My Journey into Microbiology, the Deep Sea, and Bioinformatics

Created in November 14, 2025

2025

Hello and welcome!
I’m Jojy John — a researcher, postdoctoral scholar, wife, and mother of two little ones.
This is the first post of my blog Daily Bioinformatics from Jojy’s Desk, where I share my daily work, learning, troubleshooting, and thoughts as a microbial ecologist and bioinformatician.

🌱 Where it all began

My journey started during my Bachelor’s in Microbiology at MG University in Kerala, India.
Growing up in a family that valued traditional medicine, I was fascinated by the healing ability of plants. My early research focused on antibacterial and anticancer activities of medicinal plants, hoping to connect traditional knowledge to scientific evidence.

During my Master’s, I worked on:

“Analysis of cell death patterns of THP-1 cells infected with Mycobacterium tuberculosis H37Ra and H37Rv.”

Tuberculosis holds a personal place in my heart — many in the older generation lost their lives to this disease. Understanding its biology felt meaningful and necessary.

🌊 A question that shaped my PhD

In 2016, during my PhD field visit to the Marakkanam salt pans, I held salt crystals in my hand under the blazing sun and wondered:

“Can anything survive in this?”

That question led to my PhD:

“Diversity, genomic studies, and resistance mechanisms of moderately halophilic bacteria: insights from Salinivibrio spp. from Marakkanam salt pan.”

I explored:

  • Extreme salinity environments (120–380 PPT)
  • Cultivable and uncultivable bacterial diversity
  • Whole-genome sequencing
  • Adaptation to salinity stress
  • 16S amplicon analysis
  • Biotechnological potentials:
    • enzyme production
    • heavy metal tolerance
    • UV resistance
    • plant growth promotion
    • azo dye degradation

My findings were published in Geomicrobiology Journal, Microorganisms, and Frontiers in Microbiology.

🚢 Deep-sea expeditions and ocean microbiomes

As a Project Associate at the National Institute of Oceanography, Goa, I contributed to the Environmental Impact Assessment (EIA) of polymetallic nodule mining.

This included:

  • A 36-day deep-sea research cruise
  • Sampling sediment and water using beam trawls, bongo nets, multiple corers, and more
  • Studying bacterial communities associated with deep-sea sediments and nodules
  • Isolation and identification of heavy-metal-tolerant bacteria
  • 16S metagenome analysis
  • hypoxia and microbiome
  • shot gun metagenome

I also contributed to a project on the hypoxic Arabian Sea, working from sample collection to whole-metagenome sequencing and analysis.

🧬 Becoming a computational microbial ecologist

Over time, I transitioned fully from wet lab to computational biology.
Today, my work focuses on:

🧫 Metagenomes

  • Quality filtering
  • Assembly & co-assembly
  • MAG binning and refinement
  • Annotation & functional profiling

🧬 Metatranscriptomes

  • Assembly
  • Expression profiling

🧬 Whole-genome sequencing & hybrid assembly

🔗 Multi-omics integration

📊 Statistics & modeling

  • Functional redundancy
  • Ecological niche modeling
  • Differential expression

💻 My daily toolbox

Linux, R, Python, Bash, SLURM, and a lot of troubleshooting!

👩‍🏫 Mentorship and life as a postdoc

As a postdoc, I mentor students, collaborate with labs, manage HPC workflows, and help design analytical pipelines.

But as my workload increased, I realized something important:

So much learning gets lost — in notebooks, terminals, text files, or Slack messages.

And yes… I still break conda environments.
I still troubleshoot silly errors for days.
And I still learn something new every day.

✍️ Why I created this blog

I created this space because:

  • Paper-writing is slow, but daily learning is fast.
  • I wanted a place to document my real work.
  • I want to help students and colleagues.
  • I want future collaborators and hiring committees to see my actual skills, not just my publication list.

This blog is for:

  • Microbial ecologists
  • Bioinformaticians
  • Students learning metagenomics
  • Anyone using HPC for microbiome research
  • Future collaborators
  • Curious readers

💛 Thank you for being here

Thank you for reading my story and joining the journey.
Thank you to everyone who inspired and supported me.

This blog is for all of us — learning, experimenting, fixing, failing, and growing.

Stay tuned for daily updates from my desk.
— Jojy