By: Noah Fierer April 11, 2019 It is a seemingly simple question: What percentage of bacterial and archaeal taxa in a given sample have been cultivated? Or, to phrase this another way: How well do our pre-existing culture collections cover the breadth of prokaryotic1 diversity found in environmental or host-associated samples? This topic may seem
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
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
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
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
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
By Noah Fierer, Tess Brewer, & Mallory Choudoir May 2, 2017 Typically, when we analyze 16S rRNA gene data for bacterial and archaeal community analyses we start by clustering sequences into operational taxonomic units (OTUs), i.e. clustering sequences that fall into fixed similarity thresholds (with OTUs often, but not always, defined at the ≥97% sequence
By: Noah Fierer July 22, 2016 Some of you may have seen this paper that came out recently in Nature Plants by Wubs et al. “Soil inoculation steers restoration of terrestrial ecosystems”. As a soil ecologist – this paper brings joy to my heart. It was great to read this paper as it demonstrates the
By Angela Oliverio July 6, 2016 I’m in my fourth week here in the Taupo Volcanic Zone of New Zealand on my quest to understand what eukaryotic life –especially protists– can thrive in hotsprings. A quick refresher: protists are single-celled microbial eukaryotes and include many diverse lineages like amoebae, ciliates and flagellates. While bacteria and
By Jon Leff June 14, 2016 The problem There – I did it. I made it through processing my raw amplicon (marker gene, 16S rRNA, 18S rRNA, or fungal ITS, etc.) DNA sequences. Now I have a table that tells me how many of each taxon (i.e. phylotype, OTU, etc.) are represented in each sample.