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Senior Microbiome Research Scientist Resume Example

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SENIOR MICROBIOME RESEARCH SCIENTIST
Skills

    BIOINFORMATICS AND DATA ANALYSIS

    1.Data Processing Tools for next generation sequencing data and large multi-omic datasets

  • 16S data: QIIME1/QIIME2/MOTHUR/ bioBakery workflows with AnADAMA2
  • Metagenomic shotgun sequencing data: MetaPhlAn/MetaPhlAn2/MetaPhlAn3/HUMAnN/ HUMAnN2/HUMAnN3/bioBakery workflows with AnADAMA2
  • Metatranscriptomic sequencing data: HUMAnN2/HUMAnN3/AnADAMA2
  • RNA-Sequencing data: FastqPuri/Illumina® DRAGEN RNA Pipeline/https://usegalaxy.org/ https://transcriptomics.cloud
  • Metabolomics: MeltDB/IDEOM/MetaboAnalyst-R/NMR R
  • 16S ribosomal databases: SILVA/GreenGenes/RDP/EzBioCloud
  • Metagenomic sequencing reference database: BLAST/SEED
  • Knowledgeable about challenges in microbiome data analysis
  • Knowledgeable about handling command-line tools
  • Knowledgeable about strengths/drawbacks of existing software packages available for amplicon sequencing data analysis

    • 2. Data Analysis tools for next-generation sequencing data and large multi-omic datasets

  • Predicted metagenomics: PICRUSt/PICRUSt2/Tax4Fun/Piphillin
  • R software/RStudio/MaAsLin2/WGCNA R package
  • Bioconductor/DESeq2/edgeR
  • MicrobiomeAnalyst with R/MetaboAnalyst with R/IPA (QIAGEN Bioinformatics)
  • XLSTAT/XLSTAT-R/XLSTAT-3D/PAST/Gephi/Cytoscape/Molecular Ecological Network Analysis Pipeline/SIMCA-P/Second Genome Piphillin and Sequence Editor/STRING: Protein-Protein Interaction Networks
    Functional Enrichment Analysis
  • Https://huttenhower.sph.harvard.edu/galaxy (GraPhlAn/LEfSe/NGS QC and manipulation/ Phenotype Association/MaAsLin
  • Multiple omic data integration: MEGAN4/mixOmics R/XLSTAT/Matrix eQTL R package/ OmicsIntegrator
  • Git / GitHub (managing version control in data science projects)
  • Https://www.metabolomicsworkbench.org/tools/externaltools.php
  • Https://bioinformaticshome.com/tools/proteomics/proteomics.html

    • 3. Analytical methods for host-microbiome integration

  • Dimensionality reduction (e.g., PCA/PCOA/FA/MFA/EFA/CFA/SEM/MDS/LDA)
  • Correlation-based approach (e.g., Spearman/Pearson/CCA/CIA/PA/SparCC)
  • Regression-based approach (e.g., GLMM/PLS/LASSO/Kernel association test)
  • Network-based approach (e.g., Trans-kingdom network/WGCNA/GLM)
  • Transformation based integration/Concatenation based integration/Model based integration using DIABLO/MINT pipelines in R
  • Supervised Learning Methods: Hypothesis testing and variation analysis (MANOVA/ PERMANOVA/ANOSIM) /Regression and correlation analysis/Classification (RF / SVM)
  • Unsupervised Learning Methods: Dimensionality reduction/Cluster analysis
  • Extensive knowledge in multi-omics data integration frameworks and methods/network-based multi-omics knowledge bases, visualization tools and online resources

    • 4. Microbiome data analysis

  • Community profiling/Visual exploration/Clustering &Correlation/Comparison &Classification/ Functional profiling/Biomarker analysis/Biomarker meta-analysis
  • Alpha diversity (richness, evenness, observed taxa, rarefaction curve)
  • Phylogenetic tree and Heat tree
  • Beta diversity (weighted and unweighted UNIFRAC/Bray-Curtis/Jaccard/Jenson-Shannon distance methods)
  • PERMANOVA/ADONIS/PERMDISP
  • PCA/PCOA/nMDS/PLS-DA/RDA
  • Dendrogram analysis
  • Differential expression (zero-inflated Gaussian model/FitFeature model)
  • Differential expression (edgeR/DESeq2)
  • Heatmap analysis with hierarchical clustering
  • Core microbiome analysis
  • Predicted functional analysis
  • KEGG pathway analysis
  • Joint pathway analysis
  • Biomarker analysis (e.g., LEfSe) and validation using machine learning (e.g., random forest) approach
  • Generalized Procrustes Analysis
  • Visually exploring metagenomic data with public data in 3D PCoA plot
  • Partial Least Squares Path Modeling/Structural Equation Modeling (SEM) using XLSTAT-R

    • 4. Metabolome data analysis

  • Univariate Analysis
  • Fold Change Analysis
  • T-tests
  • Volcano plot
  • One-way Analysis of Variance (ANOVA)
  • Correlation Analysis
  • Pattern Searching
  • Chemometrics Analysis
  • Principal Component Analysis (PCA)
  • Partial Least Squares - Discriminant Analysis (PLS-DA)
  • Sparse Partial Least Squares - Discriminant Analysis (sPLS-DA)
  • Orthogonal Partial Least Squares - Discriminant Analysis (orthoPLS-DA)
  • Feature Identification
  • Significance Analysis of Microarray (and Metabolites) (SAM)
  • Empirical Bayesian Analysis of Microarray (and Metabolites) (EBAM)
  • Cluster Analysis
  • Hierarchical Clustering: Dendrogram/Heatmaps
  • Partitional Clustering: K-means/Self Organizing Map (SOM)
  • Classification & Feature Selection
  • Random Forest/Support Vector Machine (SVM) /Pathway analysis/Pathway Topology Analysis /Over Representation Analysis
  • Biomarker analysis
  • Classical univariate ROC curve analyses
  • Multivariate ROC curve based exploratory analysis (Explorer)
  • ROC curve-based model evaluation (Tester)
  • Enrichment analysis with network view

    • 5. Tools for managing large amounts of data

  • Version-control systems: GitHub/Harvard Dataverse/Zenodo/Dat. Recording entire data workflow with video-capture tool asciinema and meta-data with README/JSON
  • Automation tools (Apache Spark and Apache Hbase) to validate data-quality assurance steps. Self-contained computing environment-Docker container / online platform Code Ocean/ Binder/Gigantum/Nextjournal
  • Tools to create documents that combine software code, text, and figures: Jupyter Notebook/ Terra/Seven Bridges Genomics. Stack Overflow/The Carpentries helping resources
  • Working knowledge of databases and Structured Query Language (SQL)/Linux command line
  • Familiarity with AWS/GCP cloud-computing services (e.g., Storage & Databases/Virtual machines/CloudLIIMS)

    • MOLECULAR BIOLOGY

  • DNA/RNA/protein extraction/purification,
  • QPCR, ddPCR, RT-PCR,
  • Sequencing (NGS, 16S, WGS, WGBS, Shotgun, and Nanopore)
  • DNA/RNA/protein quantification, Nanodrop, Qubit, cDNA preparation, genotyping, library preparation for sequencing
  • Microscopy, Western blot, FISH, IHC, ELISA, Luminex
  • Terminal restriction fragment length polymorphism (TRFLP), Cloning using PCR and restriction enzymes,
  • Deep knowledge/strengths and weaknesses of individual omics technologies

    • MICROBIOLOGY

  • Microbial phenotypic characterization, Aerobic and Anaerobic bacterial culturing using aseptic techniques, Culture media preparation, Optimization of media and fermentation conditions, Working with anaerobic workstations, Gram staining, Colony morphology, Cell morphology, Microbial assay of antibiotics, Microscopy, MALDI-TOF, Flow cytometry
  • FACS and biochemical ID (i.e., Vitek-MS), Lyophilization and freeze-drying of bacteria, Live/dead screening using bacterial viability kit, Bacterial counting and enumeration, Bacterial endotoxin measurements using LAL assay, Viable titer (CFU), Bioactivity assays, ELISA, SDS-PAGE, Western blot, HPLC, Bioburden, Cross-immunity assays, Spectrum of Inhibition, Bacteriocin in silico Identification, Transformation and transfection assays, Serological testing, fluorescent in‐situ hybridization

    • CERTIFICATIONS

    1. Whole genome sequencing of bacterial genomes - tools and applications

    https://coursera.org/share/bc204c6ba2d4ea856c39a1e7ed254ee4

    2. Genomic Data Science: Algorithms for DNA Sequencing

    https://coursera.org/share/556d7045d9e7f1fe6b7d2c65916dae60

    3. Data Science: Getting and Cleaning Data

    https://coursera.org/share/0ec2dfabb572eab3d0f29537ae6d70bd

    4. Data Science: R Programming

    https://coursera.org/share/691973eeb8ccde8a76efbbd93c8e4ae9

    Data Science: Advanced R Programming/Johns Hopkins University

    https://coursera.org/share/0ec2dfabb572eab3d0f29537ae6d70bd

    Databases and SQL for Data Science/IBM/

    https://coursera.org/share/092054dbda6ef79818547536120982d5

Professional Summary

Senior Microbiome Research Scientist with demonstrated expertise in conducting human clinical research on gut microbiome and deep understanding of scientific methods and data analysis techniques used

  • 11 years of nutritional science research experience (e.g., green tea/fish oil/high-fat diet) related to gut microbiome with strong background in biochemistry/molecular biology/microbiology. Demonstrated expertise in conducting human clinical research on gut microbiome [e.g., green tea liquid consumption on gut microbiome (PubMed id: 29750437)] using specific meta-omics analysis coupled with innovative computational systems
  • Deep understanding of scientific methods (e.g., 16S rRNA sequencing/shotgun metagenomics/qPCR/metabolomics) and bioinformatic platforms and computational tools (e.g., QIIME/MOTHUR) used in gut microbiome research and subsequent secondary analysis (e.g., microbial diversity/taxonomy/functional analyses) using several high-throughput software (e.g., PICRUSt/XLSTAT/PAST/R) as demonstrated in track record of publications (e.g., Microbiome journal)
  • Proven expertise in integrative analysis of gut microbiome data with host metabolites data (e.g., Nature's Communications Biology journal) and host clinical parameters (e.g., Molecular Nutrition & Food Research journal) to translate results to business opportunities. Proven experience in establishing external partnerships with global academic experts (e.g., Patrice D Cani, Belgium), scientific organizations (e.g., Research Center for Nutrition and Food Safety, China) and research institutes (e.g., APC Microbiome, Ireland) to create efficiencies in research
  • Demonstrated technical and scientific writing expertise and highly developed management skills with track record for authoring over 20 manuscripts, writing grants (e.g., NIH RO1) and protocols (e.g., standard operating procedures/data analysis pipeline), managing teams to perform techniques (e.g., DNA/RNA isolation), and communicating results to technical/non-technical audiences at meetings (e.g., Rhode Island Microbiome Symposium, 2020) and trade shows (e.g., Cambridge Healthtech Institute's Targeting the Microbiome, 2018)
  • Proven ability to manage complex projects (e.g., longitudinal analysis of gut/oral or gut/urinary microbiome; integrated multi-omics analysis), work with scientists having diverse cultural backgrounds/personalities/work styles and work and communicate effectively in cross functional (e.g., interdisciplinary research) and global teams (e.g., APC Microbiome, Ireland)
Work History
Senior Microbiome Research Scientist, 03/2020 to 09/2020
Company Name - City, State
  • Established and initiated running of new microbiome-based clinical research program (e.g., purchasing high-end instruments and arranging laboratory facilities/hiring technicians) at John G. Rangos Sr. Research Center, communicated with members of “University of Pittsburgh Center for Medicine and the Microbiome” to establish new collaborations and lead design and execution of pediatric clinical research studies
  • Served as Subject Matter Expert for all aspects of microbiome sequencing research projects (gut microbiome/urinary and respiratory tracts microbiome), resulting in development of complex operational strategies and diverse molecular and bioinformatics tools to obtain and integrate microbiomic, metagenomic, and metatranscriptomic data with host epigenetic, transcriptomic and metabolomic data to investigate mechanisms of host-microbiome interactions in variety of pediatric health conditions
  • Conceived/designed/executed new longitudinal, observational study in healthy infants to investigate association between gut microbiome and urinary tract microbiome and examine influence of demographic characteristics on development of gut/urinary microbiome by performing shotgun metagenomic sequencing on serially collected stool and urine samples. Wrote study design/sample collection protocols and experimental procedures/data analysis plan, reviewed/updated IRB protocol, and prepared questionaries with inclusion/exclusion criteria
  • Conceived and designed 5 different new studies using specific meta-omics technologies to utilize samples (stool/urine/nasopharyngeal) already collected from 4 different clinical trials and generate preliminary data for grants applications
  • · Constructed customized 16S data processing and analysis pipeline for lab. Performed downstream bioinformatics analysis on stool/urine Illumina MiSeq 16S rRNA gene sequencing FASTQ data (Argonne National Laboratory) using QIIME2 pipeline (demultiplexing with cutadapt/read joining with vsearch/quality filtering/denoising with deblur/OTU clustering with vsearch/feature table construction and summaries), generated OTU table in BIOM format and phylogenetic tree file in NEWICK format using QIIME2-phylogeny plugin
  • · Performed alpha and beta diversity analysis with QIIME2-diversity plugin/alpha rarefaction plotting with QIIME2 diversity alpha-rarefaction visualizer/ taxonomic analysis with pre-trained Naive Bayes classifier and q2-feature-classifier plugin/differential abundance testing with ANCOM and Q2-composition plugin and paired sample (pre-ear infection and post-ear infection) comparisons with q2-longitudinal
  • Predicted metagenome functional content from 16S marker gene by running PICRUSt1 pipeline to get KEGG ENZYME/KEGG orthologs and pathways and determined significant features using Linear discriminant analysis Effect Size (LEfSe) analysis. Used hclust and randomForest R packages and LEfSe analysis on 16S data to perform hierarchical clustering and biomarker discovery. Performed differential abundance analysis on 16S data using edgeR/DESeq2 and compared results with differential abundance results obtained from Zymo's shotgun metagenomic data. Performed microbe-microbe interaction (co-occurrence and anti-occurrence) analysis using QIIME2-SCNIC (Sparse Cooccurrence Network Investigation for Compositional data) plugin
  • Performed integrative transcriptome-metagenome analysis on stool/urine samples using mixOmics R package (N-integration with DIABLO) to explain molecular mechanism and impact of microbial variation on gene expression.
  • Performed integration of epigenetic data with host transcriptome data (quantitative trait loci-based integration) obtained from nasal samples using Matrix eQTL and SVA R packages. Performed differential expression analysis on RNA-Sequencing data collected from nasal samples using edgeR/ DESeq2 to prepare preliminary data and figures for COVID-19 grant applications
  • Solved issues/challenges (encountered by principal investigator in past) related to sample collection/transport/storage and wrote protocols and standardized experimental procedures to establish sample collection, transport, and preservation/DNA and RNA extraction and quantification methods by communicating with companies (e.g., ZYMO, Norgen, Argonne, COPAN, LONGHORN, Bio-Rad, VWR) and collaborating with UPMC genomic core facilities
  • Conceived new study concept/designed (e.g., sequencing depth, coverage, how many biological or technical replicate) and identified right Illumina sequencing technique and library preparation methods for Dual RNA-Sequencing of urine samples to analyze both host/microbiomes simultaneously by communicating with “Health Sciences Sequencing Core” at UPMC (William A MacDonald, Ph.D.; http://www.nextgen.pitt.edu)
  • Designed and identified right sample collection/preparation methods for urine metabolomic study samples by communicating with director of Health Sciences Metabolomics and Lipidomics Core at UPMC (Stacy Gelhaus Wendell, Ph.D.; https://www.metabolomics.pitt.edu)
  • Communicated with Oxford Nanopore Technologies Inc. (Stephanie Acosta) to set up the MinION Nanopore sequencing in lab, discuss IT/lab requirements and arrange “Rapid Start Day” onset training package to test ability of nanopore sequencing for rapid diagnosis of common pediatric infections.
  • Conceived new concept/designed study/prepared and shipped stool/urine samples for metatranscriptomics (gene activity diversity, gene expression abundance, and differential gene expression analysis) to compare abundance of expressed biological signatures with abundance of 16S general biological signatures. Communicated with ‘CD Genomics' company to execute it
  • Conceived new concept/designed study/prepared and shipped urine samples for Metagenomic Shotgun Sequencing (entire microbial composition and function/resistome and virulence profiles) using Illumina Nova-seq strategy to investigate ability of metagenomics for rapid and accurate diagnosis of urinary tract infections. Communicated with ‘ZYMO' microbiomics company to execute this plan
  • · Conceived new concept/designed study to perform ‘microbial whole genome sequencing' on longitudinal nasal samples collected from ear infection trial to investigate association between microbial evolution and treatment failure. Communicated with Dr Cooper, Vaughn Scott (Associate Director of University of Pittsburgh Center for Medicine and the Microbiome) to design this study
  • Interviewed and Supervised 2 technicians/1 clinical research assistant to provide training, guidance, and advice on bench techniques (e.g., DNA/RNA isolation) and general laboratory practices. Taught NGS technologies and its applications to PI to initiate new microbiome studies. Wrote protocols and detailed plan/materials needed to perform stool/urine culture experiments. Discussed with Department of Microbiology and Molecular Genetics (Jennifer Bomberger, Ph.D.) to initiate new collaboration for gut microbiome-focused COVID-19 grant
  • Wrote 3 different pilot-study protocols (based on 2 DNA and 2 RNA extraction kits [Norgen and Zymo] /2 types of sample collection and storage buffers) for previously stored (fresh and freeze-thaw stool samples and urine samples stored at different time points) samples to standardize techniques and investigate quality of samples before utilizing them to metagenomic and transcriptomic analysis
  • Learned and applied “CloudLIMS-based lab management” to manage biospecimens and metadata, locate stored samples, standardize operational workflows and ensure sample integrity. Learned Panther Express Purchases and ordered materials for labs
  • Conceived 4 new study concepts and grant proposals, deeply involved in writing (preliminary data development, hypothesis formulation, and grant narrative development), and submitting 3 COVID-19 grant applications in conjunction with PI for industry (Merck & Co) and NIH (RO1). Participated in writing 1 manuscript that compared conventional urine culture with 16S sequencing for diagnosis of urinary tract infections
  • Managed team to get right method/kits and perform cell-free DNA isolation from stool/urine samples to develop preliminary data for grants. Established collaboration with Professor of Microbiology and Molecular Genetics (Cooper, Vaughn Scott) and independently wrote 1 whole-genome bisulfite sequencing (WGBS)-based university level grant worth $50,000 and deserved key personnel role
Research Instructor, 11/2017 to 02/2020
Company Name - City, State

GUT MICROBIOME PROJECTS

  • Human study 1: Collaborated with Department of Epidemiology, School of Public Health, Fourth Military Medical University in China, lead study to investigate effects of green tea liquid consumption on healthy human gut and oral microbiota, collected stool/saliva samples at 3 time points (baseline/after green tea/wash out), extracted/quantified DNA, performed 16s rRNA sequencing, conducted bioinformatics analysis, analyzed data using innovative computational systems, discovered novel associations between gut and oral microbiota, wrote manuscript and published findings as corresponding author in Molecular Nutrition & Food Research journal (PubMed id: 29750437)
  • Human study 2: Traveled to Shanghai Changzheng Hospital, Pudong in China with team, collected stool samples (baseline/after intervention) from cancer patients received nutritional intervention, extracted/quantified DNA, performed 16S rRNA sequencing (BGI genomics), performed bioinformatics analysis and gut microbiome data analysis after stratifing subjects according to baseline enterotypes, identified responders vs. non-responders and translated results to business opportunities
  • Human study 3: Collaborated with Geriatric Anesthesia Research Unit at Massachusetts General Hospital to investigate gut microbiome changes in Alzheimer's disease (AD) patients and their care givers, participated in study designing, performed bioinformatics and data analysis on stool 16S rNRA sequencing/short-chain fatty acids data, executed predictive modelling/machine learning techniques to discover gut microbiome-based predictions and biomarkers for AD
  • Human study 4: Collaborated with National Institute of Cardiovascular Diseases, Dhaka, in Bangladesh and performed predictive analytics to examine if intestinal alkaline phosphatase (gut microbiome-modifying factor) deficiency is associated with ischemic heart disease and high level of intestinal alkaline phosphatase is protective against ischemic heart disease (PubMed id: 31915470)
  • Preclinical studies: Conceived study plan and investigated mechanisms of host-microbiome interactions in chronic inflammatory diseases using 3 different transgenic mouse models (FAT-1/FAT-2/FAT-1+2) differed in omega-6 and omega-3 fatty acids levels, multi-omics technologies (metagenomics/metabolomics), and innovative/modern data analysis techniques/software, resulting in outstanding publication in Nature's Communications Biology (PubMed id: 31372515 ) journal and presentations at 4 prestigious conferences

GUT MICROBIOME DATA ANALYSIS

  • Performed bioinformatics analysis on Illumina 16S gene sequencing FASTQ data using QIIME2 pipeline to perform demultiplexing with cutadapt/read joining with vsearch/quality filtering and denoising with deblur/OTU clustering with vsearch/feature table construction and summaries
  • Performed alpha and beta diversity analysis with QIIME2-diversity plugin/alpha rarefaction plotting with QIIME2 diversity alpha-rarefaction visualizer/ taxonomic analysis with pre-trained Naive Bayes classifier and q2-feature-classifier plugin/differential abundance testing with ANCOM and Q2-composition plugin. Performed enterotype analysis on genus-level microbiome data using cluster and clusterSim R packages and enterotype tutorial (https://enterotype.embl.de/enterotypes.html#intro)
  • Predicted metagenome functional content using PICRUSt1 pipeline (PMID: 30424806; PMID: 29750437; PMID: 28536285; PMID: 29793531; One cancer nutritional intervention study) and PICRUSt2 pipeline (manuscript in review with mSystems journal; two manuscripts with PI), performed PCA/PCOA/differential expression and determined significant putative KEGG orthologs and pathways using Linear discriminant analysis Effect Size (LEfSe) analysis
  • Analyzed stool 16S sequencing data and stool/serum metabolomics data and performed integrated metagenomic-metabolomic data analysis using several high-throughput microbiome data analyzing tools (QIIME, XLSTAT, XLSTAT-R, XLSTAT-3D, PAST, SIMCA-P, MENAP, Galaxy web application, MicrobiomeAnalyst with R, MetaboAnalyst and Gephi/Cytoscape graph visualization and manipulation software
  • Performed microbiome data analysis such as visual exploration (stacked bar/area plot/rarefaction curve/phylogenetic tree/heat tree), community profiling (alpha and beta diversity analysis/core-microbiome analysis), clustering analysis (heatmap with unsupervised hierarchical clustering/dendrogram/correlation analysis/pattern search), differential abundance analysis (univariate/DESeq2/edgeR) and biomarker analysis (LEfSe/RandomForest/PLS-DA), resulting in the development of customized lab data analysis pipeline
  • Disentangled host-microbe interactions driven by fatty acid status by performing dimensionality reduction and net-work-based (trans-kingdom network) /correlation-based (canonical correspondence analysis/Multiple Factor analysis)/regression-based (partial least squares) analytical approaches, resulting in achievements of 3 publications by fulfilling journal's critical expectations before acceptance
  • Performed Inter-omic analysis to reveal microbe–metabolite interactions between tissue n-6/n-3 PUFA-associated microbial community type and metabotype using Multiple Factor Analysis (MFA), partial least squares-discriminant analysis, and net-work-based analytical approaches, resulting in first one used MFA for simultaneous 2D visualization of host and microbiome features (PMID: 32318028)
  • Performed partial least squares discriminant analysis (PLS-DA)/orthogonal projections to latent structures discriminant analysis (OPLS-DA) using SIMCA-P multivariate data analysis tool, resulting in discovery of different tissue fatty acid status on global fecal and serum metabolite profiles
  • Performed PCOA/PLS-CCA to investigate influence of demographic characteristics on overall composition of human gut/oral microbiota and hierarchical Ward‐linkage clustering using XLSTAT/PAST software to identify presence of oral bacterial network in gut microbiota profile, resulting in identification of negative effects oral microbiota on gut-microbiome and its prevention by green tea consumption on gut microbiome (PMID: 29750437)
  • Analyzed liver proteomics data of lab postdoc (Lei Hao., Ph.D.) obtained from high-fat diet-based preclinical studies, identified differentially abundant proteins, performed protein-protein interaction and KEGG pathways enrichment analysis with STRING biological database/PCA and Procrustes analysis/RandomForest biomarker analysis/net-work-based association analysis between proteins and metabolic parameters using Cytoscape CoNet-plugin (manuscript with PI)
  • Wrote manuscripts, collaborated with several microbiome investigators, accomplished several first- and co-authored publications, presented findings in 5 prestigious microbiome conferences, awarded “Posters of Excellence” and 2 grants worth $150,000. Drafted and reviewed animal study protocols, managed day-to-day lab activities and mentored and trained 4 technicians/3 research fellows/6 visiting scientists/2 Ph.D. students/several summer interns
Research Fellow, 10/2012 to 10/2017
Company Name - City, State

GUT MICROBIOME PROJECTS

  • Human study 1: Collaborated with Chongqing Medical Nutrition Research Center in China, participated in study designing/data analysis/manuscript writing, and discovered significant effects of gut enterotypes on beneficial effects of dietary capsaicin (chili powder) and new evidence for personalized nutrition guidance of capsaicin intervention on health promotion linking with gut microbiota patterns (PMID: 27676396)
  • Human study 2: Collected stool samples from centenarians living in Bama County, Guangxi, in China, performed 16S rRNA sequencing to analyze gut microbiome composition/function and correlated results with their dietary omega-6 and omega-3 essential fatty acid levels. Also, collected Betta-leaves they eat every day, worked with contract research organizations (International Chemistry Testing, Inc./Advanced Food Labs, Inc) to get results of microbiological/chemistry analyses, and performed preclinical studies to examine effects of betta-leaves on gut microbiome
  • Human study 3: Collaborated with Department of Epidemiology, School of Public Health, Fourth Military Medical University, in China, performed data analysis, and wrote manuscript to examine effects of vitamin C supplementation on blood pressure and hypertension control in response to ambient temperature changes in patients with essential hypertension
  • Human study 4: Collaborated with Department of Epidemiology, School of Public Health, Fourth Military Medical University, in China, performed data analysis, and wrote manuscript to examine associations of homocysteine status and homocysteine metabolism enzyme polymorphisms with hypertension and dyslipidemia in Chinese hypertensive population
  • Human study 5: Collaborated with Research Center for Nutrition and Food Safety, Chongqing, in China, participated in network meta-analysis of randomized clinical trials aimed to assess comparative effects of walnuts, pistachios, hazelnuts, cashews, and almonds on typical lipid profiles, and wrote manuscript
  • Human study 6: Collaborated with Chongqing Medical Nutrition Research Center in China (Chao Kang. Ph.D.), wrote manuscript, and performed data analysis using R packages to examine to investigate effect of exenatide, a glucagon-like peptide-1 receptor agonist, on kidney function/obesity indices/glucose control in overweight/obese patients with type 2 diabetes mellitus (under review in Nature's Nutrition & Diabetes journal)
  • Preclinical studies: Conceived/designed/executed/completed 7 new gut microbiome-based projects to investigate role of gut microbiome for (1) opposing effects of omega-6 and omega-3 fatty acids on chronic inflammatory disease; (2) preventing effects of omega-3 fatty acids on early life antibiotics and associated obesity in later life; (3) differences in liver disease associated with omega-6 fat +alcohol and omega-3 fat +alcohol combinations; (4) prevention of anti-cancer drug-induced gut toxicities with elevated omega-3 fatty acids; (5) sex-differences in obesity/metabolic syndrome; (6) combined effects of omega-3 fat and soy isoflavones on obesity/metabolic syndrome and (7) preventive effects of maternal omega-3 fatty acids during pregnancy/lactation on offspring obesity/metabolic diseases associated with high-fat diet
  • Collaborated with Chongqing Medical Nutrition Research Center in China and participated in study designing/gut-microbiome data analysis/manuscript writing to investigate mediating role of gut microbiome for the anti-obesity effects of capsaicin (PMID: 27676396)

GUT MICROBIOME DATA ANALYSIS

  • · Collaborated with APC Microbiome Institute in Ireland to perform stool 16S rRNA sequencing, analysis of stool short-chain fatty acids and stool/serum metabolomics. Trained/mentored their Ph.D. students (Ruairi Robertson and Shane O Donnell) for 2microbiome projects (techniques/study design/data analysis) when they visited MGH. Participated in developing in-house bioinformatic tools for 16S/multi-omics data analysis by working with APC core specialist (Kiera Murphy), resulting in completion of multi-omics part of 5 different microbiome projects.
  • Established and validated bacterial culture techniques and qPCR-based quantification of gut microbiota, investigated host-microbiota interactions various mouse models (co-housing/germ-free model using antibiotics/fecal microbiota transplantation/antibiotics-induced obese mouse model) resulting in 2 publications (Nature's Sci Rep/International Journal of Obesity)
  • Performed genomic DNA isolation from stool samples using 2 different DNA extraction kits (QIAGEN / MO BIO PowerSoil), determined concentration using two different techniques (photometric/fluorospectrometric) to standardize protocols for isolation and quantification of gDNA
  • Generated and validated standard curves using gDNA isolated from 10 reference bacterial strains and performed absolute quantification of bacterial DNA of 20 bacteria at different taxonomy levels by 16S rRNA gene-based qPCR method
  • Collaborated with APC Microbiome in Ireland to perform stool 16S rRNA sequencing, analysis of stool short-chain fatty acids and stool/serum metabolomics. Performed bioinformatics analysis on Illumina 16S gene sequencing FASTQ data using QIIME1 pipeline to perform demultiplexing with cutadapt/read joining with vsearch/quality filtering and denoising with deblur/OTU clustering with vsearch/feature table construction and summaries
  • Investigated effects of maternal omega-3 fatty acids on offspring gut microbiota and sex-differences in gut microbiota on metabolic disorders using 16S rRNA gene amplicon sequencing and predicted metagenomics, resulting in 2 high-ranking publications (Microbiome journal) in peer-reviewed journals
  • Investigated role of host-gut microbiome interactions for combined effects of omega-3 fatty acids and isoflavones on obesity and metabolic disease using 16S sequencing/PICRUSt/fecal metabolomics/fecal short-chain fatty acid analysis and performed bioinformatics (QIIME2) and integrated multi-omic data analysis, resulting in 2 oral presentations given at international conferences and completion of 1 manuscript
  • Created FuncTree map based on KEGG Brite functional hierarchy to directly visualize and calculate statistical significance of functionality of predicted metagenomics data and broadly overview what kind of biological functions are present in dataset
  • Performed multivariate receiver operator characteristic (ROC) curve-based automated important feature identification and performance evaluation using MetaboAnalystR/random forest classification/PLS-DA feature ranking method
  • Performed Multiple Factors Analysis (MFA) for simultaneous 2D visualization of host and microbiome features in 4 projects. Processed FASTQ data using QIIME pipeline / performed gut microbiome and PICRUSt analysis/PCA and PLS-DA analysis on fecal and serum metabolomics data using XLSTAT-R/PAST software
  • Performed microbial co-occurrence analysis using CoNet plugin and visualized resulting network in Cytoscape and Gephi software. Established bacterial culture techniques and trained technicians, visiting scientists and research fellows to perform and analyze data in 10 different projects
  • Authored and reviewed over 15 manuscripts in total, wrote over 5 animal study protocols (IACUC), and prepared lab for annual Lab safety inspections (biosafety, chemical safety, and general lab safety and compliance requirements)
  • Supervised and trained over 6 technicians/5 graduate and 3 Ph.D. students in conducting experiments and gathering data and analyzing results to obtain valuable and actionable conclusions
  • Accomplished 4 first-authored publications, presented data/results (oral/poster) in group and department meetings and 20 different conferences (local/national/international).
  • Established 6 different professional relationships with microbiome-related laboratory personnel through effective communication and collaboration skills to promote collaboration and enhance results
  • Organized Inaugural Symposium of the International Society for Omega-3 Research (ISOR), served as Session Chair and gave oral presentation (Modulation of Gut Microbiota as a Novel Mechanism for Omega-3 Benefits) (https://omega3society.org/events/)
Postdoctoral Research Fellow, 11/2009 to 09/2012
Company Name - City, State
  • Learned commonly used molecular biology and microbiology techniques/traditional statistics and gained in-depth understanding of theories/principles underlying these methodologies by working with molecular biologist (Dr. Madhu Malo, Assistant Professor) and microbiome investigator (Dr. Richard Hodin, Professor)
  • Conceived/designed/executed 4 preclinical projects to investigate preventive/curative effects of intestinal alkaline phosphatase (IAP) on (1) high-fat diet-induced metabolic syndrome; (2) high-fructose-induced obesity and liver disease; (3) chronic-alcohol-induced liver disease and (4) early-life antibiotics and associated later-life obesity with high-fat diet, and role of IAP-mediated gut microbiome changes (bacterial stool culture/qPCR-based gut microbiota analysis) in these contexts
  • Collaborated with molecular microbiologist (Sundaram Ramasamy. Ph.D.) and performed DNA/RNA extraction and quantification from stool/tissue samples to investigate preventive effects of IAP supplementation and associated gut microbiota changes on inflammatory bowel disease (PMID: 20645323)
  • Worked with molecular biologist (Madhu S Malo) and performed terminal estriction fragment length polymorphism, phylogenetic analyses and quantitative real-time PCR of subphylum-specific bacterial 16S rRNA genes to determine role of IAP on gut microbiota homeostasis
  • Participated in 16S rRNA gene pyrosequencing to determine gut microbiome composition of antibiotics treated mice/processing and analysis of pyrosequencing data using “Research and Testing Laboratory's in-house pipeline” and vegan/ladbsv/DESeq2 R packages. Collaborated with Research and Testing Laboratory, Texas, to perform 16S rRNA gene pyrosequencing and data analysis
  • Established 3 new collaborations. Developed, established and validated standard procedures to measure bacterial endotoxin and markers of metabolic syndrome, bacterial translocation and chronic inflammation. Performed bacterial stool culture to investigate preventive effects of IAP supplementation against antibiotic-associated bacterial infections by preserving normal homeostasis of gut microbiota
  • Collaborated with other members of lab and helped them in their experiments/compiled data and sent to lab supervisor and principal investigator/regularly presented data to weekly lab meeting/reviewed and improved 3 grant applications
  • Accomplished 1 first-authored, break-through publication (PNAS journal). Co-authored 5 high-quality publications. Generated over 5 award-winning abstracts. Won several awards and grantsworth more than $400,000 (e.g., Ellison Foundation Award). Presented well-written abstracts at scientific meetings (e.g., DDW by AGA). Awarded posters of distinction and posters of merit. Changed primary focus of laboratory investigations to metabolic disease from inflammatory boweldisease
  • Translated preclinical findings with IAP to business opportunities to investigate role of IAP in patients with type 2 diabetes and ischemic heart disease and develop new IAP-based stool assay for early diagnosis
Education
M.D.: : Medicine And Research, 03/2008The Tamil Nadu Dr. M.G.R. Medical University - City

Higher Performance in Nutrition, Biochemistry and Microbiology

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School Attended

  • The Tamil Nadu Dr. M.G.R. Medical University

Job Titles Held:

  • Senior Microbiome Research Scientist
  • Research Instructor
  • Research Fellow
  • Postdoctoral Research Fellow

Degrees

  • M.D. : : Medicine And Research , 03/2008

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