About

Jingqiu Liao is an Assistant Professor in the Charles E. Via, Jr. Department of Civil & Environmental Engineering at Virginia Tech. Her areas of interest include microbiomes and ecosystem health, bacterial pathogens and food safety, and environmental antimicrobial resistance. She holds a B.S. in Ecology from the University of Science & Technology Beijing, an M.S. in Environmental Science from Peking University, and a Ph.D. in Microbiology from Cornell University, with minors in Genomics and Soil Science. She also completed an exchange program in Environmental Engineering at MIT. Liao has professional experience as a postdoctoral scientist in Systems Biology at Columbia University Irving Medical School and has worked as a research assistant in Environmental Sciences and Engineering at Peking University. Her research focuses on environmental and public health microbiology, contributing to understanding microbiomes, pathogen dynamics, and antimicrobial resistance in environmental contexts. She has received several awards, including the Larry Beuchat Young Researcher Award from the International Association for Food Protection and the Outstanding New Assistant Professor Award from Virginia Tech.

Research topics

• Genetics
• Biology
• Anatomy
• Microbiology
• Zoology
• Botany
• Computational biology

Selected publications

• Multi-scale ecological drivers shape the genome flexibility of soil-dwelling <i>Listeria monocytogenes</i>

  ISME Communications · 2026-01-01

  articleOpen accessSenior author

  Abstract Understanding bacterial genome flexibility is key to predicting evolutionary trajectories and ecological interactions. Genome flexibility has been attributed to adaptive evolution, yet the underlying ecological drivers for bacterial pathogens persisting in natural environments remain poorly understood. Listeria monocytogenes (Lm), a foodborne pathogen prevalent in the environment, serves as an ideal model in this context. Through pangenome analysis of 177 Lm isolates representing three evolutionary lineages (I, II, and III) that we isolated from soils across the USA, we detected substantial genomic variation strongly associated with climatic factors, soil properties, and bacterial community composition, particularly the relative abundance of Nitrospirae, Planctomycetes, Acidobacteria, and Cyanobacteria. These factors were linked to many gene functions, particularly those involved in cell envelope synthesis, defense mechanisms, and replication, recombination, and repair. Among Lm lineages, distinct pangenome structure were observed. Lineage III exhibited a highly open pangenome, which was attributed to local adaptation to nutrient-limited conditions and strong dispersal limitation. In contrast, lineage I maintained a more conserved pangenome, likely due to frequent homogenizing dispersal across locations. Consistent with the dispersal patterns, lineage I showed an elevated risk for transmission along environmental-human pathways, evidenced by epidemiological links between three soil-derived and 17 clinical isolates. Collectively, this study suggests the pivotal roles of abiotic factors and bacterial communities in shaping genomic diversity of Lm and potentially other bacterial pathogens in soil. It also highlights significant differences in genome flexibility and transmission dynamics across lineages of the same pathogen species, underscoring the need for tailored source tracking strategies.

  PublisherDOI

• Longitudinal multi-omics reveal phase-dependent viral adaptive strategies and functional potential during formation of algal-bacterial granular sludge

  Bioresource Technology · 2026-03-13

  article
  PublisherDOI

• Microenvironment-driven interactions between mobile genetic elements and defense systems modulate the plastisphere resistome

  Water Research · 2026-03-12

  article
  PublisherDOI

• Motile and non-motile <i>Listeria</i> species adopt distinct genomic and ecological strategies to achieve broad geographic ranges in soil

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-09

  articleOpen accessSenior authorCorresponding

  Abstract Broad geographic ranges indicate high ecological versatility and are generally associated with low extinction risk. Motility is not only a physiological feature, but also a core ecological trait for bacteria. However, the genomic foundations underlying the broad geographic ranges of motile and non-motile bacteria remain poorly understood. To address this, we analyzed 141 and 90 genomes of Listeria welshimeri and L. booriae , systematically screened from 1,004 soil samples across the United States, representing widespread motile and non-motile species, respectively. We show that L. welshimeri exhibits restricted phylogeographic structure and a weak distance-decay relationship, suggesting minimal geographic barriers to dispersal. Its high dispersal capacity likely stems from enhanced motility and effective host colonization, evidenced by strong positive selection on flagellar genes and the close relatedness to isolates from wild birds. In contrast, L. booriae displays a regionally endemic distribution and limited dispersal. With a large, open pangenome, L. booriae appears strongly adapted to local environments. This is evidenced by pronounced positive selection on genes involved in inorganic ion, amino acid, and coenzyme transport and metabolism, as well as strong associations with abiotic factors, particularly climate, and accompanying bacterial consortia. In summary, to establish widespread distributions, L. welshimeri tends to rely on movement and colonization of wildlife hosts to facilitate long-distance dispersal, while L. booriae leverages genomic plasticity and metabolic versatility that enable adaptation to diverse environmental conditions. These findings highlight the distinct genomic foundations and ecological strategies that motile and non-motile bacteria use to achieve broad geographic ranges in the environment.

  PublisherOA PDFDOI

• Assessment of a Passive Sampler for Aquifer Microbial Community Profiling and Comparison of Porous Media Applied in a Managed Recharge Scenario

  Water Environment Research · 2026-05-01

  articleSenior author

  Microbial communities play an important role in aquifer systems as both hazards (e.g., pathogens and carriers of antibiotic resistance genes) and contributors to contaminant remediation. However, monitoring native microbial communities in situ remains challenging. To address this challenge, we developed a passive sampler that employs removable cartridges containing solid media designed to recreate the aquifer environment in a controlled fashion and support consistent, repeatable, time-series sampling. With a bench-scale, continuous-loop setup circulating advanced-treated wastewater, we compared microbial community dynamics across three candidate porous media: native aquifer sediment, zirconia beads, and laboratory-grade silica sand. 16S rRNA gene amplicon sequencing revealed that native aquifer sediment best reflected influent microbial composition and temporal shifts. Native aquifer sediment also exhibited more spatial consistency in microbial diversity along the sampler. These findings suggest that native aquifer sediment is an optimal porous medium for long-term, in situ monitoring of microbial communities for managed aquifer recharge and other applications in groundwater systems.

  PublisherDOI

• Genomic diversification underlies the broad ecological range of <i>Salmonella enterica</i> serotype Typhimurium

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-21

  articleOpen accessSenior authorCorresponding

  Abstract Salmonella Typhimurium is a versatile foodborne pathogen with a broad ecological range, making it an ideal model to better understand pathogen adaptations that allow them to infect multiple hosts and persist across diverse environments. We analyzed 745 genomes of S. Typhimurium isolated from three food animal sources (bovine, swine, and poultry) and two non-food animal sources (wild birds and the environment). We found that S. Typhimurium from food animal sources generally had a more open pangenome and harbored more antimicrobial resistance genes (ARGs) than non-food animal sources. Notably, swine isolates exhibited the most open pangenome and prevalent ARGs, likely as a result of horizontal gene transfer primarily mediated by plasmids. Despite similar core genome sizes, S. Typhimurium from different sources displayed distinct patterns of positive selection in the core genome that varied in both frequency and targeted functional categories. In contrast, although accessory genome sizes varied substantially across sources, the frequency of positive selection remained similar. Using machine learning, we further identified genetic variants (e.g., virulence factors) highly predictive of sources. These findings suggest that gain and loss of accessory genes and positive selection acting on core genes facilitate differential adaptation in S. Typhimurium, contributing to its broad ecological range.

  PublisherOA PDFDOI

• Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress

  Microbiome · 2025-01-31 · 19 citations

  articleOpen access

  BACKGROUND: The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress. RESULTS: Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities. CONCLUSIONS: Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.

  PublisherOA PDFDOI

• Temporal, Seasonal, and Patient Demographic Trends Among Culture-Confirmed Human Salmonellosis Cases Identify Regional Differences in Salmonella Serotypes Reported in Virginia, USA From 2012 through 2022

  Journal of Food Protection · 2025-05-23 · 3 citations

  articleOpen access

  The U.S. federal government established a national goal of reducing the salmonellosis incidence to ≤11.5 cases/100,000 persons by 2030. To assess progress toward this goal in Virginia, we used data from culture-confirmed salmonellosis cases reported to the Virginia Department of Health during 2012-2022 (N = 11,411). A Bayesian negative binomial splines model was implemented to estimate changes in incidence/100,000 persons during 2012-2022 statewide and for specific localities (for example: county or independent city). Incidence varied substantially by locality and over time. Output from modeled incidence suggests limited progress toward federal salmonellosis reduction goals in Virginia. During 2012-2022, statewide modeled incidence ranged between 11.6 (in 2022) and 12.9 (in 2018). From 2018 to 2022, there was a consistent decrease in the modeled incidence of culture-confirmed salmonellosis in Virginia. In contrast to FoodNet trends, the inclusion of culture-independent diagnostic tests in the case definition did not significantly reduce the number of culture-confirmed cases, suggesting a high rate of reflex culturing among patients in Virginia. Among 187 Salmonella serotypes reported, 64.2% of culture-confirmed infections were attributed to six serotypes: Typhimurium (including the monophasic variant, I 4,[5],12:i:-; 20.3%), Enteritidis (18.0%), Newport (10.7%), Javiana (7.7%), Bareilly (3.9%), and Braenderup (3.6%). Trends in salmonellosis attributable to specific serotypes varied substantially; modeled incidence of infections caused by some serotypes decreased substantially (e.g., S. Typhimurium/I 4,[5],12:i:-) and others increased (e.g., S. Braenderup). This may indicate that serotype-specific trends may be masking changes in salmonellosis epidemiology and contributing to the apparent overall stability in salmonellosis incidence in Virginia; efforts to meet federal goals may need to be tailored to reduce the incidence of specific serotypes that are increasing in incidence.

  PublisherDOI

• Initializing a Public Repository for Hosting Benchmark Datasets to Facilitate Machine Learning Model Development in Food Safety

  Journal of Food Protection · 2025-02-01 · 5 citations

  articleOpen access

  While there is clear potential for artificial intelligence (AI) and machine learning (ML) models to help improve food safety, the development and deployment of these models in the food safety domain are by and large lacking. The absence of publicly available databases that host well-curated datasets that can be used to develop and validate AI /ML models represents one likely barrier. Thus, we took three previously published datasets, which we further cleaned and annotated, and made them publicly available in a repository called Cornell Food Safety ML Repository. The selected datasets include (i) presence or absence of Listeria spp. in soil samples collected across the U.S. with paired metadata for soil properties, geolocation, climate, and surrounding land use, (ii) presence or absence of Salmonella and Campylobacter in young chicken carcasses tested in processing facilities with associated meteorological and temporal metadata, and (iii) presence or absence of fecal contamination as well as E. coli concentration in New York watersheds with associated metadata for land use, water attributes, and meteorological factors. These datasets can serve as benchmark datasets for developing ML models. To demonstrate the utility of the repository, we developed customizable scripts as well as LazyPredict (a quick screening method) scripts for training different types of ML models using the shared datasets. While this repository provides an important starting point that will allow for the development and testing of ML models to predict foodborne pathogens contamination in different sources, the inclusion of further datasets is clearly needed to advance this field. This paper thus includes a call to action for the deposit of well-curated datasets that can be used for further development of predictive models in food safety. This paper will also discuss the benefits of such public databases, including the assessment of data-sharing scenarios using existing privacy-preserving techniques.

  PublisherDOI

• Assessment of a Passive Sampler for Aquifer Microbial Community Profiling and Comparison of Porous Media Applied in a Managed Recharge Scenario

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-22

  articleOpen accessSenior authorCorresponding

  Abstract Microbial communities play an important role in aquifer systems, as both hazards (e.g., pathogens, carriers of antibiotic resistance genes) and contributors to contaminant remediation. However, monitoring native microbial communities in situ remains challenging. To address this challenge, we developed a passive sampler with that employs removable cartridges containing solid media designed to re-create the aquifer environment in a controlled fashion and support consistent, repeatable, time-series sampling. With a bench-scale, continuous-loop setup circulating advanced-treated wastewater, we compared microbial community dynamics across three candidate porous media: native aquifer sediment, zirconia beads, and laboratory-grade silica sand. 16S rRNA gene amplicon sequencing revealed that native aquifer sediment best reflected influent microbial composition and temporal shifts. Native aquifer sediment also exhibited more spatial consistency in microbial diversity along the sampler. These findings suggest that native aquifer sediment is an optimal porous medium for long-term, in situ monitoring of microbial communities for managed aquifer recharge and other applications in groundwater systems.

  PublisherDOI

Frequent coauthors

• Elvin A. Kabat

  85 shared

• Flavio Gruezo

  Columbia University

  38 shared

• Bo Nilsson

  Uppsala University

  36 shared

• David Zopf

  University of Michigan–Ann Arbor

  36 shared

• Albert M. Wu

  Chang Gung University

  36 shared

• Xiaofeng Cao

  26 shared

• J Shyong

  25 shared

• David Geltner

  Massachusetts Institute of Technology

  25 shared

Education

• PhD

  Cornell University

  2020

• MS

  Peking University

  2014

• BS

  University of Science and Technology Beijing

  2011

Awards & honors

• Larry Beuchat Young Researcher Award, International Associat…
• Outstanding New Assistant Professor Award, Virginia Tech, 20…
• Major Grants Initiative Scaling Scholarship, Virginia Tech,…
• Ralph E. Powe Junior Faculty Enhancement Award, Oak Ridge As…
• Pre Tenure Faculty Research Award, 4 VA, 2023