Back by popular demand – my 7th Annual JAMS Symposium report (better late than never, right?)

The 7th Annual Joint Academic Microbiology Seminars Symposium, or JAMS Symposium for short, is an event I had been looking forward to for quite some time. Held each year in Sydney, it brings together a group of like-minded researchers for a program jam packed with talks and posters covering the latest discoveries in microbiology. And no, I won’t apologise for the pun, because frivolity is mandatory at JAMS. It’s one of the reasons why I like it so much.

This year’s event took place on Wednesday 21st March. After heading to the wrong location (important: read the instructions and don’t just turn up where it was held last time!) I made it to the lecture theatre in the Australian Museum with a few minutes to spare. Just enough time to say a quick hello to Federico Lauro and have my first laugh of many for the day – at his socks, which speak the truth for most meetings but on this occasion they were proclaiming a loud and categorical lie about the afternoon and evening ahead.

Fede opened the show with a quick run-down of the history of JAMS. For the uninitiated, check out my blog post from last time around. This year, a new acronym had emerged, with #MAMGA (Make Australian Microbiology Great Again) decreed as the most important order of business for the day. Like all the other recovering #JAMSaholics in attendance, I was not disappointed. The future of Australian microbiology is in good hands, with Yolanda Plowman from the University of Sydney leading by example as our enthusiastic MC.

First cab off the rank was Mike Manefield from UNSW. Given his involvement with JAMS from the beginning and his passion for all things microbiology, it came as no surprise to me that his talk was both whimsical and comprehensive. Mike covered a lot of ground in a short space of time, including highlights from Matthew Lee’s work on microbial organohalide respiration for bioremediation of sediment in the nearby Botany Bay, through to Sabrina Beckmann’s project using neutral red to enhance methane production by Methanosarcina. It’s fair to say that Sabrina’s presence was sorely missed at JAMS7, but her legacy most definitely lives on. It was great to have her chiming in on the fun via Twitter – in real time, all the way from Delaware!

Next up was Caroline Chénard from Nanyang Technological University in Singapore, the first of two international speakers. Caroline talked about her research on the effects of nutrient availability on marine viral communities in the Singapore and Johor Straits, which she has studied using a hybrid Illumina/Nanopore sequencing approach. The audience particularly enjoyed Caroline’s enthusiastic efforts to highlight of the importance of viruses as a globally dominant biological entity!

The final science talk before the much anticipated poster session was delivered by Chris Greening from Monash University. With a nod to a favourite late night pub anthem, he explained how some microbes are (whoa!) living on the air by scavenging atmospheric gases in order to survive. It never ceases to amaze me how gosh-darn clever microbes are! Some great collaborative research spanning several Australian labs was necessary to bring these discoveries to light.

Next, in a display of what can only be described as shameless self-promotion, I was lucky enough to take to the stage before the break for a rapid-fire introduction to the EMCR Forum and my role on the Executive team. For the uninitiated, the mission of the EMCR Forum is to serve as the voice of Australia’s early- and mid-career researchers, championing improvement in the national research environment through advocacy. The focus of the Forum is on sustainable and transparent career structures, diversity and inclusion, stable funding policies, professional development opportunities, and raising awareness of issues facing the future of science. Membership of the EMCR Forum is 100% free and open to all researchers within 15 years post-PhD. If you’re an EMCR reading this and you haven’t signed up yet, what are you waiting for? I strongly advise you to do it right now!

I quickly found out that few things in life are free, and was asked to repay the organising committee for letting me speak about the EMCR Forum by helping to judge the PhD student poster session with Belinda Ferrari from UNSW and Lisa Moore from Macquarie University. I’m joking of course – it was an honour to be asked to make such an important decision. It was uplifting to feel the energy in the room as I hung back to watch the students interact with other scientists and talk about their research. It was genuinely challenging to pick a winner for the Jeff Powell perpetual student award, so named in honour of Jeff’s gaffe at JAMS1 when he entered a poster and temporarily “won” the competition – before he was disqualified for being a postdoc! The announcement was made later in the evening, but I won’t keep you in suspense – the prize went to Vanessa Pirotta from Macquarie University for her poster describing the use of drones to collect microbes from whale snot.

The slot after the poster break at the JAMS annual symposium is traditionally the hardest – mostly because the delegates are full of cheese and wine or beer which can mess with our ability to focus properly! Luckily Talitha Santini from UQ was up to the challenge. It was inspiring to hear her talk so passionately about her research in the traditionally male dominated mining sector, and learn about how microbial communities are being engineered to bioremediate abandoned sites. For me, this was a definite highlight of the JAMS7 program.

Our final speaker was Rytas Vilgalys from Duke University in North Carolina. I had the pleasure of talking to Rytas briefly during the poster session about his sabbatical at Western Sydney University, which he was thoroughly enjoying. Rytas delivered a fascinating talk about the “wood wide web” – communication and coevolution between forest trees and their symbiotic fungi. I particularly enjoyed the colourful images of different fruiting bodies that he has captured during his career.

At the conclusion of the talks, the group meandered up the road to Harpoon Harry hotel, our venue for the evening shenanigans. After a quick drink or two to get started, the organising committee had some presentations to make. This included bottles of “Phil’s Pils”, the specially brewed JAMS7 conference beer courtesy of Phil Barker from the University of Wollongong. (Note for Sabrina – if you’re reading this, I still have a bottle for you stored safely in my cupboard for when you visit me later in the year!). While this was happening, I noticed Fede making a fuss in the corner and wondered what could possibly be going on. Eventually he whipped out a wooden toilet seat complete with metal plaques and handed it to Tom Jeffries. This new offering is known as the Co-operative Advancement of Community Award (CACA) to recognise people who “get shit done” for JAMS. Aha! The toilet seat reference made complete sense, even if it was slightly odd in fitting with JAMS tradition. Seeing Tom proudly wearing it around his neck later in the evening certainly topped off a wonderful day – a real credit to the organising committee of Yolanda Plowman, Caitlin Abbott, Shang Yu Shueh plus Mike, Fede and Tom.

I’m going to finish my JAMS7 symposium report on a personal note. The most wonderful thing about this group for me is the genuine sense of camaraderie and kindness. At several points I found myself having deep and meaningful conversations about the challenges faced by academics who are trying to consolidate their careers. At that stage I wasn’t entirely sure what the future was going to hold for me, but I was reasonably certain that my research career was coming to an end and that this would be the last JAMS symposium I would attend. Rather than feeling despondent, it was comforting to be surrounded by friends who fostered a safe space where I could talk about the serious issues I have been dealing with over the past 12 months. I woke up the next morning with a bit of a headache (!) but buoyed by the best wishes from many awesome people who were genuinely concerned about what I’ve been through and where I’m headed next. This really does mean a lot to me and I want to thank everyone for their support.

I am now happy to say that I have accepted a position at the University of South Australia, where I will be working as a grant developer starting in June – providing professional development and support services to EMCRs. I still can’t believe I’m going to get paid to do something I really enjoy! This is an opportunity for me to take my career in a new direction, where I can harness my skills, knowledge and passion to make a positive difference for others. I’ll still be tweeting as @MicrobialMe and challenging the status quo on issues I care deeply about – I don’t think that will ever change. If anyone cares to join me, you know where I’ll be.

PS – great to see the Paulsen lab from Macquarie University joining the Twitter party after JAMS7. Better late than never!


The publication paradox: why it isn’t always as simple as “just write it”

Something came to the surface today when I read a tweet insinuating that if I want to be an author on a paper, then I simply need to get off my arse and write one. If only it was that easy for everyone! I wanted to provide this perspective, not to complain but to provide an insight into why many EMCRs might be struggling with this – especially those who don’t work in academia. It’s really important that as a community we don’t stifle conversations about why we might be finding it difficult. We all experience things differently and everyone can benefit from a little understanding and support to get through the tough periods.

I’ve worked at CSIRO since January 2009. I spent six years in Brisbane and Sydney studying microbes in the rumen of livestock. During my time in Sydney I worked as the sole scientist on an industry funded project where I used metagenomic techniques to study methanogens, with the aim of identifying novel targets to reduce methane emissions from cattle. I acted as the principal investigator, laboratory technician, finance officer and report writer. I was responsible for everything from delivery of milestones to monitoring the budget. This proved to be incredibly stressful, especially towards the end of the project when I realised that the component of my work that was supposed to be the most interesting from a publication standpoint had not worked out in the way I had hoped. The industry partner was pleased with the outcomes and I received high praise for a job well done, which should have been enough. But the fact that I haven’t yet been able to convert my three years of effort into that coveted journal article continues to weigh heavily on my mind. I worry that by measuring performance based only on publications that we are skewing our perception of what’s really important – the ability to do good science and make an impact. The evidence that I can do this currently lies in my comprehensive project report. It’s publicaly available, peer-reviewed and has a DOI. Unfortunately this just isn’t good enough to demonstrate my capabilities and be competitive for career development awards – even those only available to CSIRO staff.

As my rumen methanogen project came to a close I was lucky enough to spend 5 months in the US as a Fulbright Scholar. I spent my time at the US Department of Energy Joint Genome Institute analysing genomes from type strains of Methanobrevibacter, the most common genus of rumen methanogens. When I accepted the scholarship, the project was meant to act as a stopgap until I got my next round of funding. Shortly afterwards Australia had a change in government and the focus shifted away from funding climate change research. It became clear that this was not an area I was going to be able to continue in, so I made the decision to relocate to Adelaide when I got back and started working in the field of human gut microbiology. I knew straight away that it was going to be difficult to write up my Fulbright research. The output isn’t relevant to my current research focus and provides little benefit to my new business unit. This is the reality of what it is like to work outside of academia – it is not always possible to make decisions that are in the best interests of your own career and to find time to focus on writing papers. I knew there was a group with interests in collaborating so I reached out and gave them the genome data and my preliminary analysis. While I’m still waiting to see if we can write a paper together, the information has been useful for one of their projects. It makes me feel better knowing that my effort may be translated into something more because I was able to see the bigger picture. For me, that’s what science should be about.

I’ve realised that I need to do something more to plug the publication hole. I knew that some of the data I’d generated would be very useful to a PhD student who had recently moved from CSIRO to UQ with my previous boss. She’s been able to incorporate it into a more impactful analysis and is in the process of writing the manuscript. I see this as a win for both of us, but it does mean I take a middle seat on the author list. It’s not reflective of the effort it took me to generate the data, but I’m happy that I’ve been able to contribute to something more substantial. I’ve also teamed up with one of my colleagues in Brisbane to rework the rest of the data from my rumen methanogen project. We had an abstract selected for a journal special issue and he has negotiated an extension so I can prioritise my current project work. He understands the difficulties I’m facing and I’m glad to have his support. It’s been very challenging for me to change research focus and concentrate on learning a new field while trying to find time to get those darn papers out! As someone with anxiety I need to be careful not to focus all of my energy on work and I try not to do too much outside of hours to give myself time to relax. I know from experience that the consequences of not doing this can be brutal. This is probably the main reason why the “just write it” comment has irked me so much. We shouldn’t have to be fighting with ourselves all the time, overworking and not exercising self-care in order to stay in the game. We also shouldn’t feel like we can’t be honest about the realities of what we’re facing.

So before judging someone else and the situation they find themselves in, take some time to consider that their reality may be very different to your own. It’s OK to admit when we’re struggling and it shouldn’t been seen as a sign of weakness. I’m not ashamed of where I’m at because things aren’t always easy for me. Some people really don’t understand this.



The sixth annual JAMS Symposium (aka the ultimate session for microbiologists down under)

On Wednesday 22nd March 2017 a motley crew of around 130 microbiologists gathered at the Australian Museum in Sydney for the annual JAMS Symposium. From humble beginnings the Joint Academic Microbiology Seminars Symposium has grown into what many consider to be a highlight of the year, representing the largest independent meeting in Australia of microbiologists from all disciplines. It is powered by enthusiastic volunteers and donations from sponsors – nothing would be possible without their generous support.

The concept of JAMS was born at ISME13 in Seattle from a simple idea – why don’t we get people together in Sydney to drink beer and discuss microbiology? The concept caught on and before too long a series of informal seminars were being held once a month, with a focus on allowing PhD students and ECRs to share their work with each other. In contrast, the annual JAMS symposium features presentations by established scientists hailing from all over the world, followed by dinner and drinks surrounded by old friends and new. The JAMS Inc. style is summed up best by Federico Lauro, one of the founding trio, who says “it’s simple, we just dig microbiology”. And that’s why I made the trip from Adelaide to be a part of it.

Thomas Jeffries from Western Sydney University began proceedings by calling Fede “The JAMS Yoda”. I found this gif which reminded me of the JAMS motto – minima maxima sunt – or the small things are the great things. I’m sure most people in attendance would agree with me that the microbes were the real luminous beings on show!


Mike Givstov from the University of Copenhagen in Denmark and Nanyang Technological University in Singapore kicked us off with a great presentation about the quest for anti-biofilm-biotics. He emphasised the fact that most antibiotic discovery pipelines fail to screen against bacteria in biofilm state, which is strange given that this is the preferred life-mode during infection and it is known to act as a protective shield. He gave examples where mechanisms to disrupt biofilms based on inhibition of quorum sensing or cyclic diguanylate signalling can be combined with traditional antibiotics to increase their efficacy against Pseudomonas aeruginosa.

Next we heard from Mike Taylor from the University of Auckland in New Zealand who spoke about characterising the microbiome associated with chronic rhinosinusitis (CRS). CRS affects 5% of the US population with treatment costs exceeding $8 billion in the US alone. Using 16S rRNA gene sequencing data, Mike and his team have shown that despite high variability, CRS microbiome network maps are more fragmented compared to healthy controls and exhibit decreased species diversity, suggesting that CRS is associated with community dysbiosis.

Mike Manefield’s tweet shows a captivated audience during Mike Taylor’s talk and the first of many confronting images for the afternoon, none of which came with any prior warning!


You might also be excused for thinking this is the Joint Academic Mike-robiology Seminars, with so much involvement from people named Mike …


The final talk before the break saw Perran Cook from Monash University in Melbourne enlighten us on mechanisms of anoxic microbial metabolism in permeable sediments. He presented data to support a hypothesis for dominance of diatoms in euphotic sand, with evidence for high levels of hydrogen production. He suggested that algal anaerobic fermentation drives lipid production, acting as an energy store which can be accessed once the oxygen concentration increases.


During the break I caught up with some of my favourite EMCR women in Australian microbiology, namely Ania Deutscher from the Department of Primary Industries NSW, Cath Burke from the University of Technology Sydney and Deirdre Mikkelsen from the University of Queensland. Over a glass of wine we spoke about many things, most notably around how to effectively combat the adverse effects of constantly second-guessing ourselves. We wondered if this was common for other women in our field and agreed that peer mentoring was likely to be the best medicine. I’m definitely going to keep this conversation going and I’d like to encourage others experiencing similar feelings to reach out for support. I sat down for the second session with a renewed sense of optimism and confidence that I’d found the right path forwards.

After the break Professor Liz Harry from the University of Technology Sydney gave a sweet presentation on the antimicrobial properties of Australian manuka honey. Did you catch the pun? I couldn’t resist, and apparently microbes find it hard to escape the application of manuka honey as a topical treatment for skin wounds. The antimicrobial properties can be attributed to a number of factors and work is underway to determine which is most important. Liz made an interesting point about how people may be reluctant to use honey as a treatment due to fear of the unknown, but the reality is that we don’t know everything about many of the drugs we take. She provided evidence for the ability of Australian manuka honey to reverse resistance of Staphylococcus aureus to oxacillin. We were all kept entertained by yet more pictures of lesions a subtle dig aimed at our Kiwi friends across the ditch.


Up next was Nicole Webster from the Australian Institute of Marine Science in Townsville. The audience breathed a collective sigh of relief when she promised not to show any gross pictures. Many people were excited for her to present – apparently it was a long time coming for the JAMS faithful!


Nicole’s talk described a large body of work to characterise virus assemblages found in seawater and associated with corals and sponges on the Great Barrier Reef using a functional metaviromic workflow called HoloVir. The different sample types had distinct viral profiles suggesting adaptation to specific ecological niches. Communities exhibited high diversity and low similarity to sequenced viromes, creating challenges that needed to be overcome during analysis. One additional interesting finding was that inshore virus genomes show enrichment for herbicide resistance genes, providing evidence for the effects of anthropogenic disturbance within a delicate ecosystem. The official JAMS tweet sums this talk up best:


Our final talk for the symposium was delivered by Steve Siciliano from the University of Saskatchewan in Canada. Like others in the room, I had the pleasure of seeing Steve’s talk at JAMS1 and I think all are in agreeance that he is welcome back for JAMS12! Steve told us that the most important factor driving soil microbiology in his study system is not the increase of the invasive plant smooth brome but the concomitant loss of native plant species. Using co-inertia analysis he presented a model where smooth brome structures the bacterial communities which in turn structures the fungi and archaea structure both. By this stage many of us are slightly confused which gave rise to a couple of great comments from Steve to see us to the end of the presentations.


We headed upstairs in the Australian Museum main building for dinner and drinks overlooking the Sydney skyline and harbour. It’s a beautiful spot and I swap stories with Aaron Darling about the experiences we had on our respective US sabbaticals. After the mains are served Jeff Powell is called upon to award the winner of the Jeff Powell Perpetual Student Award. Even though Steve suggested we should be trusting of Canadians, the JAMS faithful know better. Jeff was the inaugural winner of the JAMS Symposium student poster prize – but was subsequently disqualified as a postdoc who couldn’t read instructions! As the announcement was made, we were treated to some impromptu fireworks over the harbour, and so concluded the (somewhat) formal part of the evening.


The afterparty kicked on at Harpoon Harry, a short stroll from the museum and the site of the regular JAMS events. These are well worth attending if you find yourself in Sydney on the last Tuesday of the month. You could even use it as an excuse to visit – I’m sure Mike Manefield would be very welcoming to volunteers seeking to give a talk. At closing time I find myself enjoying a gin with Justin Seymour who I had just met and Maurizio Labbate who I haven’t seen in over 10 years. That’s the power of JAMS – reuniting old friends and creating new ones!

All in all, the JAMS annual symposium represents a unique and truly enjoyable event on the Australian microbiology calendar. The organising committee strive to deliver unique offerings and opportunities to emerging microbiologists in the Sydney region, with plans to expand across Australia over the coming year. If you would like more information about how to get involved, simply visit or follow @jamsorgau.

On managing mental health challenges in science

The start of the working week is probably not the best time for me to be visiting this topic, but it’s important to capitalise while the impetus is still strong. Fire in the belly, as they say. Ann Arnold (@ann_arnold) wrote this great piece for ABC news, providing advice for employers and employees about managing mental health in the workplace. This is a topic that resonates with me on a number of levels and I’ve recently found the motivation to start sharing my perspective and experiences. I hope this helps others to realise they’re not weird, or broken, or useless – this is a tough gig at the best of times and we need to support each other in order to get through it.

First things first. We need to get serious about mental health in science. Every place I have worked has been across their responsibilities for protecting staff and students against the risk of physical harm. I manage a laboratory and this means everyone needs to be inducted into the workspace and receive appropriate training before working alone. They must read the biological and chemical risk assessments, use appropriate PPE at all times and be aware of what to do in case of an emergency. In the office, we have regular ergonomic assessments and software installed on computers to make sure we take regular breaks. When I come to work I know that my body is safe. But what about my mind? We would never make someone stay in a lab that was on fire, but what about asking people to remain in a situation that’s causing them distress? Managers and colleagues need to be able to recognise the signs, be willing to offer genuine support and take positive steps towards improving the situation in the short and long term.

Recognising that someone is struggling with their mental health can be tricky. We’re all individuals who respond differently to pressure in the workplace. We also come to work as people with lives that continue when we leave at the end of the day. Try to put yourself in their shoes. Keep an eye out for changes in personality and mood. Some people are experts at repressing their feelings while others wear their heart on their sleeves. No prizes for guessing which one I am! It’s also really important to foster an environment that provides a safe space where everyone can raise their concerns and be heard. Ann’s article reminded me of an incident that triggered a change in the way I approach my own situation. My GP feels that my anxiety and depression are exacerbated by work stress, and encourages me to self-monitor and speak up when I notice the signs are pointing in the wrong direction. I can become overwhelmed when my workload becomes unmanageable – a situation familiar to many EMCRs. In a meeting of 20 or so individuals, I raised this as a concern not only for myself but because I could see it was also affecting others. Since I’ve become more aware of my own mental health issues I’m acutely “in tune” with what people around me are experiencing. A very mild superpower, if you will. My perspective was met with a chorus of laughter from several individuals which only stopped when I pointed out that their response was inappropriate. For many people, this would have shocked them into suffering in silence for the forseeable future. For me, it’s acted as the catalyst to expose how widespread and real this issue is within the scientific community.

Support can be given to your colleagues in many shapes and forms. Again, remember that everyone is an individual and it might take time to work out what you can do, if anything. Avoid the urge to jump in and be a knight in shining armour, there is often no easy fix and this approach can make things worse. My office buddy here in Adelaide knows that it helps me to hug it out when things are shitty. My “work best friend” in Sydney used to usher me out for the highly effective therapeutic combination of coffee and cake. I do miss that, it takes time to build up a relationship with someone you can trust. I know he is always just a phone call away. This is what works for me, but not everyone will want to talk about their experiences and that’s OK too. Not every situation can be rectified, and it’s often enough to know that someone cares. It’s important to be guided by their reaction. Don’t push too hard if they’re not able to talk about what’s going on, but leave the door open for a future conversation. Remember the difference between empathy and sympathy, and above all else, don’t point them in the direction of work-based counsellors! This is an example of dumbsplaining. We are well aware that these services exist and know how to access them.

Managers can go a long way towards creating a positive environment at work by offering “more carrot and less stick”. Take the time to learn about what motivates and inspires people. Encourage your staff and students by highlighting their achievements to others. Let them know they are visible and that you’re paying attention. Respect their expertise and listen when they offer feedback or raise concerns. Try not to put too much pressure on people and never push your own problems onto them. Communicate openly and articulate your expectations. Develop meaningful professional development plans and stick to them. If you make it easier for your staff and students to do their jobs to the best of their ability, you might just find it becomes easier to do yours!

I want to finish by saying I’m really appreciative of all the support I’ve received on social media. I made a new friend recently because someone was brave enough to reach out. I spent several years feeling isolated and alone, not understanding what I was going through and not knowing if there was anything I could do. That’s not the case anymore, and I can confidently say things are much better. As many others will know, mental health is a rollercoaster with unpredictable twists and turns. It is a constant process. Don’t suffer in silence. My private messaging is open on Twitter, please get in touch if you are in need of a virtual hug or something more.

My very first blog post!

First things first, I want to thank my fellow members of the Australian Academy of Science EMCR Forum executive for giving me the gentle nudge I needed to accept the position of Chair for 2017. It means a great deal to me to have their support. Nikola Bowden did a stellar job last year and has left some big shoes for me to fill. I’m really excited to see what the next 12 months will entail.

I’m often asked what the EMCR Forum is about – mostly because I try to tell anyone who will listen! It is somewhat of a tricky question to answer because it depends on what your interests are and how you choose to engage. In a nutshell, the EMCR Forum provides a national voice for all scientists up to 15 years post-PhD, irrespective of sector and discipline. Our mission is to improve the future of science in Australia through advocacy and engagement.

Since our inception in 2011 it has been possible to drive several important initiatives including implementation of the Science and Gender Equity (SAGE) Pilot; rescuing the Australian Research Council (ARC) Future Fellowship scheme from certain death; and making sure EMCR issues were front and centre during the recent National Health and Medical Research Council (NHMRC) structural review. This is a tough environment for EMCRs and we will continue to advocate on behalf of our constituents (i.e. everyone who meets the description in the paragraph above).

Thanks mainly to the efforts of Hamish Clarke and Adrian Carter, the EMCR Forum is active on Twitter (@EMCRForum) and provide regular email updates to disseminate the latest information of relevance to EMCRs. We host Science Pathways to promote professional development and will hopefully be in a position to run events locally this year. The Forum provides a unique mechanism to get involved in national conversations and we are pleased to be assisting Science and Technology Australia with Science meets Parliament this year (#SmP2017).

What does it all mean? If any of this is resonating with you, I’d like to encourage you to become a member. It’s free, so why not? Everything we do as the EMCR Forum executive is driven by feedback from EMCRs about what concerns or interests you most. Sharath Sriram (who is leaving the executive this year) puts it best by saying we are run by scientists, for science. As we move forward I’m hopeful that by fostering a positive and inclusive community of EMCRs we can work together to change the future for Australian scientists. So go on, join the conversation – we’re here for you, and we’re listening!