MICROBE 2018 recap - Microbial Ecology: Theory, XenoGI and Nanoarchaea!

So the final session I attended I was really excited about because it's a blast from my PhD past, jumping back into microbial ecology theory and extremophiles!

Eugene Koonin from NCBI started off the session discussing complexity and simplicity in the genomic era.

"No one can properly define complexity [and yet] we know it when we see it."

• When we look at gene families, we find that 70-80% of genes in prokaryotic genomes are evolutionarily conserved, belong to COGs, are apart of orthologous lineages and can be considered 'distinct evolutionary units'.
• The rest we call ORFans - comprising 10-15% of genes within a genome. These can either be 'real' or errors in annotation.
• As you increase phylogenetic distance you begin to see a decay in gene content similarity
• Simplicity is 'genome streamlining'
• Complexity is 'gene accumulation'
• Larger effective population sizes are going to limit complexity due to strong selection which will lead to genome streamlining.

To learn more about Koonin's work, check out below and also his google scholar profile:

• Genomes and Protein Universe
• Orthologs, paralogs and evolutionary genomics.
• Computational methods for gene orthology inference
• Functional and evolutionary implications of gene orthology

Eliot Bush, Harvy Mudd College
Reconstructing the history of genomic island insertions in clade of microbes using Xenogi

• Eliot presented his work on Xenogi available on github.
• So there's quite a bit software designed to detect islands in single and multiple isolates but Xenogi does this within in the context of their phylogeny; Xenogi does. This allows for the identification of islands shared between strains in a clade or determine the branch on the tree when/where this island was inserted in the organism.
• The process:
• Get genomes from Genbank at the scaffold level with synteny (gbff files)
• Phylogenetic tree input (newick format)
• The program does a global alignment and calculates synteny scores, builds gene families with the most recent common ancestor placed within the species tree, then merges the families into islands that have a common origin via a parsimony rearrangement score (check out paper).
• The output is text and BED formatted files
• They can do 4-5 genomes in about 10 min
• To do 40 genomes on a computer with 500 GB RAM it'll be about 20 hours.

You can download this program via Github OR use the Web Interface version.

Anna-Louise Reyesenbach, Portland State University

Nanoarchaeota

Source

• Nanoarchaeota is an archaeal lineage symbiotic with Crenarchaeaota.
• Nanoarcheaota exist in diverse environments and are adapted to different hosts.
• But they have not been isolated from everything - despite being inferred via 16S rRNA surveys to be widespread.
• Nanoarchaeota like to 'stick' to their hosts however have been isolated by themselves (unattached) from samples in New Zealand (visualized via electron microscopy).
• We have now been able to detect nanoarchaeotes in Yellowstone National Park, New Zealand and deep sea hydrothermal vents.
• Deep sea nanoarchaeotes are more similar to terrestial hot spring nanoarchaeotes.
• All nanoarchaetoes are ectosymbionts
• In experiments it was found that Nanoarchaeum equitans can 'scout' for new hosts - it's 'host-proper' Ignicoccus hospitalis is not around. It can attach to different hosts but this relationship is unstable and will only support a few cell divisions.
• Genomic analysis of nanoarchaeotes from New Zealand and Yellowstone National Park show they both have cycles for glycolysis and gluconeogenesis, contain archaeal flagellar genes that are expressed and lack ATP synthase.

For more on the wild world of Nanoarchaea and thermophiles check out:

• Genomics informed isolate and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment
• Some great figures in this publication
• Genetics, genomics and -omics of thermophiles

Elio Schaechter from ASM "Small Things Considered" had a nice blog post on Nanoarchaea from 2009 if you want to have a look..."A happy hot couple". 

I first became acquainted with Anna-Louise's work while a graduate student in Dave Ward's lab at Montana State University and I have always enjoyed her presentations - her lab does some great work.