Robyn Wright
@robynjwright.bsky.social
• Microbial ecology/bioinformatics (microbiome/plastisphere) • Postdoc @ Dalhousie Uni 🇨🇦 • PhD @ Warwick Uni 🇬🇧🇪🇺 • usually found trail running around Nova Scotia with my dog 🏃🏻♀️🐶 • she/her •
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
December 1, 2025 at 12:23 PM
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/
December 1, 2025 at 12:23 PM
…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/
- 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/
December 1, 2025 at 12:23 PM
…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/
- 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/
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/
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/
GitHub - R-Wright-1/GeCoCheck
Contribute to R-Wright-1/GeCoCheck development by creating an account on GitHub.
github.com
December 1, 2025 at 12:23 PM
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/
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/
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/
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...
www.microbiologyresearch.org
December 1, 2025 at 12:23 PM
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/
Hope you and your family have a lovely day, looks beautiful!
October 13, 2025 at 3:15 PM
Hope you and your family have a lovely day, looks beautiful!
…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...
You can read our full discussion here: dalmug.org/blood-refere...
Human reference microbiome profiles of different body habitats in healthy individuals
Oh and Park (2025): Human reference microbiome profiles of different body habitats in healthy individuals.
dalmug.org
April 17, 2025 at 6:00 PM
…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...
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…
The authors also suggest that…
April 17, 2025 at 6:00 PM
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…
The authors also suggest that…
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.
In this study, the authors characterised the microbiome in blood, saliva and stool of 171 healthy/10 periodontal disease participants.
Frontiers | Human reference microbiome profiles of different body habitats in healthy individuals
www.frontiersin.org
April 17, 2025 at 6:00 PM
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.
In this study, the authors characterised the microbiome in blood, saliva and stool of 171 healthy/10 periodontal disease participants.
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.
April 10, 2025 at 12:43 PM
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!
April 10, 2025 at 12:43 PM
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!
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.
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.
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.
www.biorxiv.org
April 10, 2025 at 12:43 PM
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.
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.
Congratulations!! 🥳
February 23, 2025 at 6:22 PM
Congratulations!! 🥳
I’ll be working to get it integrated with the @qiime2.org plugin and available through bioconda soon!
February 20, 2025 at 1:37 PM
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!
The new database is included from PICRUSt2 v2.6.0, and if you use it, we’d love to hear your feedback on it!
February 20, 2025 at 1:37 PM
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!
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.
February 20, 2025 at 1:37 PM
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.
February 20, 2025 at 1:37 PM
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.
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!
February 20, 2025 at 1:37 PM
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!