• Alexis wins her category at NSURP 2021 Presentations!

    Congratulations to Alexis who won her category - Medical Microbiology - at the recent NSURP 2021 Presentations. Alexis’s presentation was entitled “Application of the Competitive Lottery-Based Theory to the Cystic Fibrosis Microbiome”.

  • New research published in MBE

    New research, previously submitted as a pre-print, on the extensive structure of gene-gene associations within the accessory pangenome has now been published in Molecular Biology and Evolution (MBE). This is the first project to be published that uses Coinfinder, our recently published software that identifies gene-gene associations and dissociations within microbial pangenomes. In this paper, we use Pseudomonas spp. as a case study of an open pangenome to show that we observe structure in the “noise” of the accessory gene content. There is an ongoing debate in the literature as to whether the accessory gene content of pangenomes arises due to random drift within horizontally transferred genes or due to some level of selection on this gene content. In this work, we provide evidence that there appears to be selective pressures acting on these genes. Fiona started this work while she was a Marie Skłodowska-Curie Fellow in the McInerney research group.

  • Arooj wins research award & passes her thesis proposal!

    Congratulations are in order for Arooj who has had an eventful few weeks. In April, Arooj won an internal award from Ryerson University entitled “Research Contribution of the Term” for her contribution to our research group’s poster at the Microbiology Society Annual Conference. Arooj followed up the success of this award by passing her thesis proposal, entitled Pathoadaptation in Shigella spp. last week. Congratulations, Arooj!

  • On Planning, Patience, and Perseverance in applying for Fellowships & Funding

    We all know that Fellowships and various other funding opportunities can help progress our research goals and careers. But how we come to obtain funding isn’t always a straight-forward path. Although I can only speak from my own experience, I’ve put together a few thoughts on what has been helpful for me to keep in mind during the process.

  • New pangenome research up on bioRxiv

    Since the sequencing of bacterial genomes started to become more common-place a few decades ago, we’ve recognized the vast genetic diversity that can exist within a species (or other group of closely related genomes). In prokaryotes, this is commonly attributed to pervasive horizontal gene transfer and the relative fluidity of the genome. This collective genetic diversity, termed “the pangenome”, can be extensive (an “open” pangenome) or minimal (“closed”). This raises the question: what mechanisms govern the structure of pangenomes?

  • NSURP Summer project presentations go live

    The presentations that Gabriela and Robert put together as part of their 4 week NSURP Undergraduate Summer Projects in the Whelan lab have gone live on the NSURP website. Both students did an excellent job learning the ins and outs of the cystic fibrosis and microbiome literature in such a short amount of time, and applied what they learnt to the interpretation of 16S rRNA gene sequencing data using softwares such as R and phyloseq. They put a lot of work into these short projects and that really shows in their final presentations!

  • NSURP students finish for the summer

    Becoming an Anne McLaren Fellow this past July and opening my own research group gave me the opportunity to invite Undergraduate project students to work with me over the summer. When I announced the AMF, a friend and colleague told me about the NSURP initiative that was being run out of the US. The National Summer Undergraduate Research Project (NSURP) was put together by Drs. Michael D. L. Johnson, David A. Baltrus, and Jennifer Gardy in order to help mitigate the impact of lab closures in light of the covid19 pandemic on Undergraduate students. Given that Projects would be conducted virtually, it was feasible to apply to be a mentor from the UK. I was paired with 2 Undergraduate students interested in microbiology and how microbes can effect human/host health. Together, we learnt and applied bioinformatic tools to the study of the cystic fibrosis lung microbiome.

  • Welcome to the Whelan lab!

    Last week marked my first day as a University of Nottingham Anne McLaren Fellow. The AMF is a 3 year transitionary Fellowship that will help me establish an independent research group. I’ll be in this role part-time until the end of the year in order to give me a chance to finish up my Marie-Curie Skłodowska Actions funded research in the McInerney group.

    My research group will focus on using computational, ecological, and evolutionary techniques to study microbial communities. Specifically, I am interested in using networks and graph theory to help better understand how the microbiome contributes to health and disease. In the first instance, this will be focussed on human diseases such as cystic fibrosis and irritable bowl syndrome, but my longterm objective is to include studies of non-human and environmental microbial communities with the ultimate goal of incorporating the idea of “One Health” into my research.

    I’m excited to have the opportunity to continue my research at the UoN, and to nurture an inclusive, inquisitive, and fun research environment. I know that I am not, never have been, and never will be perfect, but it is important to me that the philosophy of my research group focusses on equality and inclusivity.

    Although right now my research “group” is really just me, I will soon be looking to co-supervise Undergraduate project students, MSc/PhDs, and Postdocs. As this website expands to include a lab manual, information on current research projects, and other goodies, I hope that you’ll reach out with any questions or inquiries!

  • I believe in equality.

    I believe in equality. I believe in fair and equal treatment of any human being without judgement of one’s skin colour, sexuality, religion, culture, gender, or identification. In the context of science and academia, I believe everyone has the same right to education and to be treated equally and fairly within this (or any) space.

  • On defending, cycling, and moving.

    It’s been a busy year! The first half was dominated by writing and defending my PhD thesis. Although everything is always easier in retrospect, dare I say that it was a rewarding process to compile the research, ideas, and opinions that I’ve had over the last 5 years into one mega-document. I wouldn’t go so far as to say that being questioned for a few hours was fun, but I am really proud to have gotten through it all with a smile! After the appropriate amount of celebration, I took a break. My partner and I (well, mostly him) spend the winter planning a 2 month bicycle tour of Canada’s East Coast. I had never been to Newfoundland before, so that was our priority. So after wrapping up a few loose ends in the lab, we flew to St. John’s and began to cycle towards home. In the end, we zigzagged 3,000km around the Maritimes, ending near the Quebec-New Brunswick border. This trip was a great way to see part of Canada, to meet so many amazing people, and to regroup after the final PhD push. Our cycling tour was also the perfect way to say (a temporary) goodbye to Canada before we started our next adventure. In October, I moved to Manchester, UK to start as a Research Associate in James McInerney’s research group. Not only is it a jump across borders and an ocean, but this also represents a slight change in research area. But I’m excited to see where the end 2 years bring!

  • McMaster's Human microbiome journal club continues into the new year!

    At our last meeting, we realized that we missed our 5-year anniversary as McMaster’s Human microbiome journal club. Although disappointed that we didn’t make it an excuse to throw a party and eat cupcakes, this landmark anniversary really speaks to the community of trainees and academics that we have here at McMaster who are dedicated to presenting the most recent findings and (sometimes) struggle through some complex mathematics all for the sake of further understanding the ins and outs of their field.

    This anniversary comes just a few months after Dr. Jennifer Stearns, the founder of our humble JC, started her own research group in the Farncombe Institute at McMaster, and was awarded the Farncombe Chair in Microbial Ecology and Bioinformatics. Jen’s group, focussing on the microbial development that accompanies infants as they become children, will of continue to expand the amount and types of microbiome research that is being conducted within the Farncombe and across McMaster University in general.

    We start this new year with hopes to continue our critical evaluation of the human microbiome literature as we incorporate new trainees and laboratories into our ranks!

  • Year in review: progress & reflection.

    I have this habit, for better or for worse, of sketching out my short- and long-term future plans every year just before the Christmas break. The short-term usually covers the next year: what conferences I’d like to attend, what professional goals I’d like to accomplish, and my often-overstated research plans to publish all the things. While its often a bit disheartening to look back on these outlines and realize how naive my publishing goals really were, I’ve found its been a really interesting exercise in self-reflection.

    Even though I’m happy to see 2016 come to an end for many (political) reasons, this year has actually been a great year of personal and professional growth for me. Many of the stories that I’ve been involved with were published, including a culturing study of the gut microbiome and a microbiome study of the cystic fibrosis lung. Ryan Buensuceso and I started a science podcast series. And the loose ends associated with my main PhD focus are beginning to be tied. It was also an amazing honour to be presented with The Karl Freeman Prize for my closing seminar in the Biochemistry department, and IIDR’s Michael Kamin Hart Memorial Scholarship for my PhD research. These awards are particularly important to me because they come internally from within the Department and Institute in which I work; these decisions aren’t being made based on a written proposal or application but on myself as a colleague and trainee.

    Looking ahead, 2017 is going to be terrifyingly awesome. If all goes to plan, I’ll be defending my PhD, taking a much deserved break (more on that later), and starting a new adventure (also more on that later). But as overwhelming as this might feel at times, this yearly-exercise of looking ahead allows me to review snapshots into the long-term goals of Fiona’s of past. For me, this is a really important way of stepping back from the every day to realize that even though I may feel that goals and deadlines change, or that I’m unsure of my day-to-day research progress, my long-term goals remain the same.

  • Engaging with the cystic fibrosis community.

    The majority of the research that I have been conducting as part of my PhD has focussed on the lung microbiota of individuals with cystic fibrosis (CF). Even though the vast majority of my science happens in front of a computer, I have been so fortunate to have had the chance to meet and engage with CF patients in our collaborating lab in Calgary led by Dr. Michael Parkins. These experiences have been so important to me; they are particularly important in helping keep the “big picture” view every time that I get caught down a rabbit hole of software comparisons or code refactoring sessions.

  • Introducing the Microbiome Working Group

    At McMaster University, I am lucky to be part of the Surette laboratory, which has many microbiome-focussed projects and personal. However, with the growing use of the 16S rRNA gene sequencing pipeline that I developed, we begun to realize how many other labs at McMaster were using microbiota datasets to help answer their research questions. This meant that often one or two researchers per-lab were studying and using microbiome-related tools in almost perfect isolation.

    In April 2015, Dr. Jennifer Stearns and I launched the Microbiome Working Group. This Group continues today as a weekly, drop-in work/discussion hour with the aim of bringing microbiome researchers together to teach and learn from one another. That’s the official tagline, anyway, but to honest: it was really as simple as wanting colleagues in this field to get to know each other! (You work with who you know, right?) In the last year and a half, we’ve seen this group develop into a small-but-mighty team of microbiome researchers interested in tackling everything from typos in R code to the greater philosophical ideas behind what we’re studying. Its been particularly rewarding to witness the growth of some of our “regulars” who started out fearing that a mis-command could delete every file on their system to absolutely falling in love with the command line.

    This was the conceptual idea that Jen and I had behind the Working Group from the beginning: For better or worse, academia is a constant cycling of trainees, and there can be large gaps in knowledge that leave a research group with a graduate once they have their degree in hand. The Working Group was a way to mitigate this. It was a way for the learner to become the teacher, and for our collective knowledge to remain available to the next generation of trainees.

  • The Graduate Experience

    Impress Magazine, a Graduate student website run out of the Department of Immunology at the University of Toronto, collected information from Graduate students across the country to compare their experiences. Everyone had something interesting to say, and it was put together into an amazing infographic! Check it out here.

  • New publication: research on how the microbiome of the nost and throat change as we age

    A recent article in the Annals of the American Thoracic Society is the result of an extensive collaboration between the Bowdish and Surette labs (colloquially referred to as the “Bowdettes”) on a study of the upper respiratory tract microbiomes. As we age, we become more susceptible to respiratory infections such as influenza and pneumonia; however, we aren’t yet sure why. The microbial communities, or microbiomes, that inhabit our noses and throats act as protectors of our respiratory tract from microbes in our environment. Previous research has identified that immune function declines with age, but an understanding of whether this is correlated with changes to the respiratory tract microbiomes remained unknown. In this study, we rectified this by collecting swabs of the anterior nares (nostril) and oropharynx (throat) from willing elderly volunteers, and profiled these microbial communities using 16S rRNA sequencing of the variable 3 region. Initial analyses of these data indicated that there were no associations of these microbiomes with gender, the residence of the participant, or other factors. Interestingly, the microbiota sampled from the noses and throats of these individuals did not look distinct from each other, meaning that the microbes found in these participants noses were similar in type and number to those found in their throats. In fact, when we combined this data with that of healthy, mid-aged adults sampled at the same locales as part of the Human Microbiome Project, we discovered that the microbiota of the elderly were very different from that of adults, and included more variability among subjects. Interestingly, we did not discover an increase in the abundance of any pathogenic species such as Streptococcus pneumoniae which often cause respiratory infections. These results are important as we consider the implications to the study of respiratory infections. We can hypothesize that the dysbiosis if the microbial communities of the upper respiratory tract with age may affect immune function, or the effectiveness of these ecological barriers, allowing pathogens such as S. pneumoniae to easily infiltrate; however, further research will have to be conducted in order to fully examine the effect these microbial changes will have on us as we age. Our paper can be found here; if you have any questions or comments, please leave us a note below or on the Surette lab website!

  • Bioinformatic how-to guide.

    Late last year, my co-authors and I published a “how to” guide for using bioinformatic tools. Although this review focusses on the tools available to the field of immunology, at least half of the article is applicable to anyone interested in getting started with these tools. The idea to write this review was based on our frustration with how many great tools exist that are severely under-utilized by immunologists. And I’m not talking about software that assumes that the user has taken 10 computer science courses; these are copy and paste, easy-to-use tools that your parents could use (sorry, Mom & Dad). We start by explaining tools that are common to all fields, including how to find a sequence of interest from a reputible, online database, how to conduct sequence alignments, and how to search for single nucleotide polyporphism (SNPs) in genes of interest. We conclude with tools that are specific to immunology, such as,, and IRIS (Immune responses in silico). Check out our review if you’re interested, but, more importantly, consider including the use of simple, easy-to-use, online bioinformatic tools in your microbiology, molecular biology, immunology, anything-ogy research approaches to generate hypotheses and gain knowledge that can save you time and money at the lab bench!

  • The influence a scientist can make.

    I posted this originally on Google+ approximately 1 year ago. In the hopes of kicking some life back into this site, I thought I would re-share it here, especially since the original post was private. Enjoy.

    A significant reason why I chose to become a scientist was the constant exposure I had to nature as a child. My friends and I were always playing outdoors, and my family’s idea of a vacation was car camping supplemented with too much hiking. My brother and I learnt how to find interest in anything from the stamp-sized swamp between our campsite and the next, to the tadpoles that would nip at our legs as our parents fished.

    Watching a lecture today given by David Suzuki reminded me of the big picture of why I’m doing what I’m doing. For him, he experienced a disconnect between his genetics research and the way science was being used by the government around the time of the Vietnam War. Such a large disconnect, in fact, that he considered leaving science altogether. While I don’t feel such a strong divide, I did realize how easy it is to get walled up in the laboratory, forgetting much of what exists beyond. I suddenly felt so disgusted with myself for not having recently taken the time to lay outside, paddle a canoe, or fish, allowing myself to really think about the research I’m doing and why it’s important to us, the envrionment, and nature as a whole- because if it’s not important to those 3 things, I don’t believe it’s worth doing.