Karthik Anantharaman

Advice from NSF: grant proposals can still include outreach, community engagement, and so on. But avoid specifying particular groups

Tomorrow at 12:45-1:30 in the EEB Track Hub in the poster hall #ASMmicrobe I am talking about microbial diversity including Asgard archaea, and an expanded tree of life from marine sediments.

Excited to be a part of this effort from Mandy Joye's group showing the role of heterotrophs in deep sea carbon cycling!

Ultrafast and accurate sequence alignment and clustering of viral genomes - Nature Methods Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.

Ultrafast and accurate sequence alignment and clustering of viral genomes | Nature Methods https://www.nature.com/articles/s41592-025-02701-7

I use this as a joke in lectures. Works every time 😂

Very excited this part of my PhD is out 🎉 We describe vent viral and microbial traits that govern viral biogeography and contribute to mounting evidence that these communities are highly endemic, and thus likely vulnerable to disruptive activities like deep sea mining
#Microbiome #DeepSeaMining

A few weeks ago we met in the Scottish Highlands to launch our HFSP @hfspo.bsky.social funded project on virus-prokaryotic interactions in wetlands and impact on the methane cycle. What a fantastic team to be part of. @karthik-a.bsky.social @soilmicrobes.bsky.social & Joanne Emerson

#phagesky #microsky

Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems - Nature Communications Viruses are pivotal players in deep-sea hydrothermal vents, shaping microbiomes by preying on key hosts. Through a global-scale analysis of vent viruses and their interactions, this study reveals that...

Excited to share our lab's latest work led by PhD student
@maggielangwig.bsky.social
describing the ecology and evolution of viruses in globally distributed hydrothermal vents.
www.nature.com/articles/s41...

Come and work with me!

The Nature Micro team is expanding and we're looking for someone to champion microbial ecology, plant micro & related areas for the journal

Knowledge of microbial ecology/plant micro is desirable but we're open to applications from all microbiologists

Link below 👇

Beneath the surface: Unsolved questions in soil virus ecology Soil virus ecology is an exciting but still nascent field of research in soil microbiology. While there has been a recent surge in soil virus research…

Our perspective on soil virus ecology research is out!

Fantastic collab with
@christinahazard.bsky.social @karthik-a.bsky.social @lukehillary.bsky.social @urineri.bsky.social @simrouxvirus.bsky.social @gtrubl.bsky.social @KurtWilliams @jeffinerca.bsky.social @graemenicol.bsky.social @JoanneEmerson

Phage interactions may contribute to the population structure and dynamics of hydrothermal vent microbial symbionts Deep-sea hydrothermal vent ecosystems are sustained by chemoautotrophic bacteria that symbiotically provide organic matter to their animal hosts through the oxidation of chemical reductants in vent fl...

Amidst all the bad news, I still want to share two new preprints from our lab group. The first is led by newly minted Dr. Michelle Hauer, in collaboration with @karthik-a.bsky.social @katiekliermicrobe.bsky.social and @maggielangwig.bsky.social
www.biorxiv.org/content/10.1...

World's only freshwater river 'Ganga' with a remarkable 50 times faster elimination of germs, says expert | Delhi News - The Times of India Despite over 60 crore visitors and countless holy dips during Maha Kumbh, the Ganga remains germ-free. A study by Padma Shri Dr. Ajay Sonkar reveals G

This was published in the top newspaper in India. So much for "news". timesofindia.indiatimes.com/city/delhi/w...

Our lab had a great time at the IBSE Microbiome Symposium. Looking forward to this in the future again.

I am in Bengaluru quite often (multiple times a month really). We should catch up sometime.

It was great to host @jeffinerca.bsky.social and learn about her inspirational work in the persistence of soil carbon. Hosted by the IBSE Microbiome Symposium at IIT Madras.

Great talk by Tanja Woyke on very exciting upcoming technological advancements in single cell genomics at @jgi.doe.gov Hosted by the IBSE Microbiome Symposium at IIT Madras.

Excited and grateful to have Brett Baker and Paul Wilmes at the IBSE Microbiome Symposium at IIT Madras. Forever amazed by their brilliant science. @archaeal.bsky.social @paulwilmes.bsky.social

Cody Martin from lab our presenting his work on deep learning and the development of 'PST' for viral ecology at the IBSE Microbiome Symposium at IIT Madras in Chennai, India.

Black and white ink cartoon of a myovirus-like phage with eyes and eyebrows looking confused with “?!?” above its head. The page is hovering above a hexagonal child’s sorting toy with different shaped holes. On the front of the toy is a simple phylogenetic tree with shapes corresponding to the holes at the end of the branches

Phage taxonomy doesn’t have to be taxing, my latest cartoon for the Phage journal. To illustrate 𝘁𝗮𝘅𝗠𝘆𝗣𝗵𝗮𝗴𝗲 lnkd.in/dAXK4sSt @milja001.bsky.social

Excited to have Jill Banfield present the opening keynote at the IBSE Microbiome Symposium at IIT Madras yesterday.

Studies only making reads available may satisfy journal requirements but do not serve the larger community.

If you work with any form of metagenomics/genomics data, and are for open access and FAIR data policies...Please consider making ALL your data public (genomes, proteins, reads, metadata).

Putting on my editor's hat for my yearly rant about scientists who do not review manuscripts enough for journals.

As a quantitative approach, consider reviewing 3X the papers submitted by you or your lab in a calendar year (the number 3X comes from if you expect 3 reviews for your own papers).

Don't have it but could look into it. Feel like the two sets may be quite complementary.

Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages - Environmental Microbiome Background Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dy...

New lab paper alert: Presenting "Prophage-DB", a database of prophages mined from public databases along with metadata. environmentalmicrobiome.biomedcentral.com/articles/10....

🚨Postdoc position(s) alert🚨 If you like to develop new bioinformatic tools for *human* microbiome analysis, are interested by virus/phages, we (JGI Viral Genomics and Microbiome Data groups) may have a great position for you ! No official job posting yet, but email or DM if you are interested !

Check out our new preprint on viruses associated with Karenia brevis blooms! 🦠 🌊 🧪 🧬 @cmarinescience.bsky.social

I just assumed a mountain came up in Wisconsin in the last 6 months that I was away!

Crucial stepping stones in freshwater microbiology - Nature Microbiology Three different studies in this issue use metagenomics to study the bacterial and viral dynamics of freshwater microbiomes, highlighting the ecological and environmental drivers of these ecosystems.

News and Views by @naturemicrobiol.bsky.social on our recent papers describing the 20-year study of ecology and evolution of viruses and bacteria in freshwater systems. @archaeal.bsky.social @quendi.bsky.social @uwmadison.bsky.social

www.nature.com/articles/s41...

Unravelling viral ecology and evolution over 20 years in a freshwater lake - Nature Microbiology A long-term metagenomic time series reveals how viruses impact diversity, ecological dynamics and evolution of freshwater microbiomes.

OUT NOW Unraveling viral ecology and evolution over twenty years in a freshwater lake

@karthik-a.bsky.social & co

www.nature.com/articles/s41...