Welcome to the Skope! The blog dedicated to the human microbiota, the collection of microorganisms that reside with and on the human body. Described as the “forgotten organ”, the human microbiota launches at birth. Soon trillions of microbes colonize the human host enabling our survival. These microbes digest dietary starches, aid immune system development, and synthesize essential vitamins. Even our mood and behavior may be linked to microbial communities. Most Skope entries cover the gut microbiota, the microbes that inhabit the intestinal tract, click Gutsy Topics. But I will also include articles on the oral microbiota, skin microbiota, ocean microbiota, soil microbiota, and many more microbial habitats. Articles in An American (US!) in Vancouver describe my graduate/international experiences, while Biologs features brief histories of microbiology and also reviews/summaries of interesting microbial articles and books. Happy exploring!
Each season of 2020 arrived with unexpected challenges, unanticipated distress, and grief. Despite the ongoing shock and uncertainty, I’m grateful for the resilience, community (socially distant), pursuits of justice, and kindness I’ve witnessed this year.
I know many of us are struggling and I almost feel awkward for the personal celebrations I’ve experience. But I also believe it’s important to hold tightly to positive memories, reflect in gratitude, and foster wonder. So…I’m sharing a list of joy (not in any particular order)!
(1) Extra time with family over spring/summer
(2) Ability to let go of unfinished research disrupted by COVID19
(3) (Currently) healthy
(4) Safe return to Canada following summertime quarantine
(5) Friendship during life transitions
(6) A post-doctoral fellowship*
(7) Beautiful BC (beaches, bears, bays, + boats)
(8) A new scicomm project**
(9) An accepted research publication***
(10) Passing my PhD defense this August…I’m Dr. Bauer!
I’ve included my thesis acknowledgments below. There are many more people that could (should) be on the list, particularly former Finlayites, non-UBC support, previous teachers/mentors, and the groundbreaking/ceiling cracking researchers that came before. Thank you.
This thesis could not have been accomplished without the support of Dr. Brett Finlay. Thank you, Brett, for the opportunity to pursue gut-systems research in the Finlay Lab and for providing academic, collaborative, and funding support throughout my doctoral studies. When I joined the Finlay lab, the current team described your leadership style as an “opportunity creator” –thank you for supporting incredible opportunities that included developing a gut-brain research crew and forging interdisciplinary research at the Djavad Mowafaghian Centre for Brain Health (Canada), Lee Kong Chian School of Medicine (Singapore), and Lleida Universitat (Spain). I am particularly grateful that you provided me the opportunity to join the CIFAR-Humans and the Microbiome Program as a reporter.
My deepest gratitude to all the members of the Finlay Lab from 2015-2020. I am grateful to all of you not only for your friendship, but also for helping develop my research skills and providing training and mentorship in new experimental techniques and data analyses. Thank you for your encouragement and guidance navigating the successes and challenges of graduate school. I’m a better scientist because of all of you. To fellow Fall 2015 lab mates—Kelsey, Sarah, and Rozlyn—thank you for your support throughout graduate studies. I wish you the best of success as we keep investigating the microbial world. Kelsey thanks for being my partner in Team MAL-BG, I’ve truly appreciated your advice, insight, and collaboration. Thank you to Andrew, Kate, and Jorge for advice in prepping for comprehensive exams, setting up committees, and maintaining work-life balance. Jorge thank you for training in the anaerobic chamber. I’m also grateful to Antonio, James, and Zack for their research perspective and advice in experimental designs. Thanks to all the members of malnutrition studies: Haggai, Anna, and Paula for providing a needed clinical and nutritional perspective. Also, a thank you to the growing Team Brain—Mihai, Nina, and Avril—I’ve enjoyed all our conversations and I’ve been challenged to think more critically and explore new research directions. Honorary Team Brain crew members, Charisse and Zakhar, thank you for your support in developing a microbe-microglia paper. Mihai,thanks for being a great bay mate and sharing alcohol-resistant makers. To you and Charisse thanks for all the long hours prepping microglia, for answering bioinformatic questions, and supporting my gut-brain projects. Finally, the lab could not function without Tahereh, Deng, and Lisa. Tahereh—thank you for the many long and challenging hours you dedicate to supporting my mouse studies, with efficiency and respect for the animals. I’m very grateful. Deng thank you especially for the warm and thoughtful Exit Seminar introduction. Lisa—thank you for supporting my research needs and helping me succeed within the Finlay Lab. Your support has been incredible.
In addition, I want to thank the expanded support team during graduate studies—both my doctoral thesis committee comprised of Dr. Jennifer Gardy, Dr. Brian MacVicar, and Dr. Lisa Osborne, as well as the Microbiology and Immunology Department at UBC. Thank you for your support and academic guidance. Also, a special thank you to Darlene Birkenhead for helping me navigate requirements and opportunities during the graduate experience.
This work was greatly supported through multidisciplinary collaboration. I am absolutely indebted to Eric Brown, currently at the Broad/Harvard, for teaching me the MAL-BG model and how to develop and critically plan research projects. I’m very grateful for your friendship and mentorship. Eli York—the microglial project could not have been accomplished without your research skills and suggestions. Thank you for introducing me to this incredible neuroimmune regulator and for your knowledge in glial biology. I wish you success in your research at Harvard University. I am also grateful to members of the CIFAR-HMB Program for allowing me to join in a transdisciplinary discussion of the microbiome and expanding my study of microbial communities to consider perspectives embedded in health, evolution, and anthropology. Dr. Brian MacVicar, Dr. Sven Pettersson, and Dr. Victoria Ayala—thank you for allowing me to visit your labs to expand my training in neurology and metabolism. I am very grateful to the mentorship and opportunities that you all provided me. I look forward to future collaboration.
Personal awards for research include a Vanier NSERC Canada Graduate Scholarship from the Canadian Federal government, Four Year Doctoral Fellowship from UBC, as well as funding from work as the Program Report of the CIFAR-Humans and the Microbiome Program. During my doctoral studies the Finlay Lab received support from the CIHR (Canada) and the Bill and Melinda Gates Foundation (United States). I’m grateful to these funding agencies for supporting research exploring the microbiome and gut-systems interactions.
Finally, this success also reflects on the love and support I received from my family. Mom—I wouldn’t be a scientist without you. Thank you for your wisdom, support, and helping me launch my work in research. Thank you for the gift of science. Dad—thank you for believing in me even when faith in myself faltered. Thank you for the knowledge of words. Khelsea—you are my best friend and role model, thank you and John for graciously opening up your home so I could write this thesis safely during a global pandemic. You are my heroes.
*More about me later
**Definitely more about me later
***Obviously more about me later (you get the idea)
Next Tuesday, February 11, marks the 5th annual International Day of Women and Girls in Science (WGS). Created by the United Nations, this day celebrates the accomplishments of women researchers and brings attention to the unique challenges experienced by women students/scientists and the continued gender gaps in STEM careers.
To promote WGS awareness, UBC Science featured 10 women researchers within the University. You can check out their bios and research here. Featured scientists include Dr. Xin Li, a professor within the Botany Department, who runs a lab at the Michael Smith Laboratories, the transdisciplinary research hub where I study/research. PhD Candidate Isobel Mouat from the Microbiology and Immunology Department shares her experience combining virology research (specifically the role of Epstein-Barr virus in autoimmune disease development) and science education.
On February 11 the Michael Smith Labs will host winners of the 2020 Early Career Invited Lecture Series–Dr. Gabi Fragiadakis (UCSF) and Dr. Giuliana Rossi (EPFL). Dr. Fragiadakis utilizes bioinformatic techniques to analyze the impact of diet on immune-microbiome interactions. Dr. Rossi’s postdoctoral research utilizes organoids (3D tissue cultures from stem cells) to examine organogenesis (formation of organs during embryonic development).
To wrap-up this post–and in celebration of Black History month–I would like to highlight an African-American microbiologist, Dr. Ruth Ella Moore. Born in 1903, Ruth Ella became the first black woman to receive a PhD in the natural sciences (Bacteriology, Ohio State University). A fashionista and polymath, Dr. Moore taught English courses and microbiology classes, she even chaired the Bacteriology Department at Howard University. She engaged in a range of research projects–studying Mycobacterium tuberculosis pathology (causative agent of tuberculosis), examining the role of oral microbes in cavity development, assessing blood factors, and exploring the impact of antibiotics on gut microbes (check out a snippet of her research here)!
Wikipedia Images: Ruth Ella Moore
We need diversity in STEM. Scientific innovations emerge through the efforts of many voices working together to dream, create, develop, and critically test and retest and retest and retest ideas.
Research can be difficult, discouraging, rewarding, confusing, and exciting. For a long time STEM has (and continues?!) to be a challenging space for women to thrive. But you and I matter.
So in honour of the women that came before…
“We must have perseverance and above all, confidence in ourselves. We must believe that we are gifted for something and that this thing must be attained.” –Marie Curie
In summer 2014–a year before I began graduate studies–the ice bucket challenge splashed across social media. Participants were filmed getting drenched with ice-cold water. Videos typically ended with nominations for others to join the ice bucket dunk or donate money towards ALS research. Within a month, the ALS Association received over 100 million USD.
ALS (Amyotrophic lateral sclerosis, Lou Gehrig’s disease) is characterized by progressive death of motor neurons within the brain and spinal cord. Broken motor neuron-muscle signalling results in loss of voluntary movement, eventually leading to death.
A (no) MYO (muscle) TROPHIC (nutrition)
ALS has no cure. Following diagnosis, half of ALS patients die within the next five years…although there are notable exceptions (theoretical physicist Dr. Stephen Hawking and NFL athlete Steve Gleason). In 1990, members of the World Federation of Neurology gathered in Spain to define the diagnostic criteria of ALS. Almost 30 years later, the Ayala lab at Institut de Recerca Biomèdica in Lleida, Spain explores how diet might improve ALS outcomes.
In November 2019 Dr. Ayala’s team published their work in Neurotherapeutics. I was able to participate in this project and, in October, I visited with members of Dr. Victoria Ayala’s lab (including lead author Dr. Pascual Torres). The Ayala Lab utilized a mouse model of ALS (G93A-SOD1) to examine the impact of dietary DHA (docosahexaenoic acid) supplementation. DHA is a fatty acid that contributes to neurocognitive development, anti-inflammatory responses, and lipid signalling. We consume DHA through our diet–key food sources include eggs, algae, fish, and nuts/seeds. ALS patients, however, display a decrease of DHA within the spinal cord.
Torres et al. report that DHA supplementation improves life expectancy and motor capabilities (stride length) in male, but not female, mice. DHA supplementation also increases DHA levels within the spinal cord of male mice. The authors suggest that increased DHA mitigates systemic inflammation likely improving ALS outcomes. A cautionary note: the G93A-SOD1 mice model genetic (familial) ALS–SOD1 gene mutations are linked to ALS. However, the majority of ALS cases have no known genetic component. Intriguingly, ALS is more common in males than females. This research highlights the importance of assessing disease pathology and putative treatments in males and females.
Questions to ponder:
Could DHA help manage specific cases of ALS? If so, what basic research/clinical trials would be needed to assess DHA efficacy? What are the limitations and/or benefits of mouse research? Are there additional mechanisms that might explain why DHA supplementation improves ALS outcomes in the G93A-SOD1 model?
Check out the publication to learn more about ALS research in the Ayala Lab. To donate to the ALS Association click here.
Me in Lleida (La Seu Vella cloisters)–stay tuned for more discussion re: international collaborations!
Last week Science published a perspective article authored by my boss B. Brett Finlay and members of the CIFAR (Canadian Institute for Advanced Research) Humans and the Microbiome Program (HMB). CIFAR-HMB explores how the microbiome influences human evolution, anthropology, and health (particularly at the “bookends” of life: perinatal development and ageing).
I’ve had the wonderful opportunity to attend CIFAR-HMB meetings as a program reporter–covering various HMB sessions and outreach initiatives. During a 2019 Toronto meeting, discussions emerged regarding disease/mortality trends. Overall rates of communicable (infectious) diseases have decreased in the past century. In contrast, the prevalence of “noncommunicable” diseases (e.g. dementia, cardiovascular disease) has risen.
Ongoing research suggests that gut microbes may contribute to the aetiology and pathology of certain “noncommunicable” conditions. If so, spreading impaired microbial communities may increase the risk of transmitting microbiota-associated disease conditions. Of course, this article addresses a largely hypothetical perspective. Don’t worry–you won’t catch heart disease from bugs within a sneeze!! However, the microbial-transmission model raises some interesting questions…
Are noncommunicable diseases truly noncommunicable? How might researchers prove that microbial transmission contributes to the direct transmission of certain “noncommunicable” disorders? And how could we prevent the spread of disease-associated microbiome communities? Check out the article and promo video!
In this post, I’ll share some 2019 highlights from the Finlay lab.
The past year included conferences, collaboration, documentaries, disturbing reports, and (of course) science!
In April 2019, the Michael Smith Laboratories held a special screening of Dr. Brett Finlay’s Let Them Eat Dirt Documentary. The documentary, based on the eponymous book authored by Dr. Marie-Claire Arrieta (former Finlay post-doc, now at the University of Calgary Arrieta Lab) and Dr. Finlay, explores links between gut microbes and health.
Written for parents and educators, the book and documentary discuss how over-sanitization impairs the establishment of a diverse gut microbiota. Reduced diversity has been linked to the rise of non-infectious disease (e.g. asthma, allergy). *To learn more about Finlay asthma research, check out “BREATHE” in the Skope’s Gutsy section.* The documentary highlights lifestyle practices that shape the microbiota and practical solutions to bolster a healthy microbiome (taking a pill labelled “probiotic wonder” does not act as a panacea for gut, metabolic, or brain disorders!).
2019 screenings occurred in Vancouver, Victoria, and Toronto…stay tuned for a wider release in 2020. Until then, check out the trailer below.
The year ended with a special report from the Council of Canadian Academies: When Antibiotics Fail. Brett Finlay chaired an expert panel that addressed antimicrobial drug resistance (AMR). Disquieting, yet critical, the report details the medical, financial, and ecological impacts of antibiotics and AMR. The panel estimates that by 2020 nearly 40% of pathogenic microbes will be resistant against first-line antimicrobials (think penicillin, ampicillin). In a fight where bad bugs outwit drugs, what are promising solutions to prevent infectious diseases in our future?
In positive news, Finlayite and Microbiology and Immunology PhD Candidate, Sarah Woodward, was awarded the UBC Science Excellence in Service Award. Sarah is a key leader in the UBC branch of Let’s Talk Science, a Canadian initiative promoting STEM programs, education, and outreach initiatives. You can learn more about Sarah’s work in our #3facts5scientists interview!
Finally, to begin the 2020 take a look at our Year in “Review”!
In Merry Christmas from the Finlay Lab I noted that 2020 would feature new blogs (and vlogs!) exploring gut-brain interactions, microbiome research, and graduate life. Here, I share some of my 2019 highlights to kickstart the new year.
This year I presented at Neuro-Immune Axis a Cell Symposium in Long Beach, CA (selected poster promo talk/poster). While the packed schedule kept me scribbling notes, visiting poster sessions, and/or networking…I took off during my lunch break to visit the Pacific Ocean. On my way to Alamitos Beach I passed by incredible mural art including this piece by Dina Saadi. Saadi–an artist based in Dubai–is known for her vibrant works featuring women. An abandoned cop car and e-scooter stood watch during my visit.
I also discussed ongoing challenges and potential of gut-brain research in a multidisciplinary review co-authored with Dr. Finlay and Dr. Tobias Rees, an anthropologist/philosopher interested in how gut microbes shape concepts of humanity TR research. This work was part of a special Bioessays review featuring voices from the Canadian Institute for Advanced Research (CIFAR) Humans and the Microbiome Program. You can watch our video preview here.
This year also featured various outreach projects. I’m a TEDx presenter! In March 2019 I shared 3 lessons I gained from examining gut microbiota-brain interactions. The day was particularly memorable as my mom and sister joined the audience.
(1) Expand Perspective (2) Value Voices (3) Acknowledge Interdependency
In October I spent several weeks in Lleida, Spain in the lab of Dr. Victoria Ayala VA Research. Dr. Ayala belongs to the Institut de Recerca Biomèdica de Lleida. In addition to practicing Catalan, learning lipidomic techniques (assessing lipid profiles in tissue samples), and presenting at lab meetings, I had the opportunity to visit some incredible Spanish cities including Barcelona (left) and Peñíscola (right). Peñíscola, a medieval walled city, has been featured in the movie El Cid and Game of Thrones episodes. The stone castle was originally built by Templar Knights before turning into the base of Papa Luna (Father Moon), also known as Pope Benedict XIII.
I’ll share more about my autumn abroad in an upcoming post.
Collaborations also expanded into the art realm! This year I had the opportunity to participate in a piece featured in the Curiosity Collider’s Collisions Festival in Vancouver. Earlier this year, Linda Horianopoulos (UBC PhD Candidate) and members of the Finlay Lab discussed gut-brain research with the incredible Dzee Louise. Dzee took our coffee conversation and created a wondrous puzzle painting entitled Crossing. To learn more about the work, check out Dzee’s blog post.
Here are grad students and the artist (Dzee far right) during the festival.
Research-Outreach-Collaboration: What a year! Here’s to new adventures in 2020. Happy exploring friends!
**Stay tuned for PART II where you’ll actually “Meet the Finlayites” and learn more about projects from researchers and graduate students in the Finlay lab.
A bit of Christmastime cheer from the friendly Finlay team. Stay tuned for more posts and video blogs in 2020. Until then, wishing you all a most wonderful time of the year. To those far from home–sending lots of love! And to all the industrious scientists–may your experiments and data analyses bring good news this season!
“Festive bay walls
Busy lab halls
Dressed in holiday style
In the air
There’s a feeling
A story of challenge, community, and collaboration…a research tale for Christmas!
Summertime has arrived (stay cool west coast)! And with it, conference season…at least in my corner of the world. For this blog post, I’ll focus on a decidedly, non-microbial subject—conference fashion*! More specifically, what should (female) researchers pack for a conference**? I don’t think there is one right answer, although there are a lot of ill-advised ones (no, please don’t pack your prom dress)! The following suggestions are based on my own experiences attending STEM-focused conferences. What are your thoughts?
Choosing what to wear…
Season and location: Is an umbrella necessary? Should you pack an extra layer or swimsuit—for me, the answer is usually yes to both! Will talks be hosted in a college amphitheater or an upscale hotel ballroom?
Advice and Investigation: Has anyone else in your lab been to this conference/or a similar type of conference? What are their suggestions? Are there photos of attendees from previous years on the conference website or social media pages? Do the conference planners provide any suggestions?
Participation and Networking: Are you attending for free food? Do you plan to personally meet with an eminent researcher or potential future boss? Will you be presenting a talk/poster?
So let’s pack….
Shoes: In the lab I wear close-toed, fully-covered shoes—mostly loafers or ankle boots. I appreciate the chance to wear different footwear: colorful ballet flats, wedges, or a trusty pair of heels. I suggest not packing anything new or potentially uncomfortable. Conferences include a surprising amount of walking—traveling from the hotel to venue, networking, poster session perusal, and spontaneous photo sessions.
Clothes: I had a female professor offer the following advice. Pack what you consider appropriate, but also include an outfit/items for a more formal and a more casual look (e.g. a black blazer/heels or your favorite science-themed shirt, respectively). These items will allow you the flexibility to dress up or relax your look. I typically wear a combination of jeans+blouse+blazer at most conferences I attend. If I’m presenting a poster or talk I’ll typically swap jeans for a more formal trouser. If I do wear a dress or pencil skirt (rarely!), I’ll keep the shoes and accessories more casual. For the most part, I prefer a “polished casual” look with a splash of elegance! I like to pack athletic wear, as well. A morning jog or outdoor excursion gets blood pumping to the brain!
Always a great outdoor excursion with these amazing brains! Finlayians at X3/X4 Kesytone Symposia 2018
Hair: Hair grooming can definitely elevate my look. When plating bugs in the lab, my hair is usually tied into a messy bun or side braid. I spend more time styling my hair at conferences (hello hair straightener, curls, or chignon). Whether you’re rocking a shaved design, beachy waves, neon locks, elegant braids, or modern updo—present a polished version of your unique style.
Remember, more important than outward aesthetic is your inner confidence. What makes you feel elegant, capable, and confident? Whether you choose a little black dress or hiking pants, present your polished self.
hmm…don’t take all your conference fashion advice from me 🙂
*Unfortunately, women still experience sexist ideologies (ahem…Dr. Tim Hunt) and often face more scrutiny for sartorial choices than male colleagues. Addressing and changing these toxic behaviors deserves an entirely separate post (or blog). For more on challenges and ways to address workplace equality, see:
My spring in Singapore has been a valuable learning experience. For the past 1.5 months, I’ve had the opportunity to attend microbiome conferences, gain new lab techniques, and work with an incredible research team at the Nanyang Technological University. Stay tuned for more Singapore updates in a future Skope post!
Of course, a perk about living in a new country is celebrating an added holiday—as you’ll recall from Holidaze! Unlike North America, Singapore observes Labour Day on May 1—the International Worker’s Day. I decided to explore Singapore’s northern neighbors during the Labour day weekend. The highlight of my whirlwind adventure was Angkor. Angkor, the ancient centre of the Khmer dynasty, lies a few miles north of Siem Reap, Cambodia. The site contains beautiful Khmer temples, notably the magnificent Angkor Wat (built by King Suryavarman II and now a UNESCO World Heritage Site), Angkor Thom (the stone-headed temple of King Jayavarman VII), Baphuon (featuring a 70-meter reclining Buddha), and Ta Phrom (Tomb Raider temple)! Originally built for Hindu worship, many of these sites were later transformed into Buddhist temples. The stone carvings reveal scenes from daily life and a blend of Hindu and Buddhist iconography.
A knowledgeable guide (thanks Mr. Sophea!) from the Happy Angkor Tour showed me around the park. Our first stop was at a quiet mountain temple. I climbed 5 stories of VERY NARROW stairs to see the reclining Buddha. While erosion certainly contributed to stair loss, my guide explained that steep, narrow staircases are an important feature of Khmer temples. Narrow stairs remind visitors that the path to heaven is never easy. Wide stairs invite a certain complacency—an opportunity to tarry near the earth during your ascent to the gods.
For me, the virtue of narrow stairs is to accept the challenge of the ascent. Graduate school has provided me with ample challenges—learning new lab techniques (troubleshooting said techniques), altering research directions, learning new analysis methods, writing papers, preparing for comprehensive exams, improving time management, building resilience, project planning (and re-planning). The amount of false starts and failures involved in this process occasionally feels daunting. But perhaps if getting a PhD was easy, I’d spend too long lingering and less time growing as a scientist. Vacation was awesome—but I’m ready to climb.
What’s your challenge? Accept the ascent—the reward at the top might amaze you.
This picture does not do the staircase justice. If ascending was a challenge—descending was (momentarily!) slightly terrifying. Many ledges were only wide enough to accommodate one sneaker!
PS—Tips for Visiting Ankor
If you have the opportunity to visit and learn about the complex history of Cambodia—you should definitely stop at Siem Reap/Angkor. While visiting the park…
Don’t withdraw or exchange Cambodia riel—it is almostimpossible to exchange the money when you leave the country. Unfortunately, high inflation rates have eroded the riel’s value. Many places accept, even prefer, US dollars.
If you are on a tight schedule, I would recommend booking a tour company (check out: http://happyangkortour.com). Due to the park’s size, walking is not an option! Bike rentals and tuk-tuks are an inexpensive option—just do some homework/route planning beforehand! There are many hidden gems around the park. Whatever your mode, wear comfortable shoes, you’ll do a lot of walking and climbing at each temple site.
These are still active worship sites—be respectful in dress and behavior.