A5045563074- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Wastewater Treatment and Nitrogen Removal
- Antibiotic Resistance in Bacteria
- Bacterial biofilms and quorum sensing
- Methane Hydrates and Related Phenomena
- Bacterial Identification and Susceptibility Testing
- CRISPR and Genetic Engineering
- Insect behavior and control techniques
- Protist diversity and phylogeny
- Vibrio bacteria research studies
- Bacterial Genetics and Biotechnology
- Probiotics and Fermented Foods
- Gut microbiota and health
- Pharmaceutical and Antibiotic Environmental Impacts
- Forensic Entomology and Diptera Studies
- Marine and coastal ecosystems
- Insect Pest Control Strategies
- Antimicrobial Resistance in Staphylococcus
- Clostridium difficile and Clostridium perfringens research
- Mycobacterium research and diagnosis
- Bacteriophages and microbial interactions
- Insect symbiosis and bacterial influences
- Trace Elements in Health
- Antibiotics Pharmacokinetics and Efficacy
University of Hong Kong
2016-2025
Chinese University of Hong Kong
2012-2025
Hospital Authority
2023-2024
Queen Mary Hospital
2019-2024
South China Agricultural University
2007-2023
Hong Kong University of Science and Technology
2010-2016
It is difficult for beginners to learn and use amplicon analysis software because there are so many tools choose from, all of them need multiple steps operation. Herein, we provide a cross-platform, open-source, community-supported pipeline EasyAmplicon. EasyAmplicon has most the modules needed an analysis, including data quality control, merging paired-end reads, dereplication, clustering or denoising, chimera detection, generation feature tables, taxonomic diversity compositional biomarker...
We investigated the diversity, spatial distribution, and abundances of ammonia-oxidizing archaea (AOA) bacteria (AOB) in sediment samples different depths collected from a transect with distances to mangrove forest territories Hong Kong. Both archaeal bacterial amoA genes (encoding ammonia monooxygenase subunit A) all supported distinct phylogenetic groups, indicating presences niche-specific AOA AOB sediments. The higher than sediments, especially vicinity trees, might indicate more...
A new species complex, the eparmata is established within subgenus Phortica s. str., based on eight known and five species, all of which are endemic to Oriental Region: P. bipartita (Toda & Peng, 1992), (Okada, 1977), lanuginosa Chen Toda, 2007, latipenis Gao, 2005, pangi Wen, setitabula unipetala 2005 zeta 2007; jadete sp. nov., kava mengda wongding nov. yena key this complex provided. Barcoding sequences (mitochondrial COI gene) were obtained for 22 specimens above-mentioned species....
Abstract Background The spread of antibiotic resistance has become one the most urgent threats to global health, which is estimated cause 700,000 deaths each year globally. Its surrogates, genes (ARGs), are highly transmittable between food, water, animal, and human mitigate efficacy antibiotics. Accurately identifying ARGs thus an indispensable step understanding ecology, transmission environmental human-associated reservoirs. Unfortunately, previous computational methods for mostly based...
Abstract Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency tools adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT ( B inning A cross a S eries ssemb l ies T oolkit) and refinement short- long-read sequencing data. employs multiple binners with thresholds to produce initial bins, then utilizes neural networks identify core sequences remove...
Anaerobic ammonium oxidation (anammox) has been recognized as an important process for the global nitrogen cycle. In this study, occurrence and diversity of anammox bacteria in deep-sea subsurface sediments South China Sea (SCS) were investigated. Results indicated that bacterial sequences recovered from habitat by amplifying both 16S rRNA gene hydrazine oxidoreductase encoding hzo all closely related to Candidatus Scalindua genus. A total 96 346 clones grouped into five subclusters: two...
The community and population dynamics of anammox bacteria in summer (wet) winter (dry) seasons estuarial mudflat sediment the Mai Po Nature Reserve were investigated by 16S rRNA hydrazine oxidoreductase (hzo) genes. phylogenetic diversity showed that sequences related to 'Kuenenia' presented but not while 'Scalindua' occurred both could be divided into six different clusters. Compared genes, hzo genes revealed a relatively uniform seasonal diversity, with relating 'Scalindua',...
In the present study diversity and abundance of nitrifying microbes including ammonia-oxidizing archaea (AOA) betaproteobacteria (beta-AOB) were investigated, along with physicochemical parameters potentially affecting them, in a transect surface sediments from coastal margin adjacent to Pearl River estuary slope deep South China Sea. Nitrifying microbial was determined by detecting amoA (ammonia monooxygenase subunit A) gene. An obvious community structure shift for both AOA beta-AOB...
Anaerobic ammonium oxidizing (anammox) bacterial community structures were investigated in surface (1-2 cm) and lower (20-21 layers of mangrove sediments at sites located immediately to the trees (S0), 10 m (S1) 1000 (S2) away from a polluted area Pearl River Delta. At S0, both 16S rRNA hydrazine oxidoreductase (HZO) encoding genes anammox bacteria showed high diversity layer sediments, but they not detectable forest. S1 S2 shared similar communities layers, which quite different that S0....
The phylogenetic diversity and abundance of ammonia-oxidizing beta-proteobacteria (beta-AOB) was analyzed along an anthropogenic pollution gradient from the coastal Pearl River Delta to South China Sea using ammonia monooxygenase subunit A (amoA) gene. Along open ocean, dominant genus changed Nitrosomonas Nitrosospira, indicating niche specificity by these two genera as both salinity influence were major factors involved. bacterial amoA gene also variable gradient, with highest in deep-sea...
ABSTRACT Sulfur is an important element in sustaining microbial communities present hydrothermal vents. oxidation has been extensively studied due to its importance chemosynthetic pathways fields; however, less known about sulfate reduction. Here, the metagenomes of chimneys located on ultraslow-spreading Southwest Indian Ridge (SWIR) were pyrosequenced elucidate associated sulfur cycle. A taxonomic summary genes revealed a few dominant bacteria that participated cycle, particularly...
Horizontal gene transfer (HGT) of operational genes has been widely reported in prokaryotic organisms. However, informational such as those involved transcription and translation processes are very difficult to be horizontally transferred, described by Woese's complexity hypothesis. Here, we analyzed all the completed genome sequences (2,143 genomes) NCBI (National Center for Biotechnology Information) database, scanned genomes with high intragenomic heterogeneity 16S rRNA copies, explored...
Despite being fundamentally important and having direct therapeutic implications, the functional genomics of clinical isolates multidrug-resistant (MDR) pathogens is often impeded by lack genome-editing tools. Here, we report establishment a highly efficient, in situ technique applicable environmental prototypic MDR pathogen P. aeruginosa harnessing endogenous type I-F CRISPR-Cas systems. Using this approach, generate various reverse mutations an epidemic genotype, PA154197, identify...
Abstract The advent of next‐generation sequencing has revolutionized microbiome research, enabling in‐depth exploration microbial communities through amplicon sequencing. widespread adoption across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high‐throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility many...
Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is frequently associated with multidrug resistance and global epidemic outbreaks, contributing significantly to morbidity mortality in hospitalized patients. However, P. aeruginosa belonging the sequence type (ST) 16 was rarely reported. Here, this report presents complete genome of YK01, ST16 isolate from patient keratitis. The reference YK01 expected provide valuable data for investigating its genomic population, enhancing...
Six imported pigs originating from Guangdong, Henan, and Hunan provinces in China during October 2015 to February 2017 were cultured found be positive for meropenem-resistant Escherichia coli The samples yielded 9 E. isolates of diverse sequence types carrying blaNDM-5 on IncX3 (8 5 farms) or IncFII (1 isolate 1 farm) plasmids. mcr-1 gene was coharbored by 4 isolates. plasmids (∼46 kb) identical nearly each other.
Pseudomonas aeruginosa ATCC 27853 was isolated from a hospital blood specimen in 1971 and has been widely used as model strain to survey antibiotics susceptibilities, biofilm development, metabolic activities of spp.. Although four draft genomes P. have sequenced, the complete genome this is still lacking, hindering comprehensive understanding its physiology functional genome.Here we sequenced assembled using Pacific Biosciences SMRT (PacBio) technology Illumina sequencing platform. We found...
The prevalence and propagation of antimicrobial resistance (AMR) are serious global public health concerns. large the ever-increasing use antibiotics in livestock is also considered a great concern. extent similarity acquired antibiotic genes (ARGs) between humans food animals driving factors underlying AMR transfer them not clear, although link ARGs both hosts was proposed. To address this question, with swine chicken as examples animals, we analyzed over 1,000 gut metagenomes from world. A...
The rise in antibiotic-resistant bacteria is causing worldwide concerns. urgent need for new antibacterial drugs calls thinking and strategies to explore novel, narrow-spectrum, pathogen-specific targets. Legionaminic acid (Leg) pseudaminic (Pse) are nonulosonic carbohydrates with structural similarity eukaryotic sialic acid, distributed numerous pathogenic Gram-negative as components of cell surface-associated glycans. They involved the host interaction, pathogenicity, antiphage defense...
Post-translational modification (PTM) of proteins is one important strategy employed by bacteria for environmental adaptation. However, PTM profiles in deep-sea microbes remain largely unexplored. We provide here insight into PTMs a hydrothermal vent microbial community through integration metagenomics and metaproteomics. In total, 2919 unique 1306 were identified, whereas the latter included acetylation, deamination, hydroxylation, methylation, nitrosylation, oxidation, phosphorylation....