Iman Rusmana
Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University. Jl. Raya Darmaga, Bogor 16680, West Java. Indonesia

Published : 38 Documents
Articles

Found 8 Documents
Search
Journal : HAYATI Journal of Biosciences

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

Abstract

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

Abstract

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.
Analysis of Intestinal Mucosal Immunoglobulin A in Sprague Dawley Rats Supplemented with Tempeh SOKA, SUSAN; SUWANTO, ANTONIUS; RUSMANA, IMAN; SAJUTHI, DONDIN; ISKANDRIATI, DIAH; JESSICA, KATHARINA
HAYATI Journal of Biosciences Vol 22, No 1 (2015): January 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1507.883 KB) | DOI: 10.4308/hjb.22.1.

Abstract

Tempeh is a well-known Indonesian fermented food made from soybean. During the fermentation process, microorganisms play an important role in the flavor, texture, and nutritional quality of tempeh. Tempeh has been show to have immuno-modulatory and immune-stimulating properties that may also be caused by the microorganisms in tempeh as they interact between the microbial population in the intestinal tract. The objective of this study was to quantify IgA gene expression at both the transcription and translation levels in Sprague Dawley (SD) rats supplemented with tempeh. A total of 6 female SD rats were divided into 3 groups of 2 rats. The first group was the control and was fed a standard diet without tempeh. The second- and third group were fed with a standard diet supplemented with raw and cooked tempeh, respectively. Ileum tissue samples were collected after tempeh supplementation for 28 days. RNA was extracted from ileum samples, and measurement of IgA gene expression was further analyzed using semi quantitative real-time PCR. The concentration of IgA protein was quantified from ileum lysate using the half sandwich ELISA method. IgA gene expressions in rats supplemented with raw, and with cooked tempeh, were 1.18 and 1.17 fold higher, respectively, compared to the control group. Moreover, IgA protein secretion levels also increased 2.46 and 2.08 fold, respectively, compared to the control group. The result of this study indicates that both raw and cooked tempeh may stimulate IgA secretion, and also that both viable and non-viable microorganisms might stimulate IgA gene expression.
Characterization of Bacteriophage Specific to Bacillus pumilus from Ciapus River in Bogor, West Java, Indonesia KUSMIATUN, ANIK; RUSMANA, IMAN; BUDIARTI, SRI
HAYATI Journal of Biosciences Vol 22, No 1 (2015): January 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.22.1.

Abstract

Bacillus pumilus is a spore-forming bacteria that is rod-shaped, gram positive, and aerobic. B. pumilus produced pumilacidins, known to have toxic effects on epithelial cells. Antibiotics were usually used to treat the disease caused by bacteria. Antibiotic typing test of B. pumilus indigenous from sewage water showed that this isolate was resistant to ampicillin and clindamycin. An alternative way was by application of bacteriophages as biocontrol agents to reduce B. pumilus in environment. The aim of this study were to isolate and characterize B. pumilus bacteriophage isolated from Ciapus River in Bogor, West Java. Bacteriophages infecting B. pumilus were isolated from river water using the double agar overlay method. Phages were defined by plaque morphology, structure, host range, and characteristic of molecular weight protein phage. Phage FBa1, FBa2, and FBa3 had narrow host range and they were specific for infecting B. pumilus. Electron microscope observation showed that phage FBa1 had icosahedral head without tail (166.67 nm in diameter), so it is called phage-like particles. Characterization of phage FBa1 by SDS-PAGE showed five proteins band. Molecular weight of FBa1 proteins was 70.9, 54.9, 33.8, 28.3, and 21.4 kDa.
Characterization of Bacteriophage Specific to Bacillus pumilus from Ciapus River in Bogor, West Java, Indonesia KUSMIATUN, ANIK; RUSMANA, IMAN; BUDIARTI, SRI
HAYATI Journal of Biosciences Vol 22, No 1 (2015): January 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.22.1.27

Abstract

Bacillus pumilus is a spore-forming bacteria that is rod-shaped, gram positive, and aerobic. B. pumilus produced pumilacidins, known to have toxic effects on epithelial cells. Antibiotics were usually used to treat the disease caused by bacteria. Antibiotic typing test of B. pumilus indigenous from sewage water showed that this isolate was resistant to ampicillin and clindamycin. An alternative way was by application of bacteriophages as biocontrol agents to reduce B. pumilus in environment. The aim of this study were to isolate and characterize B. pumilus bacteriophage isolated from Ciapus River in Bogor, West Java. Bacteriophages infecting B. pumilus were isolated from river water using the double agar overlay method. Phages were defined by plaque morphology, structure, host range, and characteristic of molecular weight protein phage. Phage FBa1, FBa2, and FBa3 had narrow host range and they were specific for infecting B. pumilus. Electron microscope observation showed that phage FBa1 had icosahedral head without tail (166.67 nm in diameter), so it is called phage-like particles. Characterization of phage FBa1 by SDS-PAGE showed five proteins band. Molecular weight of FBa1 proteins was 70.9, 54.9, 33.8, 28.3, and 21.4 kDa.
Analysis of Intestinal Mucosal Immunoglobulin A in Sprague Dawley Rats Supplemented with Tempeh SOKA, SUSAN; SUWANTO, ANTONIUS; RUSMANA, IMAN; SAJUTHI, DONDIN; ISKANDRIATI, DIAH; JESSICA, KATHARINA
HAYATI Journal of Biosciences Vol 22, No 1 (2015): January 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1507.883 KB) | DOI: 10.4308/hjb.22.1.48

Abstract

Tempeh is a well-known Indonesian fermented food made from soybean. During the fermentation process, microorganisms play an important role in the flavor, texture, and nutritional quality of tempeh. Tempeh has been show to have immuno-modulatory and immune-stimulating properties that may also be caused by the microorganisms in tempeh as they interact between the microbial population in the intestinal tract. The objective of this study was to quantify IgA gene expression at both the transcription and translation levels in Sprague Dawley (SD) rats supplemented with tempeh. A total of 6 female SD rats were divided into 3 groups of 2 rats. The first group was the control and was fed a standard diet without tempeh. The second- and third group were fed with a standard diet supplemented with raw and cooked tempeh, respectively. Ileum tissue samples were collected after tempeh supplementation for 28 days. RNA was extracted from ileum samples, and measurement of IgA gene expression was further analyzed using semi quantitative real-time PCR. The concentration of IgA protein was quantified from ileum lysate using the half sandwich ELISA method. IgA gene expressions in rats supplemented with raw, and with cooked tempeh, were 1.18 and 1.17 fold higher, respectively, compared to the control group. Moreover, IgA protein secretion levels also increased 2.46 and 2.08 fold, respectively, compared to the control group. The result of this study indicates that both raw and cooked tempeh may stimulate IgA secretion, and also that both viable and non-viable microorganisms might stimulate IgA gene expression.
Metagenomic of Actinomycetes Based on 16S rRNA and nifH Genes in Soil and Roots of Four Indonesian Rice Cultivars Using PCR-DGGE Mahyarudin, .; Rusmana, Iman; Lestari, Yulin
HAYATI Journal of Biosciences Vol 22, No 3 (2015): July 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1377.267 KB) | DOI: 10.4308/hjb.22.3.113

Abstract

The research was conducted to study the metagenomic of actinomycetes based on 16S ribosomal RNA (rRNA) and bacterial nifH genes in soil and roots of four rice cultivars. The denaturing gradient gel electrophoresis profile based on 16S rRNA gene showed that the diversity of actinomycetes in roots was higher than soil samples. The profile also showed that the diversity of actinomycetes was similar in four varieties of rice plant and three types of agroecosystem. The profile was partially sequenced and compared to GenBank database indicating their identity with closely related microbes. The blast results showed that 17 bands were closely related ranging from 93% to 100% of maximum identity with five genera of actinomycetes, which is Geodermatophilus, Actinokineospora, Actinoplanes, Streptomyces and Kocuria. Our study found that Streptomyces species in soil and roots of rice plants were more varied than other genera, with a dominance of Streptomyces alboniger and Streptomyces acidiscabies in almost all the samples. Bacterial community analyses based on nifH gene denaturing gradient gel electrophoresis showed that diversity of bacteria in soils which have nifH gene was higher than that in rice plant roots. The profile also showed that the diversity of those bacteria was similar in four varieties of rice plant and three types of agroecosystem. Five bands were closely related with nifH gene from uncultured bacterium clone J50, uncultured bacterium clone clod-38, and uncultured bacterium clone BG2.37 with maximum identity 99%, 98%, and 92%, respectively. The diversity analysis based on 16S rRNA gene differed from nifH gene and may not correlate with each other. The findings indicated the diversity of actinomycetes and several bacterial genomes analyzed here have an ability to fix nitrogen in soil and roots of rice plant.
Characterization and Identification of Cellulolytic Bacteria from gut of Worker Macrotermes gilvus Ferbiyanto, Andri; Rusmana, Iman; Raffiudin, Rika
HAYATI Journal of Biosciences Vol 22, No 4 (2015): October 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (760.677 KB) | DOI: 10.4308/hjb.22.4.197

Abstract

As a social insect, termite colony consists of three castes, i.e. reproductive, soldier, and worker castes. In their role of cellulose digestion, the worker termites use two sources of cellulolytic enzyme that include cellulases produced by the termite and the gut symbions. Macrotermes gilvus classified in mound builder termite, mostly depend on cellulolytic bacteria for cellulose digestion. This study aims to characterize cellulolytic bacteria of termite gut symbionts of worker M. gilvus and to identify the cellulolytic bacteria based on sequences of 16S ribosomal RNA (rRNA) gene. Cellulolytic bacteria of termite gut were isolated and cultured in CMC (Carboxymethyl cellulose) media. The biochemical characters of bacterial isolates were assayed using Microbact 12A and 12B. Cellulolytic activity was determined based on formation of clear zone and cellulolytic index on CMC plate media. The bacterial isolate that has the highest cellulolytic index was analyzed for its 16S rRNA gene sequences. Four isolates of cellulolytic bacteria were successfully isolated from gut of M. gilvus with aerobic and anaerobic conditions. The highest formation of cellulolytic index (2.5) was revealed by RA2. BLAST-N (Basic Local Alignment Search Tool for Nucleotides) result of 16S rRNA gene sequences of RU4 and RA2 isolates showed that the isolate has similarity with Bacillus megaterium and Paracoccus yeei, respectively. This result indicated that RA2 isolate was P. yeei, a cellulolytic bacterium of a termite gut of M. gilvus.