Tuesday, July 3, 2018

Microbiome - How important are the sample space and it's structure?

Another great talk from the symposium on probabilistic microbial modeling...

TLDW Highlights...and links to further reading, term definitions, concept reads and their upcoming workshop etc...

Microbiome abundance or relative abundance...that is the question?!

Really great talk by Shayamal Peddada about metrics for measuring and comparing abundance/relative abundance within and between microbiome samples.

Worth a watch!

For those TLDW (too long didn't watch)...

Saturday, June 23, 2018

MICROBE 2018 WrapUp - a note about Mentorship...

Disclaimer! This is a lengthy one!

25 blogs later, ASM Microbe 2018 was a jam packed conference for me! These meetings are blessings and curses because there is so much awesome stuff to see and listen to and not enough time to 'do it all'. But I am always excited when I am able to participate.

If you liked this series, I have other series posted as well, feel free to follow the blog and you'll get notified when I start posting again...hopefully. Before I sign off and my blog goes dark (until my next 'learning adventure') I wanted to take a moment to chat about mentorship.

It's challenging, being a woman in science.
It's challenging, being a minority in science.

It's difficult to get funding for everyone, especially new investigators. You have to have a track record before you can apply for funding and yet you cannot develop that track record easily without funding. It's like being offered a packaged up pair of shiny new scissors and then realizing you NEED a pair of scissors to open the package to begin with... *facepalm*

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:

Friday, June 22, 2018

MICROBE 2018 recap - Evolution of Tuberculosis

So it's Sunday...the meeting started Thursday night. Usually about this time, depending on how ambitious your schedule for the meeting, you are starting to get a little peek'ed and the sessions are starting to run together. For me - a good deal of money is spent coming to these conferences so I have a tendency to pack my schedule. This often times ends in overlapping sessions necessitating a cost/benefit analysis of whether I should risk missing the beginning of the next talk by running to the session after this one or stay in this session and listen to a talk that is perhaps less "soul-on-fire" interesting for me. In either case, you start tapping your coffee IV to make sure it's running only to realize that by this point you've probability built up a super human caffeine tolerance. Yet you still grab that cup and hold it at the morning sessions with such care and possessiveness you would think it a pot of gold.

So major kudos to Caitlin Pepperell and her ability to recapture my attention as my first coffee wore off and I started in on coffee #2. It helps that my next favorite bug - after Vibrio, is Mycobacteria

Evidence I stayed awake...the whole time:
You can decipher my notes above or just read the recap below.

MICROBE 2018 recap - Ancient Infectious Disease - Paleomicrobiology

So for this session and the rest of the meeting my laptop decided it no longer wanted to hold a charge so I was relegated to using old school methods of taking notes...my notebook and a pen! Gasp.


Didier Raoult, Faculte de Medecine; IHU Mediterranee Infection
Paleomicrobiology: Human Infections and Antiquity
"Everything was called plague back then..."
There was the Thucidides plague in Athens, the Antonine plague, Justinian plague, Black Death,then the post Columbian era syphilis and 'eruptive fever' (measles and smallpox) followed by the great wars and lice; Douai (18th century), Napoleon (19th century), WWI in the 20th century and the Bolshevic revolution.

Needless to say there's a lot of disease in our human history leaving an indelible mark...that we can find in frozen tissues, fixed tissues, mummies, bone and teeth. The most popular technique or perhaps the most used methodology you would start with in detection of pathogens is PCR.

MICROBE 2018 recap - Jumping back into AMR for a moment...

As you can probably tell I attempted to hop into as many AMR sessions as possible as that is a primary interest of mine...

So before we finish off this blog series on some ancient infectious disease and microbial ecology (upcoming...) let's hop back in briefly to Dr. Lance Price's talk and hit some of his highlighted points.

Lance Price, George Washington University
Expanding our view of zoonotic pathogens: How genomics is revealing insidious host jumps and AMR transmissions

  • So we've heard a lot about E. coli ST131 this meeting - it's broad host range, extensive resistance and wide geographic dispersal globally.
  • So in thinking about these AMR pathogens spread particularly in E. coli were learn this a lot of overlap of these E. coli STs (isolates) within the meat market and clinic. They have their own clusters, but there is also overlap.
  • Through phylogenetic analysis of different STs of E. coli we find both human and 'meat' clade ancestors suggesting independent host jumps.
    • ST10 and ST38: ancestor in meat, yet found in clinical isolates
    • ST12 found to have humans as the ancestor but has been found in food animal production isolates
  • But it's not just limited to human <> meat...enter poultry, APEC and the ColV plasmid
So policy? Given the expanding issue of these isolates many with AMR in our food animal production line... what is being done?

California has now restricted use of antibiotics in animals.
(the actual senate bill if you are interested, SB27)

  • This is all good but in the event that these jumps have already occurred and establishment of these AMR strains has happened in humans. Legislation of this sort will have little effect.
  • BUT it does have the potential, if followed long enough, for 'washing out' of sporadic spreaders.
From post about Canada's growing problem of antibiotic resistant bacteria being found in meat
and there being less food inspection agents. (https://eatinggreener.wordpress.com/tag/antibiotics/)