New pub with 57 new taxa

xvazquezc · March 10, 2026, 5:16am

Hi there,
We just published a new paper that includes 57 new taxa names already endorsed by the SeqCode, although still pending final approval. Many of them match extant placeholders in the GTDB (so they are indicated). The new names are in bold in the table below.
Thanks

Domain	Phylum	Class	Order	Family	Genus	Species	Type	Accno
Archaea	Thermoproteota	Nitrososphaeria	Nitrososphaerales	Nitrososphaeraceae	Nitrosobungeria gen. nov. (g__TH5893)	Nitrosobungeria shackeltonensis sp. nov.	BH-18_THE2	GCA_965610195
					Nitrosomicrobium gen. nov. (g__TA-21)	Nitrosomicrobium frigidum sp. nov. (s__TA-21 sp023251115)	BH-18_THE1	GCA_965610995
Bacteria	Actinomycetota	Acidimicrobiia	Acidimicrobiales	Iamiaceae	Aquihabitans	Aquihabitans niveus sp. nov.	BH-10_ACT1	GCA_965610895
			Spongiisociales (o__UBA5794)	Benthobacteraceae (f__UBA5794)	Gelisolibacter gen. nov. (g__JACDBE01)	Gelisolibacter meridionalis sp. nov.	BH-24_ACT7	GCA_965610425
		Actinomycetes	Actinomycetales	Dermatophilaceae	Cryoornithinimicrobium gen. nov. (g__Ornithinimicrobium_A)	Cryoornithinimicrobium bungerii sp. nov.	BH-23_ACT6	GCA_965610625
			Propionibacteriales	Nocardioidaceae	Nocardioides	Nocardioides polaris sp. nov.	BH-09_ACT11	GCA_965609905
		Aridivitia (c__UBA4738)	Actinopolaridales ord. nov. (o__CADDZG01)	Actinopolaridaceae fam. nov. (f__WHSQ01)	Actinopolaris gen. nov.	Actinopolaris aerotropha sp. nov.	BH-24_ACT26	GCA_965611235
			Actinosomnolentales ord. nov. (o__UBA4738)	Actinosomnolentaceae fam. nov. (f__UBA4738)	Actinosomnolentus gen. nov. (g__JACDCJ01)	Actinosomnolentus pattersoniae sp. nov. (s__JACDCJ01 sp013817655)	BH-20_ACT24	GCA_965609595
			Bungeriellales ord. nov. (o__JAHWKV01)	Bungeriellaceae fam. nov. (f__JAHWKV01)	Bungeriella gen. nov. (g__JAJCYE01)	Bungeriella frigidisoli sp. nov.	BH-23_ACT12	GCA_965612105
	Armatimonadota	Fimbriimonadia	Fimbriimonadales	Fimbriimonadaceae	Fimbriimonas	Fimbriimonas antarctica sp. nov.	BH-11_ARM2	GCA_965610675
	Bacteroidota	Bacteroidia	Chitinophagales	Chitinophagaceae	Panacibacter	Panacibacter polaris sp. nov.	BH-10_BAC2	GCA_965610815
					Wilkeslandia gen. nov.	Wilkeslandia alcanivorans sp. nov.	BH-09_BAC2	GCA_965609825
			Cytophagales	Hymenobacteraceae	Pseudopontibacter gen. nov.	Pseudopontibacter australis sp. nov.	BH-24_BAC1	GCA_965611985
		Ignavibacteria	Tepidiaquacellales (o__SJA-28)	Ventifactibacteraceae fam. nov. (f__B-1AR)	Ventifactibacter gen. nov.	Ventifactibacter hollidayae sp. nov.	BH-10_BAC5	GCA_965610795
	Cyanobacteriota	Vampirovibrionia	Obscuribacterales	Obscuribacteraceae	Psychroobscuribacter gen. nov.	Psychrobscuribacter pollutisoli sp. nov.	BH-10_CYA1	GCA_965610205
	Gemmatimonadota	Gemmatimonadetes	Cryogemmatales ord. nov. (o__JACCXV01)	Cryogemmataceae fam. nov. (f__JAHWKZ01)	Cryogemmata gen. nov.	Cryogemmata carboxiditropha sp. nov.	BH-18_GEM1	GCA_965609615
	Patescibacteria	Nanosomnibacteria class. nov. (c__UBA1384)	Nanosomnibacterales ord. nov. (o__CAILIB01)	Nanosomnibacteraceae fam. nov. (f__CAILIB01)	Nanosomnibacter gen. nov. (g__CALBLZ01)	Nanosomnibacter parvus sp. nov.	BH-11_PAT4	GCA_965609665
	Planctomycetota	Phycisphaerae	Phycisphaerales	Frigidisphaeraceae fam. nov. (f__UBA1924)	Frigidisphaera gen. nov. (g__JACVCS01)	Frigidisphaera bungerii sp. nov.	BH-11_PLA1	GCA_965611835
		Planctomycetia	Gemmatales	Gemmataceae	Cryolimnoglobus gen. nov.	Cryolimnoglobus antarcticus sp. nov.	BH-11_PLA2	GCA_965609865
	Pseudomonadota	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	Brevundimonas	Brevundimonas antarctica sp. nov.	BH-09_PSE1	GCA_965609585
		Gammaproteobacteria	Burkholderiales	Burkholderiaceae	Frigidisolicola gen. nov.	Frigidisolicola castellviae sp. nov.	BH-10_PSE17	GCA_965609575
			Dormimicrobiales ord. nov. (o__JACDCP01)	Dormimicrobiaceae fam. nov. (f__JACDCP01)	Dormimicrobium gen. nov. (g__JACDCP01)	Dormimicrobium murphyi sp. nov.	BH-24_PSE2	GCA_965610025
	Verrucomicrobiota	Verrucomicrobiae	Chthoniobacterales	Terrimicrobiaceae	Cryoterrimicrobium gen. nov.	Cryoterrimicrobium chapmaniae sp. nov.	BH-09_VER1	GCA_965610505
			Verrucomicrobiales	Verrucomicrobiaceae	Verrucomicrobium	Verrucomicrobium antarcticum sp. nov.	BH-11_VER1	GCA_965611755

m.chuvochina · March 16, 2026, 10:44am

Hello,

Thanks for notifying us!
Unfortunately, none of the type genomes made it to our database. There seems to be an issue with these assemblies, as they are not available via NCBI FTP as part of the Assembly Database. Thus, we could not download them to even consider for inclusion.

I recommend you contact NCBI and clarify with them. Let us know once the issue is resolved, and we hope to see them in the 2027 release!

Best wishes,

Masha

xvazquezc · March 16, 2026, 11:10am

Odd… I released the genomes months ago.

The only thing I can think of is that now any taxa with >1k genomes are not listed in the ftp, e.g. anything deposited as “uncultured archaeon” or “uncultured bacterium” won’t show up in the FTP. I don’t know if the GTDB deals with those, bc it’s a massive number of MAGs are at least initially deposited as such
See:
https://ftp.ncbi.nlm.nih.gov/genomes/genbank/archaea/uncultured_archaeon/latest_assembly_versions/README.txt

xvazquezc · March 16, 2026, 11:34am

The genomes are definitely in the ftp, e.g. Index of /genomes/all/GCA/965/610/505/GCA_965610505.1_BH-09_VER1
They were released in August

p.chaumeil · March 16, 2026, 5:01pm

Hi,

I took a look into why GCA_965610505.1 isn’t showing up. It seems like a mix of timing and classification issue.

Even though your genomes were released in August, they likely missed the cutoff for the RefSeq 232 assembly summary files we pulled early September.

However, the bigger issue is that NCBI has this genome assigned to the ‘soil metagenome’ taxon. Since that’s not strictly a bacterial or archaeal taxon
(more of an unknown lineage, see screenshot) it doesn’t show up in the specific assembly summaries our pipeline uses. I just checked the latest assembly summaries for bacteria and archaea, and its still not there.

You’ll probably need to reach out to NCBI to get the taxon ID updated to Bacteria or Archaea. Once that’s fixed in their system, our pipeline should pick it up.

Cheers,
Pierre

xvazquezc · March 16, 2026, 11:03pm

Thank you both.

I looked at my submission with ENA (I submitted with them), and afaik is all good with it… It’s seems to be an issue with them though… they changed the taxonomy of all 300 assemblies in the bioproject for the taxonomy of the biosamples

Let’s see how long they take to answer to my ticket…

m.chuvochina · March 17, 2026, 8:12am

Sorry to hear about that and hope that you can resolve this soon!