Thanks for reading this thread - share link at

Thanks also to the reviewers including Alice McHardy - very fair and helpful we thought. We gratefully acknowledge the large collective effort expended in administering, gathering, sequencing and uploading metagenomes into the public domain in the spirit of open science.

Join millions who have switched to Grok.

Many many to thank, particularly @aroney_samuel,.@RossenZhao, Joshua Mitchell, Rizky Nurdiansyah Mitchell Cunningham @CoralSymbioses Gene Tyson @CMR_QUT and dozens of people who have helped with the software, ms, and everyone who tolerated my enthusiasm.

SingleM is BYO genome, you can add your MAGs to the refDB to get profiles which include both known species and your novel MAGs.

Novel lineage detection + 700k profiles makes it possible to recover novel MAGs from taxons you care about. We recovered new genera from the underrepresented Muirbacteria, Wallbacteria, Riflebacteria and Fusobacteria phyla by assembling the right metagenomes.

R226-based profiles from 700k public metagenomes are at Search for your fave microbe by GTDB taxonomy there and see to get prevalence and community profiles. Got something novel? Get in touch.

A new @rust4bio approach also helps - conserved regions are already aligned to each other so distance calcs become a vector similarity search problem. Big distance => novel species. Props to for awesome PR.

Fast and RAM-efficient since most raw reads are swiftly ignored. We optimise an up-front DIAMOND BLASTX-based method. Thanks @bbuchfink / Serratus for makeidx

Perhaps most strikingly, it detects microbes that aren't in the ref db, correctly weighting their relative abundance.

It's accurate on communities of known species / non-rep strains (though can struggle with low abundance species where coverage <1X)

SingleM is a new approach to metagenome profiling. It uses conserved regions within marker genes (20aa) spanned by individual short reads. Concentrating analysis on these regions makes things easier.

This is after the huge mining efforts of SPIRE @BorkLab, SMAG, OceanMAGs etc.

In environmental samples 75% lack a genome/MAG (abundance-weighted). We aren't near to a genome for all species, not even close.

Out in @NatureBiotech: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at A 🧵

RT @Pam_Engelberts: Very excited to share the first paper out of my Postdoc @CMR_QUT:. GenomeFISH: genome-based fluorescence in situ hybrid….

RT @CMR_QUT: Our newest tool, CoverM, a unified software package which calculates several coverage statistics for contigs and genomes in an….

RT @ConversationEDU: Until now, it's been very hard for scientists to establish a detailed timeline of the early evolution of bacteria. @ww….

I learnt a whole here, from Phil Hugenholtz, Gergely J Szöllősi, Tom Williams, Adrián Davín, and many others who I have yet to meet in person.

We used Great Oxidation Event as a planet-sized "fossil" to add ancient dates to the Bacterial tree of life. The Conversation and @ScienceMagazine articles show oxygen was used by non-cyanos before that cataclysm, surprisingly.

RT @CMR_QUT: Congrats to CMR PhD student Brett Babec for taking home the best student speaker prize at this year's MGE Aus meeting 🥳 And an….