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Recent Publications

Published: 8 July 2024

Anto Budiharjo, Dyah Wulandari, Jauhara Shabrina, Risa Arum Mawarni, Anand Reyna Maulana, Nurhayati, Wijanarka Wijanarka, Laksmi Hartajanie & Lindayani

Publication Category: Sanger Sequencing

Abstract

The utilisation of enzymes in the industry has brought numerous benefits and advantages to production processes. Enzymes serve as biocatalysts, efficiently catalyzing reactions and hydrolysis in biochemical processes. However, there are challenges in applying enzymes in the industry, particularly concerning enzyme stability. The obstacle encountered in the production processes involv-ing industrial enzyme applications is the low stability of enzymes when used at high temperatures. Heat-sensitive enzymes undergo damage or denaturation. Thermophilic microorganisms are chosen because they hold the potential to produce thermophilic enzymes. The thermophilic enzymes exhibit better heat stability compared to other enzymes, making them an effective alternative for future industrial production processes. This study aims to isolate thermotoler-ant bacteria from Nglimut Hot Spring sediment, screen for cellulase and amylase-producing isolates, and molecularly identify the best isolate using 16S rRNAbarcode. The results show that 22 bacterial isolates were found in the sediment of a hot spring; TS-14 was the best isolate in producing amylase, with the highest average amylolytic index of 2.38, whereas TS-15 had the highest cellulolytic index of 2.11. Based on 16S rRNA identification, TS-14 showed an homological identity of79% with Bacillus amyloliquefaciens, while TS-15 had a 100% homological identity with Bacillus licheniformis.These re-sults were important as the first step of screening bacterial potential to pro-duce thermophilic enzymes that could be applied in the downstream pro-cessing in future industrial and biotechnology companies.

Detection of Pseudomonas aeruginosa pus wound isolate using a polymerase chain reaction targeting 16SrRNA and gyrB genes: A case from Indonesia

Published: 4 July 2024

Indra P. Jamaluddin, Susan H. Musa, Stalis N. Ethica, Arif NM. Ansori, Valensa Yosephi, Peter Y. Atmaja, Ahmad AA.Murtadlo, Sukma Sahadewa, Fara D. Durry, Maksim Rebezov, Marina Derkho, Sin W. Naw, Rahadian Zainul & Kadek Rachmawati

Publication Category: Products

Abstract

Infectious wounds on the skin surface are easily colonized by bacteria from pyogenic group that manifest as inflammation, such as Pseudomonas aeruginosa. P.aeruginosais a Gramnegative bacterium and an opportunistic pathogen known for causinginvasive state in critically ill and immunocompromised patients. The aim of thisstudy was to detect the 16S rRNAand gyrB genes in P. aeruginosausing polymerase chain reaction (PCR) method. The sample in this study was pus isolate from a 5yearold boy with leg wounds. The bacteria were isolated on brain heart infusion broth (BHIB)media and identified with molecular identification.Sequencing and BLAST analysis werecarried out to determine the similarity of gene identity by comparing sample sequence with other isolate sequences on the Gene Bank. The results of molecular identification showed amplification DNA band of around 934 base pairs (bp)for 16SrRNAand 225 bp forgyrBgene. The BLAST program demonstratedthat the sample had99.89% similarity with P. aeruginosastrain XC4 (accession code ON795960.1) for the 16SrRNAgene. Meanwhile, the gyrB gene exhibited99.10% similaritywith the P. aeruginosastrain PSA1.2 (accession code KP172300.1).

Published: 18 June 2024

Shela Emilia Permatasari & Andi Salamah
Publication Category: Sanger Sequencing

Abstract

The presence of ferritin protein in rice plants indicates a regulatory response to environmental iron stress. It prevents the destructive effects of the chain reaction resulting from Fe2+accumulation in the cell. This study aimed to detect and identify the location of the ferritin gene (OsFER) in eight local rice varieties in Indonesia. OsFER2, as the target gene was amplified using PCR, visualized by electrophoresis, and then sequenced. The sequencing results wereanalyzed using DNA Baser, BioEdit, and ClustalX2. The predicted proteins were visualized using the SWISSMODEL server, Rice Genome Annotation Project Database, and chromosome map tools. The results show that all rice varieties studied have 100% alignment similarity and OsFERcharacteristics on chromosome 11 at LOC_Os11g01530 and chromosome 12 at LOC_Os12g01530, which have striking differences. The complete protein structure of the complex is found on chromosome 12, while only a portion of alphahelix ferritin is found on chromosome 11. Differences in the position of the ferritin gene at different chromosomes impact the functional changes in the ferritin protein as an iron homeostasis key role. The two genes show different characteristics and are located at different genomic positions, suggesting a potential regulatory impact on the level of iron stress resistance in Indonesian rice varieties.

Isolation and Molecular Identification of Protease Producing Bacterium Associated
with the Brown Algae Hydroclathrus sp. from Hoga Island of Wakatobi District

Published: 7 June 2024

Nurulia Pratiwi Kaempe, Stalis Norma Ethica, Andri Sukeksi & Aprilia Indra Kartika

Publication Category: Sanger Sequencing

Abstract

Advances in fermentation technology, genetic engineering, and enzyme application technology have increased the use of enzymes. Enzymes can be produced by utilizing a source of microorganisms such as bacteria. Proteolytic bacteria or protease enzyme-producing bacteria are found in foods or plants that contain protein such as the brown seaweed Hydroclathrus sp. This study aimed to obtain protease-producing bacterium associated with marine algae Hydroclathrus sp. from waters around Hoga Island of Wakatobi District and identify the organism based on its 16S rRNA gene sequence. Isolation of bacteria from algae samples was carried out with nNutrient aAgar (NA) media, while proteolytic bacteria selection was carried out on sSkim mMilk aAgar (SMA) media. The bacterial isolates producing proteolytic-clear zone on SMA media were then identified targeting the 16S rRNA gene using the PCR (Polymerase Chain Reaction) method with 27F-1492R primers. Based on the isolation results, there were 3 unique colonies of bacteria that could be cultured from algae samples and coded HIHA-1 to HIHA-3 (HIHA stands for Hoga Island Hydrolathrus macroalgae). The selection process for protease-producing bacteria on SMA media resulted in 1 isolate of proteolytic bacteria, namely HIHA-1. Molecular identification by PCR on HIHA-1 isolate resulted in a single DNA band on the electrophoresis gel sized ~1500 bp. The sequencing results showed a DNA sequence with the size of 1421 bp sharing the highest similarity with the bacterium Exiguobacterium aestuarii strain TF-16 (homology level of 99,93%). In conclusion, the proteolytic bacterial isolate HIHA-1 associated with marine brown algae Hydroclathrus sp. was obtained and identified as Exiguobacterium aestuarii strain HIHA-1.

Abstract

 The aim of this study was to quantify and identify metabolites of Ice Nucleation Active (INA) bacteria as an anti-biofilm agent against biofilms of fish pathogens such as Aeromonas hydrophila and Streptococcus agalactiae. Ice nucleation active bacteria, which have the ability to catalyze ice nucleation, isolated from rainwater in previous studies, were used. All INA isolates were tested in several assays, including the antimicrobial test, which uses streptomycin as the positive control and none of the isolates were found positive in the antimicrobial test. As for the quorum quenching assay, it was found that four out of ten isolates were able to disturb the communication system in Chromobacterium violaceum wild type, which was used as the indicator bacteria. On the next assay, all ten isolates were tested for Biofilm Inhibition and Destruction and showed anti-biofilm activity with the highest percentage inhibition of 33.49% by isolate A40 against A. hydrophila and 77.26% by isolate A19 against S. agalactiae. C1 performed the highest destruction against A. hydrophila and S. agalactiae, with percentages of 32.11% and 51.88%, respectively. As for the GC-MS analysis, supernatants of INA bacteria contain bioactive compounds such as sarcosine and fatty acids, which are known to have antibiofilm activity against several biofilm-forming bacteria. Through 16s rRNA sequencing, identified bacteria are from the Pantoea, Enterobacter, and Acinetobacter genera. As for the conclusion, ice nucleation active bacteria metabolites tested showed positive results against pathogenic bacteria Aeromonas hydrophila and Streptococcus agalactiae in destructing and inhibiting biofilm growth.

Abstract

Gaharu bouya oil obtained from distillation of the woods from Gonystylus genus has attracted essential oil industry interest. However, the information about gaharu bouya essential oil profile is limited. The presence of Gonystylus species is also critically endangered on the IUCN Red List. Therefore, exploring the -omics profiles of Gonystylus bancanus, a native plant from Borneo Island, is important for Indonesia to conserve the population. This research investigated the metabolite profiling of G. bancanus oil, especially the volatile components of its essential oils. Distillations were performed in two technical ways: hydrodistillation on a laboratory scale and steam distillation on an industrial scale. According to LC–MS and GC–MS profiles, both essential oils displayed similar chemical compositions. This article also discusses the similarity of the chemical contents of gaharu bouya oil and agarwood oil from the gaharu superior type (Aquilaria) to support the value of the oil. This research also investigated the cytotoxicity of gaharu bouya oil against three cell lines: HeLa, MCF-7, and HT-29.

Variation in symptoms and morphology of Fusarium spp. on shallot associated with basal plate rot disease in Brebes District, Central Java Province, Indonesia

Published:
Lisa Marianah, Abdjad Asih Nawangsih, Abdul Munif, Giyanto & Efi Toding Tondok
Publication Category: Sanger Sequencing

Abstract

Basal plate rot disease is an important disease of shallots that causes losses in the field and storage. The disease is caused by Fusariumcomplex species, with different levels of virulence and host susceptibility. The six species of Fusariumspp.reported to cause basal plate rot disease of onion were F. oxysporum f.sp. cepae, F. proliferatum, F. redolens, F. solani, F. acutatumand F. tricinctum. Information about the variation in symptoms and morphology of fungi that cause basal plate rot disease on shallots, especially in Indonesia, is still very limited. Besides, the species that cause basal plate rot disease on shallots has not been molecularly confirmed using specific primers. The objective of this study was to isolate, identify, and study the variationin symptoms of the fungus associated with basal plate rot disease. The fungi were isolated from shallot plants symptomatic of basal plate rot disease collected from Brebes, Central Java Province. Eight isolates of Fusariumwith different morphologies weresuccessfully isolated and identified. Five isolates were identified as F. solani (isolate BC1, BC2, BC3, BBS1, and BBS4), two isolates as F. oxysporum f.sp. cepae (isolate BC4 and BBS6) and one isolate F. proliferatum (isolate BBS5). All eight isolates were pathogenic on shallots with different levels of virulence and symptom variations. BC4 isolate had the highest level of virulence, resulting in plant death, and was identified as F. oxysporum f.sp. cepae.

Genetic structure and current distribution of Liriomyza huidobrensis, L.sativaeand L. trifolii (Diptera: Agromyzidae) on vegetable crops in Bali, Indonesia

Published:
Wayan Eka Karya Utama1, I Wayan Supartha, Ketut Ayu Yuliadhi, I Putu Sudiarta,I Kadek Wisma Yudha, Sahabuddin Saleh, Sri Wahyuni, & Putu Angga Wiradana
Publication Category: Sanger Sequencing

Abstract

Liriomyza spp.(Diptera: Agromizidae) is a polyphagous pest that attacks various types of vegetable and ornamental plants throughout the world. The most damaging species are Liriomyza huidobrensis(Blanchard), Liriomyza sativae(Blanchard), and Liriomyza trifolii(Burgess). There have been no reports regarding mapping of population distribution and population genetics of Liriomyzain the Bali region using theCytochrome C Oxidase Subunit I (COI) approach. This research aims to map the population and genetic structure of L. huidobrensis, L. sativaeand L. trifoliion vegetable plants in Bali. This research uses a purposive sampling method which represents vegetable plantings in each district and city in Bali Province. Identification of the Liriomyzaspp.gene structure using the COI approach using LCO and HCO primers. The results of the research found that the spatial distribution of invasive leafminer fly species, namely L. sativaeand L. trifolii, was evenly distributed throughout the city districts in Bali. The distribution pattern of L. trifoliiis uniform with an S2/X value <1, while L. huidobrensisis found in the highland areas with a clustered distribution patternwith an S2/.Thegenetic distance between the three Liriomyzaspecies found in vegetable plants in Bali is much longer. This means that the three Liriomyzaspecies show very high levels of genetic differentiation in mitochondrial and nuclear genes, and differentiation between species in nuclear genes. This genetic variation can influence the ability of insects to quickly adapt to new environments and contribute to population dynamics and dispersal capacity.

Nobiletin Inhibits Breast Cancer Stem Cell by Regulating the Cell Cycle: A Comprehensive Bioinformatics Analysis and In Vitro Experiments

Published: 9
Adam Hermawan, Muthi Ikawati, Dyaningtyas Dewi Pamungkas Putri, Nurul Fatimah & Heri Himawan Prasetio
Publication Category: RNA Sequencing

Abstract

Inhibiting breast cancer stem cell (BCSC) signaling pathways is a strategic method for successfully treating breast cancer. Nobiletin (NOB) is a compound widely found in orange peel that exhibits a toxic effect on various types of cancer cells, and inhibits the signaling pathways that regulate the properties of BCSCs; however, the effects of NOB on BCSCs remain elusive. The purpose of this study was to determine the target genes of NOB for inhibiting BCSCs using in vitro three-dimensional breast cancer cell culture (mammospheres) and in silico approaches. We combined in vitro experiments to develop mammospheres and conducted cytotoxicity, next-generation sequencing, and bioinformatics analyses, such as gene ontology, the Reactome pathway enrichment, network topology, gene set enrichment analysis, hub genes selection, genetic alterations, prognostic value related to the mRNA expression, and mRNA and protein expression of potential NOB target genes that inhibit BCSCs. Here, we show that NOB inhibited BCSCs in mammospheres from MCF-7 cells. We also identified CDC6, CHEK1, BRCA1, UCHL5, TOP2A, MTMR4, and EXO1 as potential NOB targets inhibiting BCSCs. NOB decreased G0/G1, but increased the G2/M cell population. These findings showed that NOB is a potential therapeutic candidate for BCSCs treatment by regulating cell cycle.

Lactococcus Garvieae : Characterization And Ability To Inhibit The Growth Of Freshwater Aquaculture Pathogenic Bacteria

Published: 3
Mira Mawardi, Agustin Indrawati, Angela Mariana Lusiastuti & Wayan Teguh Wibawan
Publication Category: Sanger Sequencing

Abstract

Lactococcus garvieae is a gram-positive ovoid cocci bacterium formerly classified as a member of the Lactococcus genus. This study aims to isolate L. garvieae from catfish rearing pond and characterize it as a potential probiotic candidate. L. garvieae was identified and characterized through phenotypic and genotypic observation, genomic % G~C content analysis, cell surface hydrophobicity assays, acidification test, in vitro antagonism, and a profile of antimicrobial activities. The MT597595.1 accession number corresponds to L. garvieae, as determined by a molecular identification test. Biochemical characterization was performed using API 50 CH kit. The genomics %G~C content of L. garvieae was 51.8. Findings from acidification ability tests, in vitro antagonism tests, and the ability of bacteria to grow in broth medium at pH 4 reveal that L. garvieae can inhibit the growth of Aeromonas hydrophila, Streptococcus agalactiae, Streptococcus iniae, and Edwardsiella ictaluri. However, it does not suppress the growth of L. garvieae Edwardsiella tarda. Remarkably, L. garvieae has the ability to reduce the pH of neutral broth medium turning it acidic. Furthermore, L. garvieae’s hydrophobic cell surface exhibited an adhesive, hydrophobic,and protein surface cell content with a compact growth pattern consistent with postive SAT and MATH assay. Antimicrobial activity tests, encompassing 11 antibiotics, disclosed resistance to Nalidixic acid while displaying intermediate sensitivity to Streptomycin and Trimethoprim. In conclusion, L. garvieae demonstrates an inhibitory effect on the growth of pathogenic bacteria, underlining its potential as a probiotic candidate.

Bioprospecting of Rhizobia as Plant Growth Promoting Rhizobacteria Potential from Root Nodules of Groundnut (Arachis hypogaea L.)

Published: 1
Dyah Wulandari,Karyadi Baskoro, Yasmiin Mahmuudah, Florentina Kusmiyati, Alberta Rika Pratiwi & Anto Budiharjo
Publication Category: Sanger Sequencing

Abstract

Rhizobia are bacteria that symbiosis with host plant, as shown in the root nodules formation, and provide nitrogen that can be absorbed by plants in greater quantities than rhizobacteria. Available Nitrogen, which absorbed by plants, is the essential requirement for plant growth because its role in increasing yield and quality, hence it is needed in greater quantities than other nutrients. The study aimed to determine the macroscopic and microscopic diversity of rhizobia isolates from the groundnut nodules and their potential as PGPRs, andto identify 16S rRNA isolates with the best potential as PGPRs molecularly. The methods used were isolation from root nodules, screening of PGPR potential, molecular identification based on the 16S rRNA gene, and phylogenetic analysis to determine their kinship. Based on the isolation results, 17 Gramnegative isolates were obtained white to pink or orange color on AG media with various colony characteristics in terms of shape, margin, elevation, and texture. KT 20, which was selected as rhizobia isolate with the best potential as PGPR, has ammonium concentration of 23.12 ppm, synthesizes IAAwithaconcentration of 10.36 ppm, and phosphatessolubilization activity, although its ability to synthesize proteases is low. The results of molecular identification of 16S rRNA showed that KT 20 belongs to the Rhizobiumgenus witha similarity of 99.48% andbootstrap valueof 96%.

Abstract

Pseudoalteromonas viridis strain BBR56 was isolated from seawater at Dutungan Island, South Sulawesi, Indonesia. Bacterial DNA was isolated using Promega Genomic DNA TM050. DNA purity and quantity were assessed using NanoDrop spectrophotometers and Qubit fluorometers. The DNA library and sequencing were prepared using Oxford Nanopore Technology GridION MinKNOW 20.06.9 with long read, direct, and comprehensive analysis. High accuracy base calling was assessed with Guppy version 4.0.11. Filtlong and NanoPlot were used for filtering and visualizing the FASTQ data. Flye (2.8.1) was used for de novo assembly analysis. Variant calls and consensus sequences were created using Medaka. The annotation of the genome was elaborated by DFAST. The assembled genome and annotation were tested using Busco and CheckM. Herein, we found that the highest similarity of the BBR56 isolate was 98.37% with the 16 S rRNA gene sequence of P. viridis G-1387. The genome size was 5.5 Mb and included chromosome 1 (4.2 Mbp) and chromosome 2 (1.3 Mbp), which encoded 61 pseudogenes, 4 noncoding RNAs, 113 tRNAs, 31 rRNAs, 4,505 coding DNA sequences, 4 clustered regularly interspaced short palindromic repeats, 4,444 coding genes, and a GC content of 49.5%. The sequence of the whole genome of P. viridis BBR56 was uploaded to GenBank under the accession numbers CP072425–CP072426, biosample number SAMN18435505, and bioproject number PRJNA716373. The sequence read archive (SRR14179986) was successfully obtained from NCBI for BBR56 raw sequencing reads. Digital DNA–DNA hybridization results showed that the genome of BBR56 had the potential to be a new species because no other bacterial genomes were similar to the sample. Biosynthetic gene clusters (BGCs) were assessed using BAGEL4 and the antiSMASH bacterial version. The genome harbored diverse BGCs, including genes that encoded polyketide synthase, nonribosomal peptide synthase, RiPP-like, NRP-metallophore, hydrogen cyanide, betalactone, thioamide-NRP, Lant class I, sactipeptide, and prodigiosin. Thus, BBR56 has considerable potential for further exploration regarding the use of its secondary metabolite products in the human and fisheries sectors.

The potential Two Types of Green Macroalgae (Caulerpa racemosa and Caulerpa lentillifera) as a Natural Food Preservative from Jepara beach, Indonesia

Published: 5 March 2024

Gunawan WidiSantosa, Ali Djunaedi, AB Susanto, Delianis Pringgenies, Dafit Ariyanto & Aris Kabul Pranoton

Publication Category: Sanger Sequencing

Abstract

Green macroalgae, known locally as Latoh, is one of the green seaweeds consumed by the local community in Jepara and is beneficial for health. This study explores the potential of secondary metabolites from seaweed and its symbiotic bacteria as natural food preservatives and antibacterials. Seaweed samples were collected from the seagrass ecosystem of Panjang Island, Jepara, Indonesia. Subsequently, the samples were subjected to scanning electron microscopy analysis, proximate analysis, phytochemical analysis, thin layer chromatography, and highperformance liquid chromatography for amino acid analysis. A sample was subjected to a multistage extraction process using nhexane, ethyl acetate, and methanol (1:5 w/v), each for 24 h. Symbiotic bacteria from seaweed were isolated, and enzymatic (proteolytic, amylolytic, and cellulolytic) and antibacterial testing against pathogenic bacteria Staphylococcus aureusand Escherichia coliwas conducted using the disc diffusion method. The selected bacteria were subjected to molecular identification. The research showed that Caulerpa lentilliferahad an ash content of 3.24%, protein content of 0.57%, and fat content of 0.337%. Phytochemical analysis shows that the sample contains flavonoids, steroids, and alkaloids. HPLC analysis reveals that Caulerpa lentilliferahas the highest content of aspartic acid (relative area: 11.90%), glutamic acid (relative area: 13.43%), and alanine (relative area: 9.03%). Caulerpa racemosasample shows the highest detector response for glutamic acid (relative area: 12.19%), aspartic acid (relative area: 11.10%), and alanine (relative area: 9.63%). The results indicate that 14 bacterial isolates were successfully isolated, with 6isolates from Caulerpa lentilliferaand 8isolates from Caulerpa racemosa,all exhibiting enzymatic and antibacterial abilities. The research results concluded that the Latoh seaweed species Caulerpa lentillifera andCaulerpa racemosaand their symbiotic bacteria have the potential to be used as food preservatives

Published: March 2024

Anna Rakhmawati, Bernadetta Octavia & Siti Marwati

Publication Category: Amplicon Sequencing

Abstract

As the number of Covid-19 cases has increased, the production and use of face masks have also increased accordingly. This widespread use of face masks generates millions of tons of mask waste. This study analyzed the bacterial community composition of discarded masks from landfills (Piyungan, Jatibarang, Burangkeng); mangroves (Wanatirta, Tirang, Teluk Naga); and beaches (Parangtritis, Marina, Tanjung Pasir) in Yogyakarta, Semarang, Bekasi, and Tangerang, Java, Indonesia using 16S rRNA sequencing. Analyzing all samples from landfills, mangroves, and beaches revealed that the Proteobacteria phylum is the predominant. In addition, Firmicutes was the second-highest phylum in the samples from landfills and mangroves. In the meantime, Actinobacteria and Cyanobacteria dominated the phyla found in samples from beaches. Analyses at the genus level revealed that Bacillus members predominated in samples of discarded face masks from landfills. addition, the most prevalent genus found in samples from mangroves and beaches was Vibrio. According to the findings,the distribution of bacterial communities differed among the various regions. Dissimilar bacterial communities and gradient distributions were found among discarded face masks in landfills, mangroves, and beaches. It was the first examination of bacterial distribution in discarded disposable face masks from various locations.

Published: 23 February 2024

Joko Prasetyo, Nur Baitullah Juniar, Rusdi Evizal, Tri Maryono, & Cipta Ginting

Publication Category: Sanger Sequencing

Abstract

Trichoderma has the potential to suppress fungal pathogens and thus control plant diseases, including Phytophthora foot rot, which is the most devastating disease of black pepper in Lampung. Identification of a microorganism can not only rely on its morphological characteristics, but it is also necessary to identify it molecularly at the species level. This research was aimed at identifying the fungus Trichoderma sp. Margodadi isolates at the species level and to know the potential of Trichoderma sp. Margodadi isolates and their secondary metabolites to control P. capsici. This research was conducted from March to November 2021 at the Laboratory of Plant Disease, Department of Plant Protection, and the Laboratory of Agricultural Biotechnology, Faculty of Agriculture, University of Lampung. Identification of Trichoderma was done by morphological characteristics and molecular methods. The ability of Trichoderma to suppress P. capsici was tested by dual culture. The effect of secondary metabolites on the growth of P. capsici was determined in vitro at concentrations of 0% (control), 10%, 20%, 30%, and 40%. The experimental design used was a completely randomized design consisting of five treatments repeated five times. The data obtained from the test were analyzed using ANOVA, followed by the LSD test at 5%. The results of this study showed that Trichoderma sp. Margodadi isolate had a close relationship with Trichoderma asperellum and had the ability as an antagonist to inhibit the growth of P. capsici up to 47.23%, and the secondary metabolites produced could inhibit the growth of P. capsici up to 72.53% with the best concentration of 40%. 

The Potential of Bacillus altitudinis B538 and Alcaligenes faecalis B947 in PET and PCL Plastic Degradation

Published: 23 February 2024

Muthia Rahmah Dini, Mochamad Nurcholis, Maria Ulfah, Gabriela Christy Sabbathini, Sri Rezeki Wulandari & Is Helianti

Publication Category: Sanger Sequencing

Abstract

Polyethylene terephthalate (PET) plastic is the most widely used type of plastic that produces waste and causes various environmental and health problems. The treatment of PET plastic waste with chemically and mechanically recycling approaches still has shortcomings, so biological processing using microorganisms or enzymes has new potential. Two bacterial isolates from the Indonesian Culture Collection of NationalResearch and Innovation Agency (InaCC, BRIN), namely isolate InaCC B538 and InaCC B947, were further observed for their potential in PET plastic degradation. Firstly, both isolates were determined by the molecular marker 16S rDNA. The potential of both isolates was measured with following method: 10 days of degradation using PET and PCL substrates, esterase enzyme activity assay, and observation of the PET plastic surface using Scanning Electron Microscope (SEM). Species identification was performed using DNA sequencing of 16S rDNA. InaCC B538 and InaCC B947 were closely related to Bacillus altitudinis TBMAX41 and Alcaligenes faecalis AN-13, respectively. InaCC B947 isolate has a better potential in degrading PET plastic and PCL with a degradation percentage of 0.32% for PET plastic and 3.22% for PCL film for 10 days, respectively, and esterase activity of 0.06 U/ml; while InaCC B538 did not cause weight loss of PET and 2.49% for PCL, respectively, with esterase activity of 0.04 U/ml. The degradation of PET plastic by the isolates InaCC B947 was able to cause damage to the plastic surface leading to the degradation of PET plastic.

Abstract

MAS disease (Motyle Aeromonas hydrophila) is a prevalent bacterial infection that affects freshwater lobsters. This research aimed to evaluate the potential of CpG-ODN as an immunostimulant and protecting agent in Cherax quadricarinatus lobsters. The study was conducted at the Fish Health Laboratory, Pangkep State Polytechnic, Indonesia. The lobsters were divided into different groups and injected with three types of CpG-ODN (2133, 2006, 1668) or a control group using PBS. Parameters such as Total Hemocyte Count, Phagocytic Index, and Lysozyme Activity were measured at multiple time points, including before and after injection. CpG-ODN 2006 showed significant immunostimulant effects, as evidenced by a notable increase in total hemocyte count, phagocytic index, and lysozyme activity compared to the other CpG-ODN types. On the other hand, CpG-ODN 2133 exhibited potential as a protecting agent against Aeromonas hydrophila, as lobsters injected with this CpG-ODN demonstrated higher survival rates in the challenge test compared to the control group. These findings contribute to our understanding of immunostimulant strategies and protective mechanisms in freshwater lobsters. CpG-ODN, particularly CpG-ODN 2006, shows promise as an effective immunostimulant, while CpG-ODN 2133 exhibits potential as a protecting agent against A. hydrophila. Further exploration of CpG-ODN applications could lead to advancements in disease management in aquaculture.

Published: 22 February 2024

Mutia Ramadhaniaty, Vindy Rilani Manurung, Khairunnisa, Friyuanita Lubis & Ipanna Enggar Susetya
Publication Category: Sanger Sequencing
Abstract

The Nias Islands are an archipelago in the western part of North Sumatera, encompassed by the Indian Ocean, and have become a hotspot for demersal and pelagic fishes. These geographical conditions endow the waters around Nias with large fishery resources, leading to their frequent utilization as fishing grounds for Sumatera Island and its surrounding areas. This research aimed to identify the commercially important fish species with the highest catch frequency in the waters of Nias, and this identification marked the initial stage of the sustainable utilization of fish resources. The method used was DNA Barcoding using genes targeting the COI Mitochondrial locus. Therefore, 43samples were collected from several North and South Nias fish landing sites. The obtained species were classified into 3 groups based on the commodity type: demersal fish, pelagic fish, and Choncricthyes. There were 8 species of demersal fish (Caesio caerulaurea, Halichoeres scapularis, Lethrinus ornatus, Mulloidichthys flavolineatus, Parupeneus barberinus, Scarus prasiognathos, Plectropomus leopardus, andVariola albimarginata), displaying genetic distances ranging from 0.0020.275. Pelagic fish consisted of 5 species, namely Amblygaster clupoides, Caranx ignobilis, Caranx sexfasciatus, Ferdauia ferdau, andScomberomorus commerson, displaying genetic distances ranging from 0.0020.267. The next commodities were Chondrichthyeswith 9 species (Carcharhinus sealei, Himantura leoparda, Neotrygon kuhlii, Paragaleus randalli, Pateobatis jenkinsii, Rhynchobatuscf laevis, Spyrna lewini, Taeniura meyeni, andUrogymnus granulatus), displaying genetic distance ranging from 00.271.This value indicates that migratory species such as Chondrichthyeshave quite extensive movements so that the genetic distance between species and between populations tends to be low.

Published: 13 February 2024

Yuliza, Andi Salamah & Hardini Puspitaningrum
Publication Category: Sanger Sequencing
Abstract

Pemphis acidulais a wild plant in rocky or sandy coastal areas and mangrove ecosystems. Different geographic characteristics may affect plant adaptability and have an impact on the emergence of various genotypes. This study was performed to reveal the phenetic relationship and genetic variation of P. acidu-lain 3 different areas in Tomini Bay, Gorontalo Province, Indonesia. We took 3 samples from each location and analysed them using 14 morphological char-acters and molecular approaches based on ISSR markers and ITS gene. The results showed that P. acidulaon Olele had bigger sizes in some morphological features compared to the plants in other study areas. The phenetic analysis showed that P. acidulaat Biluhu and Dulanga were more closely related, alt-hough P. acidulaat the 3 locations had 100% similarity. Genetic variation anal-ysis showed the highest genetic similarity based on ISSR markers was found in Dulanga and Biluhu samples (76.8%). Phylogenetic based on ITS gene re-vealed that Olele samples were in the same clade with P. acidula accession from GenBank (genetic distance 0-0.19%), while Biluhu samples were a sister group (genetic distance 24.97-25.03%) even though their percentage identity corre-sponds to P. acidula (81.34%). Plant adaptation to different habitat conditions may affect the genetic diversity of P. acidula.

Abstract

Forkhead box O3 (FOXO3) is a transcription factor that regulates stress resistance, metabolism, cell cycle, and apoptosis. Several studies exhibited the association of the FOXO3 polymorphism rs2802292 with human longevity and protects individuals from degenerative diseases. The emergence of degenerative diseases in the elderly is associated with the accumulation of senescent cells that secrete a secretome known as a senescence-associated secretory phenotype (SASP) consists of several cytokines, chemokines, growth factors, proteases.

Environmental Metagenomic Analysis of “ESKAPE” Pathogens in the Pediatric Intensive Care Unit of General Hospital Yogyakarta Indonesia

Published: 7 February 2024

Ludhang Pradipta Rizki, Indah Kartika Murni,Abu Tholib Aman & Titik Nuryastuti
Publication Category: Amplicon Sequencing
Abstract

Healthcare-associated infections (HAIs) are infections that occur while receiving health care, develop in a hospital or other healthcare facility, and first appear 48 hours or more after hospital admission, or within 30 days after having received health care. HAIs are linked to high mortality rates, prolonged stays, increased hospital overhead costs, and financial burdens on patients. Bacterial transmission from medical personnel or the environment, or patient-to-patient contact are all potential causes of these infections. A molecular epidemiology approach is needed to examine the contribution of risk factors and the distribution of “ESKAPE” pathogens within the hospital environment. In this study, we conducted a comprehensive analysis of the distribution of ESKAPE bacterial pathogens in the environment of pediatric intensive care units over a 30-day time interval using shotgun metagenomics. We collected samples from handwashing sinks, the floor around patients, and ventilator screens and tubes in the pediatric intensive care unit (PICU) of General Hospital, Yogyakarta, Indonesia in March 2022. We determine taxonomic profiles and also detect resistome, and virulome distribution of ESKAPE pathogens on various environmental surfaces through shotgun metagenomic sequencing. The microbiomes of the floor, sink, and mechanical ventilator exhibit a diverse composition of microbial communities, featuring significant species richness based on Shannon and Simpson’s index. These microbiomes encompass a wide array of microbial species, including ESKAPE bacterial pathogens, as well as profiles related to resistome and virulome. ESKAPE pathogens, especially Acinetobacter baumannii, predominated in the PICU environment. Most virulome have been associated with metabolism/nutrition and adhesion. Noteworthy findings include resistome genes characterized by mechanisms like efflux pumps (MDR) and alterations in antibiotic targets.

Diversity of Santigi (Pemphis acidula J.R.Forst. & G.Forst.), A Mangrove Association in Tomini Bay, Sulawesi, Indonesia

Published: 29 January 2024

Dewi Wahyuni K. Baderan, Sukirman Rahim, Melisnawati H. Angio, Muh. Nur Akbar, Magfirahtul Jannah, Yuliana Retnowati & Ramli Utina
Publication Category: Sanger Sequencing
Abstract
Pemphis acidulais a wild plant in rocky or sandy coastal areas and mangrove ecosystems. Different geographic characteristics may affect plant adaptability and have an impact on the emergence of various genotypes. This study was performed to reveal the phenetic relationship and genetic variation of P. acidu-lain 3 different areas in Tomini Bay, Gorontalo Province, Indonesia. We took 3 samples from each location and analysed them using 14 morphological char-acters and molecular approaches based on ISSR markers and ITS gene. The results showed that P. acidulaon Olele had bigger sizes in some morphological features compared to the plants in other study areas. The phenetic analysis showed that P. acidulaat Biluhu and Dulanga were more closely related, alt-hough P. acidulaat the 3 locations had 100% similarity. Genetic variation anal-ysis showed the highest genetic similarity based on ISSR markers was found in Dulanga and Biluhu samples (76.8%). Phylogenetic based on ITS gene re-vealed that Olele samples were in the same clade with P. acidula accession from GenBank (genetic distance 0-0.19%), while Biluhu samples were a sister group (genetic distance 24.97-25.03%) even though their percentage identity corre-sponds to P. acidula (81.34%). Plant adaptation to different habitat conditions may affect the genetic diversity of P. acidula.

The first report of dark septate endophytes from Indonesian Pinusmerkusii and its symbiosis role as a plant growth promoter in nursery condition

Published: 27 January 2024

Jumadil Akhir, Elis Ninaherliyana, Surono & Sri Wilarso Budi
Publication Category: Sanger Sequencing
Abstract
To encourage the healthy growth of Pinus merkusii Pinus merkusii Jungh et de Vriese seedlings at the seedling stage, Dark Septate Endophytic (DSE) fungi were used as growth promoters. In this study, four DSE strains, i.e., Apls 1.5.3,Pls 32.1, Hs14.6a,and Hs14.6c isolated from P. merkusiiroots, were tested for their ability to stimulate the growth of P. merkusiiseedlings. After 14 weeks of incubation in nursery conditions, P. merkusiiseedlings inoculated with four DSE strains experienced a higher increase in heightand stem diameter when compared to the control treatment. Overall, thebiomass results of P. merkusiiseedlings treated with the DSE strains performed better than those of the control. Root colonization of P. merkusiiseedlings showed thatthe 4 DSE strains significantly outperformed the control. The Hs14.6c strain outperformed the other strains and controls regardingnutrient (nitrogen) uptake. The findings of this study are the first to show that the DSE Apls 1.5.3 strain is similar to Cylindroccarpon, the Hs14.6a and Hs14.6c strains are similar to Cladophialophorasp., andthe Pls 32.1 strain is similar to Oncopodiella trigonellabased on identification results and phylogenetic trees and can be in symbiosis with seedsof P. merkusii, a pine species native to Indonesia.
Abstract

The development of meat analogues focuses on sustainable production and requires attention to their nutritional, physicochemical, and sensory values. Anchovy protein isolate (API) is a novel and potential binding agent in the development of meat analogues. This study aimed to produce API and evaluate the physical, proximate, and sensory qualities of patty meat analogue (PMA) with the addition of API. The preparation method for API uses pH-shifting. The ratios of API added to the meat analogues were 0 % (F0), 4 % (F1), 8 % (F2), and 12 % (F3) per textured vegetable protein (TVP) weight. Furthermore, PMA was analysed for physical, proximate, and sensory properties. API had 87.23 % dry basis (db) protein content. The amino acid composition of API generally complied with the nutritional requirements of adults and children. The addition of API significantly affected the physical properties, proximate composition, and sensory (taste) qualities of PMA (p < 0.05). The protein content of PMA met Indonesian national standards (SNI) and was similar to both McDonald’s and ground beef patty based on United States Department of Agriculture (USDA) standards. F3 was found to be the best based on its physical, proximate, and sensory properties.

Seroconversion, genotyping, and potential mosquito vector identification of Japanese encephalitis virus in pig sentinel settings in Bali, Indonesia

Published: 8 January , 2024

I Made Kardena, Anak Agung Ayu Mirah Adi, I Nyoman Mantik Astawa , Ida Bagus Made Oka, Shafi Sahibzada, Mieghan Bruce, & Mark O’Dea

Publication Category: Sanger Sequencing

Abstract

Background and Aims: Despite the endemicity of Japanese encephalitis virus (JEV) in humans and animals in the Province of Bali, Indonesia, there is little data on whether seroconversion to the virus occurs in pigs, JEV genotypes circulating, and it’s potential mosquito vectors in the area. The aims of this study were to (i) Determine whether JEV infection in Balinese pigs occurs before reaching their sexual maturity, (ii) identify the genotypes of circulating JEV, and (iii) identify potential JEV mosquito vectors at the study sites in urban and peri-urban areas of Bali. Materials and Methods: Sixteen 1-week-old Landrace piglets from two different sows were housed in Denpasar. Similarly, 18 one-week-old mixed-breed piglets of two different sows were housed in Badung Regency. The piglets were bled every 1 to 4 weeks for up to 24 weeks. Serum samples from the 11 piglets were tested for antibodies against JEV, and seroconversion- suspected sera were titrated using an enzyme-linked immunosorbent assay. Blood of seroconverted sera from pigs were tested using polymerase chain reaction (PCR) to detect the genetic sequence of JEV. The mosquitoes in the sentinels were trapped throughout the study period to identify the potential mosquito vectors of JEV. Results: Antibodies were detected in most of the selected piglets’ sera from weeks 1 to 24 of their age. However, sera of pig B9 collected from the sentinel setting in Badung Regency showed a four-fold increase in antibody titer from week 4 to week 8, indicating seroconversion. PCR testing of blood from B9 (pooled blood sample collected from week 5 to week 8) identified JEV nucleic acids, which were phylogenetically classified as belonging to the JEV genotype III. Meanwhile, 1271 of two genera of mosquitoes, Anopheles spp. and Culex spp. were trapped in the pig sentinels. Conclusion: JEV seroconversion likely occurs before the pig reaches sexual maturity in Badung Regency. Sequence data indicate that JEV genotype III is circulating in the pig sentinel setting in the regency; however, circulating genotypes need to be clarified through increased surveillance. Meanwhile, Culex spp. and most likely Culex quinquefasciatus and Anopheles spp. were the dominant mosquitoes present in the study sites set in the urban area of Denpasar and peri-urban areas of Badung, Bali, indicating that these are likely vectors in spread of JEV in the region

Abstract

This research aims to quantify antiquorum sensing and antibiofilm activity of f phyllosphere bacteria against biofilm formed by pathogenic fish bacteria such as Aeromonas hydrophila, Streptococcus agalactiae, and Vibrio harveyi. Antiquorum sensing assay using Chromobacter violaceum as indicator bacteria and antibiofilm assay showed six phyllosphere bacteria have antiquorum sensing and antibiofilm activities against tested bacteria. The highest inhibition and destruction activity was showed by metabolite of JB 3B and EJB 5 F against A. hydrophila, respectively. Determination using light microscope and scanning electron microscope performed decreaing in biomass of biofilm observed after treated with metabolite from phyllosphere bacteria.

Metagenomic data of bacterial 16S rRNA in the cemetery soil samples in Surakarta City, Indonesia

Published: 14 December 2023

Triastuti Rahayu, Erma Musbita Tyastuti, Ambarwati Ambarwati,  Lina Agustina, Noor Alis Setiyadi,  Nazia Jamil, & Yasir Sidiq
Publication Category: Amplicon Sequencing

Abstract

Cemetery soils most likely contain degradative bacteria which possibly have beneficial potencies. However, the bacterial exploration in these potencies is still limitedly conducted in Indonesia. The raw sequence data of total bacteria in the cemetery soils through metagenomic analysis have been revealed. The data were obtained by collecting soil samples from six spots of two major Cemetery areas, which were Pracimaloyo (P) and Bonoloyo (B), in Surakarta City, Central Java, Indonesia. The six sample spots consisted of two samples from P area with respectively 20 cm and 140 cm depths and four samples of each two samples from B area with 20 and 40 cm depths. The total DNA was subsequently extracted from the collected soils using ZymoBIOMICS DNA Miniprep Kit. The total DNA then was amplified using a couple of 16S rRNA primers through Illumina HiSeq 2500 PE250 (Novogen, Korea) environment system. The raw sequence data has been submitted to the National Center for Biotechnology Information (NCBI) with project ID PRJNA997385. The archived sequence can be accessed in the NCBI website with the following URLs https://www.ncbi.nlm.nih.gov/sra/PRJNA997385. A brief analysis of the sequence data showed that the most common phyla in 20 cm-depths were Proteobacteria (29.5%), Actinobacteria (21.6%), and Firmicutes (19.2%), while Actinobacteria were the most found in 140 cm-depths with 34.2% followed by Proteobacteria (21.9%) and Firmicutes (16.6%). This data would be the first report of total bacterial sequence from cemetery soils in Indonesia.