Noah Fierer

Rapid species-level metagenome profiling and containment estimation with sylph - Nature Biotechnology The microbial composition of metagenomes is identified in seconds by profiling against large databases.

If you haven't yet, check out Sylph - very useful tool (but I don't know how well it would work for your particular analyses): www.nature.com/articles/s41...

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

Please do send along any questions/comments that emerge from the discussion. You could also invite the lead author to join

Spatiotemporal dynamics in airborne fungi and fungal allergens across the United States A 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...

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

Feel free to shoot the lead author (Hoffert) an email - he can share the hi-res version. Hopefully the final version for publication will be higher resolution.....

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

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...

A cross-environment comparison of nontuberculous mycobacterial diversity Nontuberculous 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...

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/...

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)

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).

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)

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)

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)

A periodic table of bacteria?: Mapping bacterial diversity in trait space Bacterial 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...

I agree with both of these papers. Given that they were published >10 years ago, why is the 'hologenome' concept still a thing?

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses - BMC Biology Background The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metag...

See Table 1 of this paper: bmcbiol.biomedcentral.com/articles/10....

Correct - if you filtered a few liters of your saliva for DNA extraction, you would undoubtedly have far far higher DNA yields than a few liters of household water

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

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

Continent-wide assessment of the strain-level diversity of Bradyrhizobium, a dominant soil bacterial genus Global 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...

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...

Bacteria break through one-micrometer-square passages by flagellar wrapping Confined 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...

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)

Excellent work (and very well-written)

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?

This looks awesome. Open to PhD students from the US?

👆 Yes. 100% agreed.

So happy it is still winter here in Colorado

Alignment, Classification and Tree Service Align your 16S rRNA sequences using the SINA alignment tool.

Might be a useful alternative: www.arb-silva.de/aligner/

The figure shows study sites at the Savannah River Site in SC, USA, and the edge transects used in the study.

This is a multipanel figure showing bacteria/archaea and fungi turnover across edge transects in different blocks with pH and canopy cover.

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....