Noah Fierer

A plea: If you are leading a faculty search and you expect 100s of applications - please do not request letters up front! You are basically telling your colleagues that you do not value their time.

nature.comSelf-generated hydrogel ejects bacterial cells for localized biofilm dispersion - Nature MicrobiologyBacillus subtilis biofilms locally disperse by ejecting motile cells through osmotic pressure generated by their poly-γ-glutamic acid hydrogel, a mechanism resembling that through which Cnidaria eject...

18 Sept

It is rare to find a paper that really blows my mind. This is one of those papers: www.nature.com/articles/s41...

@louisschipper.bsky.social

15 Aug

@jeffinerca.bsky.social FYI - you can enter NZ even without your NZETA approved.

Noah Fierer reposted

Louis Schipper

1 Aug

Lecturer position in soil science opportunity (equivalent to Assistant Prof. Looking forward to seeing some great applicants. elhs.fa.ap1.oraclecloud.com/hcmUI/Candid...

elhs.fa.ap1.oraclecloud.comLecturer in Soil ScienceTake the next step in your academic career, conducting original research in soil science and contributing to teaching the next generation of scientists within the Earth and Environmental Sciences Team...

biorxiv.orgA representative of a ubiquitous bacterial lineage parasitically feeds on host RNACellular metabolism is widely understood as an integrated network of redox reactions, energy conservation, and biosynthetic pathways. Here we show that across diverse prokaryotic lineages, loss of red...

23 June

This study is amazing: www.biorxiv.org/content/10.6...

biorxiv.orgPredicting optimal growth temperatures of bacteria using learned structural information from a single proteinTemperature is a fundamental determinant of bacterial physiology and ecology. Optimal growth temperature (OGT) is highly variable across species, contributing to differences in where and when species ...

19 June

New preprint up: the power of protein language models - using a single gene (adenylate kinase) to predict the temperature optima of bacteria and bacterial communities from genomes or metagenomes www.biorxiv.org/content/10.6...

journals.asm.orgPredicting oxygen levels in microbial habitats using a metagenome-based approach | mSystemsOxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages diffe...

18 June

Ever wanted to use metagenomic data to infer oxygen levels (or the oxygen preferences of whole bacterial communities)? We have the tool for you: journals.asm.org/eprint/9GUIR...

enviromicro-journals.onlinelibrary.wiley.comRethinking Alpha Diversity in Marker‐Gene Microbiome Studies: Dominance Matters More Than RichnessMarker-gene microbiome surveys systematically under-sample rare taxa, causing alpha diversity metrics to reflect dominance rather than true richness. This conceptual mismatch can lead to misleading e...

12 May

Really useful paper explaining why richness/diversity metrics are rarely informative when applied to microbial community sequencing data: enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

nytimes.comAfter Prison, a Financial Titan Plots an Unlikely Comeback

The recent NY Times article on Oath (a soil inoculant company) warrants a mini-thread, so here we go: www.nytimes.com/2026/05/01/b... (1/9)

The company appears to be using 'soil stars' (their term) to promote the company. These are all great scientists, but where are the agronomists? h/t @agronomistag.bsky.social (6/9)

OK - this is just cringe: (7/9)

nytimes.comAfter Prison, a Financial Titan Plots an Unlikely Comeback

The recent NY Times article on Oath (a soil inoculant company) warrants a mini-thread, so here we go: www.nytimes.com/2026/05/01/b... (1/9)

Is this just snake oil being sold by well-funded salesmen? I don't know, but if the soil microbial inoculant industry has taught me anything over the years, it is to maintain a high degree of skepticism (4/9)

I know every company is trying to hop on the AI hype train. Maybe AI could be useful here, but I doubt it. This just seems more like marketing copy than journalism (5/9)

nytimes.comAfter Prison, a Financial Titan Plots an Unlikely Comeback

The recent NY Times article on Oath (a soil inoculant company) warrants a mini-thread, so here we go: www.nytimes.com/2026/05/01/b... (1/9)

First, the article appears to be a blatant attempt to restore the reputation of the company's billionaire founder (and convicted felon). Using 'journalism' for reputation laundering is not new, but it is still cringe-worthy (2/9)

The article is essentially unpaid advertising touting their microbial inoculants (see text). I realize this is not a science article, but big claims require big evidence. Same goes for their website (www.oathsoillife.com/pages/scienc...) - inoculants led to a 50% increase in SOC??? (3/9)

biorxiv.orgEvidence for endemism and local adaptation in Antarctic soil bacteriaAntarctic soils represent one of the more extreme environments for microbial life on Earth, yet they harbor heterogeneous and diverse microbial communities. Biologists have long hypothesized that Antarctic microorganisms are unique from those found on other continents due to the extreme geographic isolation and the cold, dry, and challenging conditions typical of Antarctica. To test this hypothesis, we focused on a cosmopolitan bacterial genus, Arthrobacter, that is widely distributed across global soils. We first profiled a global metagenomic dataset from both Antarctic and non-Antarctic surface soils to quantify the distributions of Arthrobacter strains. Despite high strain-level diversity, 90% of the strains found in the Antarctic soils were only found on the continent. We then used cultivation-based phenotypic analyses and strain-level genomic comparisons to assess how Antarctic strains and non-Antarctic strains differ in their traits and environmental preferences. Not only did we find evidence of endemism, but Antarctic Arthrobacter also have genomic characteristics and environmental tolerances that suggest they are uniquely adapted to Antarctic conditions. ### Competing Interest Statement The authors have declared no competing interest. U.S. National Science Foundation, NSF 21-567, EAR 1950681 Australian Research Council, FT240100502, DE250101210

6 May

New pre-print out - we sought to determine if Antarctic soil bacteria are really endemic to the continent. Would love feedback. www.biorxiv.org/content/10.6...

21 Apr

I was excited to read this paper until I got to this section describing their Methods. Big claims require better evidence. www.pnas.org/doi/10.1073/...

31 Mar

Another day of microbiome scientists jumping the shark

26 Jan

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

biorxiv.orgbiorxiv.org

biorxiv.orgSpatiotemporal dynamics in airborne fungi and fungal allergens across the United StatesA broad diversity of fungi can be found in the near-surface atmosphere, with both the amounts and types of airborne fungi varying across space and time. However, the specific spatiotemporal patterns i...

8 Jan

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

academic.oup.comConstructing a “periodic table” of bacteria to map diversity in trait spaceAbstract. Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmen

6 Jan

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...

journals.asm.orgA cross-environment comparison of nontuberculous mycobacterial diversity

8 Dec 2025

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....

academic.oup.comValidate User

10 Oct 2025

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...

biorxiv.orgA cross-environment comparison of nontuberculous mycobacterial diversityNontuberculous mycobacteria (NTM) are a group of environmental bacteria that encompass nearly 200 described species, some of which can cause chronic pulmonary infection in humans. What makes these inf...

6 Aug 2025

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...

28 July 2025

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/...

science.orgscience.org

biorxiv.orgA periodic table of bacteria?: Mapping bacterial diversity in trait spaceBacterial diversity can be overwhelming. There is an ever-expanding number of bacterial taxa being discovered, but many of these taxa remain uncharacterized with unknown traits and environmental prefe...

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...

Perhaps more importantly, the workflow for generating the 'periodic table' is adaptable so it can ultimately be expanded to incorporate additional traits/taxa (5/6).

We hope the approach and our draft 'periodic table' are useful and encourage future efforts to systematically characterize trait variance across the bacterial tree of life.(6/6)

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...

Here we focused on 6 traits - inferring those traits (including autotrophy, O2 tolerance, phototrophy, etc.) using genome-based models across >50,000 bacterial 'species' (thanks @ace-gtdb.bsky.social!) (3/6)

Our draft 'periodic table' of bacterial diversity, like the periodic table of the elements, provides a interpretable & concise way to visualize and explore bacterial diversity in trait space (see Figs 4-5) - linking phylogeny to trait distributions in a quantifiable manner (4/6)

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...

Work was motivated by the challenges associated with linking taxonomic/phylogenetic information to knowledge of what we know (or think we know) about bacterial traits (2/6)

rdcu.beGuidelines for preventing and reporting contamination in low-biomass microbiome studiesNature Microbiology - In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize...

21 June 2025

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

biorxiv.orgContinent-wide assessment of the strain-level diversity of Bradyrhizobium, a dominant soil bacterial genusGlobal surveys of soil bacteria have identified several taxa that are nearly ubiquitous and often the most abundant members of soil bacterial communities. However, it remains unclear why these taxa ar...

30 May 2025

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...

biorxiv.orgBacteria break through one-micrometer-square passages by flagellar wrappingConfined spaces are omnipresent in the micro-environments, including soil aggregates and intestinal crypts, yet little is known about how bacteria behave under such conditions where movement is challe...

21 May 2025

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

8 May 2025

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)

7 May 2025

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?

@julianresasco.bsky.social

20 Apr 2025

So happy it is still winter here in Colorado

Noah Fierer reposted

Julian Resasco

3 Apr 2025

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....

rdcu.beEffects of Geosmin on the Behavior of Soil Protists

17 Mar 2025

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

link.springer.comA comprehensive survey of soil microbial diversity across the Antarctic continent - Polar BiologyAntarctic soils are unique from those found nearly anywhere else on Earth yet can still harbor a broad diversity of microorganisms able to tolerate the challenging conditions typical of the continent....

21 Feb 2025

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...

boulderblue.comAir Quality Testing Services – Allergen Detection with Boulder BlueEnsure a healthier space with cutting-edge air quality testing services from Boulder Blue. Our genomic tests help detect indoor allergens.

20 Feb 2025

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

26 Jan 2025

Both the porcupine and I enjoyed the powder today

@nealahenderson.bsky.social

24 Jan 2025

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....

Noah Fierer reposted

Neal Henderson

20 Jan 2025

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

15 Jan 2025

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/...)

12 Jan 2025

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

10 Jan 2025

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?

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

4 Jan 2025

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