Microbiome ANCHOR: Advancing Novel Computational and High-quality Omics Research. Microbiome Conference, June 8-10, 2026. Oak Island, Nova Scoatia. An intimate microbiome meeting to foster connections and share ideas about microbial communities, the methods used to study them, and their diverse applications. microbiome-anchor.ca

Save the Date: Microbiome ANCHOR is a new Canadian microbiome conference taking place June 8-10, 2026 at Oak Island Resort in Nova Scotia. Registration opens in January and space will be limited: head to microbiome-anchor.ca and join the mailing list so you don't miss out!

Metabolic redundancy is required for microbial polyethylene assimilation 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...

Metabolic redundancy is required for microbial polyethylene assimilation. Cellular and metagenomic analyses show that redundancy of the fatty acid metabolism is essential to process the enormous pool of oxidised aliphatic metabolites generated by weathered PE #plastic www.biorxiv.org/content/10.6...

A synthetic bacterium that degrades and assimilates poly(ethylene terephthalate) 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...

Paper alert!
We have created a bacterium that eats plastic! We named it PETBuster! Great work by PhD student Dekel Freund @dekel-freund.bsky.social.
www.biorxiv.org/content/10.1...

We hope that drawing attention to some of these issues will encourage more researchers to carry out similar methods! Our pipeline is freely available on GitHub, which we hope will be useful. We designed it for use w/Kraken output, but would happily modify for others like Kaiju if anyone wants. 6/6

…leading to lower nucleotide identity between sequenced reads & ref. genomes, but checking genome coverage still identifies taxa that are clearly not present and is particularly useful for verifying taxa of interest. MAG assembly could help here, but will miss much of the diversity present. 5/

…in ref. genomes.
- in blood & tumour datasets, M. tuberculosis has no reads mapped to ref. genome & the only species with >1% genome present have the same parts of the genome in multiple samples & are likely contaminants.
- marine & soil samples have lower representation in databases… 4/

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

We use our new tool GeCoCheck (github.com/R-Wright-1/G...) to remove 99.7% of false positive taxa in simulated samples.

Real samples are a bit more complicated, but we show that:
- in stool samples, H. pylori lack any reads mapping to ref. genome & are likely from contaminating phage sequences… 3/

From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools 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...

Obtaining high precision & high recall is an ongoing issue in metagenomic taxonomic classification. We’ve used parameter adjustments for this in simulated samples (www.microbiologyresearch.org/content/jour...), but in environmental samples this quickly leads to very low % of reads classified. 2/

New preprint out with Ben Fisher, André Comeau & @betascience.bsky.social!

www.researchsquare.com/article/rs-8...

TLDR: we recommend checking the genomic coverage of metagenomic taxonomic classifications from a tool like Kraken to remove false positives w/out large drops in recall. 1/

Hope you and your family have a lovely day, looks beautiful!

Not that you care, but I still wanted to let you know that if I see a paper full of bogus citations with your name on it, I'm not talking to you anymore.

I was so triggered by a paper I was reading this morning, I am drinking my second coffee.

…the differences they identify using logFC between different body sites can be used clinically to identify the health status of an individual. We felt that the study needed a much larger sample size before this would be appropriate.

You can read our full discussion here: dalmug.org/blood-refere...

We found the alpha diversity results to be particularly striking: they find that alpha diversity follows the pattern blood > saliva > stool. As this appears to be in contrast to most existing literature, we’d have loved to see more discussion of these results.

The authors also suggest that…

Frontiers | Human reference microbiome profiles of different body habitats in healthy individuals

Last week, we read “Human reference microbiome profiles of different body habitats in healthy individuals” (published here: www.frontiersin.org/journals/cel...)

In this study, the authors characterised the microbiome in blood, saliva and stool of 171 healthy/10 periodontal disease participants.

After a long hiatus, we’re back to writing up blog posts of our DalMUG journal club discussions! You can see all of our previous posts here: dalmug.org

We also changed the name of the new database - what seemed like a lighthearted joke a few months ago didn’t feel so lighthearted anymore. But the genomes and annotations within the database are not changed, so all of the information above in the thread is still correct.

I’ve also overhauled the Wiki pages a bit, so I hope it’s easier for users to find the information they need. It’s already available through conda but I’m still working on the Q2 plugin!

PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2 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.

We’ve now updated the PICRUSt2 new database preprint!

www.biorxiv.org/content/10.1...

No major changes here: the database used is the same but we’ve added some comparisons of computational resources required and a few extra discussion points.

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

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:

rdcu.be/eg4OA

1/

A call for healing and unity | mBio 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.

My editorial simultaneously published in all of @asm.org's journals addresses the ongoing effort by the administration to halt efforts to diversify science. It should be obvious from ASM Journals' efforts over the years, but we aren't fans journals.asm.org/doi/10.1128/...

Congratulations!! 🥳

I’ll be working to get it integrated with the @qiime2.org plugin and available through bioconda soon!

We’ve also expanded the number of EC number and KO annotations by about 1.3-fold, and it’ll be easy for users to add their own functions to the database with HMMs now.

The new database is included from PICRUSt2 v2.6.0, and if you use it, we’d love to hear your feedback on it!

This has expanded the number of genomes present from 19,493 to 26,868 bacterial and 406 to 1,002 archaeal. This means that the genomes more closely match study sequences and therefore better represent a range of different environments.

We now use genomes annotated with Eggnog and phylogenetic trees from GTDB, so we can easily update the genomes as well as the functions included in the future.

Figure giving an overview of the PICRUSt2 database - Figure 1 from the preprint. It includes the steps taken for database construction, functions included in the previous oldIMG and new MPGA databases, number of taxa included in both databases, composition of simulated samples, and the performance of the oldIMG and MPGA databases on the simulated samples from different environments.

I started thinking about how we could make the PICRUSt2 database easy to update and expand about 5 years ago now, so it’s exciting to finally have something that others can use!

PICRUSt2-MPGA: an update to the reference database used for functional prediction within PICRUSt2 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...

I guess I’ll start off on here with my last tweet?

I’m pleased to share my new preprint with @betascience.bsky.social, where we introduce a new database for PICRUSt2 functional predictions.

www.biorxiv.org/content/10.1...

Big news - part 1 of the 2025 Canadian Bioinformatics Workshop Series has arrived! Learn more and apply here: bioinformatics.ca/workshops/cu...