Fierer Lab

Exploring the structure and function of microbial communities

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Insights, rants, shameless self promotion, etc. from the Fierer lab and its affiliates.

Lumping versus splitting – is it time for microbial ecologists to abandon OTUs?

By Noah Fierer, Tess Brewer, & Mallory Choudoir 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 similarity level). A

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Ecosystem restoration: what do soil and feces have in common?

By: Noah Fierer 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 likely importance of

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Field reflections from NZ: microbial eukaryotic life in hot springs

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 archaeal taxa have long been appreciated

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Microbial community data in R: Introducing mctoolsr

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. This table is often referred to

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