Anantharaman Microbiome Laboratory

Computational Biology, Microbial and Viral Ecology, Human and 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

Integrating Microbial and Viral Ecology with Data Science to Study

Human Health, Ecosystem Change, and Biogeochemistry

Comic created by Dinesh Kumar Kuppa Baskaran

OUR RESEARCH

The fundamental focus of our laboratory is to understand the basic biology of phage and metabolic interactions in environmental and host-associated microbiomes, and their overall impacts on microbiome fluctuation, ecosystem change, and biogeochemistry. Our research occurs at the interface of three diverse fields, namely, Computational Biology, Microbial and Viral Systems Ecology, and Biogeochemistry.

  • We are developing bioinformatics approaches and tools to study uncultivated viruses, with a specific focus on bacteriophages (phages). Through our open access software and tools, we hope to enable and drive microbial and viral ecology studies in the future.
  • We are integrating omics approaches with ecological data to enhance our ability to predict microbiome, ecosystem, and host health states.
  • We utilize a combination of fieldwork, laboratory experiments, and multi-omics based approaches to investigate the microbial and viral ecology of environmental systems such as deep-sea hydrothermal vents, oxygen minimum zones, the pelagic ocean water column, freshwater ecosystems, and peatland soils.

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Developing omics-based computational biology and bioinformatics approaches to advance microbial and viral ecology

We are developing new bioinformatic approaches to identify and characterize viruses, microbes, and their interactions and connections in microbiomes based on different types of omics data. Tools developed by our laboratory include VIBRANT (to study and characterize viruses and viral auxiliary metabolic genes), METABOLIC (to identify microbial metabolism and quantify community interactions based on metabolism), PROPAGATE (to identify the activity of proviruses), vRHYME (to enable binning of viral genomes from metagenomes), ViWrap (to enable comprehensive characterization of viruses from metagenomes). More recent developments include Protein Set Transformer (to relate viral genomes based on shared protein content), CheckAMG (to identify and curate auxiliary genes in viral genomes), and Prophage-DB (a comprehensive database of prophage genomes, proteins, and associated metadata).

Microbial and viral community interactions

Recent advances in DNA sequencing and bioinformatics approaches have enabled the recovery of thousands of strain-resolved microbial genomes from a single ecosystem, thereby providing a window into fine scale microbial interactions and metabolic networks in complex communities. Broadly, we are interested in studying three types of interactions in microbial communities – virus-microbe, microbe-microbe, and microbial “metabolic handoffs”. We focus on virus-microbe interactions involving “auxiliary metabolic genes”, which are host-derived genes utilized by viruses in selfishly altering microbial metabolism. We’re also investigating virus-microbe interactions through the lens of virus life cycles and life-history switches. We study microbe-microbe interactions, and “metabolic handoffs” primarily focused on sulfur metabolism. We seek to quantify and predict the impact of such interactions on biogeochemical cycling at cellular, ecosystem, and global scales.

Microbial sulfur metabolism

Microorganisms control and modulate transformations associated with the element sulfur in natural and engineered systems. Sulfur plays a central role in biochemistry, impacts carbon and nitrogen turnover in various environments, and is critical to maintaining the health of oceans in the future. We use biotic sulfur transformations as a model to study the evolution and ecology of microbial energy metabolism and viral auxiliary metabolism.

OUR RESEARCH IS FUNDED BY

                           

                                               

The Brugger Family Foundation