Thanks, we also implemented the Qiime2 pipeline with SILVA reference as wrapper script – it works well :-)

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

Don't miss out on the 3rd West Pacific Marine Biology Symposium @ UQ Brisbane, 25–28 Nov.

Reg & abstracts open: tinyurl.com/wpmbs2025
Early-bird regos now extended to 14 Oct, so you can still secure discounted registration rates!

@cnrs.fr
@cnrsbiologie.bsky.social
UQ Centre for Marine Science

- Tangaroaeota phyl. nov. (former RBG-13-66-14)

- Ryujiniota phyl. nov. (former UBA6262) and

- Spongiamicota phyl. nov. (former UBA8248)

In summary, we contributed to the understanding of taxonomic and functional diversity in benthic prokaryotic communities across Western Pacific sediments.

... aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments.

We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages & proposed names for 3 phyla:

- metagenomics based taxonomy revealed clusters across all samples, that mainly aligned with depth & sediment type

- Thermoproteota & Asgardarchaeota were the most abundant archaeal phyla; Archaea relative abundances > 50% in some samples

- Metabolic capabilities ranged from ...

Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent o...

Led by @Jiauri Sun & in collab with @Takuro Nunoura and team - we analysed shallow coastal & deep subseafloor sediment cores (0.01 to 600m below the seafloor) in the Western Pacific:

www.microbiologyresearch.org/content/jour...

We found that:

GTDB Release 10-RS226 (16th April 2025) has been published
gtdb.ecogenomic.org

Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released!

(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)

ecoevorxiv.org/repository/v...

... there is now (2025) a new rule 72 in the ICNP that says "if ... the proposed name is a synonym of a pro-validly published and pro-legitimate Candidatus name of the same rank, then that Candidatus name must be reused"

Yes, it will be interesting to see how this all plays out - SeqCode vs ICNP.
Using previously introduced names is beneficial indeed, and supports taxonomic stability. It seems that the ICSP has realised that as well ...

Re Minisyncoccota paper #1: Besides the Code controversy, it is a good and longstanding practice to consider previous names, when proposing a new name for a lineage. Unfortunately, these authors did not consider this.

But, there is obviously a controversy brewing when it comes to authors publishing names under the ICNP that are in conflict with #SeqCode validated names. This is possible since the ICSP does not (yet) recognize SeqCode names. Hopefully that will change soon.

Not so fast 😊 , #Patescibacteriota is a validly published phylum name under the #SeqCode and is here to stay ;-)

Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous bacterial phylum Patescibacteriota phyl. nov. Abstract. Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metaboli

Originally defined by Rinke et al. (2013) as Candidatus Patescibacteria, the phylum #Patescibacteriota now has a validly published name and an official type!

Explore the lifestyle, biogeography, and metabolic capabilities of its type genus, #Patescibacterium, here: doi.org/10.1093/isme...

#SeqCode

Btw based on phylogenetic diversity, #Patescibacteriota is the fourth-largest phylum in the bacterial domain 😀

The paper:

- covers nomenclatural types for higher ranks including the phylum Patescibacteriota

- includes genomic characterization, metabolic reconstruction, and biogeographical analysis of Patescibacterium

- explores the occurrence of long gene coding insertions in the 23S rRNA sequences

Proposal of Patescibacterium danicum gen. Nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. Nov Abstract. Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metaboli

Great collaboration with Phil Hugenholz @xrefugee13.bsky.social, Tanja Woyke, Per Halkjær Nielsen, and many more:

"Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous bacterial phylum Patescibacteriota phyl. nov."

doi.org/10.1093/isme...

Hmm seems like bsky is not like Twitter/X once was, not much of a discussion here ... or nobody does amplicon sequencing any more 🤣😱🤔

Futuristic visionbof a rRNA gene analysis pipeline, illustrated by AI

#Amplicon #16S pipeline in 2025

Hi all, since my lab has moved (from ⛱️ to ⛰️), we now need to establish a new #Amplicon pipeline, mostly 16S but also ITS (fungi).
So my question is, is QIIME 2 still state of the art, or are there other/ better tools/workflows out there now? Thanks ☺️

Best #paper #acknowledgements ever 😀
So honest.

"Thanks finally to five anonymous reviewers .... and to R.N. whose editorial generosity bears no small responsibility for this paper's rescue from an early grave. .... I've supplied all errors myself."
doi.org/10.1093/jos/...

Bluesky’s science takeover: 70% of Nature poll respondents use platform Roughly 6,000 readers answered our poll, with many declaring that Bluesky was nicer, kinder and less antagonistic to science than X.

Roughly 6,000 readers answered our poll, with many declaring that Bluesky was nicer, kinder and less antagonistic to science than X

https://go.nature.com/42tH8Ai

Apoorva Prabhu (@aprabhu90.bsky.social) Postdoctoral Research Associate - Sydney Institute of Marine Science Honorary Postdoc- University of Technology, Sydney PhD at the Australian Centre for Ecogenomics, The University of Queensland, Bri...

Big congrats to aprabhu90.bsky.social - this is the 2nd paper from her PhD project! 👏

Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses Our spatio-temporal metagenomic study of a subtropical estuary successfully identified viruses and their potential hosts. Viral contigs were detected using a consensus approach comprising geNOMAD and...

New #marine #virus paper out 😀
"Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses"

> we proposed 2 new Magrovirales families:
- Apasviridae (magrovirus group A)
- Krittikaviridae (magrovirus group E)

> and 1 new order:
- Adrikavirales

doi.org/10.1111/1462...

Have you tried it?

Great 👍

Christian Rinke ‪Prof in Environmental Microbiology, University of Innsbruck, AUT & Honorary Associate Prof, UQ, AUS‬ - ‪‪Cited by 16,361‬‬ - ‪microbial evolution & ecology‬ - ‪multi-omics‬ - ‪microbial plastic degra...

Please add me as well:
scholar.google.com.au/citations?us...

The #microbial #climate #feedback hypothesis is already becoming reality ...

"shift in methane carbon isotopes suggests microbial emissions drove record high atmospheric methane growth"
#science 🧪
www.pnas.org/doi/10.1073/...

If archaeal viruses count, please add me as well- cheers

Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. nov. https://www.biorxiv.org/content/10.1101/2024.11.01.618662v1 Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall

Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. nov. www.biorxiv.org/content/10.1101/2024.11....