A5067632164- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Neonatal Respiratory Health Research
- Anesthesia and Neurotoxicity Research
- Antibiotic Resistance in Bacteria
- Bacteriophages and microbial interactions
- Indoor Air Quality and Microbial Exposure
- Bacillus and Francisella bacterial research
- Probiotics and Fermented Foods
- Infant Development and Preterm Care
- Plant Pathogens and Fungal Diseases
- Birth, Development, and Health
- Plant-Microbe Interactions and Immunity
- Plant Pathogenic Bacteria Studies
- Chronic Obstructive Pulmonary Disease (COPD) Research
- Diet and metabolism studies
- Bacterial Identification and Susceptibility Testing
- Mycotoxins in Agriculture and Food
- Aquaculture disease management and microbiota
- Enterobacteriaceae and Cronobacter Research
- Pharmaceutical and Antibiotic Environmental Impacts
- Listeria monocytogenes in Food Safety
- Molecular Biology Techniques and Applications
- Tracheal and airway disorders
National University of Singapore
2012-2022
Singapore Centre for Environmental Life Sciences Engineering
2013-2022
Nanyang Technological University
2013-2022
Children's Hospital
2020
Singapore Institute for Clinical Sciences
2020
Vanderbilt University Medical Center
2020
University of Indonesia
2012
Abstract The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity individuals genomic datasets and led to reduced medical relevance for a large proportion world’s population. Population-specific reference genome as well genome-wide association diverse populations are needed address this issue. Here we describe pilot phase GenomeAsia 100K Project. This includes whole-genome sequencing dataset from 1,739 219 population groups 64 countries across Asia....
The gut microbiota evolves as the host ages, yet effects of these microbial changes on physiology and energy homeostasis are poorly understood. To investigate potential effects, we transplanted old or young mice into germ-free recipient mice. Both groups showed similar weight gain skeletal muscle mass, but receiving a transplant from donor unexpectedly increased neurogenesis in hippocampus brain intestinal growth. Metagenomic analysis revealed age-sensitive enrichment butyrate-producing...
The atmosphere is vastly underexplored as a habitable ecosystem for microbial organisms. In this study, we investigated 795 time-resolved metagenomes from tropical air, generating 2.27 terabases of data. Despite only 9 to 17% the generated sequence data currently being assignable taxa, air harbored diversity that rivals complexity other planetary ecosystems. airborne organisms followed clear diel cycle, possibly driven by environmental factors. Interday taxonomic exceeded day-to-day and...
Abstract Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed breed in fecal decaying organic matter, but microbiome they harbour transport is largely uncharacterized. We sampled 116 individual blowflies from varying habitats on three continents subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic metagenomic analyses of host-associated at species level. Both fly host segregate based principal...
Through several observational and mechanistic studies, microbial infection is known to promote cardiovascular disease. Direct of the vessel wall, along with risk factors, hypothesized play a key role in atherogenesis by promoting an inflammatory response leading endothelial dysfunction generating proatherogenic prothrombotic environment ultimately clinical manifestations disease, e.g., acute myocardial infarction or stroke. There are many reports DNA isolation even few studies viable...
Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains tiny nuclear genome despite at least two rounds of whole duplication (WGD) since common ancestry with grapevine and other species. We used third-generation assembly several complete chromosomes to reconstruct most recent lineage-specific ancestral genomes led modern U. gibba structure. Patterns subgenome dominance in WGD, both architectural transcriptional, are suggestive allopolyploidization, which may have...
Abstract True flies are insects of the order Diptera and encompass one most diverse groups animals on Earth. Within dipterans, Schizophora represents a recent radiation that was used as model to develop pipeline for generating complete mitogenomes using various sequencing platforms strategies. 91 from 32 different species were sequenced assembled with high fidelity, amplicon, whole genome shotgun or single molecule approaches. Based novel mitogenomes, we estimate origin within...
Rationale: Long-term antibiotic use for managing chronic respiratory disease is increasing; however, the role of airway resistome and its relationship to host microbiomes remains unknown.Objectives: To evaluate resistomes relate them environmental using ultradeep metagenomic shotgun sequencing.Methods: Airway specimens from 85 individuals with without (severe asthma, obstructive pulmonary disease, bronchiectasis) were subjected sequencing an average depth exceeding 20 million reads....
Evidence is accumulating that the establishment of gut microbiome in early life influences development atopic eczema. In this longitudinal study, we used integrated multi-omics analyses to infer functional mechanisms by which modulates eczema risk. We measured functionality and metabolome 63 infants between ages 3 weeks 12 months with well-defined cases controls a sub-cohort from Growing Up Singapore Toward healthy Outcomes (GUSTO) mother-offspring cohort. At weeks, allergen-sensitized were...
The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising meteorological tower aircraft, we conducted synchronized measurements parameters airborne biomass ( n = 480) in air column up 3,500 m. taxonomic analysis metagenomic data revealed differing patterns microbial community composition with respect time day height above ground. temporal spatial...
Abstract Investigation of the microbial ecology terrestrial, aquatic and atmospheric ecosystems requires specific sampling analytical technologies, owing to vastly different biomass densities typically encountered. In particular, ultra-low nature air presents an inherent challenge that is confounded by temporal fluctuations in community structure. Our pipeline advances field bioaerosol research significantly reducing times from days/weeks/months minutes/hours, while maintaining ability...
Abstract Background The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In double-blind randomized controlled study, 153 infants born by elective received an infant formula supplemented with either synbiotic, prebiotics, or unsupplemented until 4 months old. Vaginally were included reference group. Stool samples collected day 3 till week 22. Multi-omics deployed to investigate impact...
Second-generation sequencing (SGS) generates millions of reads that need to be aligned a reference genome allowing errors. Although current aligners can efficiently map small number mismatches, they are not well suited for handling large mismatches. The efficiency improved using various heuristics, but the sensitivity and accuracy alignments sacrificed. In this article, we introduce Basic Alignment tool Mismatches (BatMis)--an efficient method align short k BatMis is Burrows-Wheeler...
Abstract Here, we describe taxonomical composition, as well seasonal and diel dynamics of airborne microbial communities in West Siberia. A total 78 biomass samples from 39 time intervals were analysed, within a temperature range 48 °C (26 to − 22 °C). We observed 5–170-fold decrease DNA yield extracted the winter compared summer, nevertheless, yielding sufficient material for metagenomic analysis. The included Actinobacteria Proteobacteria, Ascomycota Basidiomycota fungi major components,...
While there is increasing knowledge about the gut microbiome, factors influencing and significance of resistome are still not well understood. Infant commensals risk transferring multidrug-resistant antibiotic resistance genes (ARGs) to pathogenic bacteria. The rapid spread bacteria a worldwide public health concern. Better understanding naïve infant may build evidence base for antimicrobial stewardship in both humans food industry. Given high carriage rate extended spectrum beta-lactamase...
Abstract Background Bacillus cereus is ubiquitous in nature, found environments such as soil, plants, air, and part of the insect human gut microbiome. The ability to produce endospores biofilms contribute their pathogenicity, classified two types food poisoning: diarrheal emetic syndromes. Here we report gap-free, whole-genome sequences B. strains isolated from air samples analyse potential. Results Genome assemblies consist one chromosome seven plasmids each. genome size strain SGAir0260...
ABSTRACT Bacillus altitudinis strain SGAir0031 ( Firmicutes ) was isolated from tropical air samples collected in Singapore. Its genome assembled using short reads and single-molecule real-time sequencing, comprising one chromosome with 3.81 Mb plasmid 32 kb. The consists of 3,820 protein-coding genes, 81 tRNAs, 24 rRNAs.
Abstract Background: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger projects take on complexity data storage for high volumes samples. This has created a need low-cost laboratory information management systems (LIMS) that contain flexible fields accommodate unique nature individual labs. Many labs do not have dedicated technology position, so LIMS must also be easy setup maintain with minimal technical proficiency. Findings: MetaLIMS is...
Bacillus velezensis strain SGAir0473 (Firmicutes) was isolated from tropical air collected in Singapore. Its genome assembled using short reads and single-molecule real-time sequencing comprises one chromosome with 4.18 Mb. The consists of 3,937 protein-coding genes, 86 tRNAs, 27 rRNAs.
Klebsiella pneumoniae is ubiquitous in the environment and a member of three-species biofilm model. We compared genome sequence an environmental isolate, K. strain KP-1, to those two clinical strains (NTUH-K2044 MGH 78578). KP-1 possesses strain-specific prophage sequences that distinguish it from strains.
Micrococcus luteus strain SGAir0127 was isolated from indoor air samples collected in Singapore. The assembly, based on single-molecule real-time sequencing reads, resulted two contigs, one chromosomal contig with a length of 2.57 Mbp and nonchromosomal 8.68 kbp. genome has total 2,564 genes.