Polyethylene (PE) is amongst the most recalcitrant synthetic polymers, and only a limited number of microbes have been shown to utilise it as their sole carbon and energy source. Here, we investigated...

Polyethylene terephthalate (PET) is the fourth most commonly used plastic worldwide. Like all plastics, post-consumer PET is poorly managed and accumulates in the environment, posing significant ecolo...

Contribute to R-Wright-1/GeCoCheck development by creating an account on GitHub.

In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While differ...

Background: Obtaining high precision while maintaining high recall is an ongoing problem for metagenomic taxonomic classification in microbial ecology research. Parameter adjustments can achieve this ...

Oh and Park (2025): Human reference microbiome profiles of different body habitats in healthy individuals.

Dalhousie Microbiome User Group (DalMUG).

Summary: PICRUSt2 is a bioinformatic tool that predicts microbial functions in amplicon sequencing data using a database of annotated reference genomes. We have constructed an updated database for PICRUSt2 that has substantially increased the number of bacterial (19,493 to 26,868) and archaeal (406 to 1,002) genomes as well as the number of functional annotations present. The previous PICRUSt2 database relied on many timely and computationally intensive manual processes that made it difficult to update. We constructed a new streamlined process to allow regular upgrades to the PICRUSt2 database on an ongoing basis, and used this process to create a new database, PICRUSt2-SC (Sugar-Coated). Additionally, we have shown that this updated database contains genomes that more closely match study sequences from a range of different environments. The genomes contained in the database therefore better represent these environments and this leads to an improvement in the predicted functional annotations obtained from PICRUSt2. Availability: PICRUSt2 source code is freely available at https://github.com/picrust/picrust2 and at https://anaconda.org/bioconda/picrust2. The latest version of PICRUSt2 at the time of writing is also archived: https://doi.org/10.5281/zenodo.15119781. The PICRUSt2-SC database comes pre-installed with PICRUSt2 from version 2.6.0 onwards. Step-by-step instructions for making the updated database are at https://github.com/picrust/picrust2/wiki/Updating-the-PICRUSt2-database. All code used for the analyses and figures in this manuscript is at https://github.com/R-Wright-1/PICRUSt2-SC\_application\_note and https://doi.org/10.5281/zenodo.15119770. ### Competing Interest Statement The authors have declared no competing interest.

Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.

Executive orders signed since 20 January 2025 aim to end programs intended to diversify the scientific workforce via equitable and inclusive practices and processes; cut federal funding for research and innovation; and stifle scientific communications. They represent a stunning reversal of policies that have been the bedrock of the U.S. scientific research enterprise and its leadership in the world, and therefore not surprisingly they have been met with a number of legal challenges. Some of the executive orders have been blocked by temporary restraining orders, and others are pending judicial review.

Summary PICRUSt2 is a bioinformatic tool that predicts microbial functions in amplicon sequencing data using a database of annotated reference genomes. We have constructed an updated database for PICR...