Research • Microbiology & Molecular Diagnostics

Jannatul Ferdaus
Jame

Advancing molecular diagnostics and microbial genomics to improve pathogen detection, surveillance, and public health outcomes

B.Sc. Microbiology @ BRAC University
Microbial Genomics
Molecular Diagnostics & Pathogen Surveillance

My Journey into Microbiology Research

Jannatul Ferdaus Jame

Decoding the Microbial World for Public Health

Growing up in Dhaka, Bangladesh, I witnessed firsthand how waterborne diseases and antibiotic-resistant infections disproportionately affect communities with limited access to diagnostic infrastructure. This sparked my determination to understand pathogens at the molecular level and develop tools that bring reliable detection to where it is needed most.

As a microbiology student at BRAC University, I found my calling at the intersection of wet-lab experimentation and computational analysis. From culturing Legionella pneumophila on selective media to performing 16S rRNA sequencing analysis with QIIME2, I discovered that combining traditional microbiology with bioinformatics and genomics opens powerful new avenues for pathogen surveillance and antimicrobial resistance tracking.

My research now spans molecular diagnostics, probiotic mechanisms, and environmental microbiology. Whether I am conducting PRISMA-guided systematic reviews of 180+ probiotic studies, building predictive models for antibiotic resistance, or mapping Legionella contamination hotspots in urban water systems, my goal remains the same: translating microbial science into actionable public health solutions.

My Mission

I am dedicated to advancing molecular diagnostics and microbial genomics to improve the detection and surveillance of waterborne and clinically relevant pathogens. My research bridges wet-lab microbiology, bioinformatics, and data science to develop reproducible, evidence-based approaches for public health challenges.

Through PCR-based pathogen detection, microbiome analysis pipelines, systematic reviews, and predictive modeling for antimicrobial resistance, I work to strengthen global health surveillance and make diagnostic tools more accessible to underserved communities.

My Microbiology Research Journey

Molecular Diagnostics

From PCR optimization and primer design to dnaJ gene-based identification of Legionella pneumophila, I develop and refine molecular tools for accurate pathogen detection in environmental and clinical samples.

Bioinformatics & Genomics

Leveraging 16S rRNA analysis with QIIME2, BLAST, and phylogenetic tools alongside Python and R to analyze microbial communities, track diversity patterns, and build reproducible data pipelines.

Public Health Impact

Committed to translating laboratory findings into real-world solutions, from community water safety programs to AMR surveillance models that inform hospital infection control strategies.

Core Research Questions

PCR and molecular diagnostics

Molecular Diagnostics & Pathogen Surveillance

How can PCR and NGS-based methods be optimized to improve detection and surveillance of waterborne and clinically relevant pathogens? Investigating molecular tools such as dnaJ gene targeting for Legionella identification and developing environmental surveillance workflows for contamination hotspot mapping.

Gut microbiome and probiotics

Probiotic Mechanisms & Host-Microbe Interactions

What are the strain-specific mechanisms through which probiotics modulate gut microbiota and mucosal immunity? Examining antimicrobial peptide secretion, SCFA metabolism, and TLR2/NF-kB signaling pathways through systematic reviews and meta-analytic modeling across 180+ studies.

Antimicrobial resistance laboratory

Antimicrobial Resistance & Microbial Genomics

How can computational approaches improve prediction and tracking of antimicrobial resistance patterns? Leveraging bioinformatics, machine learning, and 16S rRNA sequencing to analyze microbial community dynamics and forecast resistance profiles for informed public health interventions.

Current Research at Stamford University

Conducting a PRISMA-guided systematic review of 180+ studies examining strain-specific effects of Lactobacillus and Bifidobacterium on gut microbiota composition and mucosal immunity, identifying mechanistic pathways involving antimicrobial peptide secretion, SCFA metabolism, and TLR2/NF-kB signaling. Performing meta-analytic modeling using RevMan, JASP, and R (metafor, vegan) to compare effect sizes across studies while standardizing CFU dosage and controlling for delivery-route variability. Additionally preparing a review manuscript on AMPK activation beyond metabolism, integrating AMPK signaling and neurocardiac inflammatory pathways to explore metformin's role in ICNS neuroinflammation and arrhythmogenic remodeling.

Microbiology laboratory research

Areas of Expertise

Wet-Lab & Molecular Biology

  • BSL-2 Pathogen Handling & Microbial Culture
  • PCR Optimization (Gradient/Multiplex) & qPCR
  • Genomic DNA Extraction & Gel Electrophoresis
  • Membrane Filtration & Selective Media Preparation
  • Legionella Detection & AMR Pattern Assessment

Bioinformatics & Genomics

  • 16S rRNA Analysis (QIIME2, DADA2, USEARCH)
  • BLAST & Phylogenetic Analysis
  • Alpha/Beta Diversity Metrics & PCA/PCoA
  • Meta-Analysis & Effect Size Modeling
  • Systematic Reviews (PRISMA Framework)

Computational Analysis

  • Python (Pandas, NumPy, SciPy, scikit-learn)
  • R (tidyverse, ggplot2, vegan, phyloseq, metafor)
  • Machine Learning for AMR Prediction
  • Data Visualization & Pipeline Automation
  • Git/GitHub & Reproducible Research

Key Projects

Probiotic Mechanisms Research - Gut Microbiome

Probiotic Mechanisms & Health Benefits: Systematic Review

2024 – Present

Conducted a PRISMA-guided systematic review of 180+ studies examining strain-specific effects of Lactobacillus and Bifidobacterium on gut microbiota composition and mucosal immunity. Identified mechanistic pathways involving antimicrobial peptide secretion, SCFA metabolism, and TLR2/NF-kB signaling. Performed meta-analytic modeling using RevMan, JASP, and R (metafor, vegan) to compare effect sizes, standardizing CFU dosage and controlling for delivery-route variability. Published in Exploration of Drug Science (2025).

Studies

180+ reviewed

Tools

RevMan, R, JASP

Status

Published

View Publication
Legionella Water Testing - Molecular Laboratory

Legionella pneumophila Detection in Urban Water Systems

2024

Selectively isolated and molecularly identified Legionella pneumophila from various water sources across Dhaka, Bangladesh using dnaJ gene-targeted PCR. Collected 42 water samples from 12 sites, applying acid, heat, and chlorine pretreatment to reduce non-Legionellae organisms. Cultured on optimized BCYE media and confirmed isolates via PCR, gel electrophoresis, and 16S rDNA and dnaJ gene sequencing. Published in Journal of Preventive, Diagnostic and Treatment Strategies in Medicine (2024).

Samples

42 collected

Sites

12 locations

Method

dnaJ gene PCR

View Publication
AMPK Molecular Signaling - Cardiac Research

AMPK Activation Beyond Metabolism: Metformin & ICNS Neuroinflammation

2025 – Present

Preparing an integrative review manuscript proposing a mechanistic framework linking metformin-induced AMPK activation to modulation of intrinsic cardiac nervous system (ICNS) neuroinflammation and downstream arrhythmogenic remodeling. Synthesizing interdisciplinary literature spanning cardiometabolic pharmacology, neuroinflammation, autonomic neuroscience, and cardiac electrophysiology to establish an "AMPK-ICNS-arrhythmia axis." Expected submission May 2026.

Focus

AMPK Signaling

Scope

Interdisciplinary

Status

In Preparation

Microbiome Data Analysis and Visualization

Microbiome Data Analysis & Visualization

2024

Processed 16S rRNA sequencing data using QIIME2 and R to analyze microbial diversity and community shifts under varying environmental conditions. Generated OTU heatmaps, PCA plots, and phylogenetic trees to identify microbial indicators of environmental stress. Automated analysis pipelines to improve reproducibility and reduce processing time across datasets.

Antibiotic Resistance Surveillance - Petri Dish

Antibiotic Resistance Surveillance & Prediction

2023

Analyzed 5-year clinical isolate data to quantify multidrug-resistant E. coli and Staphylococcus aureus trends and identify emerging AMR patterns. Built predictive models using logistic regression and random forests to forecast resistance profiles, informing hospital infection control strategies. This project demonstrated the power of combining microbiological data with machine learning for actionable public health surveillance.

Data

5-year dataset

Models

LR, Random Forest

Impact

Hospital IC

Publications & Presentations

Mechanisms of Action and Health Benefits of Probiotics: A Comprehensive Review

Alam, S. T., Rayhan, A. B. H., Ahmed, M. U., Khan, M. T., Jame, J. F., Islam, M. M., Raj, M. A. R., & Uddin, M. A. (2025). Exploration of Drug Science, 3, 1008129.

DOI: 10.37349/eds.2025.1008129 Published

Selectively Isolation and Molecular Identification by dnaJ Gene of Legionella pneumophila Found in Various Water Sources in Dhaka, Bangladesh

Hossain, M. I., Ahmed, M. U., Toni, J. R., Khan, M. T., Hassan, M. N., Jame, J. F., Rayhan, A. B. H., & Alam, S. T. (2024). Journal of Preventive, Diagnostic and Treatment Strategies in Medicine.

DOI: 10.4103/jpdtsm.jpdtsm_68_24 Published

AMPK Activation Beyond Metabolism: Metformin and ICNS Neuroinflammation

Jame, J. F., Ahmad, I., & Jahin, T. (2026). Review manuscript integrating AMPK signaling and neurocardiac inflammatory pathways.

In Preparation

Selected Conference Presentations & Invited Talks

Maine Public Health & Microbiology Education Summit (2025)

Data-driven healthcare resource allocation and infectious disease forecasting

BRAC University Research Symposium 2023-2024

Applied microbiology: pathogen surveillance, sanitation analytics, and community education for public health

Bangladesh Innovation Summit (2023)

Community-driven water testing kits and hygiene programs for low-income schools

Bangladesh HealthTech Summit (2024)

Mobile diagnostics and low-cost microbiological testing for rural health equity

4th International Conference on Sustainable Technologies for Industry 4.0 (2022)

Inclusive health education tools for visually impaired students

Let's Connect

I am actively seeking research collaborations in molecular diagnostics, microbial genomics, and pathogen surveillance. Particularly interested in projects involving PCR/NGS-based detection, microbiome analysis, antimicrobial resistance, and public health microbiology.

Email

jannatul.ferdaus.jame@g.bracu.ac.bd

Phone

+880-1301511539

LinkedIn

linkedin.com/in/jannatul-ferdaus-jame

GitHub

github.com/jame-jpg

Based in Dhaka, Bangladesh

Currently at BRAC University, Department of Microbiology. Available for research collaborations, conference presentations, and opportunities in molecular diagnostics, microbial genomics, and public health microbiology.

Whether you're interested in collaborative research, need expertise in molecular diagnostics, or want to discuss microbial genomics and public health, I'd love to hear from you.

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