A5046669989- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Ethics in Clinical Research
- Indoor Air Quality and Microbial Exposure
- Molecular Biology Techniques and Applications
- Inorganic Chemistry and Materials
- SARS-CoV-2 and COVID-19 Research
- Bacteriophages and microbial interactions
- Conservation Techniques and Studies
- Liver Disease Diagnosis and Treatment
- Bacterial Identification and Susceptibility Testing
- Gene expression and cancer classification
- Gastrointestinal motility and disorders
- Gastroesophageal reflux and treatments
- Odor and Emission Control Technologies
- Legionella and Acanthamoeba research
- Diabetes and associated disorders
- Bacterial biofilms and quorum sensing
- COVID-19 Clinical Research Studies
- Soil Carbon and Nitrogen Dynamics
- Bioinformatics and Genomic Networks
- Wastewater Treatment and Nitrogen Removal
Northwestern University
2019-2025
Harvard University
2024
Massachusetts General Hospital
2024
Shanghai Public Security Bureau
2021
Zhejiang University
2016-2018
Abstract Background High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only viable portion communities at scale. There as yet not one best solution this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular (e.g., qPCR or sequencing). While these met moderate success, most them focused on resulting...
Abstract Background Characterization of microbial activity is essential to the understanding basic biology communities, as function a microbiome defined by its biochemically active (“viable”) community members. Current sequence-based technologies can rarely differentiate activity, due their inability distinguish live and dead sourced DNA. As result, our structures potential mechanisms transmission between humans surrounding environments remains incomplete. solution, 16S rRNA transcript-based...
The field of microbiome research continues to grow at a rapid pace, with multi-omics approaches becoming widely used interrogate diverse samples. However, due lagging awareness and implementation standards data stewardship, many datasets are produced that not comparable, reproducible, or reusable. In 2021, the National Microbiome Data Collaborative launched its Ambassador Program, which utilizes community-learning model annually train cohort early-career researchers in stewardship best...
Environmental surveillance is a critical tool for combatting public health threats represented by the global COVID-19 pandemic and continuous increase of antibiotic resistance in pathogens. With its power to detect entire microbial communities, metagenomics-based methods stand out addressing need. However, several hurdles remain be overcome order generate actionable interpretations from metagenomic sequencing data infection prevention. Conceptually technically, we focus on viability...
Abstract Background Effective surveillance of microbial communities in the healthcare environment is increasingly important infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but currently challenged by several limitations: (1) they not powerful enough extract valid signals out background noise for low-biomass samples, (2) do distinguish between viable and nonviable organisms, (3) reveal load quantitatively. An additional practical challenge...
Closely related species are typically assumed to demonstrate similar phenotypes driven by underlying conserved genotypes. When monitoring for the effect of antimicrobials on types that may be selected for, this assumption prove incorrect, and identification additional genetic markers necessary.
Abstract Background Microscopic colitis (MC) is a common cause of chronic diarrhea, predominantly among older adults. Emerging evidence suggests that perturbations gut microbiome and metabolome may play an important role in MC pathogenesis. Objective To comprehensively characterize alterations the microbial metabolic composition MC. Design We established longitudinal cohort adult patients with two control groups individuals – diarrhea controls age- sex-matched without diarrhea. Using stool...
Abstract A key question in microbial community analysis is determining which features are associated with properties such as environmental or health phenotypes. This statistical task impeded by characteristics of typical profiling technologies, including sparsity (which can be either technical biological) and the compositionality imposed most nucleotide sequencing approaches. Many models have been proposed that focus on how relative abundance a feature (e.g. taxon pathway) relates to one...
Abstract Background Characterization of microbial viability is essential to the understanding basic biology communities, as function a microbiome defined by its biochemically active (“viable”) community members. Current sequence-based technologies can rarely differentiate viability, due their inability distinguish live and dead sourced DNA. As result, our structures potential mechanisms transmission between humans surrounding environments remains incomplete. solution, 16S rRNA...
Abstract A One Health approach is essential in combating antibiotic and antimicrobial resistance. Chlorhexidine (di)gluconate (CHG), a widely used antiseptic medical intensive care units (MICU), has recently come under scrutiny. However, studies on CHG tolerance, particularly interconnected indoor environments, are limited. We comprehensively explored tolerance MICU environments from chemical, microbial, molecular perspectives. Using microcosm experiments field surveys, we demonstrated that...
Abstract This protocol describes the snap freezing process for liquid-phase environmental microbial samples. Compared with standard freezing, it better maintains integrity of cells.
Abstract Microbial samples collected from built environment surfaces can be very low-biomass. This poses a critical challenge to extract valid signals out of the background noises for downstream analyses. Upon comparing and optimizing several extraction methods, our results demonstrated that bead-beating heat lysis followed by liquid-liquid was optimal method, as opposed widely used column- magnetic bead-based methods. Adapted Lucigen MasterPure Complete DNA RNA Purification Kit manual, this...
Abstract The application of propidium monoazide (PMA) treatment is partially impeded by the failure to obtain consistent results. Though reason multifaceted, lack explicitly outlined protocols exacerbates issue. Here we present an optimized protocol with steps and notes described in detail. This helpful achieve results across samples batches.
Abstract This is a protocol to collect microbiome samples from built environment surfaces using swabs as the collection device, followed by extracting biomass swab heads liquid buffer solutions for downstream processing. The also describes cultivation pipeline capture large fraction of indoor diversity. Additionally, it provides steps pool multiple together if needed.
Abstract Effective surveillance of microbial communities in the healthcare environment is increasingly important infection prevention. However, current workflows are insufficient for proper risk assessment. Upon evaluating and optimizing techniques, we recommend best practices introduce a well-structured workflow metagenomics-based environmental that appropriate low-biomass samples, distinguishes viability, quantitative. The was developed using representative microbiome sample, which created...
Abstract Background: High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only viable portion communities at scale. There as yet not one best solution this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular (e.g. qPCR or sequencing). While these met moderate success, most them focused on resulting...
Abstract As the scientific literature grows exponentially and research becomes increasingly interdisciplinary, accurate high-throughput reference deduplication is vital in evidence synthesis studies (e.g., systematic reviews, meta-analyses) to ensure completeness of datasets while reducing manual screening burden. Existing tools fail fulfill these emerging needs, as they are often labor-intensive, insufficient accuracy, limited clinical fields. Here, we present RefDeduR, a text-normalization...
Objective To explore the application value of automatic nucleic acid extractor combined with vacuum concentrator in forensic DNA extraction. Methods Gradient samples human peripheral venous blood were collected at 40, 80, 120, 160, 200, 240, 280 and 320 fold dilution. The each gradient treated no inhibitor, black oil, rust, fruit acid, tin foil indigo, respectively. was used for purification extraction above samples. extracted eluent （6 μL） taken amplification directly, rest concentrated by...