scholarly journals Molecular identification of bacteria by fluorescence-based PCR-single-strand conformation polymorphism analysis of the 16S rRNA gene.

1995 ◽  
Vol 33 (10) ◽  
pp. 2601-2606 ◽  
Author(s):  
M N Widjojoatmodjo ◽  
A C Fluit ◽  
J Verhoef
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Identification ◽  
Single Strand Conformation Polymorphism ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Conformation Polymorphism Analysis ◽  
Identification Of Bacteria ◽  
The 16S Rrna Gene ◽  
Conformation Polymorphism

scholarly journals Bacterial Community Dynamics during Production of Registered Designation of Origin Salers Cheese as Evaluated by 16S rRNA Gene Single-Strand Conformation Polymorphism Analysis

2003 ◽  
Vol 69 (7) ◽  
pp. 3840-3848 ◽  
Author(s):  
Frédérique Duthoit ◽  
Jean-Jacques Godon ◽  
Marie-Christine Montel
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Gram Positive ◽  
Leuconostoc Pseudomesenteroides ◽  
The 16S Rrna Gene ◽  
Conformation Polymorphism

ABSTRACT Microbial dynamics during processing and ripening of traditional cheeses such as registered designation of origin Salers cheese, an artisanal cheese produced in France, play an important role in the elaboration of sensory qualities. The aim of the present study was to obtain a picture of the dynamics of the microbial ecosystem of RDO Salers cheese by using culture-independent methods. This included DNA extraction, PCR, and single-strand conformation polymorphism (SSCP) analysis. Bacterial and high-GC% gram-positive bacterial primers were used to amplify V2 or V3 regions of the 16S rRNA gene. SSCP patterns revealed changes during the manufacturing of the cheese. Patterns of the ecosystems of cheeses that were provided by three farmers were also quite different. Cloning and sequencing of the 16S rRNA gene revealed sequences related to lactic acid bacteria (Lactococcus lactis, Streptococcus thermophilus, Enterococcus faecium, Leuconostoc mesenteroides, Leuconostoc pseudomesenteroides, Lactobacillus plantarum, and Lactobacillus pentosus), which were predominant during manufacturing and ripening. Bacteria belonging to the high-GC% gram-positive group (essentially corynebacteria) were found by using specific primers. The present molecular approach can effectively describe the ecosystem of artisanal dairy products.

scholarly journals Molecular identification of bacteria isolated from culture medium of rotifer fed on fishery waste diet

2020 ◽  
Vol 21 (6) ◽  
Author(s):  
Stenly Wullur ◽  
HATOPAN NAPITUPULU ◽  
LETHA LOISE WANTANIA ◽  
ELVY LIKE GINTING ◽  
VEIBE WAROUW ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Identification ◽  
Culture Medium ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Seawater Salinity ◽  
Identification Of Bacteria ◽  
The 16S Rrna Gene

Abstract. Wullur S, Napitupulu H, Wantania LL, Ginting EL, Warouw V, Tallei TE, Rumengan IFM. 2020. Molecular identification of bacteria isolated from culture medium of rotifer fed on fishery waste diet. Biodiversitas 21: 2735-2740. The aim of this study was 16S-rRNA sequences based molecular identification of bacteria isolated from culture medium of rotifer fed with fishery waste diet (FWD). We cultured rotifer Brachionus rotundiformis in sterilized seawater (salinity 25 ppt) using FWD, following the procedure in Patent No. P00201609066. Bacteria from the culture were collected, homogenized, diluted 10 to 1000 fold, spread on agar plates and incubated at 370C for 24 to 48 hours. Representative colonies of the bacteria according to their morphologies were isolated for further characterization. Genomic DNA of the isolates were extracted, and the 16S rRNA gene of the isolates were amplified. Polymerase Chain Reaction (PCR) product of each isolate was sequenced and queried against the NCBI GenBank database. Six different isolates based on size, color, elevation, margin, and colony were observed during 24-48 hours incubation at 370C. The 16S rRNA genes of the six isolates were successfully amplified and produced DNA band at 1300-1500 bp, with quality value equal to or greater than 20 (QV20+) of each entire sequence around 941-1253 bases. Basic Local Alignment Search Tool (BLAST) queries in the NCBI GenBank and EzBioCloud database using the 16S-rRNA gene sequences showed that the six isolates belong to four different genera, i.e: Bacillus, Staphylococcus, Vibrio, and Alteromonas.

scholarly journals Molecular identification of bacteria isolated from culture medium of the gold-lipped pearl oyster Pinctada maxima larvae

2020 ◽  
Vol 21 (11) ◽  
Author(s):  
Stenly Wullur ◽  
HATOPAN NAPITUPULU ◽  
ELVY LIKE GINTING ◽  
NOLDY GUSTAF FRANS MAMANGKEY ◽  
LETHA LOUISIANAWANTANIA ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Identification ◽  
Culture Medium ◽  
Pearl Oyster ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Identification Of Bacteria ◽  
Pinctada Maxima ◽  
The 16S Rrna Gene

Abstract. Wullur S, Napitupulu H, Wantania LL, Ginting EL, Mamangkey NGF, Smolak R, Ogello E. 2020. Molecular identification of bacteria isolated from culture medium of the gold-lipped pearl oyster Pinctada maxima larvae. Biodiversitas 21: 5291-5297.  This study was conducted for the molecular identification of bacteria species isolated from culture medium of the gold-lipped pearl oyster, Pinctada maxima larvae. The pearl oysters were cultured using live-microalgae (Isochrysis sp) and fish waste diet (FWD) as food sources.  Bacteria were isolated from the oyster larvae and identified based on the 16S rRNA gene sequence. The isolated bacteria were grown on agar plates and incubated at 37°C for 24 to 48 hours. Representative colonies of the bacteria were selected and cultured for molecular analysis.  The 16S rRNA genes of the bacteria were amplified and the sequences were matched with the NCBI GenBank database. Seven different colonies were observed based on morphological characters. Similarity test by conducting the Basic Local Alignment Search Tool (BLAST) in the NCBI GenBank database, using the 16S rRNA gene sequences showed that the seven isolates colonies possess high similarity to five bacteria species i.e. Pseudomonas pachastrellae, Vibrio alginolyticus, Bacillus filamentosus, Bacillus cereus and Idiomarina fontislapidosi belonging to four different genera i.e. Bacillus, Staphylococcus, Vibrio, and Alteromonas.

Rapid identification of bacteria by real-time amplification and sequencing of the 16S rRNA gene

2006 ◽  
Vol 66 (1) ◽  
pp. 156-164 ◽  
Author(s):  
Inge Vliegen ◽  
Jan A. Jacobs ◽  
Erik Beuken ◽  
Cathrien A. Bruggeman ◽  
Cornelis Vink
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Real Time ◽  
Rapid Identification ◽  
Rrna Gene ◽  
Identification Of Bacteria ◽  
Time Amplification ◽  
The 16S Rrna Gene

scholarly journals THE 16S rRNA GENE MARKER-BASED MOLECULAR IDENTIFICATION OF CULTURABLE COLIFORM BACTERIA ISOLATED FROM FORAMINIFERA CALCARINA DERIVED FROM PRAMUKA ISLAND WATERS, THE SERIBU ISLAND DISTRICT, JAKARTA PROVINCE

2020 ◽  
Vol 13 (1) ◽  
pp. 10-18
Author(s):  
Mochamad Untung Kurnia - Agung ◽  
Agus Tri Askar ◽  
Yuli Andriani ◽  
Lintang Permatasari Yuliadi
Keyword(s):  
Coral Reef ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Identification ◽  
Bay Of Bengal ◽  
Coliform Bacteria ◽  
Gene Marker ◽  
Rrna Gene ◽  
Gene Markers ◽  
The 16S Rrna Gene

Contamination of coliform bacteria in benthic foraminifera has been reported due to pollution of organic wastes in the aquatic environment around coral reef ecosystems and this event was known to interfere the process of foraminifera shell formation which in turn resulted the disruption of the role of foraminifera in the process of formation of coral reef bottom sediments. The aim of this research is to identify the isolates of culturable coliform bacteria that contaminate foraminifera Calcarina species isolated from the waters of the Pramuka Island, the Seribu Island district, Jakarta Province using the 16S rRNA gene markers. Foraminifera sampling was carried out in the waters of Pramuka Island, the Seribu Island district, Jakarta Province in 5 (five) stations, while the process of bacterial isolation and molecular identification were carried out at the Laboratory of Microbiology and Molecular Biotechnology (MICROMOL), Faculty of Fisheries and Marine Sciences (FPIK), University Padjadjaran. Molecular identification was carried out using the Polymerase Chain Reaction (PCR) method based on the 16S rRNA gene markers. Sequencing is done by sending PCR results to 1st Base, sequencing service company, in Singapore and then, the aligning of sequencing results with databases in genBank was done using  the Basic Local Alignment Search Tool (BLASTTM) program available on the National Center for Biotechnology Information (NCBI) website. The results of 16S rRNA gene amplification from the five isolates produced amplicons of ± 1400 bp length with concentrations ranging from 157.5 µg / mL-230 µg / mL and with a purity ratio ranging from 1.477-1.769. While the results of BLAST and phylogenetic analysis showed that the five isolates were closely related to the isolate Eschericia coli strain inspire99 (Acc No. JQ315935.1), which was isolated from the waters of the Bay of Bengal, India. These results also indicate the existence of ecological connectivity between the waters of the Bay of Bengal in India and the waters of Pramuka Island in Indonesia.

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