suggesting a possible cross-feeding between B. subtilis strain 29784 and these beneficial microbes. Taken together, the data indicate that Bs29784 exerts its described probiotic effects through a combined action of its metabolites on both the host and its microbiome.

scholarly journals Facklamia ignava sp. nov., Isolated from Human Clinical Specimens

1998 ◽  
Vol 36 (7) ◽  
pp. 2146-2148 ◽  
Author(s):  
Matthew D. Collins ◽  
Paul A. Lawson ◽  
Rafael Monasterio ◽  
Enevold Falsen ◽  
Berit Sjöden ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Electrophoretic Analysis ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Clinical Specimens ◽  
Sequencing Studies ◽  
Taxonomic Methods ◽  
Rrna Gene Sequencing

Two strains of a hitherto-undescribed gram-positive, catalase-negative coccus isolated from human sources were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains are genealogically identical and constitute a new line close to, but distinct from, Facklamia hominis. The unknown bacterium was readily distinguished from F. hominis by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Facklamia ignava sp. nov. The type strain of Facklamia ignava is CCUG 37419.

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