Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University

Published : 5 Documents

Found 5 Documents

Comparison of DNA Extraction Methods for Microbial Community Analysis in Indonesian Tempe Employing Amplified Ribosomal Intergenic Spacer Analysis SEUMAHU, CECILIA ANNA; SUWANTO, ANTONIUS; RUSMANA, IMAN; SOLIHIN, DEDY DURYADI
HAYATI Journal of Biosciences Vol 19, No 2 (2012): June 2012
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (136.378 KB) | DOI: 10.4308/hjb.19.2.93


Tempe fermentation involved complex microbial communities which are only revealed partially through culture dependent methods. Culture-independent methods would be potential to unravel this complex microbial fermentation. Appropriate DNA extraction is an essential tool to obtain reliable data from culture independent method. In this study, we employed two commercial DNA extraction methods to find the best one for microbial community characterization employing amplified ribosomal intergenic spacer analysis (ARISA). Our result showed that PowerFood Microbial DNA Isolation Kit-MOBIO (PFMDIK) is an excellent method for microbial DNA extraction from tempe. It gave high quantity and quality of DNA suitable for PCR amplification of 16S-23S rRNA intergenic spacer to yield a diverse and reproducible ARISA profile.
Bacterial and Fungal Communities in Tempeh as Reveal by Amplified Ribosomal Intergenic Sequence Analysis SEUMAHU, CECILIA ANNA; SUWANTO, ANTONIUS; RUSMANA, IMAN; SOLIHIN, DEDY DURYADI
HAYATI Journal of Biosciences Vol 20, No 2 (2013): June 2013
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (142.073 KB) | DOI: 10.4308/hjb.20.2.65


Tempeh is an Indonesian traditional fermented food produced using Rhizopus as a starter culture. In practice, however, the starter culture as well as fermentation processes would yield a polymicrobial fermentation, which generated a unique tempeh flavor and texture. This condition makes Indonesian tempeh as one of the most complex fermented food, while at the same time would make it difficult to scale up tempeh production with uniform quality and consistency. The aim of this study was to compare a number of tempeh microbial communities employing Amplified Ribosomal Intergenic Sequence Analysis (ARISA). Fresh tempeh samples were obtained from tempeh producers in Java and Moluccas. 16S rRNA gene libraries and DNA sequencing were employed to analyze further the nature of bacterial diversity in two selected tempeh samples. The results of our study showed that different tempeh producer possessed different Bacterial ARISA (BARISA) or fungi ARISA (FARISA) profiles.  However, BARISA profiles were found to be more discriminative than FARISA, and therefore BARISA would be more useful for tempeh genetic fingerprint or barcoding.
The Dynamics of Bacterial Communities During Traditional Nata de Coco Fermentation SEUMAHU, CECILIA ANNA; SUWANTO, ANTONIUS; HADISUSANTO, DEBORA; SUHARTONO, MAGGY THENAWIJAYA
Microbiology Indonesia Vol 1, No 2 (2007): August 2007
Publisher : Indonesian Society for microbiology

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One of the important problems in traditional Nata de Coco (Nata) fermentation is production inconsistency due to strain or genetic variability reflecting mixed microbial communities involved in this process. This research was aimed at examine the population dynamics of the bacterial community during the fermentation processes. Samples were collected daily for six days from fermentation media derived from “good” and “bad” Nata fermentation. We compared the levels of bacterial diversity through amplified 16S-rRNA (ARDRA). DNA was extracted directly from the fermentation media and 16S-rRNA gene was amplified employing Universal Bacterial Primers. The amplicons were cloned into pGEM-T Easy vector, and restriction enzymes HaeIII and RsaI were used to generate ARDRA profiles. ARDRA phylotypes of DNA extracted from the fermentation medium obtained from different Nata qualities were compared. Phylotype profiles demonstrated unique bacterial community profiles for different conditions of Nata quality, which could be developed as a parameter to monitor Nata quality during fermentation. In this research we found that the dynamics of the bacterial population involved in Nata fermentation were a crucial factor for determining traditional Nata quality.
Isolation and Identification of Protease Enzyme Producing Bacteria from Fermentation of Gonad Sea Urchin (Echinothrix calamaris) Jamaludin, Siani La; Rehena, Johanis Fritzgal; Seumahu, Cecilia Anna; Rumahlatu, Dominggus
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 23, No 4 (2018): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (652.56 KB) | DOI: 10.14710/ik.ijms.23.4.187-198


Bekasang of gonad sea urchin is one of the traditional fermentation products which generally involves microorganism spontaneous fermentation. Fermented paste products have a long shelf life and are processed quite easily using protease enzymes. Good exploration of producing protease from bakasang is needed to obtain the protease enzyme-producing microorganism with different characters. The method used in this research is screening with clear zone, measuring the activity of crude extract of protease enzyme characterization of bacteria through gram staining. Identification of potential microorganisms through 16S rRNA sequence. The results showed that there were eight isolates of protease enzyme-producing bacteria (G1, G2, G3, G4, G5, G6, G7, and G8) indicated by clear zones around single-colonic bacterial streaks. Only five bacterial isolates (G1, G4, G6, G7, and G8) were tested for the enzyme activity. These isolates have characteristics of positive gram bacteria. The interpretation of the results of molecular analysis using PCR and BLASTN sequences of 16S rRNA gene from five bacterial isolates, showed the identity of bacteria as: G1 was Staphylococcus piscifermentans strain CIP103958 with 99% similarity; Isolate G4 was Staphylococcus saprophyticus strain ATCC 15305 with 99% similarity; Isolate G6 was Staphylococcus condimenti F-2 strain with 99% similarity; Isolate G7 was Bacillus amyloliquefaciens subsp. plantarum strain FZB42 with 99% similarity; And G8 isolates was Lactobacillus plantarum strain JCM 1149 with 99% similarity.
Agrotech Journal Vol 3, No 1 (2018): Agrotech Journal (ATJ)
Publisher : Universitas Sembilanbelas November Kolaka

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1039.065 KB) | DOI: 10.31327/atj.v3i1.524


Galoba durian is one of the endemic floras from Maluku. Galoba durian is a species belonging to the Amomum genera Zingiberaceae family. It is also used as a medicinal plant for waist and kidney diseases. Based on the color of the fruit, galoba durian is divided into two nmely red galoba durian and green galoba durian. Distribution of this plant in Ambon can found in a few places such as highland and coastal area. Different locations influence phenotypic of plants, but may not show different genetic characteristic. Genetic diversity can detected by molecular markers. Genetic characterization from galoba durian using RAPD markers has not been done before. This study aimed to analyze genetic diversity from galoba durian using molecular markers RAPD. Samples of plants are used red galoba durian from Hatu and green galoba durian from Hatalae. The result of the first study, characterization of the morphology of the galoba durian, showed that both galoba have almost similar characteristics. Further DNA was tested by qualitative and quantitative. Result shows good qualitative and quantitative of DNA genomic. The second study was amplification by PCR-RAPD. DNA amplifications were performed using 3 primers out of 9 screened random primers. The primers selection was based on hight polymorphism. DNA amplification has 36 bands which were 100% polymorphic. The size of each bands from visualization of agarose was determined by linear regression. Number of band amplified was range from 120 to 1612 bp. Polymorphic band of RAPD showed the highest  genetic diversity. It can be concluded that the two plants of galoba durian are different species