Feng Ju

Westlake University · Division of Environment and Resources

Understanding environmental and biological influences on the dynamics of microbial communities has received great attention in microbial ecology. Here, utilizing large time-series 16S rRNA gene data, we show that in activated sludge of an environmentally important municipal wastewater treatment plant, 5-year temporal dynamics of bacterial community...

Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This...

Understanding which/how antibiotic resistance genes (ARGs) contribute to increased acquisition of resistance by pathogens in aquatic environments are challenges of profound significance. We explored the co-occurrence and removal versus enrichment of ARGs and human bacterial pathogens (HBPs) in municipal sewage sludge digesters. We combined metageno...

Wastewater treatment plants (WWTPs) are implicated as hotspots for the dissemination of antibacterial resistance into the environment. However, the in situ processes governing removal, persistence, and evolution of resistance genes during wastewater treatment remain poorly understood. Here, we used quantitative metagenomic and metatranscriptomic ap...

Metformin (MET), a worldwide used drug for type 2 diabetes, has been found with the largest amount by weight among all drugs in aquatic environment, including the drinking water systems where this emerging micropollutant is inevitably transformed during chlorination process. Whether MET chlorination byproducts Y (C4H6ClN5) and C (C4H6ClN3) exist in...

Antibiotic resistance genes (ARGs) are a well-known environmental concern. Yet, limited knowledge exists on the fate and transport of ARGs in deep freshwater reservoirs experiencing seasonal hydrological changes, especially in the context of particle-attached (PA) and free-living (FL) lifestyles. Here, the ARG profiles were examined using high-thro...

Metagenomics has in the last decade greatly revolutionized the study of microbial communities. However, the presence of artificial duplicate reads mainly raised from the preparation of metagenomic DNA sequencing library and their impacts on metagenomic assembly and binning have never brought to the attention. Here, we explicitly investigated the ef...

Metformin is the first-line antidiabetic drug and one of the most prescribed medications worldwide. Because of its ubiquitous occurrence in global waters and demonstrated ecotoxicity, metformin, as with other pharmaceuticals, has become a concerning emerging contaminant. Metformin is subject to transformation, producing numerous problematic transfo...

Evidence for microbial degradation of polyvinyl chloride (PVC) has previously been reported, but little is known about the degrading strains and enzymes. Here, we isolate a PVC-degrading bacterium from the gut of insect larvae and shed light on the PVC degradation pathway using a multi-omic approach. We show that the larvae of an insect pest, Spodo...

With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment.

Clogging has attracted increasing attention as one of the key problems affecting the development and application of constructed wetland (CW) technology. However, there is a lack of systematic research on the evolution history, hot spots, frontiers and direction classification of CW clogging, lack of research papers on how to effectively solve clogg...

Despite the growing awareness of antibiotic resistance genes (ARGs) spreading in the environment, there is a knowledge gap on the fate and transport of ARGs in particle-attached (PA) and free-living (FL) lifestyles in deep freshwater ecosystems experiencing seasonal hydrological changes. Here, we examined the ARG profiles using high-throughput quan...

A self-stabilizing microbial community lays the foundation of the efficient biochemical reactions of the anaerobic digestion (AD) process. Despite extensive profiling of microbial community dynamics under varying operating parameters that have been documented, the effects of food waste (FW) to feeding sewage sludge (FSS) ratios on the microbial ass...

Micro/nano-sized plastics (MPs/NPs) existing in wastewater system are the potential threats to nitrogen (N) biotransformation. Constructed wetlands (CWs) as wastewater treatment systems are considered the important barriers preventing MPs/NPs from entering the open water. However, little is known about how the accumulation of MPs/NPs affects microb...

Cyanobacterial harmful algal blooms (CyanoHABs) are globally intensifying and exacerbated by climate change and eutrophication. However, microbiota assembly mechanisms underlying CyanoHABs remain scenario-specific and elusive. Especially, cyanopeptides, as a group of bioactive secondary metabolites of cyanobacteria, could affect microbiota assembly...

Background The abundance of clinically important antibiotic resistance determinants in wastewater has raised concerns regarding their dissemination into the environment and transmission to animals and humans. However, the high bacterial diversity and complexity of environmental microbiomes makes it challenging to comprehensively detect and quantify...

The antibiotic resistance crisis underlies globally increasing failures in treating deadly bacterial infections, largely due to the selection of antibiotic resistance genes (ARG) collection, known as the resistome, in human gut microbiota. So far, little is known about the relationship between gut antibiotic resistome and host metabolic disorders s...

Background Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown. Here we used culture-independe...

Abstract The interactions between the gut microbiome and metabolome play an important role in human health and diseases. Current studies mainly apply statistical correlation analysis between the gut microbiome and all the identified metabolites to explore their relationship. However, it remains challenging to identify the specific metabolic functio...

Background During wastewater treatment, the wastewater microbiome facilitates the degradation of organic matter, reduction of nutrients, and removal of gut parasites. While the latter function is essential to minimize public health risks, the range of parasites involved and how they are removed is still poorly understood. Results Using shotgun met...

Cyanobacterial harmful algal blooms (CyanoHABs) are globally intensifying and exacerbated by climate change and eutrophication. However, microbiota assembly mechanisms underlying CyanoHABs remain scenario specific and elusive. Especially, cyanopeptides, as a group of bioactive secondary metabolites of cyanobacteria, could affect microbiota assembly...

Microbial degradation of polyvinyl chloride (PVC) is eco-friendly and economically attractive but extremely challenging due to the lack of a molecular understanding of the degrading strains and enzymes. Motivated by the serendipitous discovery that the larva of an agricultural invasive insect pest, Spodoptera frugiperda, effectively survived PVC fi...

Hadal zones are marine environments deeper than 6,000 m, most of which comprise oceanic trenches. Microbes thriving at such depth experience high hydrostatic pressure and low temperature. The genomic potentials of these microbes to such extreme environments are largely unknown. Here, we compare five complete genomes of bacterial strains belonging t...

Taxonomic convergence is common in bacterial communities but its underlying molecular mechanism remains largely unknown. We thus conducted a time-series transcriptional analysis of a convergent two-species synthetic community that grew in a closed broth-culture system. By analyzing the gene expression and monitoring the community structure, we foun...

The rise of antibiotic resistance as one of the most serious global public health threats has necessitated the timely clinical diagnosis and precise treatment of deadly bacterial infections. To identify which types and doses of antibiotics remain effective for fighting against multi-drug-resistant pathogens, the development of rapid and accurate an...

The widely used antidiabetic drug metformin has become an emerging contaminant of water systems. In a prior study, we demonstrated the marked mammalian toxicity of the disinfection-derived byproducts (DBPs) Y (yellow, C4H6ClN5) and C (colorless, C4H6ClN3), and here assess the distribution, formation, and ecotoxicity of these in Chinese urban water...

Background Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically diverse assemblages can be and what causes them to transition between states remains poorly understood. We studied monthly activated sludge (AS) samples collected over 9 years from a full-scale wastewater...

Microbial degradation of polyvinyl chloride (PVC) is eco-friendly and economically attractive, but extremely challenging due to the lack of mechanistic understanding on the degrading strains and enzymes. Motivated by an accidental discovery that the larva of an agricultural invasive pest, Spodoptera frugiperda, effectively survived solely on PVC fi...

Although there is growing evidence that micropollutants can be microbially converted in rapid sand filters of drinking water treatment plants (DWTPs), little is known about the biotransformation pathways and associated microbial strains in this process. Here, we constructed sand filter columns filled with manganese or quartz sand obtained from full...

Large water diversion projects are important constructions for reallocation of human-essential water resources. Deciphering microbiota dynamics and assembly mechanisms underlying canal water ecosystem services especially during long-distance diversion is the prerequisite for water quality monitoring, biohazard warning and sustainable management. Us...

Large water diversion projects are important constructions for reallocation of human-essential water resources. Deciphering microbiota dynamics and assembly mechanisms underlying canal water ecosystem services especially during long-distance diversion is the prerequisite for water quality monitoring, biohazard warning and sustainable management. Us...

Objective: To investigate the association between human gut antibiotic resistome and the progression of type 2 diabetes (T2D) in a large cohort study. Design: The present study included 1210 participants from the Guangzhou Nutrition and Health Study. We depicted the landscape of human gut antibiotic resistome with shotgun metagenomic data and exami...

Mainstream anaerobic ammonium oxidation (anammox) represents one of the most promising energy-efficient mechanisms of fixed nitrogen elimination from wastewaters. However, little is known about the exact processes and drivers of microbial community assembly within the complex microbial biofilms that support anammox in engineered ecosystems. Here, w...

Sludge lysate is an unavoidable and refractory liquid produced from the waste activated sludge hydrothermal pyrolysis, which contains plenty of hazardous refractory organic compounds and value-added organic resources. Here, the proof of concept for an integrated strategy that couples technically compatible pretreatment to microbial electrolysis ass...

River networks are one of the main routes by which the public could be exposed to environmental sources of antibiotic resistance, that may be introduced e.g. via treated wastewater. In this study, we applied a comprehensive integrated analysis encompassing mass-flow concepts, chemistry, bacterial plate counts, resistance gene quantification and sho...

Although several molecular-based studies have demonstrated the involvement of ammonia-oxidizing archaea (AOA) in ammonia oxidation in wastewater treatment plants (WWTPs), factors affecting the persistence and growth of AOA in these engineered systems have not been resolved. Here, we show a seasonal prevalence of AOA in a full-scale WWTP (Shatin, Ho...

The global rise and spread of antibiotic resistance greatly challenge the treatment of bacterial infections. Wastewater treatment plants (WWTPs) harbor and discharge antibiotic resistance genes (ARGs) as environmental contaminants. However, the knowledge gap on the host identity, activity and functionality of ARGs limits transmission and health ris...

Antarctica is an isolated and relatively simple ecosystem dominated by microorganisms, providing a rare opportunity to study the spread of airborne microbes and to predict future global climate change. However, little is known about on the diversity and potential sources of microorganisms in the marine atmosphere along the Antarctica coast. Here we...

Antibiotic-resistant pathogens pose a significant threat to human health. Several dispersal mechanisms have been described, but transport of both microbes and antibiotic resistance genes (ARGs) via atmospheric particles has received little attention as a pathway for global dissemination. These atmospheric particles can return to the Earth's surface...

Background: Neither the abundance of the exo/endoglucanase GH modules nor the taxonomy affiliation is informative enough in inferring whether a genome is of a potential cellulolytic microbe or not. By interpreting the complete genomes of 2642 microbe strains whose phenotypes have been well documented, we are trying to reveal a more reliable genotyp...

Metformin (MET), a worldwide used drug for type 2 diabetes, has been found with the largest amount by weight among all drugs in aquatic environment, including the drinking water sources where chlorination inevitably transforms MET into chlorination byproducts. Although MET has health-promoting properties, whether or how its chlorination byproducts...

Complex microbial biofilms orchestrating mainstream anaerobic ammonium oxida-tion (anammox) represent one of the most promising energy-efficient mechanisms of fixed nitrogen elimination from anthropogenic waste waters. However, little is known about the ecological processes that are driving microbial community assem-bly leading to functional anammo...

Co-digestion of food waste with sewage sludge is widely applied for waste stabilization and energy recovery around the world. However, the effect of solid retention time (SRT) on the microbial population dynamics, metabolism and interspecies interaction have not been fully elucidated. Here, the influence of SRT between 5 and 25 days on the performa...

Designed for retaining suspended particles, rapid sand filters (RSFs) are widely used in drinking water treatment. There is increasing evidence that microbial processes within RSFs contribute to the transformation and removal of organic carbon, nitrogen, and metal pollutants. Here, we linked microbial composition and functional profiles with treatm...

Motivation: Microbiome-metabolome association studies have experienced exponential growth for an in-depth understanding of the impact of microbiota on human health over the last decade. However, analyzing the resulting multi-omics data and their correlations remains a significant challenge due to the lack of a comprehensive computational tool that...

Neither the abundance of the exo/endoglucase GH modules nor the taxonomy affiliation is informative enough in inferring whether a genome is of a potential cellulolytic microbe or not. By interpreting the complete genomes of 2642 microbe strains whose phenotypes have been well documented, we are trying to reveal a more reliable genotype and phenotyp...

Mycobacterium often presents as an abundant bacterial genus in activated sludge in many wastewater treatment plants (WWTPs), but the species-level taxonomy and functions remain poorly understood. In this study, we profiled the mycobacterial communities in eleven WWTPs from five countries by pyrosequencing the rpoB amplicons and searching against a...

Bacterial community in activated sludge (AS) is diverse 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 signif...

Due to complexity and variety of pharmaceutical wastewater composition, little is known as for functionally important microflora of pharmaceutical wastewater treatment plants (pWWTPs). We compared bacterial composition and diversity of pWWTPs (27 sludge samples collected from 12 full-scale pWWTPs) with those of other industrial (iWWTPs) (27 samples...

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 sampling method to identify overlooked diversity and the hidden dynamics of microbes; detect cross-asso...

Background: Methanogenic biodegradation of aromatic compounds depends on syntrophic metabolism. However, metabolic enzymes and pathways of uncultured microorganisms and their ecological interactions with methanogenic consortia are unknown because of their resistance to isolation and limited genomic information. Results: Genome-resolved metagenom...

To comprehensively understand the profile of free-living bacteria and potential bacterial pathogens in sewage treatment plants (STPs), this study applied high-throughput sequencing-based metagenomics approaches to investigate the effects of activated sludge (AS) treatment process and ultraviolet (UV) disinfection on the community of bacterial patho...

Although the health of rivers is threatened by multiple anthropogenic stressors with increasing frequency, it remains an open question how riverine microbial communities respond to emerging micropollutants. Here, by using 16S rDNA amplicon sequencing of 60 water samples collected during different hydrological seasons, we investigated the spatio-tem...

Understanding the influences of biotic and abiotic factors on microbial community structure and methanogenesis are important for its engineering and ecological significance. In this study, four biogas digesters were supplied with the same inoculum and feeding sludge, but operated at different sludge retention time (7 to 16 days) and organic loading...

The effectiveness and treatment conditions of FeCl3- and AlCl3-coagulated municipal sewage sludge from chemically enhanced primary treatment (CEPT) using anaerobic digestion (AD) and the structure of microbial community were investigated. The results based on 297 measurements under different operational conditions demonstrate good average AD perfor...

Anaerobic technology has been applied for the treatment of solid wastes and wastewater since the 1880s. This chapter reviews the most recent advance in molecular microbial characterization techniques, i.e., metagenomics, as well as its applications in anaerobic technology, from the exploration of the intriguing science of anaerobes to industrial en...

Improvement on the bioconversion of cellulosic biomass depends much on the expanded knowledge on the underlying microbial structure and the relevant genetic information. In this study, metagenomic analysis was applied to characterize an enriched mesophilic cellulose-converting consortium, to explore its cellulose-hydrolyzing genes, and to discern g...

A metagenomic approach and network analysis was used to investigate the wide-spectrum profiles of antibiotic resistance genes (ARGs) and their co-occurrence patterns in 50 samples from 10 typical environments. In total, 260 ARG subtypes belonging to 18 ARG types were detected with an abundance range of 5.4 × 10(-6)-2.2 × 10(-1) copy of ARG per copy...

The ubiquitous occurrence of microorganisms gives rise to continuous public concerns regarding their pathogenicity and threats to human environment, as well as potential engineering benefits in biotechnology. The development and wide application of environmental biotechnology, for example in bioenergy production, wastewater treatment, bioremediatio...

The objective of this study was to investigate the Microbial community shifts of bacteria, especially nitrifiers and denitrifiers, in the biofilm of two rotating biological contactor (RBC) trains with different running times along the plug flowpath. The microbial consortia were profiled using multiple approaches, including 454 high-throughput seque...

Methanogenesis from wastewater-borne organics and organic solid wastes (e.g., food residues) can be severely suppressed by the presence of toxic phenols. In this work, ambient (20 °C) and mesophilic (37 °C) methane-producing and phenol-degrading consortia were enriched and characterized using high-throughput sequencing (HTS). 454 Pyrosequencing ind...

Metagenomic technique was employed to characterize the seasonal dynamics of activated sludge (AS) communities in a municipal wastewater treatment plant (WWTP) over 4 years. The results indicated that contrary to Eukaryota (mainly Rotifera and Nematoda), abundances of Bacteria and Archaea (mainly Euryarchaeota) were significantly higher in winter th...

The metagenomic approach was applied to characterize variations of microbial structure and functions in raw (RW) and treated water (TW) in a drinking water treatment plant (DWTP) at Pearl River Delta, China. Microbial structure was significantly influenced by the treatment processes, shifting from Gammaproteobacteria and Betaproteobacteria in RW to...