MICROBE 2018 recap - What's New in the Tree of Life?

So I started the meeting in great form...late for the the 'Meet the Experts' Session! DOH! But I did get to hear quite a bit from Barny Whitman and Brian Hedland about the state of taxonomy today.

Notable tidbits:

• We all know that funding is scarce in this administration (insert ugly cry face) but it looks like studies trying to tease apart taxonomy are particularly underfunded despite the interest (and huge debate!) in the topic - about 2% funding for taxonomy.

The huge debate you ask? Yes - I dare you to walk into a bar of microbiologists and yell "OTUs forever, species SUCK!" or "There are no species!!!!" - My guess is you'll start running very quickly from the mob with pitchforks and lighted torches soon.

Why the debate? Well historically before we had molecular techniques to assist in defining or analyzing microbes what did we have? A microscope and chemical assays to see what the bugs were eating and producing right?

ASM MICROBE 2018 DISPLAY

That's some bad-ass sketching if I don't say myself.

So organisms were classified on shape (bacilli, coccoid, bacilli-coccoid, filament...), chemical assays that define cellular metabolism or cell components (ie. cell wall). Lumen learning has a quick decent breakdown of this if you are interested. Hum over the phylogenetics portion if you are unfamiliar with this but the other sections in this post are a good primer for how we go about organizing the chaos - Lumen Learning Methods of Classifying and Identifying Microorganisms.

Chaos? Yes - because as the advent of sequencing, especially high throughput 'next gen' sequencing, came about all of a sudden we had genetic information to complement morphology.

ASM MICROBE 2018 DISPLAY

If you are interested in how we go about using high throughput sequencing to do a variety of studies - check my (now outdated) Blog Series on the Workshop on Genomics (click on the Blog hyperlinks in the schedule) and then if you are intrigued and in the field - go take one of their Workshops!

With sequencing studies we were finding the microbes which we thought were in the same species were actually quite different genetically and it was becoming difficult to reconcile or find a 'threshold' or 'gold standard' for how we can marry morphological characterization and genetic cut offs. It started and is still held to some degree that 70% DNA/DNA hybridization or 97% 16S rRNA homology were gold standards for defining species then the topic of average nucleotide identity between genomes (ANI) popped up. Tiedje's group has a nice 2007 paper on these terms and their correlations. 

So DO microbes form species or OTUs or nothing at all? I could spend a lot of blog acreage breaking this down but there are several lovely publications on the subject that I think you should check out and make your own decision - pick up a beer and join the debate!

Doolittle, W. Ford, and R. Thane Papke. "Genomics and the bacterial species problem." Genome biology 7.9 (2006): 116.

Papke, R. Thane, et al. "Searching for species in haloarchaea." Proceedings of the National Academy of Sciences 104.35 (2007): 14092-14097.

Gevers, Dirk, et al. "Re-evaluating prokaryotic species." Nature Reviews Microbiology 3.9 (2005): 733.

Cohan, Frederick M. "What are bacterial species?." Annual Reviews in Microbiology 56.1 (2002): 457-487.

Becraft, Eric D., et al. "The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park." Frontiers in microbiology 6 (2015): 590.

Olsen, Millie T., et al. "The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat." Frontiers in microbiology 6 (2015): 604.

Nowack, Shane, et al. "The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light." Frontiers in microbiology 6 (2015): 626.

Dixit, Purushottam D., Tin Yau Pang, and Sergei Maslov. "Recombination-driven genome evolution and stability of bacterial species." Genetics 207.1 (2017): 281-295.

Rodriguez-R, Luis M., et al. "How much do rRNA gene surveys underestimate extant bacterial diversity?." Applied and environmental microbiology (2018): AEM-00014.

and finally - just click on this link to learn how metagenomics has contributed to the conversation! 

This but scratches the surface! If you come across more or pinnacle publications please post in the comments.

• If you are looking for funding to sequence your organism - check out JGI they fund microbial genome sequencing projects to bolster the microbial genomes available in the databases.

The Joint Genome Institute does have an impressive array of a variety of genomes and several tools you can use to compare publicly available genomes. Check out their Integrated Microbial Genomes and Genome Portal links. 

In terms of 'how do we define or know if we have a new species?', this question still persists. In the session the question was brought up on how you 'publish' a new species really? Do you have to culture/isolate it? Do you have to sequence it and show a genetic cohesiveness to the organisms you are calling one species? With molecular techniques taking off - finding the uncultured world (microbial dark matter) the bottleneck becomes getting these isolated cultures and yet we are seeing new species defined everyday in the literature based on genetics and a defining 'feature' not seen before in named species. Barny's comment on that was pretty much - well the gold standard remains, get a xenic (pure) culture - BUT if you can get a reviewer to buy your arguments and evidence of calling a bacterium a new species based on genetic analysis and perhaps a defining metabolic feature then have at it. Each journal will have it's own set of metrics and will ultimately decide, however to get your organism into culture collections as a 'new species' it would need to be in pure culture and submitted/described as such. There are no real regulations or 'best practices' in place for how you go about taking your unknown and figuring out if it 'qualifies' as a new species, you have to just see how similar it is to what is known, follow the super lose guidelines, maybe try and get it into culture, figure out what is novel about it then write it up - submit is and cross your fingers right?

A google search for best practices in microbial species classification doesn't turn up any guidelines...but it does turn up many parts of the debate and a lot of suggestions. 

So the debate continues...