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:

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

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.

http://theoatmeal.com/comics/pens

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
• ST95 has a human ancestor, has been found in meat and isolates have been obtained from poultry falling into ST95 characterized as APEC (Avian Pathogenic E. coli). So there is potential for human isolates moving into poultry, acquiring plasmid then spilling back over into humans and meat.
• ST117 has been an emerging APEC problem in poultry but there is evidence of spillover into humans and in food production animals (meat) and is causing sporadic spread.

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/)

MICROBE 2018 recap - Tales of Biogas Core Microbial Communities: The Research, The Rant, The Learning Process

"Research is easy! You have your hypothesis, your starting point, experimentation, perhaps some optimizations and options you take along the way followed by results, analysis and whalah, you are done and have forever changed the world..."

... SAID NO ONE EVER!

Here's an example from a mathematical modeling of infectious disease class I took several years back while still in grad school.

The plan:

Everything goes smoothly...splendidly even, and we all take tea breaks as our analyses run seamlessly without errors or missing/wrongly formatted data leading to a totally understandible, interpretable results that confirms all our hypotheses...

Reality:

By the end, I think we all just wanted a stiff drink.

And this is research! 

The glory and terribleness of it - it's exciting, frustrating and above all a learning process.

MICROBE 2018 recap - Tiny Drivers of Evolution - HGT in Microbes

Dr. Michael Brockhurst, University of Sheffield
Causes and consequences of horizontal gene transfer (HGT) in microbes

We are now in the world of temperate phages...and one plasmid that we'll hear about later.

• Temperate phages have a two-stage life cycle, lytic and lysogenic (where they 'hide' by integrating in the genome and becoming a prophage).
• So what are the benefits of interacting and integrating temperate phages as a bacterium?
• Lots of horizontal gene transfer
• Accelerated evolutionary adaptation potential - how so?
• When you have phages jumping in and out of genomes leaving and taking DNA with them, you have the potential for mutational events and rearrangements...genes get turned on and off - this is all fuel for evolutionary adaptation (or just death, ya death can happen too).
• Increased competitiveness

Story Time...

MICROBE 2018 recap - Antibiotics and Evolution of Resistance - Poster Talk Take Home Messages

So another round of Poster Talks, this time on Antibiotic Resistance...let's boil these posters down to their take home messages and provide some links for further information!

Anna Seekatz - University of Michigan
Longitudinal impact of prophylactic antibiotic use on the gut microbiota and antimicrobial
resistance genes

Methods: 

• Use of cefazolin, clindamycin, vancomycin
• Up to 7 stool samples collected before and after antibiotic administration
• 16S rRNA gene sequencing
• qPCR to identify antibiotic resistance genes
• Mixed model analysis

THM: "While ultimately your gut microbiota does 'drift' away from itself over time, a short pulse of antibiotics DOES produce a discernable 'bump' in the population composition immediately following antibiotic administration"

Further Reading:

• Seekatz, Anna Maria, and Vincent Bensan Young. "Clostridium difficile Infection and the Tangled Web of Interactions Among Host, Pathogen, and Microbiota." Gastroenterology 154.6 (2018): 1573-1576.
• Francino, M. P. "Antibiotics and the human gut microbiome: dysbioses and accumulation of resistances." Frontiers in microbiology 6 (2016): 1543.
• Shreiner, Andrew B., John Y. Kao, and Vincent B. Young. "The gut microbiome in health and in disease." Current opinion in gastroenterology 31.1 (2015): 69.
• Jakobsson, Hedvig E., et al. "Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome." PloS one 5.3 (2010): e9836.
• Raymond, Frédéric, et al. "The initial state of the human gut microbiome determines its reshaping by antibiotics." The ISME journal 10.3 (2016): 707.

MICROBE 2018 recap - Microbes that Know No Borders - Emergence and Transmission

Dr. Julian Parkhill, Sanger Institute
Signatures of emergence and transmission in bacterial pathogens

Dr. Parkhill has been involved on analysis of transmission and emergence of pathogens for almost 2 decades now. A glance through his publication record shows involvement in epidemic analysis and antimicrobial resistance in Burkholderia, Campylobacter, Neisseria, Legionella, Cholera, Mycobacteria and has assisted in the development of tools and analysis for better visualization and annotation of sequence data, faster phylogenetic analysis, whole genome sequencing, SNPs and AMR, population structure and much more.

Today we looked at Extraintestinal Pathogenic E. coli (ExPEC) and Uropathogenic E. coli (UPEC), and once again we are looking at ST131 in particular as we did in the AMR Highlights blog.

• ST131 clones are said to have emerged in 2000, sequentially acquiring fluoroquinolone resistance followed by beta-lactam resistance (blaCTXM15), rapidly expanded and have remained stable ever since in terms of population size.

But is this really 'emergence'?

MICROBE 2018 recap - Microbes that Know No Borders - AMR, Humans and Animals

Dr. Susan Sanchez is from the College of Veterinary Medicine at the University of Georgia. She is the section head for Microbiology and Molecular Biology, the Assistant Director of the Biomedical Health Science Institute and the Chair of One Health.

Her research interests include: (i) Antimicrobial resistance (AMR) spread in humans and animals (ii) Staphylococcus and Salmonella with a focus on MRSA and (iii) Diagnostic testing for zoonses present in animals.

Her talk focused on how AMR spreads between humans and animals. Interestingly she started off by saying her adviser had said a long time ago that clinical microbiology is dead, we have antimicrobials. I think we can all agree, that is not true. Estimates suggest that a failure to address AMR could lead to 10 million deaths by 2050.

MICROBE 2018 - A moment to appreciate Art, Anecdotes, Imagination and Stress Poop...

Taking a brief break to appreciate the imaginative and artistic side of the ASM General meeting...

1990s-esk Viewmaster! 

The vendors were out in full force with creative ways of drawing in the crowd including video games where you shoot microbes, lots of spin the wheels, scavenger hunts followed by a claw game and of course throw backs to the childhoods of many of the attendees such as Karius...

There were plenty of buttons to collect throughout the conference as you made your way through the exhibition hall listening to poster talks, viewing posters and perusing vendors. You could easily establish your pen collection for the next year and giant microbes are always a staple in many of the vendor give aways (red blood cell via Eppendorf) and Chicken Pox via ATCC.

In the world of art both Trilobite Glassworks and Artologica were in attendance as well.

HIV magnet - Trilobite Glassworks

ComputerPhage - Trilobite Glassworks.
Also featured, several stickers courtesy of
ASM and other vendor booths

The computerphage by Trilobite Glassworks was made almost entirely of computer parts salvaged by her husband. Given my husband is a software engineer I thought he'd get a kick out of that.

MICROBE 2018 recap - Bioinformatics - PhaME: from Reads to Genomes to SNP phylogenies and more...

Karen Davenport, LANL:

From Raw Reads to  Trees: Whole Genome Single Nucleotide Polymorphisms Phylogenetics Across the Tree of Life

This presentation may win for longest title.

So Los Alamos National Laboratories (LANL) puts out lots of different bioinformatics tools with their more well known tools, from my perspective, being PhaME (bioRxiv paper), EDGE (NAR paper) and GOTTCHA (NAR paper). 

I was a part of a group from WRAIR that tested their EDGE platform when it was originally being developed. While it has a lot of good software integrations (packaging up of open source software for pathogen detection, surveillance and other analyses), for me, 'black box' bioinformatics solutions always have their caveats. I see these 'all-in-one' answers as exploratory tools that require validation at the very least with other pipelines. Additionally, with the large software packages like EDGE, if there is no comprehensive manual or links to manuals of programs integrated into the system then I am suspicious of the 'default' settings and why they were set in that way. I've have had many a reviewer ask for justifications on my data analysis set ups and if you cannot justify your settings (default or not) then you don't understand what the analysis is really doing to your data. Perhaps I just have an innate distrust of machine default outputs.

To LANL and the EDGE team's credit this is posted on their readthedocs site for EDGE:

"While the design of EDGE was intentionally done to be as simple as possible for the user, there is still no single ‘tool’ or algorithm that fits all use-cases in the bioinformatics field. Our intent is to provide a detailed panoramic view of your sample from various analytical standpoints, but users are encouraged to have some insight into how each tool or workflow functions, and how the results should best be interpreted." 

Like they read my mind...this is good advice for any tool(s) that you use.

MICROBE 2018 recap - Bioinformatics - Microbial Genomes Atlas (MiGA)

So I don't typically tweet during meetings because it's hard enough to listen and take notes without attempting to be witty and post on twitter accurately at the same time, it's just not one of my gifts. My twitter account in general comes and goes much like this blog with my postings limited to what I find interesting in the field or what I am learning in the field. So - like this blog, my twitter goes dark here and there and lights up when I'm inspired to share. I'm impressed I have as many followers as I do - thank you faithful followers!

BUT, for this talk I found this amusing enough given we were in a bioinformatics software talk that we saw this...

@ASMicrobiology #ASMicrobe at the new #Bioinformatics Tools and Discovery session... While loading the talk on MiGA we get an "out of memory" error. The humor is not lost on me. pic.twitter.com/eJQ1xBDHcb

— Mel Melendrez (@UseqMiseq) June 8, 2018

"Out of Memory" is what that says. So I was amused for sure.

So I have my moments of within meeting tweeting.

During this talk we were updated on the Microbial Genomes Atlas (MiGA).

MICROBE 2018 recap - Bioinformatics - Comparison of Metaproteomics Tools

So Dr. Pratik Jagtap is from my current stomping grounds...Minnesota. He's a research assistant professor at the University of Minnesota, Minnesota Supercomputing Institute (MSI). His work focuses on tool development for proteomic analysis specifically for Galaxy-P and he has an impressive array of publications in the field. His latest 2018 offering:

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework

Stalking his twitter account it is chock full of great links to studies and research being conducted in the are of proteomics so if that's a field of interest to you I recommend you follow his account.

In this particular presentation he was investigating the latest metaproteomic software offerings and evaluating their performance with an oral microbiome set courtesy of Rudney and colleagues 2015. He wasn't specific as to which Rudney 2015 article but I'm guessing it's this one - which appears to have links to fastq datasets from an oral microcosm study. Or it could be this publication from 2015 which Rudney is on, but not first or last author which talks about an oral microbiome dataset used specifically for Galaxy P, though I cannot be sure because the article is paywalled.

Comparison studies in bioinformatics are always informative because it sets down metrics by which we can start using to interrogate these programs and evaluate which ones are best for our experimental design, which are potentially flawed, what are the pros and cons for each such that we can justify their use or exclusion in our studies.

MICROBE 2018 recap - Bioinformatics - Machine Learning and Microbial Ecology

I confess...if 'machine learning' is in the title I am immediately crawling into my hole of computational fear at the impending deluge of terminology I will most likely have to google 90% of.

I was pleasantly surprised with Demetrius' presentation - so kudos on describing how machine learning is applied to microbial ecology and making it palatable for those of us unversed in machine learning.

Demetrius DiMucci: Boston University

A machine learning approach for predictive and 

explanatory microbial ecology

I really liked how Demetrius started off, my imperfect quote, more of a paraphrase below:

"Pretend you are a community ecologist - who has isolated your community and sequenced everything that is there. With thousands of organisms you want to learn what's causing the function of this community... a typical approach is 'reductionist' meaning you isolate using media (culturing). This is quite impractical for 1000's of organisms, so what do we do? We cheat!"

Always a great way to grab attention... Let's Cheat!

MICROBE 2018 recap - Bioinformatics - Gi-Scanner

So half, if not more, of my life is dedicated to using (and breaking) bioinformatic software, so of course, when I heard there was a whole poster talk session on new bioinformatic tools I grabbed my computer staked out a sweet spot where I could charge everything up and waited for the black-box buttons to be pushed...

Dr. Sophie Shaw (right) and I

Before I jump in...a shout out to my lovely fellow bioinformatician who I haven't seen in 4 years (we met at the Workshop for Genomics in 2014) yet prolifically follow on twitter and instagram. We found eat other at Daniel McDonald's poster presentation for the American Gut Project...awww Dr. McDonald bringing together globally floating around bioinformaticians since 2018.

Alright - back to the session: First up -

YoungJae Hur, Seoul National University: 

Gi-Scanner: An algorithm to predict genomic islands by 

comparative genomics

So, the first thing I typically do when someone touts a new piece of software is google/google scholar it. I want to find the software page...github, sourceforge, lab webpage - I like going to the source, looking at documentation and making my own assessments. Alas for Gi-Scanner it is not published or available on a website yet. I was a bit confused in the presentation as to whether we were looking at a piece of software to identify genomic islands OR if we are waiting on a database of genomic islands for V. cholerae identified by their software but that their software may not actually be available for public use. I want to think the former - that the software will be readily available soon and that the database will also be published/available for those interested in particular with V. cholerae.

MICROBE 2018 recap - MicrobioOMG - American Gut

Everybody Poops!

So I met Daniel McDonald several years ago when I was involved in the Workshop for Genomics which takes place in the Czech Republic every year (register it's awesome!). Avid python programmer, working in Rob Knight's group (I profiled Rob Knight for the genomics workshop in 2014), involved in coding and all things metagenomic using a tool called QIIME.

Quick plug for QIIME2. I am a bioinformatician...which means I am routinely breaking software in the name of biology! I am also a self-taught programmer (yes, my software engineer husband gasped at that too), which means, I can read code but I'm still a novice at writing it. SO, I know just enough to be truly annoying to these bioinformatics software developers. The QIIME crew are really fantastic and you don't have to fear about posting questions on their forum, unlike Stack Overflow which few novices would ever dare post on. They are supportive and really want you to use their tools and make them better, shout outs to Thermokarst and Nicholas_Bokulich who have dealt with me. Two more of the biggest metagenomics analysis packages that I have used are:

• MOTHUR v1.4 (Pat just recently overhauled the package, I have yet to dive in. He offers a ton of workshops on Mothur and R by the way)
• Github
• Wiki
• Workshops
• MGRAST - Completely online, nice crew of developers routinely overwhelmed which is good and bad right? You have tool that is so streamlined it's becoming super popular and everyone wants to use it, but that means finding the funding and manpower to keep it going. It's a very slick interface. They are very responsive to helpdesk emails. There are limitations and make sure you know what you are doing with your data when you set up the analysis. The metadata input is very specific in it's requirements so don't be shy about asking questions if you get errors in uploading. Sometimes using their API is a lot faster than the GUI interface on the webpage. At least that's been my experience.

I digress - back to the American Gut Project!

MICROBE 2018 recap - Astrobiology: Ancient Fats and Modern Genes

Paula Welander is an Assistant Professor of Earth System Science at Stanford University. Her lab is
focused on lipid biomarker studies in modern bacteria, specifically hopanoids and sterols. On her page she discusses the interest in lipids preserved in the rock record and how they might be signatures of early life, however we know little of evolutionary history and function of these molecules in modern bacteria. Without a fuller understanding of the function and history of these molecules in the 'here and now' it becomes difficult to interpret what we are seeing in the rock record. Her lab aims to fill this gap.

So let's learn about some 'fat' microbes.

MICROBE 2018 recap - Astrobiology: Linking phylogeny, physiology and the rock record

Alright...admittedly the full title of this one was a bit scary for me as the only words, or more accurately, word, I really felt I had a grasp on was 'phylogeny' - yes that was it, 17 words in this title and I was like "I know what a phylogeny is":

Energy controlled distribution of isotopes in biocatalytic systems: A means of linking phylogeny, physiology and the rock record.

But I powered through.

Shawn McGlynn is from the Tokyo Institute of Technology, Earth-Life Science Institute (ESLI) his research interests include - microbial interactions, metalloproteins, early life and it's emergence, stable isotope techniques and microbial ecology. 

To learn more about his research and love of of Japanese hot springs check out his Research Story: Bridging disciplines and continents and check out his google scholar profile.

So we start with the question of:

"How do we elucidate the history of biological catalysis with the material record (sulfur isotopes)?"

MICROBE 2018 recap - Astrobiology: The History of the World, A Microbial Perspective

So I made it on time to this session...

Before I launch into the glory of astro-micro-biology - I was amused by the starting comments of the session. ASM hands out guidelines for sessions that include the suggestion that you should present learning objectives for the session...so we know what we are getting ourselves into. This was the only session where I saw this presented. It was actually kind of neat; high school student, college student, graduate student, seasoned full professor-die-hard-academic... we all benefit from organizing our thoughts and goals. So kudos to the Astrobiology session for doing this! And kudos to ASM for their app on this meeting - it made tracking and zooming to sessions as well as 'rating' sessions and talks very easy.

Jennifer B. Glass is an Assistant Professor at Georgia Tech with a primary research interest in Biogeochemistry. If we shamelessly stalk her on google we find her interests include: (i) anaerobic oxidation of methane, (ii) greenhouse gas cycling - focus methane/nitrous oxide, (iii) biogeochemical cycling (iv) marine microbiology as it pertains to anaerobic metabolisms (v) integrating omic and geochemical datasets and (vi) coevolution of microbial metabolisms and ocean chemistry over Earth's history - whew!

She's been a NASA Astrobiology Postdoc, PEO Scholar and NSF Graduate Research Fellow and if you'd like to take a look at her lab and research check out her website and google scholar profile!

My favorite part of her lab page -

Failure required, tears optional, please don't lick the science!