ORCID Profile
0000-0003-1804-5314
Current Organisation
UNSW Sydney
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Publisher: American Chemical Society (ACS)
Date: 27-08-2018
Abstract: Wastewater treatment plants (WWTPs) are considered reservoirs of viruses, but the ersity and dynamic changes of viruses are not well understood. In this study, we recovered 8478 metagenomic viral contigs (mVCs >5 kb) from two WWTPs (Shatin, 2806 Shek Wu Hui, 5672) in Hong Kong. Approximately 60% of the mVCs were poorly covered (<35% of genes in identified mVCs) by the current NCBI and IMG/VR viral databases. The temporal profile of the newly identified mVCs among 98 Shatin AS s les collected monthly (for approximately 9 years) revealed the presence of periodic dynamics at an interval of approximately one year (341 days). The spatial distribution pattern of the virome in the wastewater treatment systems showed that shared viral clusters (viral populations categorized based on shared gene content and network analysis) can be globally found among similar s les of wastewater treatment systems, indicating the presence of core viral communities among geographically isolated wastewater treatment systems. These results not only supplemented the current virome database of engineered systems but also, to some extent, expanded the understanding of long-term cyclical development and spatial distributions of viral communities in wastewater treatment systems.
Publisher: Oxford University Press (OUP)
Date: 02-02-2018
DOI: 10.1093/BIOINFORMATICS/BTY053
Abstract: Much global attention has been paid to antibiotic resistance in monitoring its emergence, accumulation and dissemination. For rapid characterization and quantification of antibiotic resistance genes (ARGs) in metagenomic datasets, an online analysis pipeline, ARGs-OAP has been developed consisting of a database termed Structured Antibiotic Resistance Genes (the SARG) with a hierarchical structure (ARGs type-subtype-reference sequence). The new release of the database, termed SARG version 2.0, contains sequences not only from CARD and ARDB databases, but also carefully selected and curated sequences from the latest protein collection of the NCBI-NR database, to keep up to date with the increasing number of ARG deposited sequences. SARG v2.0 has tripled the sequences of the first version and demonstrated improved coverage of ARGs detection in metagenomes from various environmental s les. In addition to annotation of high-throughput raw reads using a similarity search strategy, ARGs-OAP v2.0 now provides model-based identification of assembled sequences using SARGfam, a high-quality profile Hidden Markov Model (HMM), containing profiles of ARG subtypes. Additionally, ARGs-OAP v2.0 improves cell number quantification by using the average coverage of essential single copy marker genes, as an option in addition to the previous method based on the 16S rRNA gene. ARGs-OAP can be accessed through smile.hku.hk/SARGs. The database could be downloaded from the same site. Source codes for this study can be downloaded from iaole99/ARGs-OAP-v2.0. Supplementary data are available at Bioinformatics online.
Publisher: MDPI AG
Date: 24-12-2022
DOI: 10.3390/V15010053
Abstract: Viruses are the most abundant form of life on earth and play important roles in a broad range of ecosystems. Currently, two methods, whole genome shotgun metagenome (WGSM) and viral-like particle enriched metagenome (VLPM) sequencing, are widely applied to compare viruses in various environments. However, there is no critical assessment of their performance in recovering viruses and biological interpretation in comparative viral metagenomic studies. To fill this gap, we applied the two methods to investigate the stool virome in hepatocellular carcinoma (HCC) patients and healthy controls. Both WGSM and VLPM methods can capture the major ersity patterns of alpha and beta ersities and identify the altered viral profiles in the HCC stool s les compared with healthy controls. Viral signatures identified by both methods showed reductions of Faecalibacterium virus Taranis in HCC patients’ stool. Ultra-deep sequencing recovered more viruses in both methods, however, generally, 3 or 5 Gb were sufficient to capture the non-fragmented long viral contigs. More lytic viruses were detected than lysogenetic viruses in both methods, and the VLPM can detect the RNA viruses. Using both methods would identify shared and specific viral signatures and would capture different parts of the total virome.
Publisher: Springer Science and Business Media LLC
Date: 07-05-2013
DOI: 10.1007/S00248-013-0238-8
Abstract: The microbial community plays an essential role in the high productivity in mangrove wetlands. A proper understanding of the spatial variations of microbial communities will provide clues about the underline mechanisms that structure microbial groups and the isolation of bacterial strains of interest. In the present study, the ersity and composition of the bacterial community in sediments collected from four locations, namely mudflat, edge, bulk, and rhizosphere, within the Mai Po Ramsar Wetland in Hong Kong, SAR, China were compared using the barcoded Illumina paired-end sequencing technique. Rarefaction results showed that the bulk sediment inside the mature mangrove forest had the highest bacterial α- ersity, while the mudflat sediment without vegetation had the lowest. The comparison of β- ersity using principal component analysis and principal coordinate analysis with UniFrac metrics both showed that the spatial effects on bacterial communities were significant. All sediment s les could be clustered into two major groups, inner (bulk and rhizosphere sediments collected inside the mangrove forest) and outer mangrove sediments (the sediments collected at the mudflat and the edge of the mangrove forest). With the linear discriminate analysis scores larger than 3, four phyla, namely Actinobacteria, Acidobacteria, Nitrospirae, and Verrucomicrobia, were enriched in the nutrient-rich inner mangrove sediments, while abundances of Proteobacteria and Deferribacterias were higher in outer mangrove sediments. The rhizosphere effect of mangrove plants was also significant, which had a lower α- ersity, a higher amount of Nitrospirae, and a lower abundance of Proteobacteria than the bulk sediment nearby.
Publisher: Springer Science and Business Media LLC
Date: 08-01-2021
DOI: 10.1038/S41467-020-20422-7
Abstract: The gut microbiota is reported to modulate the immune response in hepatocellular carcinoma (HCC). Here, we employ metagenomic and metabolomic studies to characterise gut microbiota in patients with non-alcoholic fatty liver disease (NAFLD) related cirrhosis, with or without HCC, and evaluate its effect on the peripheral immune response in an ex vivo model. We find that dysbiosis characterises the microbiota of patients with NAFLD-cirrhosis, with compositional and functional shifts occurring with HCC development. Gene function of the microbiota in NAFLD-HCC supports short chain fatty acid production, and this is confirmed by metabolomic studies. Ex vivo studies show that bacterial extracts from the NAFLD-HCC microbiota, but not from the control groups, elicit a T cell immunosuppressive phenotype, characterised by expansion of regulatory T cells and attenuation of CD8 + T cells. Our study suggest that the gut microbiota in NAFLD-HCC is characterised by a distinctive microbiome/metabolomic profile, and can modulate the peripheral immune response.
Publisher: Springer Science and Business Media LLC
Date: 12-2018
Publisher: Springer Science and Business Media LLC
Date: 13-02-2018
Publisher: Springer Science and Business Media LLC
Date: 11-08-2018
DOI: 10.1007/S00253-018-9287-8
Abstract: Bacterial community in activated sludge (AS) is erse and highly dynamic. Little is known about the mechanism shaping bacterial community composition and dynamics of AS and no study had quantitatively compared the contribution of abiotic environmental factors and biotic associations to the temporal dynamics of AS microbial communities with significantly different ersity. In this study, two full-scale sewage treatment plants (STPs) with distinct operational parameters and influent composition were s led biweekly over 1 year to reveal the correlating factors to whole and sub-groups of AS bacterial community ersity and dynamics. The results show that the bacterial communities of the two STPs were entirely different and correlated with the influent composition and operating configurations. Bacterial associations represented by cohesion metrics and the environmental factor temperature were the primary correlated factors to the temporal bacterial community dynamics within each STP. The STP with high ersity and evenness could treat influent with higher suspended solid and a shorter sludge retention time, and was less correlated with environmental factors, implying the importance of ersity for AS system.
Publisher: Frontiers Media SA
Date: 18-02-2019
Publisher: Public Library of Science (PLoS)
Date: 11-01-2012
Publisher: MDPI AG
Date: 11-2022
DOI: 10.3390/PATHOGENS11111279
Abstract: The microbiome has been implicated in the development of metabolic conditions which occur at high rates in people with schizophrenia and related psychoses. This exploratory proof-of-concept study aimed to: (i) characterize the gut microbiota in antipsychotic naïve or quasi-naïve people with first-episode psychosis, and people with established schizophrenia receiving clozapine therapy (ii) test for microbiome changes following a lifestyle intervention which included diet and exercise education and physical activity. Participants were recruited from the Eastern Suburbs Mental Health Service, Sydney, Australia. Anthropometric, lifestyle and gut microbiota data were collected at baseline and following a 12-week lifestyle intervention. Stool s les underwent 16S rRNA sequencing to analyse microbiota ersity and composition. Seventeen people with established schizophrenia and five people with first-episode psychosis were recruited and matched with 22 age-sex, BMI and ethnicity matched controls from a concurrent study for baseline comparisons. There was no difference in α- ersity between groups at baseline, but microbial composition differed by 21 taxa between the established schizophrenia group and controls. In people with established illness pre-post comparison of α- ersity showed significant increases after the 12-week lifestyle intervention. This pilot study adds to the current literature that detail compositional differences in the gut microbiota of people with schizophrenia compared to those without mental illness and suggests that lifestyle interventions may increase gut microbial ersity in patients with established illness. These results show that microbiome studies are feasible in patients with established schizophrenia and larger studies are warranted to validate microbial signatures and understand the relevance of lifestyle change in the development of metabolic conditions in this population.
Publisher: Wiley
Date: 15-12-2017
Abstract: The human gut microbiota is an important reservoir of antibiotic resistance genes (ARGs). A metagenomic approach and network analysis were used to establish a comprehensive antibiotic resistome catalog and to obtain co‐occurrence patterns between ARGs and microbial taxa in fecal s les from 180 healthy in iduals from 11 different countries. In total, 507 ARG subtypes belonging to 20 ARG types were detected with abundances ranging from 7.12 × 10 −7 to 2.72 × 10 −1 copy of ARG/copy of 16S‐rRNA gene. Tetracycline, multidrug, macrolide‐lincosamide‐streptogramin, bacitracin, vancomycin, beta‐lactam and aminoglycoside resistance genes were the top seven most abundant ARG types. The multidrug ABC transporter, aad E, bac A, acr B, tet M, tet W, van R and van S were shared by all 180 in iduals, suggesting their common occurrence in the human gut. Compared to populations from the other 10 countries, the Chinese population harboured the most abundant ARGs. Moreover, LEfSe analysis suggested that the MLS resistance type and its subtype ‘ erm F’ were representative ARGs of the Chinese population. Antibiotic inactivation, antibiotic target alteration and antibiotic efflux were the dominant resistance mechanism categories in all populations. Procrustes analysis revealed that microbial phylogeny structured the antibiotic resistome. Co‐occurrence patterns obtained via network analysis implied that 12 species might be potential hosts of 58 ARG subtypes.
Publisher: MDPI AG
Date: 11-04-2022
DOI: 10.3390/PATHOGENS11040457
Abstract: Alteration of the gut virome has been associated with colorectal cancer (CRC) however, when and how the alteration takes place has not been studied. Here, we employ a longitudinal study in mice to characterize the gut virome alteration in azoxymethane (AOM)-induced colorectal neoplasia and identify important viruses associated with tumor growth. The number and size of the tumors increased as the mice aged in the AOM treated group, as compared to the control group. Tumors were first observed in the AOM group at week 12. We observed a significantly lower alpha ersity and shift in viral profile when tumors first appeared. In addition, we identified novel viruses from the genera Brunovirus, Hpunavirus that are positively associated with tumor growth and enriched at a late time point in AOM group, whereas members from Lubbockvirus show a negative correlation with tumor growth. Moreover, network analysis revealed two clusters of viruses in the AOM virome, a group that is positively correlated with tumor growth and another that is negatively correlated with tumor growth, all of which are bacteriophages. Our findings suggest that the gut virome changes along with tumor formation and provides strong evidence of a potential role for bacteriophage in the development of colorectal neoplasia.
Publisher: Oxford University Press (OUP)
Date: 12-03-2016
DOI: 10.1093/BIOINFORMATICS/BTW136
Abstract: Motivation: Environmental dissemination of antibiotic resistance genes (ARGs) has become an increasing concern for public health. Metagenomics approaches can effectively detect broad profiles of ARGs in environmental s les however, the detection and subsequent classification of ARG-like sequences are time consuming and have been severe obstacles in employing metagenomic methods. We sought to accelerate quantification of ARGs in metagenomic data from environmental s les. Results: A Structured ARG reference database (SARG) was constructed by integrating ARDB and CARD, the two most commonly used databases. SARG was curated to remove redundant sequences and optimized to facilitate query sequence identification by similarity. A database with a hierarchical structure (type-subtype-reference sequence) was then constructed to facilitate classification (assigning ARG-like sequence to type, subtype and reference sequence) of sequences identified through similarity search. Utilizing SARG and a previously proposed hybrid functional gene annotation pipeline, we developed an online pipeline called ARGs-OAP for fast annotation and classification of ARG-like sequences from metagenomic data. We also evaluated and proposed a set of criteria important for efficiently conducting metagenomic analysis of ARGs using ARGs-OAP. Availability and Implementation: Perl script for ARGs-OAP can be downloaded from iofuture/Ublastx_stageone. ARGs-OAP can be accessed through smile.hku.hk/SARGs. Contact: zhangt@hku.hk or tiedjej@msu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: Elsevier BV
Date: 03-2023
Publisher: Elsevier BV
Date: 10-2019
DOI: 10.1016/J.ENVINT.2019.104998
Abstract: The omnipresence of filterable bacteria that can pass through 0.22-μm membrane filters demands a change in the sterile filtration practice. In this study, we identified that filterable bacteria enriched from a surface water are members of the Bacteroidetes, Proteobacteria, Spirochaetae, Firmicutes, and Actinobacteria. Filterable bacteria displayed superior filterability during the entire bacterial growth phase, especially at the exponential phase. Maximal passage percentages were comparable at different cell densities, and achieved earlier at high cell density. Furthermore, filter retention for the investigated bacteria is independent of liquid temperature. However, cultivation temperature could affect the growth of some specific filterable bacteria and lead to variability in the passage percentage. Additionally, membrane materials, pore size and filtering flux greatly affected the passage of filterable bacteria. The majority of filterable Hylemonella and SAR324 could pass through 0.1-μm polyvinylidene fluoride and polyethersulfone filters but could not pass through 0.1-μm polycarbonate and mixed cellulose esters filters. Taken together, our results demonstrated that the ultra-small size of filterable bacteria, membrane characteristics and filtration operational conditions could challenge the validity of the 0.22/0.1-μm sterilizing grade filters in providing bio-safety barriers.
Publisher: American Chemical Society (ACS)
Date: 26-06-2018
Abstract: Temporal microbial community studies have broadened our knowledge of the dynamics and correlations among microbes in both natural and artificial engineering systems. Using activated sludge as a model system, we utilized the intensive longitudinal s ling method to identify overlooked ersity and the hidden dynamics of microbes, detect cross-associations among microbes after detrending, and reveal the central microbial dynamics during sludge bulking and foaming. We discovered that the accumulative alpha ersity in activated sludge s led daily over 392 days could be as high as 14 000 OTUs, and that the bacterial community dynamics followed a gradual succession, drifting away from the initial observed day and displaying a significant time-dependent trend. Cross-associations among bacteria were modulated after removing potential spurious correlations based on autocorrelation in microbial time series. Moreover, clusters of bacteria displaying rapid turnover were discovered during the beginning, ongoing, and fading of sludge bulking and foaming, and their physicochemical parameters are resolved. These identified groups of bacteria and their related environmental factors could potentially supply clues to form hypotheses for treating operational problems, such as sludge bulking and foaming.
Publisher: Springer Science and Business Media LLC
Date: 28-11-2017
No related grants have been discovered for Xiao-Tao JIANG.