Anantharaman Microbiome Laboratory

Computational Biology & AI, Microbial & Viral Ecology, Human & Environmental Microbiomes

VIBRANT is a software for the recovery and annotation of bacterial/archaeal viruses and determination of auxiliary metabolic genes.

Beautiful sunsets over our field site - Guaymas Basin in the Gulf of California, Pacific Ocean

Hydrothermal vents at East Pacific Rise in the Pacific Ocean spewing hydrothermal fluid at 310 Celsius. Photo credit: WHOI

Black smoker hydrothermal vents at East Pacific Rise in the Pacific Ocean. Photo credit: WHOI

Local field site for sampling peatland soils - Cherokee Marsh, WI

PhD student James Kosmopoulos conducting sampling of peat deposits at Cherokee Marsh

Former PhD student Patricia Tran conducting winter sampling on Lake Mendota

A solitary crab near a black smoker hydrothermal vent at East Pacific Rise in the Pacific Ocean. Photo credit: WHOI

Tubeworms thrive in the East Pacific Rise hydrothermal systems in the Pacific Ocean. Photo credit: WHOI

Spectacular "erupting" hydrothermal vents at Guaymas Basin in the Gulf of California, Pacific Ocean. Photo credit: Schmidt Ocean Institute

PhD student Dinesh Kumar Kuppa Baskaran conducting summer sampling on Lake Mendota

Graduate students Peter Badciong (left) and Dinesh Kumar Kuppa Baskaran (right) sampling from Lake Mendota

Filamentous sulfur oxidizing bacteria colonize a hydrothermal marker. Photo credit: Schmidt Ocean Institute

A Giant Pacific Octopus calls Guaymas Basin home. Photo credit: Schmidt Ocean Institute

(Left to right) Min Chen, Xing Huang, Dinesh Kumar Kuppa Baskaran, Peter Badciong, and James Kosmopoulos at Evergreen Phage Meeting 2025

Hydrothermal mirrors reflect the colors of life. Photo credit: Schmidt Ocean Institute

Karthik sampling at sea. Photo credit: Thom Hoffman

The CTD rosette: workhorse of sampling at sea

(Left to right) Cody Martin, Katie Klier, Maggie Langwig, and Karthik Anantharaman at the Ohio State University Viromics Workshop 2022

Hydrothermal life through the lens of shimmering plumes. Photo credit: Schmidt Ocean Institute

Sampling biofilms in the deep sea. Photo credit: Schmidt Ocean Institute

High throughput water filtration for viruses at sea

(Left to right) Etan Dieppa Colon, Kun Zhou, James Kosmopoulos, Xing Huang, and Zhichao Zhou at the Ohio State University Viromics Workshop 2023

Tube worms and mussels at the East Pacific Rise hydrothermal systems in the Pacific Ocean. Photo credit: WHOI

A fish swims yards away from 370 Celsius hydrothermal fluids. Photo credit: WHOI

(Left to right) James Kosmopoulos, Cody Martin, Maggie Langwig, and Karthik Anantharaman at the 5th IBSE International Symposium in Chennai, India

Hydrothermal mirrors reflect the colors of life. Photo credit: Schmidt Ocean Institute

ViWrap is a scalable user-friendly pipeline to identify, bin, and classify viruses and predict virus-host relationships from metagenomes.

vRhyme is a software for the reconstruction of viral MAGs from metagenomes (virus genome binning).

Propagate is a software for the estimation of prophage activity, i.e. if a prophage was in the lysogenic (dormant) or lytic (active) stage of infection.

METABOLIC is a scalable software to study microbial metabolic traits and functional profiles of a microbiome/community based on microbial genomes.

(Left to right) Cody Martin, James Kosmopoulos, and Katie Klier at ISME19 in Cape Town, South Africa

Lab celebrating Bactoberfest, 2025.

Lab at pumpkin picking in Madison, 2025.

Discovering and engineering the hidden biology of microbial systems

We combine computational biology, AI, environmental microbiology, phage biotechnology, and bioengineering to understand microbial life and develop solutions for environmental and human health challenges.


 

Cartoon describing a phage infection of a bacterium created by PhD student Dinesh Kumar Kuppa Baskaran. This image won the competition conducted by the Catalysts for Science Policy (CaSP) club at UW Madison in collaboration with Delta Beer Lab brewery and was used in production of their Half-Life Hazy IPAs!

OUR RESEARCH IS FUNDED BY

                           

                             

 

                 The Brugger Family Foundation