Eat, sleep, autoclave, repeat…

For several months now, my university is in code red due to the high cases of corona infections and deaths. In case you would have missed it, we’re in a global pandemic and that poses challenges for everyone. Code red means that theoretical courses cannot take place on campus and all students are following online classes. In this regard, I’m grateful that I still have the opportunity to get up every morning and go to the lab to perform my experiments. It is one of the few things giving me a routine and a sense of purpose in these strange times.

Though I really enjoy working in the lab, it is kind of odd, since there’s only half of the staff working. As a consequence, you can (not seldom) find us thesis students video calling our mentors to make sure we’re following the right protocol and we’re working with the correct tubes, boxes and machines etc. It is a bit of a weird sight, though! To limit the spreading of SARS-CoV-2, we are also not allowed to eat together or hold big meetings in the same room. Consequently, all co-workers are spread over the entire floor to follow the online meetings to discuss recent advances in our work and brainstorm about future possibilities.

A rare benefit of the current situation is that I can manage my course material better. Since I work a lot in the lab in Antwerp, and my courses would normally have been given in Leuven, there was no possibility to attend all the courses live and, in the meantime, perform all my planned experiments. Now, I can access all the recordings of the lessons online and process them at my own pace. So, in this regard, it is not all bad, I guess. Nevertheless, it can get quite lonely. Social isolation is real, for any age group and what I experience form my immediate environment it that it is taking its toll on students as well. All we really have to do is to perform at the moment when it is expected from us. And although we, as second masters, have enough maturity and study experience to make it work this way, without any form of relaxation, it gets pretty fast you, yourself and your books (plus your not easily transformable lactobacilli) for the rest of the year. As ‘proof of concept’, most of my classmates I have only recently met at the exam, which was the biggest social event this academic year since March 2020, thus that says a lot! Notwithstanding, health comes first, and we need to keep doing the same old until things get better and the virus loses its grip in the society.

All I want to say is that I’m looking forward to my vaccine and to more normal times, but isn’t that true for everyone?

Lactobacilli and Bioengineers, a relationship under tension

My last semester as a master student ‘Cellular and Genetic engineering’ has recently started. At this moment of my study, I have had countless lectures about how we scientists can genetically alter micro-organisms to not only study them and try to understand them, but also to implement them in all kinds of sustainable applications. Thus, theoretically I should now be capable of translating any bio-application you can think of into a complex working genetic circuit, eventually resulting in an organism that does exactly what it was intended for. So, bestowed with all this knowledge and a healthy confidence, I threw myself on my master thesis. The research objective of my project is the functional characterization of specific genes in different lactobacilli. These bacteria are the favorite bacteria of the Lebeer lab, living at mucosal surfaces of the human body, including our skin, respiratory tract, gut, urogenital tract etc. Lactobacilli are considered beneficial for normal human functioning and one way to acquire them is via food. The lactobacilli that I am currently investigating were previously isolated form either carrot juice fermentations during the ‘Ferme Pekes’ project or from healthy human vaginas in the ‘Isala’ study. In short, I need to figure out why these specific lactobacilli are so interesting for us and which genes make them so interesting.

Starting the project, I was already picturing all the possible real-life applications that could stem from my research, a new probiotic, an innovative bioactive compound, a cure for cancer or HIV, world peace … who knew? My enthusiasm quickly met the reality of the situation. Lactobacilli aren’t all keen to cooperate with me on this. In fact, they do their utmost best to resist all my efforts to introduce genetic constructs, while this is necessary to elucidate their special traits. So, with a profound reality check, it was time to get back to the basics of genetic engineering!

Genetic engineering altogether comprises an extensive set of techniques to modify DNA either randomly or at very specific sites. One thing that most of these techniques have in common, is that they depend on the introduction of little pieces of DNA along with some molecular cut/paste tools (1.). Once inside, these tiny tools help me to find my genes of interest and specifically alter them by changing their code. For example, by cutting some parts out or replacing them by a self-designed code, the gene becomes disrupted. Because of this, the bacterium cannot access it anymore what causes it to lose a specific characteristic. And so, a mutant is born! By then comparing this mutant with the unaltered bacteria (called ‘wild-type’) in all kinds of tests, I can check which trait my mutant has lost. This way, genetic engineering helps to link genes to bacterial characteristics, enabling us to understand them better. However, most bacteria are naturally not really inclined to take up any additional genetic information from the environment, such as my tools and constructs. This is more scientifically termed as ‘transformation resistant’. Since this is the first critical step to carry out any type of genetic modification, it forms a major bottleneck for their further investigation. Until I can get the constructs inside, I cannot modify them, and I cannot link their traits to their genes. Luckily, scientists have evolved ways to give nature a hand. But, while some bacteria only need a little push, others require complete treatments and still others will stubbornly continue to resist any type of transformation. Unfortunately for my colleagues and me, most lactobacilli belong to these last two categories, what definitely complicates the relationship with our beloved research object.

The most common way to get any type of large molecule into a bacterial cell is by electrotransformation1. In short this means that by giving bacteria a strong electropulse, we can make little holes in their cell walls3.  As long as these pores are present, the cells are made permeable and a passage for the uptake of DNA is available2. However, randomly firing some electrical pulses at a bacterial culture will most often not seal the deal. In fact, most bacteria need a thorough preparation by which their cell wall is temporarily weakened and more willingly to become electropermeable3. In this respect, the major challenge for lactobacilli is that these preparation protocols are quite variable between species, and even between strains3. Finding the right electrotranformation protocol is therefore often done via a time-consuming trial and error method. Nonetheless, it remains an extremely important step in successful genetic manipulation. Hence, a large part of my work this year at LAMB consists of the optimization of the electrotransformation protocol of the earlier mentioned fermentative and vaginal lactobacillus strains.  

Although this resistance of lactobacilli towards artificial transformation slows down our ability to elucidate their function in the human body and fermented foods, I also must highlight that this does not inherently mean something bad. Whereas it implies that under natural conditions these bacteria are also not prone to take up undesired or dangerous genetic information, such as antibiotic resistance genes or virulence genes. This genetic robustness makes them safer and favors their use in fermented foods and probiotics.

References:

  1. Börner, R. A., Kandasamy, V., Axelsen, A. M., Nielsen A. T., Bosma, E. (2019) ‘Genome editing of lactic acid bacteria: opportunities for food, feed, pharma and biotech’, FEMS Microbiology Letters, 336(1), doi.org/10.1093/femsle/fny291
  2. Luft, C. and Ketteler, R. (2015) ‘Electroporation Knows No boundearies: The Use of Electrostrimulation for siRNA Delivery in Cells and Tissues’, Journal of Biomolecular screening, 20(8), pp. 932-942. doi:10.1177/1087057115579638.
  3. Wang, C., Cui, Y. and Qu, X. (2020) ‘Optimisation of electrotransformation (ETF) conditions in lactic acid bacteria (LAB)’, Journal of Microbiological Methods, 174 (march), p. 105944. doi:10.1016/j.mimet.2020.105944.

NSURP 2020 #NoLabNoProblem

An often overlooked aspect of this pandemic is the unfortunate loss of unique opportunities for young scientists to cultivate a deeper love for science, develop new skills, connect with (inter)national mentors, grow their professional networks, and open doors to new opportunities. University labs, companies and other institutions normally organize summer projects to enrich young researchers’ learning.

“NSURP is a community-driven initiative to create rewarding remote summer research opportunities for BIPOC undergraduate students in the microbial sciences.”

However, due to COVID-19, most summer programs were cancelled and the impact of these disruptions are especially profound on BIPOC (Black, Indigenous, People of Color) students. The National Summer Undergraduate Research Project (NSURP) is a grassroots project started by a team of microbiologists (Dr. Michael D. L. Johnson, Dr. David A. Baltrus and Dr. Jennifer Gardy) who recognize the importance of summer research experiences and who want to support BIPOC students in finding their love of science in those projects. NSURP is designed to:

  1. Matchmake BIPOC undergraduate students on a (inter)national level to microbiology laboratory mentors who can provide a remote summer research project experience.
  2. Provide a BIPOC science and professional development seminar series for those students.
  3. Provide a platform for the matched students to present their research online in an official capacity.

Total matched NSURP students in the summer of 2020

I had the incredible opportunity to be matched with two amazing students (Vanessa and Gabriel). We first had an introductory meeting about the research done at the Lebeerlab, my PhD and their interests. The next step was to work out a feasible summer project in which they could flourish, learn about a different side of microbiology and be free to incorporate their own intake. A big thanks to our post-doc Irina Spacova is here at place for helping out with the framework of the projects and the co-supervision 😊.

Both students chose to work on a literature review about two entirely different subjects (cfr. testimonies of students below). We planned a Skype meeting every week to discuss the subject, their progress and generally just talk about our lives and the academic world. A funny anecdote is that we only had a few overlapping hours as our time zones were very different (Eastern Standard Time versus Central European Time) but we made it work. Next, we even organized a virtual “Welcome to our lab”-tour (inspired by MTV cribs) where I showed them around our lab with the occasional meet & greet with a lab member.

Granted, the remote guidance was challenging but over the course of a few months, I can fondly say that I am genuinely proud of the way they worked out their projects; the in-depth knowledge they generated; and the critical scientific attitude they built. At the end both, Vanessa and Gabriel, finished an excellent mini-review and presented their work gracefully for prof. Sarah Lebeer. I am wishing them a bright future and the very best for all their new ventures. Hope to see you both soon in real-life 😊.

A big thanks goes out to the organizing committee of NSURP. I truly appreciate all the effort and organization that went into making this possible.

Testimony NSURP students

Check out their presentations and abstracts

Name: Vanessa Ibrahim
Affiliation: Harvard College
Title project: Microbial fingerprinting of trace evidence in forensic research with a focus on sexual assault cases

“This summer I had the amazing opportunity to work under Sarah and learn more about her work with the Isala project. More specifically, my project was to conduct a literature review on the human microbiome and its potential in forensic casework, particularly in cases of sexual assault. Through the process of researching for and writing this literature review, I was able to take away a lot of key concepts including how prevalent cases of sexual assault are worldwide, how next-generation sequencing has paved the way for the field of microbial forensics, and how body-fluid identification using microbial fingerprinting could be a valuable tool in the prosecution of sexual assaults. Special thanks to prof. dr. Sarah Lebeer, dr. Irina Spacova, and Sarah Ahannach for all of their guidance over the last few months!”

Name: Gabriel Aborisade
Affiliation: University of Maryland
Title project: When a commensal becomes a pathogen: the role of microbe-microbe interactions with GBS as a model organism

“I participated in NSURP because I wanted to gain more experience writing literature reviews related to microbial research.  I also aimed to organize my research thoughts and transfer skills accrued for future use, such as graduate programs and fellowships/grants applications.

During the program, I completed a guided literature review titled “When a commensal becomes a pathogen: the role of microbe-microbe interactions with group B Streptococcus as a model organism.” I thoroughly enjoyed the experience; though it was daunting at times due to my workload outside the program, I persevered and pulled through due to my mentor, Sarah, incessantly following up and encouraging me. Constructive feedbacks I received were also quite helpful. I got to see where I stood in terms of writing a quality academic paper. I was also able to practice my time management skills and use my persistence and work ethic.

I was quite happy with my progression throughout the NSURP program. I got to see myself grow in knowledge and skill. For instance, at the beginning of the project, I found it difficult briskly going through a journal and deducing the main point and deciding if it would be useful for my project or not but over the weeks, I got better at that by day. I also got better at utilizing my primary resources: my mentor, Sarah, google scholar, and my university’s online library database.

Practically, the project provided me something different in terms of doing research. My undergraduate research experiences mostly focused on doing bench lab work and field sampling, but this was the first time I spent so much time on the internet digging for journals relevant to my research topic. Furthermore, I felt my participation also made me a more exciting candidate for my graduate school applications. Though not 100% in line with my graduate school focus, my review topic was intriguing, and faculty members I conversed with listened with interest, asked questions, and picked more interest in me. 

I am incredibly grateful for this opportunity. After further reflection, I realize that this experience has built on my molded interest in microbial research and asserts my desire to pursue an academic career. This experience may seem to be only valuable academically, but I find it incredibly valuable personally.”

Diverse inside and out: vaginal microbes differ with ethnicity?

Every time I read about a study on the microbiota composition whether it is from the gut, skin, or vagina, I wonder with which bacteria am I sharing my body. As a Peruvian researcher living in Belgium and now being involved in the Isala project, I also wonder about my vaginal microbiota composition and the ones from women like me: women with non-Belgian ethnicity but living in Belgium for several years. Perhaps our vaginal microbiota has changed over time and became similar to women with Belgian ethnicity? Or our ethnic background is “resisting” the possible Belgian environmental influence?

Now, probably you are asking yourself, what is ethnicity? Are ethnicity and race the same? Well the answers are complex. While ethnicity refers to cultural characteristics (e.g. language, accent, religion, social customs, food and dietary preferences or restrictions), race refers to physical characteristics that define a person as being a member of a specific group (e.g. skin/hair/eye color, physical build) (Sociologist Julie Maes, personal communication). From a scientific point of view, classifying individuals by their physical appearance lacks of validity, as demonstrated by genetic studies where the genetic differences within individuals of a certain “racial group” is higher than between “racial groups”1. From a social point of view, race is a category forged historically through oppression, slavery, and conquest2. Even though ethnicity and race have different meanings, they are usually used interchangeably.

Initial studies that gave the first insights on vaginal microbiota composition included only Caucasian women. These studies showed that the vaginal microbiota often was dominated by lactobacilli. Further studies conducted mainly in the United States included women from different ethnic groups showed that women from different ethnic background display a different healthy vaginal bacterial composition, with lactobacilli not playing the most prominent role3. Thus, it was found that the healthy vaginal microbiome of women from European ancestry are less diverse (dominated by Lactobacillus species) than those of African ancestry (non-Lactobacillus dominated)4. To the question ‘does a healthy vagina always needs to be dominated by Lactobacillus?’, more research is needed including different ethnic groups to understand what a “healthy vaginal microbiome” really means. However, apparently, we always need Lactobacillus species during pregnancy5. Interestingly, research has indicated that the presence of Lactobacillus species plays a positive role during pregnancy. Even more, the vaginal microbiome composition of pregnant women tends to be dominated by Lactobacillus species however it becomes less lactobacillus dominant during the post-partum irrespective of community structure during pregnancy and independent of ethnicity6. This makes the question on the relevance of the presence of lactobacilli even more interesting.

Why is there a difference? For the moment, the answers are unclear. Host genetics and environmental factors might contribute to the difference, however these factors don’t explain all of the variation seen in the vaginal microbiota of different ethnic backgrounds.

In the context of the Isala project, we aimed to include women from different ethnic groups, but because it is a Citizen Science project, we were unsure whether we could reach them. These uncertainties are common in research and several factors play a role for citizen participation7. Interestingly, based on the questionnaires, almost 11% of the participants, identify themselves with one or more culture(s) different from the Belgian one. Moreover, in terms of nationality, our project includes women from 99 different countries!  In this way, Isala’s volunteers are contributing to disentangle the effects of sociodemographic, behavioral, environmental, and genetic factors on vaginal microbiota composition.

We look forward to study the vaginal microbiome in other countries in collaboration with partner institutions, hopefully we will start a new Isala-like project in a multiethnic country like Peru, so fingers crossed!

Special thanks to Lore van Praag and Julie Maes for their help to verify the concepts of ethnicity and race.

References

  1. Rosenberg NA, Pritchard JK, Weber JL, et al. Genetic structure of human populations. Science 2002;298:2381-5
  2. https://genderedinnovations.stanford.edu/terms/race.html
  3. Ravel, J., P. Gajer, Z. Abdo, G. M. Schneider, S. S. K. Koenig, S. L. McCulle, S. Karlebach, R. Gorle, J. Russell, C. O. Tacket, R. M. Brotman, C. C. Davis, K. Ault, L. Peralta and L. J. Forney (2011). “Vaginal microbiome of reproductive-age women.” Proceedings of the National Academy of Sciences 108(Supplement 1): 4680-4687
  4. Serrano MG, Parikh HI, Brooks JP, et al. Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy. Nat Med. 2019;25(6):1001-1011.
  5. Romero, R., Hassan, S.S., Gajer, P. et al. The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome 2, 4 (2014). https://doi.org/10.1186/2049-2618-2-4
  6. MacIntyre, D., Chandiramani, M., Lee, Y. et al.  The vaginal microbiome during pregnancy and the postpartum period in a European population.  Sci Rep 5, 8988 (2015).
  7. Redwood, S., & Gill, P. S. (2013). Under-representation of minority ethnic groups in research–call for action. The British journal of general practice: the journal of the Royal College of General Practitioners, 63(612), 342–343.