An Ni Zhang

An Ni Zhang
Massachusetts Institute of Technology | MIT · Department of Biological Engineering

Doctor of Philosophy

About

40
Publications
10,900
Reads
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646
Citations
Citations since 2017
35 Research Items
640 Citations
2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
Introduction
Additional affiliations
August 2018 - present
Massachusetts Institute of Technology
Position
  • PostDoc Position
Description
  • Alm Lab http://almlab.mit.edu/anni_zhang.html
September 2014 - July 2018
The University of Hong Kong
Position
  • PhD
September 2014 - July 2018
The University of Hong Kong
Position
  • Research Assistant

Publications

Publications (40)
Article
Full-text available
Background: Integrons, especially the class 1 integrons, are major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs). However, comprehensive knowledge of the types, content, and distribution of integrons in bacterial taxa is lacking to evaluate their contribution. Results: We have constructed a new integrase...
Article
Full-text available
Background: The lack of pure cultures limits our understanding into 99% of bacteria. Proper interpretation of the genetic and the transcriptional datasets can reveal clues for the enrichment and even isolation of the not-yet-cultured populations. Unraveling such information requires a proper mining method. Results: Here, we present a method to i...
Preprint
Full-text available
The increasing accumulation of antibiotic resistance genes (ARGs) in pathogens poses a severe threat to the treatment of bacterial infections. However, not all ARGs do not pose the same threats to human health. Here, we present a framework to rank the risk of ARGs based on three factors: "anthropogenic enrichment", "mobility", and "host pathogenici...
Article
Background: Metagenomic analysis reveals that antibiotic-resistance genes (ARGs) are widely distributed in both human-associated and non-human-associated habitats. However, it is difficult to equally compare ARGs between samples without a standard method. Methods: Here, we constructed a comprehensive profile of the distribution of potential ARGs...
Article
Full-text available
Background Bacterial communities are essential to the biogeochemical cycle in riverine ecosystems. However, little is presently known about the integrated biogeography of planktonic and sedimentary bacterial communities in large rivers. ResultsThis study provides the first spatiotemporal pattern of bacterial communities in the Yangtze River, the la...
Article
Antibiotic resistance, which is encoded by antibiotic-resistance genes (ARGs), has proliferated to become a growing threat to public health around the world. With technical advances, especially in the popularization of metagenomic sequencing, scientists have gained the ability to decipher the profiles of ARGs in diverse samples with high accuracy a...
Article
Full-text available
Antibiotic-associated diarrhea (AAD) affects a significant proportion of patients receiving antibiotics. We sought to understand if differences in the gut microbiome would influence the development of AAD. We administered a 3-day course of amoxicillin-clavulanate to 30 healthy adult volunteers, and analyzed their stool microbiome, using 16S rRNA ge...
Preprint
Full-text available
A bstract Patients receiving antibiotics often suffer from antibiotic-associated diarrhea (AAD). AAD is of clinical significance as it can result in premature antibiotic discontinuation and suboptimal treatment of infection. The drivers of AAD however, remain poorly understood. We sought to understand if differences in the gut microbiome, both at b...
Article
Full-text available
Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that are high-risk. Here, we developed an ‘omics-based’ framework to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our fra...
Article
Class 1 integrons (CL1s) are one of the major contributors to the horizontal transfer of antibiotic resistance genes (ARGs). However, our knowledge of CL1 in the environment is still very limited due to the limitations of the current PCR primers and the sequencing methods adopted. This study developed a new primer coupled with PacBio sequencing to...
Article
Full-text available
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...
Preprint
Full-text available
The spread of bacterial antibiotic resistance across human and environmental habitats is a global public health challenge. Wastewater has been implicated as a major source of antibiotic resistance in the environment, as it carries resistant bacteria and resistance genes from humans into natural ecosystems. However, different wastewater environments...
Article
The benefits of extensive artificial sweeteners use come at a cost of their ubiquitous occurrence in the aquatic environment. Biodegradation is crucial for the removal of artificial sweeteners in the environment, yet comprehensive characterizations of the degradation consortia that degrade these compounds have not been initiated. Here, we performed...
Preprint
Full-text available
Background The antibiotic resistant genes (ARGs) have been emerging as one of the top global issue s in both medical and environmental fields. The metagenomic analysis has been widely adopted in ARG-related studies, revealing a universal presence of ARGs in diverse environments from medical settings to natural habitats, even in drinking water and a...
Article
With the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move towards standardized comparisons among laboratories. Three widely employed DNA extraction methods (Fast...
Article
Full-text available
We designed novel quantitative real-time polymerase chain reaction (qPCR) primers for the polyphosphate kinase 1 (ppk1) gene, targeting eight individual “Candidatus Accumulibacter” (referred to as Accumulibacter) clades. An evaluation of primer sets was conducted regarding the coverage, specificity, and PCR efficiency. (i) All primer sets were desi...
Article
Full-text available
Motivation: Environmental dissemination of antibiotic resistance genes (ARGs) has become an increasing concern for public health. Metagenomics approaches can effectively detect broad profiles of ARGs in environmental samples; however, the detection and subsequent classification of ARG-like sequences are time consuming and have been severe obstacle...

Questions

Question (1)
Question
Hello, I have one simple question about the double split experiment.
Is the interpretation for single photon interference the same with single electron interference, the quantum mechanics?
There's some other explanation that the photon can travel through natural wormholes.
I'm quite confusing about this.
Thanks!

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Projects

Project (1)
Project
qPCR primer design; Reactor operation; Time series analysis of activated sludge samples.