Tyler Barnum

How thoughtful experimental design can empower biologists in the omics era - Nature Communications Here, the authors discuss principles of experimental design that are relevant for all biology research, along with special considerations for projects using -omics approaches, highlighting common expe...

I am really excited to see this article on basic experimental design principles published. Definitely will be mandatory reading for incoming graduate students in my lab. Maggie Wagner who led this article did an amazing job with the illustrations of basic principles www.nature.com/articles/s41...

Phosphite oxidizers 🤝 Methanogens
In our new paper on “Lithosyntrophy” we show that phosphite oxidation drives methanogenesis through interspecies H2 transfer. Lithosyntrophy establishes a novel mechanistic link between the #phosphorus and carbon redox cycles

Woah, super cool! A class in how to piece apart metabolism in an enrichment culture, super interesting, and raises new questions of its own. Are you willing to speculate if there are any other lithotrophic metabolisms that involve syntrophy?

Yup the review I shared says this about terminal oxidases.

Perchlorate-reducing bacteria with Cld (super interesting, which I studied!) have so far always been facultative aerobes. Some obligate anaerobes without Cld can reduce perchlorate but ClO2 is removed chemically and no O2 is produced.

Well, GenomeSPOT uses amino acid frequency, so we think it reflects selection for aerobic or anaerobic metabolism. For gene-based, it depends. They can use O2-utilizing and O2-sensitive genes instead of just Cco, SOD, etc. One example: doi.org/10.1016/j.fr...

When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence - Nature Reviews Microbiology Hypoxic environments in which anaerobes dwell experience episodic oxygenation, which can be toxic to these organisms, yet many anaerobes have the capacity to tolerate substantial levels of oxygen. In ...

Yes! They use those enzymes to deplete (detoxify) oxygen, but have other enzymes that are sensitive to oxygen.

See: doi.org/10.1038/s415...
Possibly some genome annotations here: doi.org/10.1101/2023...

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve.

Preprint 📝: biorxiv.org/content/10.1...

🧵 1/n

Our latest, lead by @ahoiching.bsky.social, uncovering physiological vulnerabilities and helping to explain growth rate limitation in SAR11.

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.biorxiv.org/content/10.1... #jcampubs

Very cool work. "The absence of cell cycle regulation genes may ... [predict] upper bounds on growth rates obtainable by these organisms" is a cool thought - we're all sick of not knowing *why* some taxa are harder to cultivate! Do you plan to expand on the prelim analysis?

The latest publication from our lab!

The famous "glomalin" from arbuscular mycorrhizal (AM) fungi is not a protein but a polysaccharide from AM fungi, so we renamed it "glomalose". Glomalin-related proteins are bacterial proteins stuck in this glomalose.
nph.onlinelibrary.wiley.com/doi/10.1111/...

Illustration showing a graduation ceremony, with speaker addressing graduates: “Let the example of my fluke success guide nearly all of you to crushing disappointment”.

Success in academia often has more to do with luck, patronage and the job market than “hard work”.
Good academics acknowledge this.
I worked hard, but I was in the right place at the right time on occasion. Historians far more talented than I have fallen between the cracks.

The biogeochemical cycling of chlorine Chlorine has important roles in the Earth's systems. In different forms, it helps balance the charge and osmotic potential of cells, provides energy for microorganisms, mobilizes metals in geologic f...

For way more on the very interesting element chlorine, see my short review here: doi.org/10.1111/gbi....

2/2 HOCl (bleach) is oxidized Cl produced by our immune system, but also seems impactful in various oxic habitats. HOCl is understudied, and there seems to be a lot left to learn about how microbes adapt to oxidative stress from Cl.

Some comparative genomics: doi.org/10.1038/s413...

Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles | Microbiology Spectrum The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have co...

1/2 The broader DMSO reductase family is massive and catalyzes key parts of various biogeochemical cycles (N, Cl, I, Ar, Se, etc.). The majority of this family has unknown functions -- yet these enzymes often support respiration, making it easier to assay substrates.

doi.org/10.1128/spec...

Beyond anaerobic respiration—new physiological roles for DmsABC and other S-/N-oxide reductases in Escherichia coli | Journal of Bacteriology Bacterial urinary tract infections are debilitating and frequently recurring in human populations worldwide, and Escherichia coli strains are a major cause of these infections. In this study, we have ...

Neat study: the classic enzyme DMSO reductase also acts on various other S-/N-oxides that are produced by reactions with HOCl. Two quick reasons a microbiologist should take note for their research:

doi.org/10.1128/jb.0...

In our study, we showed that intestinal Methanosarcinales have reduced genomes and obligately dependent on H2 and CH3 compounds for #CH4 production. They lost the Wood–Ljungdahl pathway and membrane complexes (Rnf, Fpo, Ech).
academic.oup.com/femsec/artic...
@femsjournals.bsky.social @femsmicro.org

TIL you can add .txt to a biorxiv fulltext link and get plain text. Handy for pasting into LLMs, e.g., the new BindCraft revision www.biorxiv.org/content/10.1...

We're gearing up to tackle new kingdoms of life, thanks to generous support from @wellcometrust.bsky.social. Get in touch!

Read more on our blog: cultivarium.substack.com/p/fungi-and-...

New images could change cancer diagnostics, but ICE detained the Harvard scientist who analyzes them Without scientist Kseniia Petrova’s expertise, no one can fully unlock the data’s potential, putting crucial advancements in early cancer detection at risk.

Almost every line of this story would have been simply unbelievable a few months ago:

—Pioneering cancer researcher;
—*Arrested* at airport in Boston;
—Now indefinite ICE detention in Louisiana;
—"Crime": not declaring some frog-embryo samples for research.

Read it.
www.nbcnews.com/news/us-news...

I got a 404 webpage not found. You have an extra "n" at the end of your link. Fixed link: asm.org/climatesolutions

(Thanks for sharing!)

I told everyone! 😏 If you want to co-culture CPR/DPANN epibionts, try to filter-purify them and add them into pure cultures. For Minisyncoccus they used 0.45 um filters and a suspected host. I'd recommend 0.2 um filters and a panel of various isolates.

tylerbarnum.com/2021/05/14/t...

Empowering Microbial Discovery: Your Guide to Genetic Tractability — Cultivarium — Cultivarium Rapidly identify reported genetic methods and papers for your organism, including electroporation, transposon mutagenesis, and CRISPRi.

Unlock new organisms quickly with a genetic methods “cheat-sheet”🔬

Our Portal’s new Reported Methods section streamlines access to established genetic tools and related literature.

Read more here: tinyurl.com/yj33bnyr

Hi Ameet!

Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut - Nature Microbiology Metagenomic immunoglobulin sequencing (MIg-seq) uncovered patterns of IgA antibody binding of bacterial strains in the healthy human gut microbiome.

Our technique for studying strain-level IgA binding in the microbiome is out now at @naturemicrobiol.bsky.social! Fascinated by IgA since Sean Spencer told me about it, here we make some fundamental discoveries about strain-level IgA dynamics in the healthy human gut (1/5) doi.org/10.1038/s415...

Super cool - amoebae and ciliates live in close association with lots of weird, host-associated bacteria. Including CPR/Patescibacteria.

Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut - Nature Microbiology Metagenomic immunoglobulin sequencing (MIg-seq) uncovered patterns of IgA antibody binding of bacterial strains in the healthy human gut microbiome.

OUT NOW: Metagenomic immunoglobulin sequencing (MIg-seq) reveals IgA coating of microbial strains in the healthy human gut

by Justin Sonnenburg, Matt Olm, Sean Spencer & co

#microsky

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

bsky.app/profile/cult...

Cultivarium Portal The World's microbial strain information at your fingertips.

More improvements to come and feedback is welcome. What features would be most helpful to you? Sign up here: portal.cultivarium.org/welcome

Thinking about a microbe with few or no genetic tools? This makes it easy to see examples in relatives. You will also see if you could be the first to develop genetic methods in a particular lineage. I hope this helps reward researchers who work on the frontier of microbiology.

I want to highlight a new resource for microbiology on the @cultivarium.bsky.social portal: we’ve created a database of published genetic methods for every microorganism. And if your microbe *doesn’t* have genetic tools, we point you to the closest relative that does.