Publications by authors named "Patrick K H Lee"

70 Publications

Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association.

Environ Res 2021 Oct 9:112183. Epub 2021 Oct 9.

Corporación Corpogen Research Center, Bogotá, Colombia.

In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.
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http://dx.doi.org/10.1016/j.envres.2021.112183DOI Listing
October 2021

Multi-omics analysis to decipher the molecular link between chronic exposure to pollution and human skin dysfunction.

Sci Rep 2021 Sep 15;11(1):18302. Epub 2021 Sep 15.

Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France.

Environmental pollution is composed of several factors, namely particulate matter (PM, PM), ozone and Ultra Violet (UV) rays among others and first and the most exposed tissue to these substances is the skin epidermis. It has been established that several skin disorders such as eczema, acne, lentigines and wrinkles are aggravated by exposure to atmospheric pollution. While pollutants can interact with skin surface, contamination of deep skin by ultrafine particles or Polycyclic aromatic hydrocarbons (PAH) might be explained by their presence in blood and hair cortex. Molecular mechanisms leading to skin dysfunction due to pollution exposure have been poorly explored in humans. In addition to various host skin components, cutaneous microbiome is another target of these environment aggressors and can actively contribute to visible clinical manifestation such as wrinkles and aging. The present study aimed to investigate the association between pollution exposure, skin microbiota, metabolites and skin clinical signs in women from two cities with different pollution levels. Untargeted metabolomics and targeted proteins were analyzed from D-Squame samples from healthy women (n = 67 per city), aged 25-45 years and living for at least 15 years in the Chinese cities of Baoding (used as a model of polluted area) and Dalian (control area with lower level of pollution). Additional samples by swabs were collected from the cheeks from the same population and microbiome was analysed using bacterial 16S rRNA as well as fungal ITS1 amplicon sequencing and metagenomics analysis. The level of exposure to pollution was assessed individually by the analysis of polycyclic aromatic hydrocarbons (PAH) and their metabolites in hair samples collected from each participant. All the participants of the study were assessed for the skin clinical parameters (acne, wrinkles, pigmented spots etc.). Women from the two cities (polluted and less polluted) showed distinct metabolic profiles and alterations in skin microbiome. Profiling data from 350 identified metabolites, 143 microbes and 39 PAH served to characterize biochemical events that correlate with pollution exposure. Finally, using multiblock data analysis methods, we obtained a potential molecular map consisting of multi-omics signatures that correlated with the presence of skin pigmentation dysfunction in individuals living in a polluted environment. Overall, these signatures point towards macromolecular alterations by pollution that could manifest as clinical sign of early skin pigmentation and/or other imperfections.
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http://dx.doi.org/10.1038/s41598-021-97572-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8443591PMC
September 2021

Surface touch network structure determines bacterial contamination spread on surfaces and occupant exposure.

J Hazard Mater 2021 08 17;416:126137. Epub 2021 May 17.

Department of Mechanical Engineering, University of Hong Kong, Hong Kong, China; School of Public Health, University of Hong Kong, Hong Kong, China. Electronic address:

Fomites are known to spread infectious diseases, but their role in determining transmission risk remains unclear. The association of surface touch networks (STNs), proposed to explain this risk, with real-life surface contamination has not yet been demonstrated. To construct STNs, we collected surface touch data from 23 to 26 scholars through 2 independent experiments conducted in office spaces for 13 h each. In parallel, a tracer bacterium (Lactobacillus bulgaricus) was spread by a designated carrier in each experiment during normal activities; the subsequent extent of surface contamination was assessed using qPCR. The touch data were also analyzed using an agent-based model that predicted the observed contamination. Touching public (door handles) and hidden public (desks, chair seatbacks) surfaces that connected occupants, sparse hand-to-hand contact, and active carriers contributed significantly to contamination spread, which was also correlated with the size of the social group containing carriers. The natural and unsupervised experiments reflected realistic exposure levels of mouths (1-10 ppm of total contamination spread by one root carrier), nostrils (~1 ppm), and eyes (~0.1 ppm). We conclude that the contamination degree of known and hidden public surfaces can indicate fomite exposure risk. The social group effect could trigger superspreading events through fomite transmission.
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http://dx.doi.org/10.1016/j.jhazmat.2021.126137DOI Listing
August 2021

Dysbiosis of the Urinary Bladder Microbiome in Cats with Chronic Kidney Disease.

mSystems 2021 Aug 27;6(4):e0051021. Epub 2021 Jul 27.

Centre for Companion Animal Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Konggrid.35030.35, Hong Kong SAR.

Although feline urinary tract diseases cause high morbidity and mortality rates, and subclinical bacteriuria is not uncommon, the feline urinary microbiome has not been characterized. We conducted a case-control study to identify the feline urinary bladder microbiome and assess its association with chronic kidney disease (CKD), feline idiopathic cystitis (FIC), and positive urine cultures (PUCs). Of 108 feline urine samples subjected to 16S rRNA gene sequencing, 48 (44.4%) samples reached the 500-sequence rarefaction threshold and were selected for further analysis, suggesting that the feline bladder microbiome is typically sparse. Selected samples included 17 CKD, 9 FIC, 8 PUC cases and 14 controls. Among these, 19 phyla, 145 families, and 218 genera were identified. were the most abundant, followed by . Notably, four major urotypes were identified, including two urotypes predominated by Escherichia or and two others characterized by relatively high alpha diversity, Diverse 1 and Diverse 2. Urotype was associated with disease status ( value of 0.040), with the Escherichia-predominant urotype being present in 53% of CKD cases and in all of the Escherichia coli PUC cases. Reflecting these patterns, the overall microbial composition of CKD cases was more similar to that of E. coli PUC cases than to that of controls ( value of <0.001). Finally, PUC cases had microbial compositions distinct from those of controls as well as CKD and FIC cases, with significantly lower Shannon diversity and Faith's phylogenetic diversity values. Despite the clinical importance of urinary diseases in cats, the presence of resident urine microbes has not been demonstrated in cats, and the role of these microbes as a community in urinary health remains unknown. Here, we have shown that cats with and without urinary tract disease harbor unique microbial communities in their urine. We found no evidence to suggest that the bladder microbiome is implicated in the pathogenesis of feline idiopathic cystitis, a disease similar to bladder pain syndrome/interstitial cystitis in humans. However, cats with chronic kidney disease had dysbiosis of their bladder microbiome, which was predominated by Escherichia and had a community structure similar to that of cats with Escherichia coli cystitis. These findings suggest that chronic kidney disease alters the bladder environment to favor Escherichia colonization, potentially increasing the risk of overt clinical infection.
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http://dx.doi.org/10.1128/mSystems.00510-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8407359PMC
August 2021

Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching.

Microbiome 2021 06 5;9(1):129. Epub 2021 Jun 5.

School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.

Background: The human skin microbiome has been recently investigated as a potential forensic tool, as people leave traces of their potentially unique microbiomes on objects and surfaces with which they interact. In this metagenomic study of four people in Hong Kong, their homes, and public surfaces in their neighbourhoods, we investigated the stability and identifiability of these microbiota traces on a timescale of hours to days.

Results: Using a Canberra distance-based method of comparing skin and surface microbiomes, we found that a person could be accurately matched to their household in 84% of tests and to their neighbourhood in 50% of tests, and that matching accuracy did not decay for household surfaces over the 10-day study period, although it did for public surfaces. The time of day at which a skin or surface sample was taken affected matching accuracy, and 160 species across all sites were found to have a significant variation in abundance between morning and evening samples. We hypothesised that daily routines drive a rhythm of daytime dispersal from the pooled public surface microbiome followed by normalisation of a person's microbiome by contact with their household microbial reservoir, and Dynamic Bayesian Networks (DBNs) supported dispersal from public surfaces to skin as the major dispersal route among all sites studied.

Conclusions: These results suggest that in addition to considering the decay of microbiota traces with time, diurnal patterns in microbiome exposure that contribute to the human skin microbiome assemblage must also be considered in developing this as a potential forensic method. Video Abstract.
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http://dx.doi.org/10.1186/s40168-021-01082-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8180031PMC
June 2021

A global metagenomic map of urban microbiomes and antimicrobial resistance.

Cell 2021 Jun 26;184(13):3376-3393.e17. Epub 2021 May 26.

Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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http://dx.doi.org/10.1016/j.cell.2021.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8238498PMC
June 2021

Microbial Communities in Full-Scale Wastewater Treatment Systems Exhibit Deterministic Assembly Processes and Functional Dependency over Time.

Environ Sci Technol 2021 04 30;55(8):5312-5323. Epub 2021 Mar 30.

School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.

Microbial communities constitute the core component of biological wastewater treatment processes. We conducted a meta-analysis based on the 16S rRNA gene of temporal samples obtained from diverse full-scale activated sludge and anaerobic digestion systems treating municipal and industrial wastewater (collected in this study and published previously) to investigate their community assembly mechanism and functional traits over time, which are not currently well understood. The influent composition was found to be the main driver of the microbial community's composition, and relatively large proportions of specialist (26.1% and 18.6%) and transient taxa (67.2% and 68.1%) were estimated in both systems. Deterministic processes, especially homogeneous selection events (accounting for >53.8% of assembly events), were consistently identified as the dominant microbial community assembly mechanisms in both systems over time. Significant and strong correlations (Pearson's = 0.51-0.92) were detected between the dynamics of the temporal community and the functional compositions in both systems, which suggests functional dependency. In contrast, the occurrence of sludge bulking and foaming in the activated sludge system led to an increase in stochastic assembly processes (i.e., limited dispersal and undominated events), a shift toward functional redundancy and less community diversity, a decreased community niche breadth index, and a more compact co-association network. This study illustrates that the mechanism of microbial community assembly and functional traits over time can be used to diagnose system performance and provide information on potential system malfunction.
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http://dx.doi.org/10.1021/acs.est.0c06732DOI Listing
April 2021

Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome.

Anim Microbiome 2020 Feb 7;2(1). Epub 2020 Feb 7.

Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.

Background: As one of the most densely populated microbial communities on Earth, the gut microbiota serves as an important reservoir of antibiotic resistance genes (ARGs), referred to as the gut resistome. Here, we investigated the association of dietary nutritional content with gut ARG diversity and composition, using publicly available shotgun metagenomic sequence data generated from canine and feline fecal samples. Also, based on network theory, we explored ARG-sharing patterns between gut bacterial genera by identifying the linkage structure between metagenomic assemblies and their functional genes obtained from the same data.

Results: In both canine and feline gut microbiota, an increase in protein and a reduction in carbohydrate in the diet were associated with increased ARG diversity. ARG diversity of the canine gut microbiota also increased, but less strongly, after a reduction in protein and an increase in carbohydrate in the diet. The association between ARG and taxonomic composition suggests that diet-induced changes in the gut microbiota may be responsible for changes in ARG composition, supporting the links between protein metabolism and antibiotic resistance in gut microbes. In the analysis of the ARG-sharing patterns, 22 ARGs were shared among 46 genera in the canine gut microbiota, and 11 ARGs among 28 genera in the feline gut microbiota. Of these ARGs, the tetracycline resistance gene tet(W) was shared among the largest number of genera, predominantly among Firmicutes genera. Bifidobacterium, a genus extensively used in the fermentation of dairy products and as probiotics, shared tet(W) with a wide variety of other genera. Finally, genera from the same phylum were more likely to share ARGs than with those from different phyla.

Conclusions: Our findings show that dietary nutritional content, especially protein content, is associated with the gut resistome and suggest future research to explore the impact of dietary intervention on the development of antibiotic resistance in clinically-relevant gut microbes. Our network analysis also reveals that the genetic composition of bacteria acts as an important barrier to the horizontal transfer of ARGs. By capturing the underlying gene-sharing relationships between different bacterial taxa from metagenomes, our network approach improves our understanding of horizontal gene transfer dynamics.
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http://dx.doi.org/10.1186/s42523-020-0022-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7807453PMC
February 2020

Profiling Airborne Microbiota in Mechanically Ventilated Buildings Across Seasons in Hong Kong Reveals Higher Metabolic Activity in Low-Abundance Bacteria.

Environ Sci Technol 2021 01 21;55(1):249-259. Epub 2020 Dec 21.

School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.

Metabolically active bacteria within built environments are poorly understood. This study aims to investigate the active airborne bacterial microbiota and compare the total and active microbiota in eight mechanically ventilated buildings over four consecutive seasons using the 16S rRNA gene (rDNA) and the 16S rRNA (rRNA), respectively. The relative abundances of the taxa of presumptive occupants and environmental origins were significantly different between the active and total microbiota. The Sloan neutral model suggested that ecological drift and random dispersal played a smaller role in the assembly of the active microbiota than the total microbiota. The seasonal nature of the active microbiota was consistent with that of the total microbiota in both indoor and outdoor environments, while only the indoor environment was significantly affected by geography. The relative abundances of the active and total taxa were positively correlated, suggesting that the high-abundance members were also the greatest contributors to the community-level metabolic activity. Based on the rRNA/rDNA ratio, the low-abundance members consistently had a higher taxon-level metabolic activity than the high-abundance members over seasons, suggesting that the low-abundance members may have the ability to survive and thrive in the indoor environment and their impact on the health of occupants cannot be overlooked.
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http://dx.doi.org/10.1021/acs.est.0c06201DOI Listing
January 2021

Airborne Bacteria in Outdoor Air and Air of Mechanically Ventilated Buildings at City Scale in Hong Kong across Seasons.

Environ Sci Technol 2020 10 10;54(19):11732-11743. Epub 2020 Sep 10.

School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China.

Studies of the indoor airborne microbiome have mostly been confined to a single location and time point. Here, we characterized, over the course of a year, the geographic variation, building-function dependence, and dispersal characteristics of indoor and outdoor airborne microbiomes (bacterial members only) of eight mechanically ventilated commercial buildings. Based on the Sloan neutral model, airborne microbiomes were randomly dispersed in the respective indoor and outdoor environments and between the two environments during each season. The dominant taxa in the indoor and outdoor environments showed minor variations at each location among seasons. The airborne microbiomes displayed weak seasonality for both indoor and outdoor environments, while a weak geographic variation was found only for the indoor environments. Source tracking results show that outdoor air and occupant skin were major contributors to the indoor airborne microbiomes, but the extent of the contribution from each source varied within and among buildings over the seasons, which suggests variations in local building use. Based on 32 cases of indoor airborne microbiome data, we determined that the indoor/outdoor (I/O) ratio of PM was not a robust indicator of the sources found indoors. Alternatively, the indoor concentration of carbon dioxide was more closely correlated with the major sources of the indoor airborne microbiome in mechanically ventilated environments.
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http://dx.doi.org/10.1021/acs.est.9b07623DOI Listing
October 2020

Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5' End of ORFeomes.

mSystems 2020 Aug 11;5(4). Epub 2020 Aug 11.

School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China

Codon usage bias exerts control over a wide variety of molecular processes. The positioning of synonymous codons within coding sequences (CDSs) dictates protein expression by mechanisms such as local translation efficiency, mRNA Gibbs free energy, and protein cotranslational folding. In this work, we explore how codon usage affects the position-dependent content of hydrogen bonding, which in turn influences energy requirements for unwinding double-stranded DNA (dsDNA). We categorized codons according to their hydrogen bond content and found differential effects on hydrogen bonding encoded by codon variants. The specific positional disposition of codon variants within CDSs creates a ramp of hydrogen bonding at the 5' end of the ORFeome in CDSs occupying the first position of operons are subjected to selective pressure that reduces their hydrogen bonding compared to internal CDSs, and highly transcribed CDSs demand a lower maximum capacity of hydrogen bonds per codon, suggesting that the energetic requirement for unwinding the dsDNA in highly transcribed CDSs has evolved to be minimized in Subsequent analysis of over 14,000 ORFeomes showed a pervasive ramp of hydrogen bonding at the 5' end in and that positively correlates with the probability of mRNA secondary structure formation. Both the ramp and the correlation were not found in The position-dependent hydrogen bonding might be part of the mechanism that contributes to the coordination between transcription and translation in and A Web-based application to analyze the position-dependent hydrogen bonding of ORFeomes has been developed and is publicly available (https://juanvillada.shinyapps.io/hbonds/). Redundancy of the genetic code creates a vast space of alternatives to encode a protein. Synonymous codons exert control over a variety of molecular and physiological processes of cells mainly through influencing protein biosynthesis. Recent findings have shown that synonymous codon choice affects transcription by controlling mRNA abundance, mRNA stability, transcription termination, and transcript biosynthesis cost. In this work, by analyzing thousands of , , and genomes, we extend recent findings by showing that synonymous codon choice, corresponding to the number of hydrogen bonds in a codon, can also have an effect on the energetic requirements for unwinding double-stranded DNA in a position-dependent fashion. This report offers new perspectives on the mechanism behind the transcription-translation coordination and complements previous hypotheses on the resource allocation strategies used by and to manage energy efficiency in gene expression.
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http://dx.doi.org/10.1128/mSystems.00613-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426154PMC
August 2020

Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses.

Microbiome 2020 07 24;8(1):111. Epub 2020 Jul 24.

Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL, 61801, USA.

Background: Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H transfer between organotrophs and methanogens. However, many metabolic processes are thermodynamically sensitive to H accumulation and can be inhibited by H produced from co-occurring metabolisms. Strategies for driving thermodynamically competing metabolisms in methanogenic environments remain unexplored.

Results: To uncover how anaerobes combat this H conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology-methanogenic bioreactors. Through analysis of 17 anaerobic digesters, we recovered 1343 high-quality metagenome-assembled genomes and corresponding gene expression profiles for uncultured lineages spanning 66 phyla and reconstructed their metabolic capacities. We discovered that diverse uncultured populations can drive H-sensitive metabolisms through (i) metabolic coupling with concurrent H-tolerant catabolism, (ii) forgoing H generation in favor of interspecies transfer of formate and electrons (cytochrome- and pili-mediated) to avoid thermodynamic conflict, and (iii) integration of low-concentration O metabolism as an ancillary thermodynamics-enhancing electron sink. Archaeal populations support these processes through unique methanogenic metabolisms-highly favorable H oxidation driven by methyl-reducing methanogenesis and tripartite uptake of formate, electrons, and acetate.

Conclusion: Integration of omics and eco-thermodynamics revealed overlooked behavior and interactions of uncultured organisms, including coupling favorable and unfavorable metabolisms, shifting from H to formate transfer, respiring low-concentration O, performing direct interspecies electron transfer, and interacting with high H-affinity methanogenesis. These findings shed light on how microorganisms overcome a critical obstacle in methanogenic carbon cycles we had hitherto disregarded and provide foundational insight into anaerobic microbial ecology. Video Abstract.
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http://dx.doi.org/10.1186/s40168-020-00885-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7382037PMC
July 2020

Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants.

Microbiome 2020 06 26;8(1):100. Epub 2020 Jun 26.

School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.

Background: Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous microbiota. Given the roles of the skin microbiota have on healthy and undesirable skin phenotypes and the relationships between PAHs and skin properties, we hypothesize that exposure of PAHs may be associated with changes in the cutaneous microbiota. In this study, the skin microbiota of over two hundred Chinese individuals from two cities in China with varying exposure levels of PAHs were characterized by bacterial and fungal amplicon and shotgun metagenomics sequencing.

Results: Skin site and city were strong parameters in changing microbial communities and their assembly processes. Reductions of bacterial-fungal microbial network structural integrity and stability were associated with skin conditions (acne and dandruff). Multivariate analysis revealed associations between abundances of Propionibacterium and Malassezia with host properties and pollutant exposure levels. Shannon diversity increase was correlated to exposure levels of PAHs in a dose-dependent manner. Shotgun metagenomics analysis of samples (n = 32) from individuals of the lowest and highest exposure levels of PAHs further highlighted associations between the PAHs quantified and decrease in abundances of skin commensals and increase in oral bacteria. Functional analysis identified associations between levels of PAHs and abundance of microbial genes of metabolic and other pathways with potential importance in host-microbe interactions as well as degradation of aromatic compounds.

Conclusions: The results in this study demonstrated the changes in composition and functional capacities of the cutaneous microbiota associated with chronic exposure levels of PAHs. Findings from this study will aid the development of strategies to harness the microbiota in protecting the skin against pollutants. Video Abstract.
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http://dx.doi.org/10.1186/s40168-020-00874-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320578PMC
June 2020

Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing.

Water Res 2020 Jul 18;178:115815. Epub 2020 Apr 18.

Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, UK. Electronic address:

In the past decade, the characterisation of the microbial community in anaerobic digestion was primarily done by using high-throughput short-read amplicon sequencing. However, the short-read approach has inherent primer bias and low phylogenetic resolution. Our previous study using Illumina MiSeq suggested that the heterogeneity of AD microbiome was operation-driven. To advance our knowledge towards the complexity of the AD microbiome, we performed full-length 16S rRNA gene amplicon sequencing using PacBio Sequel for a more accurate phylogenetic identification. To this end, purified DNA samples from 19 global anaerobic digesters were sequenced. Sixteen methanogenic archaea were identified at the species level. Among them, Methanosarcina horonobensis and Methanosarcina flavescens had significant presence under specific operating conditions. Methanothrix concilii presented in all digesters sequenced. Unexpectedly, over 90% of the Smithella detected were closely related to alkane-degrading Smithella strains D17 and M82, not Smithella propionica. Using LEfSe and network analysis, the interspecies relationship between the fermentative and syntrophic bacteria was addressed. Comparison of the short- and long-read sequencing results were performed and discussed. From sample preparation to data analysis, this work characterised the digester microbiomes in a superior resolution.
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http://dx.doi.org/10.1016/j.watres.2020.115815DOI Listing
July 2020

Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the Operon of Type Ia Methanotrophs.

mSystems 2019 Jul 23;4(4). Epub 2019 Jul 23.

School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China

Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. In methanotrophic bacteria, enzymes in the methane oxidation metabolic module (KEGG module M00174, conversion of methane to formaldehyde) are encoded in four operons (, , , and ). Recent reports have suggested that methanotrophs in acquired methane monooxygenases through horizontal gene transfer. Here, we used a genomic meta-analysis to infer the transcriptional and translational advantages of coding sequences from the methane oxidation metabolic modules of different types of methanotrophs. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes () from type Ia methanotrophs. We found that this nucleotide bias increases the level of codon bias by decreasing the GC content in the third base of codons, a strategy that contrasts with that of other coding sequences in the module. Further codon usage analyses uncovered that codon variants of the type Ia coding sequences deviate from the genomic signature to match ribosomal protein-coding sequences. Subsequently, computation of transcription and translation metrics revealed that the coding sequences of type Ia methanotrophs optimize the usage of codon variants to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins. Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth's system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.
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http://dx.doi.org/10.1128/mSystems.00342-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6650546PMC
July 2019

Designing and Engineering AM1 for Itaconic Acid Production.

Front Microbiol 2019 9;10:1027. Epub 2019 May 9.

School of Energy and Environment, City University of Hong Kong, Hong Kong, China.

(formerly ) AM1 is a methylotrophic bacterium with a versatile lifestyle. Various carbon sources including acetate, succinate and methanol are utilized by AM1 with the latter being a promising inexpensive substrate for use in the biotechnology industry. Itaconic acid (ITA) is a high-value building block widely used in various industries. Given that no wildtype methylotrophic bacteria are able to utilize methanol to produce ITA, we tested the potential of AM1 as an engineered host for this purpose. In this study, we successfully engineered AM1 to express a heterologous codon-optimized gene encoding aconitic acid decarboxylase. The engineered strain produced ITA using acetate, succinate and methanol as the carbon feedstock. The highest ITA titer in batch culture with methanol as the carbon source was 31.6 ± 5.5 mg/L, while the titer and productivity were 5.4 ± 0.2 mg/L and 0.056 ± 0.002 mg/L/h, respectively, in a scaled-up fed-batch bioreactor under 60% dissolved oxygen saturation. We attempted to enhance the carbon flux toward ITA production by impeding poly-β-hydroxybutyrate accumulation, which is used as carbon and energy storage, via mutation of the regulator gene . Unexpectedly, ITA production by the mutant strain was not higher even though poly-β-hydroxybutyrate concentration was lower. Genome-wide transcriptomic analysis revealed that mutation in the ITA-producing strain led to complex rewiring of gene transcription, which might result in a reduced carbon flux toward ITA production. Besides poly-β-hydroxybutyrate metabolism, we found evidence that PhaR might regulate the transcription of many other genes including those encoding other regulatory proteins, methanol dehydrogenases, formate dehydrogenases, malate:quinone oxidoreductase, and those synthesizing pyrroloquinoline quinone and thiamine co-factors. Overall, AM1 was successfully engineered to produce ITA using acetate, succinate and methanol as feedstock, further supporting this bacterium as a feasible host for use in the biotechnology industry. This study showed that PhaR could have a broader regulatory role than previously anticipated, and increased our knowledge of this regulator and its influence on the physiology of AM1.
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http://dx.doi.org/10.3389/fmicb.2019.01027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6520949PMC
May 2019

Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome.

mSystems 2019 Mar-Apr;4(2). Epub 2019 Mar 26.

School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.

The importance of microorganisms to human skin health has led to a growing interest in the temporal stability of skin microbiota. Here we investigated the dynamics and assembly of skin fungal communities (mycobiomes) with amplicon sequencing of samples collected from multiple sites on 24 healthy Chinese individuals across four seasons (in the order of winter, spring, summer, and autumn in a calendar year). We found a significant difference in community compositions between individuals, and intrapersonal community variation increased over time at all body sites. Within each season, the frequency of occurrence of most operational taxonomic units (OTUs) was well fitted by a neutral model, highlighting the importance of stochastic forces such as passive dispersal and ecological drift in skin community assembly. Despite the significant richness contributed by neutrally distributed OTUs, skin coassociation networks were dominated by taxa well-adapted to multiple body sites (forehead, forearm, and palm), although hub species were disproportionately rare. Taken together, these results suggest that while skin mycobiome assembly is a predominantly neutral process, taxa that could be under the influence of selective forces (e.g., host selection) are potentially key to the structure of a community network. Fungi are well recognized members of the human skin microbiota and are crucial to cutaneous health. Common cutaneous diseases such as seborrheic dermatitis and dermatophytes are linked to fungal species. Most studies related to skin microbial community dynamics have focused on Western subjects, while non-Western individuals are understudied. In this study, we explore the seasonal changes of the skin mycobiome in a healthy Chinese cohort and identify ecological processes that could possibly give rise to such variations. Our work reveals the dynamic nature of host skin fungal community, highlighting the dominant roles neutral forces play in the seasonal assembly of skin mycobiome. This study provides insight into the microbial ecology of the human skin microbiome and fills a knowledge gap in the literature regarding the dynamics of skin fungal community.
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http://dx.doi.org/10.1128/mSystems.00004-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6435813PMC
March 2019

Rare Taxa Exhibit Disproportionate Cell-Level Metabolic Activity in Enriched Anaerobic Digestion Microbial Communities.

mSystems 2019 Jan-Feb;4(1). Epub 2019 Jan 22.

School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR.

Microbial communities are composed of populations with vastly different abundances and levels of metabolic and replicative activity, ranging from actively metabolizing and dividing to dormant or nonviable. The 16S rRNA/rDNA ratio is an emerging tool for evaluating cell-level metabolic activity independent of abundance. In this study, we used five long-term enriched model anaerobic digestion (AD) communities to investigate community composition, diversity, structure, and in particular activity based on the rRNA/rDNA ratio. We cross-validated the 16S amplicon-based results using two alternative operational taxonomic unit (OTU) formation methods (conventional 97% sequence similarity and 100% sequence similar zero-radius OTUs by UNOISE3) and compared these to metagenome-derived population genomes and metatranscriptomes. Significant positive correlations were observed between microbial total activity and abundance with both the amplicon- and omic-based methods. All three methods revealed disproportionately high transcription/abundance ratios for some rare taxa but lower ratios for most abundant taxa for all the communities, which was further corroborated by the high replication rate (iRep) of most low-abundance population genomes. Variation in microbial activity levels is increasingly being recognized as both an important dimension in community function and a complicating factor in sequencing-based survey methods. This study extends previous reports that rare taxa may contribute disproportionately to community activity in some natural environments, showing that this may also hold in artificially maintained model communities with well-described inputs, outputs, and biochemical functions. These results demonstrate that assessment of activity levels using the rRNA/rDNA ratio is robust across taxonomic unit formation methods and is independently corroborated by omics methods. The results also provide insight into the comparative advantages and disadvantages of different taxonomic unit formation methods in amplicon sequencing studies, showing that UNOISE3 provides comparable microbial diversity, structure, and activity information as the 97% sequence similarity method but potentially loses some phylogenetic diversity and creates more "phantom taxa" (which are present in the RNA pool but not the corresponding DNA pool).
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http://dx.doi.org/10.1128/mSystems.00208-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343076PMC
January 2019

Smart Food Waste Recycling Bin (S-FRB) to turn food waste into green energy resources.

J Environ Manage 2019 Mar 8;234:290-296. Epub 2019 Jan 8.

School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Special Administrative Region. Electronic address:

Effective treatment of food waste is inherently difficult due to several factors, including its heterogeneous composition, high moisture content, and low heating value. To address these issues, this study aims to convert food waste into an energy resource using naturally occurring fermentative microorganisms embedded in wooden biochips (bio-catalysis), utilizing a "Smart Food Waste Recycling Bin" (S-FRB) system. High-throughput 16S rRNA gene sequencing analysis identified the major aerobic and facultatively anaerobic bacteria with alpha-diversity in terms of the Phylogenetic Diversity index ranging from 40.8 (initial stage) to 24.5 (mature stage), which indicates the microbial communities are relatively homogeneous and effective for use in the S-FBR. Operational results indicated that the organic content of food waste traded in the system increased from 53% up to 72% in the final end-product and achieved a mass reduction rate of approximately 80%. The heating value of the end-product, which was 3300 kcal/kg waste when measured by the differential scanning calorimeter (DSC) method, confirmed its high potential as a biofuel. Overall, the S-FRB system presents a practical approach for food waste treatment that solves the putrescible waste problem and maximizes utility through resource circulation.
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http://dx.doi.org/10.1016/j.jenvman.2018.12.088DOI Listing
March 2019

Author Correction: A comparative genomics and reductive dehalogenase gene transcription study of two chloroethene-respiring bacteria, Dehalococcoides mccartyi strains MB and 11a.

Sci Rep 2018 Aug 17;8(1):12571. Epub 2018 Aug 17.

Department of Civil and Environmental Engineering, National University of Singapore, Singapore, 117576, Singapore.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
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http://dx.doi.org/10.1038/s41598-018-30575-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6098029PMC
August 2018

Modular Metabolic Engineering for Biobased Chemical Production.

Trends Biotechnol 2019 02 28;37(2):152-166. Epub 2018 Jul 28.

School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR. Electronic address:

Microorganisms can manufacture a wide range of biobased chemicals that are useful for diverse industrial applications. However, the overexpression of heterologous enzymes in recombinant strains often leads to metabolic imbalance, resulting in growth retardation and suboptimal production of the target compounds. Here we discuss the recent development of modular metabolic engineering approaches that enable the global fine-tuning of engineered pathways by modularizing the synthetic pathway in single or multiple hosts. In particular, we highlight applications with microbial consortia. To build a vibrant biobased economy, multivariate modular metabolic engineering (MMME), modular coculture engineering (MCE), and spatiotemporal and integrative genome-scale metabolic modeling can be exploited to expedite strain optimization and improve the production of a broad variety of high-value biobased chemicals.
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http://dx.doi.org/10.1016/j.tibtech.2018.07.003DOI Listing
February 2019

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion.

Biotechnol Biofuels 2018 23;11:117. Epub 2018 Apr 23.

B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.

Background: Although anaerobic digestion for biogas production is used worldwide in treatment processes to recover energy from carbon-rich waste such as cellulosic biomass, the activities and interactions among the microbial populations that perform anaerobic digestion deserve further investigations, especially at the population genome level. To understand the cellulosic biomass-degrading potentials in two full-scale digesters, this study examined five methanogenic enrichment cultures derived from the digesters that anaerobically digested cellulose or xylan for more than 2 years under 35 or 55 °C conditions.

Results: Metagenomics and metatranscriptomics were used to capture the active microbial populations in each enrichment culture and reconstruct their meta-metabolic network and ecological roles. 107 population genomes were reconstructed from the five enrichment cultures using a differential coverage binning approach, of which only a subset was highly transcribed in the metatranscriptomes. Phylogenetic and functional convergence of communities by enrichment condition and phase of fermentation was observed for the highly transcribed populations in the metatranscriptomes. In the 35 °C cultures grown on cellulose, -related and -related bacteria were identified as major hydrolyzers and primary fermenters in the early growth phase, while -related bacteria were major secondary fermenters and potential fatty acid scavengers in the late growth phase. While the meta-metabolism and trophic roles of the cultures were similar, the bacterial populations performing each function were distinct between the enrichment conditions.

Conclusions: Overall, a population genome-centric view of the meta-metabolism and functional roles of key active players in anaerobic digestion of cellulosic biomass was obtained. This study represents a major step forward towards understanding the microbial functions and interactions at population genome level during the microbial conversion of lignocellulosic biomass to methane. The knowledge of this study can facilitate development of potential biomarkers and rational design of the microbiome in anaerobic digesters.
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http://dx.doi.org/10.1186/s13068-018-1121-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5911951PMC
April 2018

A comparison of methods used to unveil the genetic and metabolic pool in the built environment.

Microbiome 2018 04 16;6(1):71. Epub 2018 Apr 16.

Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.

Background: A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting.

Results: We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community.

Conclusions: Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.
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http://dx.doi.org/10.1186/s40168-018-0453-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902888PMC
April 2018

Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification.

Front Microbiol 2018 27;9:280. Epub 2018 Feb 27.

School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong.

Nitrification plays a crucial role in global nitrogen cycling and treatment processes. However, the relationships between the nitrifier guilds of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) are still poorly understood, especially in freshwater habitats. This study examined the physiological interactions between the AOB and NOB present in a freshwater aquarium biofilter by culturing them, either together or separately, in a synthetic medium. Metagenomic and 16S rRNA gene sequencing revealed the presence and the draft genomes of -like AOB as well as -like NOB in the cultures, including the first draft genome of . The nitrifiers exhibited different growth rates with different ammonium (NH) or nitrite concentrations (50-1,500 μM) and the growth rates were elevated under a high bicarbonate (HCO) concentration. The half-saturation constant ( for NH), the maximum growth rate (μ), and the lag duration indicated a strong dependence on the synergistic relationships between the two guilds. Overall, the ecophysiological and metagenomic results in this study provided insights into the phylogeny of the key nitrifying players in a freshwater biofilter and showed that interactions between the two nitrifying guilds in a microbial community enhanced nitrification.
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http://dx.doi.org/10.3389/fmicb.2018.00280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5835065PMC
February 2018

Individual and household attributes influence the dynamics of the personal skin microbiota and its association network.

Microbiome 2018 02 2;6(1):26. Epub 2018 Feb 2.

School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong.

Background: Numerous studies have thus far characterized the temporal dynamics of the skin microbiota of healthy individuals. However, there is no information regarding the dynamics of different microbial association network properties. Also, there is little understanding of how living conditions, specifically cohabitation and household occupancy, may be associated with the nature and extent (or degree) of cutaneous microbiota change within individuals over time. In this study, the dynamics of the skin microbiota, and its association networks, on the skin of urban residents over four seasons were characterized.

Results: Similar to western cohorts, the individuals of this cohort show different extents of variations in relative abundance of common skin colonizers, concomitant with individual- and household-associated changes in differential abundances of bacterial taxa. Interestingly, the individualized nature of the skin microbiota extends to various aspects of microbial association networks, including co-occurring and excluding taxa, as well as overall network structural properties. Household occupancy is correlated with the extent of variations in relative abundance of Propionibacterium, Acinetobacter, and Bacillus over multiple skin sites. In addition, household occupancy is also associated with the extent of temporal changes in microbial diversity and composition within a resident's skin.

Conclusions: This is the first study investigating the potential roles household occupancy has on the extent of change in one's cutaneous microbiota and its association network structures. In particular, we show that relationships between the skin microbiota of a resident, his/her cohabitants, and those of non-cohabitants over time are highly personal and are possibly governed by living conditions and nature of interactions between cohabitants within households over 1 year. This study calls for increased awareness to personal and lifestyle factors that may govern relationships between the skin microbiota of one individual and those of cohabitants, and changes in the microbial association network structures within a person over time. The current study will act as a baseline for future assessments in comparing against temporal dynamics of microbiota from individuals with different skin conditions and for identifying residential factors that are beneficial in promoting the dynamics of the skin microbiota associated with health.
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http://dx.doi.org/10.1186/s40168-018-0412-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797343PMC
February 2018

City-scale distribution and dispersal routes of mycobiome in residences.

Microbiome 2017 10 4;5(1):131. Epub 2017 Oct 4.

School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.

Background: Pathogenic and allergenic bacteria and fungi within the indoors can bring detrimental health effects on the occupants. We previously studied the bacterial communities found in households located throughout Hong Kong as well as the skin surfaces of the occupants. As a complementary study, here, we investigated the fungal communities (mycobiome) in the same residences and occupants and identified factors that are important in shaping their diversity, composition, distribution, and dispersal patterns.

Results: We observed that common skin and environmental fungal taxa dominated air, surface, and skin samples. Individual and touch frequency strongly and respectively shaped the fungal community structure on occupant skin and residential surfaces. Cross-domain analysis revealed positive correlations between bacterial and fungal community diversity and composition, especially for skin samples. SourceTracker prediction suggested that some fungi can be transferred bidirectionally between surfaces and skin sites, but bacteria showed a stronger dispersal potential. In addition, we detected a modest but significant association between indoor airborne bacterial composition and geographic distance on a city-wide scale, a pattern not observed for fungi. However, the distance-decay effects were more pronounced at shorter local scale for both communities, and airflow might play a prominent role in driving the spatial variation of the indoor airborne mycobiome.

Conclusions: Our study suggests that occupants exert a weaker influence on surface fungal communities compared to bacterial communities, and local environmental factors, including air currents, appear to be stronger determinants of indoor airborne mycobiome than ventilation strategy, human occupancy, and room type.
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http://dx.doi.org/10.1186/s40168-017-0346-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5628474PMC
October 2017

Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome.

Water Res 2017 11 20;124:77-84. Epub 2017 Jul 20.

Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA. Electronic address:

Anaerobic digester (AD) microbiomes harbor complex, interacting microbial populations to achieve biomass reduction and biogas production, however how they are influenced by operating conditions and feed sludge microorganisms remain unclear. These were addressed by analyzing the microbial communities of 90 full-scale digesters at 51 municipal wastewater treatment plants from five countries. Heterogeneity detected in community structures suggested that no single AD microbiome could be defined. Instead, the AD microbiomes were classified into eight clusters driven by operating conditions (e.g., pretreatment, temperature range, and salinity), whereas geographic location of the digesters did not have significant impacts. Comparing digesters populations with those present in the corresponding feed sludge led to the identification of a hitherto overlooked feed-associated microbial group (i.e., the residue populations). They accounted for up to 21.4% of total sequences in ADs operated at low temperature, presumably due to ineffective digestion, and as low as 0.8% in ADs with pretreatment. Within each cluster, a core microbiome was defined, including methanogens, syntrophic metabolizers, fermenters, and the newly described residue populations. Our work provides insights into the key factors shaping full-scale AD microbiomes in a global scale, and draws attentions to the overlooked residue populations.
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http://dx.doi.org/10.1016/j.watres.2017.07.050DOI Listing
November 2017

Physiological and molecular characterizations of the interactions in two cellulose-to-methane cocultures.

Biotechnol Biofuels 2017 7;10:37. Epub 2017 Feb 7.

B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.

Background: The interspecies interactions in a biomethanation community play a vital role in substrate degradation and methane (CH) formation. However, the physiological and molecular mechanisms of interaction among the microbial members of this community remain poorly understood due to the lack of an experimentally tractable model system. In this study, we successfully established two coculture models combining the cellulose-degrading bacterium 743B with Fusaro or Gö1 for the direct conversion of cellulose to CH.

Results: Physiological characterizations of these models revealed that the methanogens in both cocultures were able to efficiently utilize the products produced by during cellulose degradation. In particular, the simultaneous utilization of hydrogen, formate, and acetate for methanogenesis was observed in the - cocultures, whereas monocultures of were unable to grow with formate alone. Enhanced cellulose degradation was observed in both cocultures, and the CH yield of the - cocultures (0.87 ± 0.02 mol CH/mol glucose equivalent) was among the highest compared to other coculture studies. A metabolic shift in the fermentation pattern of was observed in both cocultures. The expression levels of genes in key pathways that are important to the regulation and metabolism of the interactions in cocultures were examined by reverse transcription-quantitative PCR, and the expression profiles largely matched the physiological observations.

Conclusions: The physiological and molecular characteristics of the interactions of two CH-producing cocultures are reported. Coculturing with or not only enabled direct conversion of cellulose to CH, but also stabilized pH for , resulting in a metabolic shift and enhanced cellulose degradation. This study deepens our understanding of interspecies interactions for CH production from cellulose, providing useful insights for assembling consortia as inocula for industrial biomethanation processes.
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http://dx.doi.org/10.1186/s13068-017-0719-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5297212PMC
February 2017

Microbiota fingerprints lose individually identifying features over time.

Microbiome 2017 01 9;5(1). Epub 2017 Jan 9.

School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong, Special Administrative Region of China.

Background: Humans host individually unique skin microbiota, suggesting that microbiota traces transferred from skin to surfaces could serve as forensic markers analogous to fingerprints. While it is known that individuals leave identifiable microbiota traces on surfaces, it is not clear for how long these traces persist. Moreover, as skin and surface microbiota change with time, even persistent traces may lose their forensic potential as they would cease to resemble the microbiota of the person who left them. We followed skin and surface microbiota within households for four seasons to determine whether accurate microbiota-based matching of individuals to their households could be achieved across long time delays.

Results: While household surface microbiota traces could be matched to the correct occupant or occupants with 67% accuracy, accuracy decreased substantially when skin and surface samples were collected in different seasons, and particularly when surface samples were collected long after skin samples. Most OTUs persisted on skin or surfaces for less than one season, indicating that OTU loss was the major cause of decreased matching accuracy. OTUs that were more useful for individual identification persisted for less time and were less likely to be deposited from skin to surface, suggesting a trade-off between the longevity and identifying value of microbiota traces.

Conclusions: While microbiota traces have potential forensic value, unlike fingerprints they are not static and may degrade in a way that preferentially erases features useful in identifying individuals.
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http://dx.doi.org/10.1186/s40168-016-0209-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5234115PMC
January 2017

Toxicity of ZnO and TiO to Escherichia coli cells.

Sci Rep 2016 10 12;6:35243. Epub 2016 Oct 12.

School of Biological Sciences, Univ. of Hong Kong, Pokfulam Road, Hong Kong.

We performed a comprehensive investigation of the toxicity of ZnO and TiO nanoparticles using Escherichia coli as a model organism. Both materials are wide band gap n-type semiconductors and they can interact with lipopolysaccharide molecules present in the outer membrane of E. coli, as well as produce reactive oxygen species (ROS) under UV illumination. Despite the similarities in their properties, the response of the bacteria to the two nanomaterials was fundamentally different. When the ROS generation is observed, the toxicity of nanomaterial is commonly attributed to oxidative stress and cell membrane damage caused by lipid peroxidation. However, we found that significant toxicity does not necessarily correlate with up-regulation of ROS-related proteins. TiO exhibited significant antibacterial activity, but the protein expression profile of bacteria exposed to TiO was different compared to HO and the ROS-related proteins were not strongly expressed. On the other hand, ZnO exhibited lower antibacterial activity compared to TiO, and the bacterial response involved up-regulating ROS-related proteins similar to the bacterial response to the exposure to HO. Reasons for the observed differences in toxicity and bacterial response to the two metal oxides are discussed.
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http://dx.doi.org/10.1038/srep35243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378928PMC
October 2016
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