Fierer Lab

Exploring the structure and function of microbial communities

Unclogging the peer review pipeline

Noah Fierer June 3, 2021 Peer review is a key part of science. Thorough reviews provide a critical check on the quality of scientific papers. Personally, nearly every paper I’ve been involved with has been greatly improved by going through the peer review process. Yes – crappy science still passes through peer review (exhibit A

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Publishing a scientific paper

Noah Fierer 2/21/2021 A short series of slides on the process of publishing a scientific paper (a.k.a. learning how the sausage is made). The process is confusing and rarely intuitive, so hopefully this is helpful. This is not meant to be a comprehensive overview, just some general tips to help early career researchers navigate the

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What’s in a number? Estimating microbial richness using DADA2

February 17th, 2020 Corinne Walsh & Noah Fierer Soils are often touted as harboring some of the most diverse microbial communities of any habitat on Earth. We typically expect to detect on the order of thousands of different bacterial taxa in a given soil sample using culture-independent sequencing methods. However, richness (number of distinct taxa

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The ‘hidden’ costs of microbial community analyses

February 13th, 2019 By: Noah Fierer DNA sequencing is clearly a powerful tool for analyzing microbial communities. It is now somewhat routine to take a sample of feces, tap water, or bellybutton lint and use DNA sequencing-based approaches to analyze the microbes living therein. We also know that the cost of generating DNA sequence data

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Garbage in, garbage out: Wrestling with contamination in microbial sequencing projects

August 15th, 2018 By: Noah Fierer, Jessica Henley, and Matt Gebert   They are insidious. They are difficult to eliminate. They strike fear in the hearts of microbiologists worldwide.  Hard drive failures? Third reviewers? Bedbugs lurking in conference hotels? Nope. Contaminants in your high-throughput sequence data. High-throughput sequencing approaches are now routinely used to characterize

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Do all animals need microbes?

By Tobin Hammer, Jon Sanders, & Noah Fierer May 18th, 2018 NOTE: A more complete discussion of these ideas is now available in the corresponding publication (available here). Have you—like us—ever written a paper or grant proposal with a statement along the lines of “All animals host microbial symbionts that play critical roles in many

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Is RNA a useful measure of microbial activity?

December 20, 2017 By Noah Fierer Let’s say a microbial ecologist wants to identify which bacteria are active in a given environmental sample at a given point in time. For example, you may want to determine which bacteria are active in a desert soil after a large rainfall event. This is often done by comparing

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Intragenomic heterogeneity and its implications for ESVs

By Angela Oliverio and Noah Fierer October 9, 2017 In a recent blog post, we focused on the advantages and disadvantages of using exact sequence variants (ESVs) versus OTUs to cluster marker gene sequences for microbial community analyses. Just to recap – let’s say we sequenced a pool of 16S rRNA genes from a bacterial

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