JAMS10: Day 2’s a journey through antibiotics, hot spring microbes, microbiome medicines, more nitrifiers, attachment, and scientific thinking

Day 2 of the JAMS10 Symposium started with Tim van Opijnen from Boston College giving us a whirlwind tour of his lab’s work on detecting antibiotic resistance mechanisms, using entropy as a predictor for an organism’s fate and the hundreds of ways tolerance can occur in an antibiotic specific manner. Next up was Dianne Newman from California Institute of Technology discussing the agathokakological (a mix of good and evil – love a vocab lesson to start a talk!) roles for redox active phenazine antibiotics produced by Pseudomonas aeruginosa

The third presentation in the session was Roland Hatzenpichler from Montana State University introducing us to metagenomic studies of archaea from Yellowstone Hot Springs, a relatively low complexity environment, to test hypotheses about organisms predicted to be methanogenic. The final speaker in this international session was Ashlee Earl from The Broad Institute of MIT and Harvard giving us insights into Enterococcus. Big props to Tim and Ashlee for planning ahead for the effects of a hurricane and pre-recording their talks!

In the afternoon the second poster session was held along with a panel session on working outside academia. Four scientists with diverse positions came together to discuss their paths from their PhDs out of academia, how they picked up the necessary skills for their current roles and how much they rely on their technical training in their everyday work. It was inspiring to hear that some panellists didn’t know what they wanted to do, even at the stage of completing their PhDs, that non-linear career paths are normal and there can be plenty of successes and satisfaction on a non-traditional career path after a PhD.

The afternoon international session started off with Samuel Forster from Monash University walking us through developing medicines using information from microbiomes, followed by Iruka Okeke from the University of Ibadan discussing adherence in E. coli, the exceptional bacterial coloniser of the digestive tract. Sebastian Lücker from Radboud University Nijmegen continued the conversation on nitrifying organisms and in situ detection of nitrifying microbes in complex samples.

These presentations were followed by Lone Gram from the Technical University of Denmark exploring why bacteria produce antibiotics and if they truly are secondary metabolites. The final speaker of this session was James Prosser from the University of Aberdeen who wrapped up the talks with a fascinating discussion (without any slides!) of scientific thinking in microbial ecology including inference, biased hypotheses based on arbitrary observations, assumptions and qualities of good hypotheses. Jim put forward the idea that it’s not technical challenges that limit progress in microbial ecology, but a lack of a scientific approach. 

The last task of the day was to wrap up the conference and announce the prize winners. Shang Yu Shueh was awarded the JAMS Community Advancement and Co-operation Award (the trophy is a toilet seat to recognise that the winner got sh*t done!). The wonderful support of the sponsors allowed for many poster presenters to be recognised for their hard work. Congratulations to all the winners!

Thanks to the JAMS10 organising committee for another excellent microbiology meeting and for creating a space for environmental and fundamental microbiology. The team of 45 pulled off an extremely professional event after pivoting from in-person to online with short notice. The only thing that was missing was the roar of applause at the end of a fabulous symposium! For more information visit jams.org.au or check out the #JAMS10 hashtag on Twitter.

JAMS10: SARS-CoV-2, fungal tree of life, halogenated pollutants, nitrifying microbes, symbionts and machine learning (and it’s only day 1!)

A new world needs a new way of conferencing and JAMS has taken full advantage of new technologies to make that happen. This year marks the 10th annual symposium of Joint Academic Microbiology Seminars (JAMS) so, despite the COVID-19 pandemic, the executive committee was determined to get everyone together to celebrate. 

New outbreaks around Australia and the world meant getting together in person was off the cards, so the team quickly pivoted to use GatherTown to create a custom online meeting place called JAMSTown. Every attendee makes an avatar that moves around the online conference space, and turning on microphones and cameras means attendees can chat and see each other in real time – it’s quick to set up and easy to get the hang of. There are plenary halls for the two streams, Sydney and Kuala Lumpur, a poster hall where attendees can chat with the poster presenters, places to chat and even a games room and beach! Zoom was used to bring together people from all around the world to talk about microbiology research.

The online symposium opened up opportunities to attract big names in microbiology from around the world. The first joint session brought us three plenary speakers, two on SARS-CoV-2 detection on surfaces and in wastewater, and the third on mycology. Forest Rohwer from San Diego University gave us a whirlwind tour of sampling and using genomics to detect if SARS-CoV-2 virus was hanging out on commonly touched, rarely disinfected surfaces in San Diego, Janelle Thompson from Nanyang Technological University introduced us to wastewater surveillance for COVID-19 and Jonathon Plett from Western Sydney University explored the impact of genomic sequencing on mycologists’ understanding of the fungal tree of life.

The poster session in JAMSTown was a good analogue of an in-person poster session. The platform allows poster presenters and visitors within a small area to talk and see each other using their computer’s microphone and camera, so the interaction and Q&A part of a poster session is still possible. There were 57 posters submitted by JAMS attendees; that’s a lot of posters to visit in two poster sessions!

After a break, the JAMS founders panel discussed the development of JAMS in the 10 years since it’s foundation, their ideas for JAMS for the next 10 years (hand it over to the young ones!) and Australian microbiology. There’s always plenty of laughs when Federico Lauro, Mike Manefield, Ian Paulsen, Mike Kertesz and Andy Holmes get together. 

In the second international session of the day, Jianzhong He from the National University of Singapore taught us about detoxifying halogenated organic pollutants and Mike Jetten from Radboud University Nijmegen introduced us to new anerobic microbes (‘spookmicrobes’) involved in the nitrogen and methane cycles. 

In the second part of the session Jillian Petersen from the University of Vienna took us on a tour across 400 million years of microbial symbiosis with marine clams and Holger Daims from University of Vienna gave us insights into new discoveries in the ecology and function of nitrifying microbes. The final speaker of the session, Lauren Cowley from the University of Bath, taught us about machine learning for attributing locations for Salmonella enteritidis infections in the UK.

Big thanks go out to all the JAMS10 sponsors! Without their support this online conference would not have been possible. Thanks to HelloBio for sponsoring a competition to win free tickets to JAMS10; I was very excited to be a winner! Overall an amazing day filled with a diversity of microbiology and speakers from across the globe – looking forward to a lot more microbiology on day 2 of JAMS10 tomorrow. For more information visit jams.org.au.

Tiny life sticking to growing green things

Communicating science to non-scientists is important, but often the jargon scientists use makes their work impenetrable, even to other scientists. So how can scientific writing become less obscure and more approachable? Randall Monroe, the creator of xkcd webcomics, gave it a go with his annotation of a Saturn V rocket blueprint. The annotation used only the 1000 most commonly used words, so instead of Saturn V the name of the rocket became Up Goer Five.

So can scientific communication in my field (microbiology and genetics) be effective using only the 1000 most commonly used words? In the interests of simplifying my writing, I wrote a summary of my PhD project using only the 1000 most commonly used words (using this text editor):

This study wants to find the ‘small pieces’ which are important for tiny life (the helping ones) to stick to growing green things. Pseudomonas tiny life are some of the best helping tiny life and one of the most well-known ones, Pseudomonas protegens Pf-5, can control problems in growing green things used for food. But in the field, helping tiny life show does not stick to growing green things very often or very well. This study will look at the whole set of ‘small pieces’ important for P. protegens Pf-5 to stick to growing green things. Making tiny life stick better to growing green things will help lower problems with growing green things and better the return from growing green things used for food, which are important both here and around the world.

This is hilarious and obviously oversimplified (to the point of not making sense in a lot of places). For comparison, this is the ‘normal’ version of my project summary:

The project aims to identify the essential genes for colonisation of plant surfaces by biocontrol bacteria. Pseudomonas bacteria are some of the most successful biocontrol bacteria and one of the most well-known strains, Pseudomonas protegens Pf-5, has the ability to control diseases that affect cotton, wheat, pea, maize, tomatoes and potatoes. Despite this, field trials of biocontrol bacteria show a lack of reliability and persistence on plant surfaces. This project will conduct a genome-wide study of genes essential for P. protegens Pf-5 colonisation of plant surfaces. Enabling reliable colonisation of crop roots by biocontrol bacteria will contribute to lowering plant disease and increasing crop yields, which are important both in Australia and internationally.

From this exercise I learned that some level of complicated language is important to communicate a precise meaning (important in science), but not every complicated word is necessary. Sometimes the language I choose can be off-putting to the reader, make my work harder to understand and appear pretentious even when I don’t mean it to.

So overall, science writing in my field using the 1000 most used words is not practical and makes it harder, not easier to understand (even nonsensical in places). But it’s an interesting exercise to see just how much jargon you’ve used or if a simpler word will do in place of a complicated one. And wouldn’t we all like simpler rather than complex!