News

Paper published in Nature

Synergistic degradation of fucoidans in the ocean

Andi’s incredible paper was published in Nature today. I think this paper charts the way forward, and Andi really showed us how its done from start to finish. I’m really glad I got to work with him and our good friend Akshit on this.

Fucoidan is a heteropolymer of fucose made by brown algae in the ocean, and its chemical complexity requires hundreds of enzymes to degrade. Andi enriched a community that degrades this polymer from ocean water, and through pure wizardry (… LCMS if you want to be a stickler about it) found that the degradation of fucoidan by synthetic communities is extremely easy to predict due to synergistic interactions between degraders.

This description really does no justice to the paper, and I really can’t recommend reading this paper enough. Also, Andi is an amazing writer and this paper is pure prose start to finish.

Go Andi!

Shaul visits ICTP in Trieste

I (Shaul) will be visiting Jacopo Grilli’s lab, and give a talk at the Quantitative Life Science division at ICTP.

Paper published in mSystems

Influence of heterotrophs on phage infection of marine picocyanobacteria

Shaul’s last(?) paper from his time at Penny Chisholm’s lab. Allison found that Prochlorococcus only recovered from phage infection if heterotrophs were around, but not if it grew in monoculture.

The twist: after regrowth Prochlorococcus was resistant to the phage - so far so good - BUT! This was, to the best we could tell, not due to genetic changes.

More weirdness in the paper.

Rahul will give a flash talk at ICBP in Genoa

Rahul will give a talk at the 12th international conference on biological physics. He will talk in the “ECOLOGY AND EVOLUTION OF COMMUNITIES” session on Thursday July 2nd about our extracellular enzyme consumer-resource model.

Shaul will talk at KITP

I (Shaul) was invited to attend the KITP program: Coarse-graining Microbial Ecology: from Genes to Physiological Strategies to Communities across Environments. You can watch most of the talks by clicking the link (including mine).

Hard to express how good this was. Impossibly good lineup of speakers, including at the Non-equilibrium Dynamics, from Active Matter to Evolutionary Dynamics conference that was running at the same time.

Paper published in Nature

Genome-wide sweeps create ecological units in the human gut microbiome

Another fun collaboration with Martin Polz’s lab. Annie found a way to identiy genome-wide selective sweeps from isolate genomes, and identifies populations that swept through the globe. These populations are more strongly associated than traditional species definitions with host states such as disease.

Samira and Elle join for a research internship

We are very glad to welcome both Samira and Elle to the lab. They will be working together with Lior about predicting carbon decomposition phenotypes from genomes.

Marco defends his master’s thesis

Marco Sing graduated with a master’s degree today. Marco is the first student to graduate from the lab, and he defended his thesis with top marks. Great job Marco and thanks for spending this time with us.

Paper published in Nature Communications

Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum.

David Seki, currently a postdoc with Michi Wagner, found a mutualism that may explain E. coli’s prevalence in infant guts. David found that E. coli and B. bifidum can form a mutualism where E. coli supplies cystein to auxotrophic Bifidobacteria, and they in turn feed it fucose left over from extracellular HMO degradation.

Paper published in Nature

Microbial iron oxide respiration coupled to sulfide oxidation.

A nice collaboration with Songcan from Alex Loy’s group just down the corridor. Songcan found a new microbial sulfur metabolic pathway that is globally widespread and can be a large contributor to the sulfur cycle.

Joana got a DOC fellowship

Joana got the flagship doctoral fellowship of the Austrian Science Fund (FWF).
Announcement link

Shaul will speak at the Microbial Population Biology GRC

I (Shaul) was invited to speak at the Microbial Population Biology Gordon Resarch Conference (GRC). Scary good linup of speakers, as always, and I am very happy to have been invited to talk in the session lead by Tami Lieberman