I am a molecular biologist with biomedical and agricultural backgrounds. I currently run a Next Generation Sequencing facility which is under the ithree institute.
My main expertises are in creating Next Generation Sequencing libraries including short gun genome sequencing, 16S/ITS metagenomics sequencing and RNA sequencing (transcriptomic and RNA seq) using commercial kits and custom protocols. I also have hand-on experience working with sequencing instruments including 454 Roche sequencing, Illumina MiSeq and HiSeq2500. My interests are in molecular biology, immunology, genetics, epigenetics, bioinformatics and 3D printing technologies for laboratory.
I completed my Bachelor and Honours degree in biomedical science major in microbiology and immunology from the University of Adelaide. I then joined the group at Waite Research Institute (University of Adelaide), completed my PhD in molecular entomology. My PhD research was on understanding the molecular mechanism of inducible immune tolerant against pesticide in Helicoverpa armigera. After my PhD, I joined Murdoch University, and did research on investigating the effect of lethal stresses on the cellular biology of Tephritid fruit flies (Queensland and Mediterranean fruit flies). I extensively focused on RNA sequencing and RNA seq data analysing in both my PhD and my postdoctoral research. Prior to my current position at UTS, I worked at the Next Generation Sequencing Facility at Western Sydney University.
Next generation sequencing, molecular biology, automated liquid handling system, 3D printing for laboratory use
Gaio, D, DeMaere, M, Anantanawat, K, Chapman, T, Djordjevic, S & Darling, A 2020, 'Post-weaning shifts in microbiome composition and metabolism revealed by over 25,000 pig gut metagenome assembled genomes'.View/Download from: Publisher's site
ABSTRACT Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50,000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5% of which were classified as >70% complete with a <10% contamination rate, and 24.4% were nearly complete genomes. Here we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental program in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic "signatures" that characterize the microbiome development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut, identifying 294 carbohydrate active enzymes. We tracked the shifts in abundance of these enzymes across time, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs, raising the possibility of modifying the piglet microbiome through the tailored provision of carbohydrate substrates.
Gaio, D, DeMaere, M, Anantanawat, K, Eamens, G, Liu, M, Zingali, T, Falconer, L, Chapman, T, Djordjevic, S & Darling, A 2020, 'Community composition and development of the post-weaning piglet gut microbiome'.View/Download from: Publisher's site
ABSTRACT We report on the largest metagenomic analysis of the pig gut microbiome to date. By processing over 800 faecal time-series samples from 126 piglets and 42 sows, we generated over 8Tbp of metagenomic shotgun sequence data. Here we describe the animal trial procedures, the generation of our metagenomic dataset and the analysis of the microbial community composition using a phylogenetic framework. We assess the effects of intramuscular antibiotic treatment and probiotic oral treatment on the diversity of gut microbial communities. We found differences between individual hosts such as breed, litter, and age, to be important contributors to variation in the community composition. Treatment effects of the antibiotic and probiotic treatments were found but were subtle, while host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appears to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life.
Anantanawat, K, Pitsch, N, Fromont, C & Janitz, C 2019, 'High-throughput Quant-iT PicoGreen assay using an automated liquid handling system.', BioTechniques, vol. 66, no. 6, pp. 290-294.View/Download from: Publisher's site
Workflows in NGS facilities require high-standard practices and high-throughput pipelines to process the large number of samples received in a timely manner. Downstream protocols such as NGS library preparation require accurate estimation of nucleic acid concentrations, which can be achieved using fluorescent dye-based nucleic acid measurement. Here, we report a protocol for preparing a 384-well Quant-iT PicoGreen assay. The protocol allows the concentrations of 184 DNA samples to be measured simultaneously in duplicate in only 1 h using an Eppendorf epMotion 5075 liquid handling system. The advantages of this high-throughput approach include a reduction in both reagents (10x less reagents compared to a standard protocol) and time (3 h for 384 samples compared with 3 days).
ABSTRACT We developed Hackflex, a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 11 times more libraries for high-throughput Illumina sequencing to be generated at a fixed cost. We call this new method Hackflex. Quality of library preparation was tested by constructing libraries from E. coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. We demonstrated that Hackflex can produce high quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. Using Hackflex, we were able to achieve a per sample reagent cost of library prep of A$8.66, which is 8.23 times lower than the Standard Nextera Flex protocol at advertised retail price. An additional simple modification to the protocol enables a further price reduction of up to 11 fold or about A$6.50/sample. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programs where sequencing large numbers of libraries is beneficial.
Anantanawat, KJ, Glatz, R & Keller, MA 2016, 'Effect of induced tolerance to Bt toxin on the egg size of Helicoverpa armigera and parasitism by Trichogramma pretiosum', Physiological Entomology, vol. 41, no. 3, pp. 267-273.View/Download from: Publisher's site
© 2016 The Royal Entomological Society Larvae of Helicoverpa armigera (Hübner) can develop a form of Bt tolerance after exposure to sub-lethal doses of Bt-toxin subclass Cry1Ac. Increasing levels of tolerance are produced over generations of larval exposure, which are not related to DNA sequence changes, and are largely maternally transmitted. The characteristic of maternal transmission, combined with the importance of egg parasitoids to cotton pest management, raises questions about the effects of Bt tolerance/exposure on the eggs of H. armigera and on some key metrics of egg parasitism. In the present study, the effect of inducible tolerance on eggs of H. armigera and parasitism by Trichogramma pretiosum (Riley) is investigated. First, the volumes of eggs laid by susceptible and tolerant H. armigera females are compared. In addition, the effect of inducible tolerance on egg parasitism is determined by comparing parasitism success, the number of adult wasps emerged per host egg, and the proportion of male and female offspring emerged per host egg. The results obtained suggest that Cry1Ac-tolerance is associated with increased egg volume, even after just one generation of sub-lethal exposure. When tolerant H. armigera are freed from ongoing sub-lethal exposure, a corresponding decrease in egg volume is not detected. Although there is no difference in the percentage of eggs parasitized, there is an increase in the number of emergent parasitoids, especially males, from eggs laid by tolerant H. armigera. These results confirm that maternally-transmitted Bt tolerance is reflected in the phenotype of the eggs of tolerant offspring, which affects egg parasitism.