The Anantharaman Lab

Anantharaman Microbiome Lab @UWMadison. Microbial/Viral ecology, omics, biogeochemistry with a focus on sulfur metabolism in environmental and human microbiomes

[Karthik Anantharaman @KarthikGeomicro]

Congrats 🎉 to our student @patriciatran_ for winning an #ISME18 best poster award! Woot woot. @quendi @UWBact @AnantharamanLab

[Karthik Anantharaman @KarthikGeomicro]

Excited to showcase our new @AnantharamanLab paper co-led by @ZhichaoZhou_CHN and Emily St. John focused on the microbial ecology of globally distributed deep sea hydrothermal vent chimneys. Super collaboration with @alr_thermophile. https://t.co/sffDjklEma.

[Karthik Anantharaman @KarthikGeomicro]

Honored to receive the ASM Early Career Award for Environmental Research. And more so, Super honored to be receiving this with @Firestone_Lab. @UWBact @AnantharamanLab

[Karthik Anantharaman @KarthikGeomicro]

Proud advisor moment! Sad to see my first PhD student @KrisKieft leave. But onto a fantastic future career ahead! Congratulations Kris on a fabulous PhD. The @AnantharamanLab was truly honored to have you be a part of our family and will miss you.

[Karthik Anantharaman @KarthikGeomicro]

Interested in viromics or viruses in microbiomes? Our new manuscript describing the virus binner vRhyme is out! Led by @AnantharamanLab PhD student @KrisKieft in collaboration with @lindskalan @SalamMicrobes @TeemoDoScience @UWBact @UWMadisonMDTP https://t.co/aFLEJyiBaZ

[Karthik Anantharaman @KarthikGeomicro]

New @AnantharamanLab paper describing sulfur metabolism in #colorectalcancer #microbiome is out! Led by MD-PhD student Elise Cowley through a fantastic collaboration w/ Patricia Wolf, Rex Gaskins, and @Ridlon_Lab. @UWMadisonMDTP @UWBact https://t.co/pdYu4apcIz

[Karthik Anantharaman @KarthikGeomicro]

Our new paper describing PropagAtE - our software for prophage activity estimation is out! Use this to study the ecology of prophages in genomes/metagenomes in diverse ecosystems and microbiomes. @KrisKieft @AnantharamanLab @UWMadisonMDTP @UWBact https://t.co/QrWnlH6NH1

[Mizrahi Lab @LabMizrahi]

METABOLIC is a novel scalable software by @AnantharamanLab which allows for characterization of microbial metabolic predictions, exchanges & interactions, individual contributions to biogeochemical cycling & community-scale functional network construction https://t.co/dzFoyZFRsC

[Trina McMahon 🌪 @quendi]

Super excited to pass along this awesome work! ⁦@patriciatran_⁩ ⁦@AnantharamanLab⁩ Do you like microbial genomes and bio geochemistry??? Look no further https://t.co/0Th1n4GAUB

[The Anantharaman Lab @AnantharamanLab]

@Rachel_L_Harris @KarthikGeomicro @UWBact Glad you like it. Feel free to reach out to us if you have questions or if we can help in any way.

[The Anantharaman Lab @AnantharamanLab]

@Rachel_L_Harris @KarthikGeomicro @UWBact Yes they were paired - from same vent/ sample. Using paired metagenomes/metatranscriptomic are best for analyses. However, even if you do not have a matching set of transcriptomes, there are still a number of possible analyses including relative activity comparisons

[The Anantharaman Lab @AnantharamanLab]

@Rachel_L_Harris @KarthikGeomicro @UWBact Yes that is correct. Using the read data is not mandatory, but including it enables coverage analyses which (1) determine the abundance of individual steps in biogeochemical cycles, (2) compute MW scores that can look at metabolic connections in the community.

[Karthik Anantharaman @KarthikGeomicro]

Our paper describing the software METABOLIC is out. We've got some great analyses and visualizations for microbial metabolism, pathways, metabolic interactions, and biogeochemical cycles from microbial genomes and metagenomes. @AnantharamanLab @UWBact https://t.co/y5egaEG0CG

[Microbiology Doctoral Training Program @UWMadisonMDTP]

If you're interested in viral genomics, this new review by #MDTP student @KrisKieft is for you!

@UWBact @AnantharamanLab

[Karthik Anantharaman @KarthikGeomicro]

Our new review on the state of viral/phage genomics led by super-talented Ph.D student @KrisKieft is now out! We discuss conventions, biases, ideologies, and the future of virus genomics. @AnantharamanLab @UWBact https://t.co/XwKUY5bOYd

[Microbiology Doctoral Training Program @UWMadisonMDTP]

Want to bin virus genomes from metagenomes?

Then #MDTP student @KrisKieft has the right tool for you!

Congrats to Kris, current student @salamzader, and trainers @lindskalan @KarthikGeomicro on their preprint!

https://t.co/KMZBIDzhcm

@UWBact @AnantharamanLab @madmicrobiome

[Karthik Anantharaman @KarthikGeomicro]

Why is there a Pseudomonas when there is no Realmonas?

[Kristopher Kieft @KrisKieft]

Excited to share ‘vRhyme’, a new bioinformatics tool for binning viruses and phages into viral metagenome-assembled genomes (vMAGs)! @AnantharamanLab @UWMadisonMDTP @UWBact https://t.co/9Y09uSCmlX

[Karthik Anantharaman @KarthikGeomicro]

Our viral genome binner "vRhyme" is available on github. All feedback/comments welcome. @KrisKieft https://t.co/dnY7zpkZUV