In Vitro Propagation of Medicinal Plant Orthosiphun Stamineus (Misai Kucing) Through Axillary Branching and Callus Culture

Orthosiphun stamineus is a herbaceous plant that is popularly known as Misai Kucing. It is widely used in traditional medicine as diuretic agent. This study was divided into two parts that was the in vitro production of complete plantlet through axillary branching and callus culture derived from leaf explant. In axillary branching method, sterilization was conducted using 0.02mg/100ml of mercuric chloride followed by rinsing with 20% and 50% of Clorox for 20 minutes and 5 minutes respectively. This sterilization method was able to remove the contaminants from the surface of the axillary stem and almost 70% of the explants were survived. Axillary bud was placed on Murashige and Skoog (MS) basic medium and cultured for 1 month. The in vitro shoot was inoculated on MS medium which was supplemented with different concentrations of BAP and NAA. The medium that contained 1.0mg/L of BAP gave the best shoot multiplication (13.25) and shoot length (6.23cm) after 8 weeks in culture. Root formation in term of percentage of root (70%) and the number of root produced (10.50) were the best when shoot inserted into medium contained 6mg/L IBA after 3 weeks in culture. However, MS medium that was supplemented with 2 mg/L IBA enhanced in the root length (3.85 cm). Meanwhile, in callus culture, the leaf explant was placed on MS medium containing with various concentrations of 2,4-D for induction of callus. The optimum level of callus induction and proliferation rate (0.42) were obtained with 4mg/L 2,4-D. The callus cells were tested in medium with Evan’s Blue staining and the result showed that the cells were embryogenic. However, the shoot induction from the callus was failed in all tested mediums containing different combinations of BAP and 2,4-D

Preliminary screening of bacterial and fungal communities from spontaneous fermentation of Durian pulps (tempoyak) using high-throughput amplicon sequencing

Fermentation is a method used to prolong the shelf-life and taste of fruit. Tempoyak is a fermented food made from durian pulps. Accumulating works were conducted to isolate and characterize the microbial communities using culture-dependent methods, with little effort in identifying the diversity using culture-independent approaches like next-generation sequencing (NGS) in tempoyak. The culture-dependent method showed several limitations such as tedious technique in plating, biasness in morphological identification and incompatibility of media selection for microbial growth. To date, the NGS allowed identification of the unculturable microbes up to species level. The purpose of this study is to screen the microbial communities in tempoyak using amplicon sequencing by targeting 16S rRNA and ITS2 for determining the diversity of bacterial and fungal communities respectively. On the other hand, this study also compared the complex microbial structure from the first day, T0 to day 14, T14 of the fermentation process. Here, we observed that sample T14 showed more diverse in both bacterial and fungal populations as compared to sample T0. Overall, genus Lactobacillus are the most abundant microbes representing the bacterial community. This study highlighted the importance of the NGS in characterizing the complex microbial communities in fermented food, for which could be useful to screen for potential unculturable microbial communities hindered by the limitation of culture-dependent approach

ITS1 amplicon sequencing of feline gut mycobiome of Malaysian local breeds using Nanopore Flongle

The gut mycobiome exhibits major influence on the gastrointestinal health and disease but received less attention due to low abundance. This study characterizes the fungal community and compares the microbial diversity between indoor and outdoor cats. Genomic DNA was extracted and sequenced by targeting the Internal Transcribed Spacer 1 (ITS1) region using Flongle flow cell on MinION™ sequencing platform. Results show the phylum Ascomycota and genus Peniophorella were numerous in indoor cats, whereas the Basidiomycota and Pichia were abundant in outdoor cats. Peniophorella formed the core mycobiome in both feline populations. Furthermore, alpha (p value = 0.0207) and beta diversities (p value = 0.009) results showed significant differences between the two groups. Overall, indoor cats have greater amounts of Peniophorella, whereas outdoor cats have higher Trichosporon and unclassified Sordariaceae. The study also suggests that keeping a cat indoors or left as a stray will affect their respective gut mycobiome

High-throughput amplicon sequencing of gut microbiome sea cucumber in Pahang, Malaysia

Sea cucumbers are soft-bodied marine organisms found in the benthic environment which are known as trepang, gamat or timun laut by locals. Sea cucumbers are commercially exploited for their body extracts due to their therapeutic properties and as culinary demands. Moreover, sea cucumbers are host to complex community of microbes. However, less efforts were documented on the identification of these microbial communities using high-throughput sequencing approach. The purpose of this study is to identify the gut microbiome of the sea cucumber from Stichopus ocellatus species. For this study, the sea cucumbers were collected from a coastal area in Pahang, Malaysia. The gut contents were sampled and processed fresh upon collection and maintained on ice prior delivery to the storage facility. The DNA was extracted prior two steps Polymerase Chain Reaction (PCR) for amplicon library preparation by targeting the V4 region of 16S rRNA. The prepared libraries were sequenced using the Illumina iSeq 100 system. The raw data were analysed using QIIME2 and other bioinformatics software. Here, we observed that the gut of Stichopus ocellatus is home for the genera of Vibrio, Tropicibacter, Desulfopila and Halioglobus. Remarkably, the bacteria from the genus Vibrio are the most abundant bacteria colonising the gut microenvironment. This study suggests baseline microbial community that inhibit the gut of sea cucumber that may confer biotechnological important bacteria for pharmaceutical applications and drug development

High-throughput amplicon sequencing of gut microbiome sea cucumber in Pahang, Malaysia

Sea cucumbers are soft-bodied marine organisms found in the benthic environment which are known as trepang, gamat or timun laut by locals. Sea cucumbers are commercially exploited for their body extracts due to their therapeutic properties and as culinary demands. Moreover, sea cucumbers are host to complex community of microbes. However, less efforts were documented on the identification of these microbial communities using high-throughput sequencing approach. The purpose of this study is to identify the gut microbiome of the sea cucumber from Stichopus ocellatus species. For this study, the sea cucumbers were collected from a coastal area in Pahang, Malaysia. The gut contents were sampled and processed fresh upon collection and maintained on ice prior delivery to the storage facility. The DNA was extracted prior two steps Polymerase Chain Reaction (PCR) for amplicon library preparation by targeting the V4 region of 16S rRNA. The prepared libraries were sequenced using the Illumina iSeq 100 system. The raw data were analysed using QIIME2 and other bioinformatics software. Here, we observed that the gut of Stichopus ocellatus is home for the genera of Vibrio, Tropicibacter, Desulfopila and Halioglobus. Remarkably, the bacteria from the genus Vibrio are the most abundant bacteria colonising the gut microenvironment. This study suggests baseline microbial community that inhibit the gut of sea cucumber that may confer biotechnological important bacteria for pharmaceutical applications and drug development

Gut microbiome and metabolome of sea cucumber (Stichopus ocellatus) as putative markers for monitoring the marine sediment pollution in Pahang, Malaysia

Antibiotic contamination in the marine environment forms an emerging threat to marine ecosystems. This study aimed to compare the gut and coelomic microbiota of Stichopus ocellatus with sediments between two coastal districts of Pahang, which potentially conferring as putative biomarkers for sediment pollution monitoring. The composition of the bacteria communities was determined using 16S rRNA V3-region gene amplicon sequencing, while hybrid whole-genome sequencing was employed to analyze the genome of Vibrio parahaemolyticus. The trace elements and antibiotic compositions were access using high-throughput spectrometry. The alpha- and beta-diversity of bacteria in gut and sediment samples from Kuantan differed substantially within (p-value = 0.017604) and between samples (p-value <0.007), respectively. Vibrio genera predominated in Kuantan samples, while Flavobacterium and Synechococcus_E genera predominated in Pekan samples. Vibrio parahaemolyticus revealed the presence of tet(35) and blaCARB-33 genes that conceived resistance towards tetracycline and betalactam antibiotics, respectively, which were detected in sediment and gut samples

Toxic trace elements in selected edible rhizomes of medicinal plants using INAA and ICP-MS techniques

Consumption the crop is one of the main sources of dietary exposure to toxic trace elements. In order to assess the level of toxic trace elements from selected herbs and to make an assumption on their consumption level of concern, fourteen elements in Zingiber zerumbet(lempoyang), Boesenbergia rotunda (temu kunci), Zingiber officinale var rubrum (halia bara) and Zingiber officinale roscoe (halia) have been determined via ICP-MS (Cd, Be, Ti, Pb) and INAA (As, Al, Ba, Cr, Co, Sb, Sr, Th, U and V) methods. It was revealed that the concentrations of these elements in most selected rhizomes did not exceed the standard dangerous toxic level. However, 47% cadmium accumulationa was detected in Zingiber officinale var rubrum grown in poly-bags

Gut microbiome and metabolome of sea cucumber (Stichopus ocellatus) as putative markers for monitoring the marine sediment pollution in Pahang, Malaysia

Antibiotic contamination in the marine environment forms an emerging threat to marine ecosystems. This study aimed to compare the gut and coelomic microbiota of Stichopus ocellatus with sediments between two coastal districts of Pahang, which potentially conferring as putative biomarkers for sediment pollution monitoring. The composition of the bacteria communities was determined using 16S rRNA V3-region gene amplicon sequencing, while hybrid whole-genome sequencing was employed to analyze the genome of Vibrio parahaemolyticus. The trace elements and antibiotic compositions were access using high throughput spectrometry. The alpha- and beta-diversity of bacteria in gut and sediment samples from Kuantan differed substantially within (p-value = 0.017604) and between samples (p-value <0.007), respectively. Vibrio genera predominated in Kuantan samples, while Flavobacterium and Synechococcus_E genera predominated in Pekan samples. Vibrio parahaemolyticus revealed the presence of tet (35) and blaCARB-33 genes that conceived resistance towards tetracycline and beta-lactam antibiotics, respectively, which were detected in sediment and gut samples