Another day of microbiome scientists jumping the shark

Looking for a tool to estimate abundances of aerobes versus anaerobes directly from metagenomes? Here you go: www.biorxiv.org/content/10.6...

New preprint up on airborne fungi across the US with a focus on fungal allergens - would love feedback. www.biorxiv.org/content/10.6...

New paper up - inspired by the periodic table of the elements, we attempted to organize bacterial diversity in genome-inferred trait space academic.oup.com/ismej/advanc...

New paper out looking at mycobacterial diversity across soils, premise plumbing, and surface waters to try to figure out the source of environmentally-acquired mycobacterial infections: journals.asm.org/doi/epdf/10....

New paper out demonstrating how we can use strain-level analyses of soil metagenomes to investigate the biogeographical patterns exhibited by a dominant group of soil bacteria (Bradyrhizobium) academic.oup.com/ismej/advanc...

New preprint led by Matt Gebert focused on the environmental reservoirs of nontuberculous mycobacterial (NTM) pathogens. NTM disease is environmentally acquired, but routes of exposure unclear. Our work implicates premise plumbing as the main culprit! www.biorxiv.org/content/10.1...

After 15 years, the authors of the infamous 'arsenic life' paper are still trying to argue that their findings are legit and not just a product of 'major errors'? Unbelievable. The authors' response to the retraction is infuriating. Time to let it go. www.science.org/doi/10.1126/...

New pre-print from my group - project led by PhD student Michael Hoffert. We set out on a daunting mission to generate a 'periodic table' of bacterial diversity (1/6) www.biorxiv.org/content/10.1...

Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io

New study out - we developed a pipeline for targeted assembly of genomes from (complex) soil metagenomes to examine the strain-level diversity and ecology of a dominant soil bacterial genus (Bradyrhizobium). Feedback appreciated. www.biorxiv.org/content/10.1...

This is cool - bacteria wrap their flagella to propel themselves through narrow passages www.biorxiv.org/content/10.1...

Just your regular reminder that 'sterile' doesn't mean 'DNA-free'! (this rant brought to you by yet another published DNA-based study conducted in a low biomass system where appropriate controls do not appear to have been included)

Dear fellow olds - recognize that the term 'next generation sequencing' is confusing to those that never had experience with the first generation. Also - what 'generation' are we on anyways?

So happy it is still winter here in Colorado

Excited to share PhD student Claire Winfrey’s (w/ @noahfierer.bsky.social & me) new paper in @esajournals.bsky.social Ecology! She examines how edge effects in habitat fragments shape soil microbial communities. Check it out 🦠 🧪 🌎 esajournals.onlinelibrary.wiley.com/doi/full/10....

New study out from my group showing how the volatile geosmin (the wonderful 'smell of dirt') serves as a cue to influence the behavior of soil protists rdcu.be/edCJj

New paper out that (we hope) will be useful to anyone with an interest in Antarctic soil microbial communities: link.springer.com/article/10.1...

We are trying to recruit folks from across the US that might be willing to be involved in a beta test of a new project to quantify airborne allergen loads in their homes. If interested (no cost), sign up here: boulderblue.com

Both the porcupine and I enjoyed the powder today

For years I've heard it said by univ admins that 'research is a net cost to the univ'. I guess we are about to find out if that is really true....

Lovely day to get out and XC ski in North Boulder Park. I recognized three Olympians out there during my 1 hour ski…one gold medalist, and one other medalist. There were probably other Olympians out there I didn’t recognize. Thanks to Boulder Nordic Club for grooming! bouldernordic.org #Boulder

Yet another reminder that RNA levels are not necessarily predictive of growth rate in mixed microbial communities (from this paper: www.pnas.org/doi/10.1073/...)

Lucky to be able to spend the morning skiing in Rocky Mt Natl Park

Another day with a SciEnCV-induced headache. Who thought just preparing a biosketch should be turned into a major time sink and source of frustration?

Cool work by @mattolm.bsky.social identifying the specific bacteria targeted by gut antibodies www.nature.com/articles/s41...

Damn - these cookies slap cooking.nytimes.com/recipes/1023...

Yikes - large earthquake in Port Vila, Vanuatu. Wonderful people and beautiful place (spent 2 weeks there in 2023). Hoping for the best...

Basically every ecology paper: "We found a strong link between X and Y at this site, so this is how the world works." The plot.

Why are Punnett squares still a thing? (asks the guy currently helping his daughter with 9th grade biology homework)

Dear microbial ecologists - I don't care how many MAGs you generated - what matters is what new insights you can glean from all those genomes (rant over)

In recognition of World Soils Day, here are 3 kitties snuggling together on a Namibian soil

Friendly welcoming party in Namibia

Cool to see that pH is not only an important determinant of microbiome structure in soil and freshwater environments, but also the human gut! www.nature.com/articles/s41...

Phytophthora takes down an indoor farming company: pitchbook.com/news/article...

Anyone have an alternate protocol suitable for ONT genomic/metagenomic library preps? The 'official' ONT protocol is kind of a pain in the ass....

With the recent improvements in ONT sequencing, I don't think we'll ever go back to Illumina for most of our sequencing work

Summary of our recent paper using Twitter data (primarily) to track seasonal allergies across the US: cires.colorado.edu/news/social-...

New paper out - social media (namely Twitter) is good for something - tracking spatial/temporal patterns in seasonal allergies across the US: academic.oup.com/pnasnexus/ar...

Yesterday vs today - gotta love Colorado

I have a request: Can you send me your 'tips & tricks' for managing/organizing research projects? I ask as I'm teaching a grad class next week on this topic. Any and all suggestions much appreciated.

This is a cool paper by @nonresidentdesi.bsky.social et al. Bacteria feeding off the carcasses of their prey. www.biorxiv.org/content/10.1...

This is really cool. Nematodes use siderophores to locate their bacterial prey: www.pnas.org/doi/abs/10.1...

Opening for an asst professor in environmental geochemistry at UC Berkeley: aprecruit.berkeley.edu/JPF04075

Maybe not everything is everywhere - the bacterial equivalent of a kiwi bird is discovered in New Zealand www.nature.com/articles/s41...

New paper out from my group - a practical guide to machine learning in microbial ecology. Hope it is useful! journals.asm.org/doi/10.1128/...

Finally got a photo of nearly everyone in the lab group! Using pizza as bait was the key.

Maybe scheduling a shut down of Canvas for maintenance during the last week of classes wasn't a great idea

This was a fun study to work on - what we know (or think we know) about bacterial amino acid auxotrophies www.nature.com/articles/s41...

An important (and useful) paper that uses data to actually quantify the 'peer review crisis': journals.asm.org/doi/10.1128/...