Science on Display | Bellevue University 
The Nebraska salt marshes are a very unique ecosystem and one of the few places in the US where the ground water is naturally salty. They are a relic of ancient oceans that once covered central North America. Conservation of natural areas has historically typically emphasized plant and insect ecology, however it is important to start at the basis, by looking at the microbial changes that often show signs of distress, or start the recovery, months or years before changes become evident in the larger ecosystem. To provide a better understanding of the Nebraska salt marsh micro-ecosystem, we performed a 16-month study to analyze and compare the salt marsh microbiome throughout different seasons.
The research team that performed this study was composed of a group of dedicated Bellevue University and international visiting students that performed different parts of this study over a two-year time period. The team found that the salt marsh microbiome is resilient, but also shows both temporal and spatial variations that are concurrent with seasonal variations in salinity, temperature, and vegetation growth. The study also identified several new species for which the whole genomes were determined. Surprising was the discovery of several antibiotic resistance markers (AMR) and human pathogenic strains of Vibrio cholerae and Pseudomonas in these somewhat secluded marsh ecosystems.
In the end the study was able to determine which species are critical for the health of the salt marsh microbiome, and this could help in future conservation and microbial stewardship efforts to preserve the marshes from further degradation and loss. The result were published this week in the journal ‘Microorganisms’: https://www.mdpi.com/2076-2607/13/10/2369
This is not only a great scientific achievement, but also a great illustration of the collaborative science research success at BU. The research was partially sponsored by the 2024-25 EPSCoR NE grant (to Dr. John Kyndt) and the Wilson Undergraduate Research Enhancement fund at BU. Two of the co-authors are BU students that were sponsored by the EPSCoR grant, one student was from the Delphin summer research program, and two other ones were from the Erasmus research student exchange program between BU and Erasmus University in Belgium.
This research was a collaboration between Bellevue Biology students: Emma Stock, Ketlyn Rota, Brandi Dunn, and Maddy Vasquez, a student from our Delfin summer research program (summer 2024) Daniela Hernandez-Velazquez from the Universidad Veracruzana (Mexico), visiting students Alyssia Lespes and Solenn Bosmans (spring 2025) from the Erasmus University Brussels (Belgium), and Jace Smith who provided additional bioinformatics support, all under the guidance of Dr. John Kyndt.
The results provide a baseline understanding of the microbial processes that support these important ecosystems, and can be used to monitor the future health of the marshes. With increasing urban development near the Nebraska salt marshes there are increasing challenges with effluent contamination of the marshes and, alternatively, potential transfer of these pathogenic and AMR containing species to neighboring developments. Preserving these wetlands is not only important for the ecosystem of the marsh and the health of the environment, but also allows us to get a historical glimpse of the evolution and adaptation of species to more extreme environments.
If you are interested in joining projects like these, there are more student opportunities to join in this type of research. For more information contact Dr. John Kyndt (jkyndt@bellevue.edu).
Thanks to the student exchange program between their Erasmus University (EhB, Brussels, Belgium) and Bellevue University, two new students are currently working at Bellevue University as Science Lab Assistants. For the past three years students visiting from EhB have had the opportunity to gained practical experience aligned with their Erasmus studies in the area of biomedical lab technology. This year the lab is joined by Alyssia Lespes and Solenn Bosmans, who are performing a 4 week long research internship.
EhB each year has ‘international days’ and Dr. John Kyndt yearly gives a presentation to the second-year students about the ongoing research at BU, as an invitation for them to join for an internship. Dr. Kyndt is originally from Belgium and earned his Ph.D. in Biochemistry at the University of Ghent and build the connections with EhB through former colleagues that are Faculty at that University.
Both Solenn and Alyssia have been involved in several projects during their research stay at BU and spent countless hours performing DNA extractions and completed many library preparations for Illumina and Oxford Nanopore sequencing. In particular, they have played a crucial role in helping with the mushroom sequencing and identification project in collaboration with NE Game and Parks, and they have helped to complete the skin microbiome study and the NE salt marsh microbiome study for which Dr. Kyndt has an grant from EPSCoR Nebraska.
Alyssia, who originates from the Limburg region in Belgium, and Solenn, who calls the Brussels region home, will be at Bellevue University until May 11. They live in student housing and also attend some of the BU science classes during their stay to compare the educational differences between the two universities. They also participated alongside Bellevue University students at the Nebraska Academy of Sciences 2025 annual meeting at UNL on April 25.
“Coming to Bellevue University and learning from Dr. Kyndt has been an amazing opportunity so far! We have learned a lot about various sequencing techniques, and working on different research topics has been incredibly educational” said Alyssia & Solenn.
The students are graduating in June, and Alyssia plans to pursue her master’s degree in forensic sciences. Solenn expects to work in industry or a hospital in a biomedical technology role after graduation.
Having students from other countries work and learn at Bellevue University enhances the overall student experience and benefits both students from other countries as well as students enrolled at Bellevue University.
“Since have signed an inter-university agreement with Erasmus this will also allow our science students the opportunity to travel to Belgium and study there, and we are actively looking at funding support for such efforts” said Dr. Kyndt.
Bellevue University, in collaboration with the Winogradsky Institute of Biology and GEOMAR, announces the discovery of a new bacterium, Thioalkalicoccus limnaeus strain Um2, found in a hydrothermal system from Russia’s Baikal rift zone. The bacterium thrives in warm, alkaline, and slightly salty waters and contains bacteriochlorophyll b, which enables it to perform photosynthesis using internal tube-like structures.
When compared to similar bacteria, strain Um2 was found to be related to other Thioalkalicoccus species but shows genetic differences. The team has sequenced the first-ever complete genome of a Thioalkalicoccus bacterium and is proposing strain Um2 as the new reference strain for this species.
“This discovery advances our understanding of how bacteria survive in extreme environments,” said Dr. John Kyndt, Professor at Bellevue University. “Studying its ability to photosynthesize in harsh conditions and its interactions in complex microbiomes could lead to new ways to harness solar energy, and possibly contribute to environmental cleanup.”
The discovery of strain Um2 offers potential applications in environmental science, particularly in removing pollutants from water. Further comparison of its metabolic processes could also help discover new molecules for biotechnological practices.
For more details, read the full article here: https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.006657#.
This blog was originally written by Dani Knipp and reposted with permission from the BU Newsroom site: https://news.bellevue.edu/bellevue-university-partners-in-discovery-of-new-bacterium-from-russias-baikal-rift-zone/
Summer is almost over, but do you ever wonder what microbes are possibly in your swimming pool? You may not know that some species can easily survive chlorine and can be abundant in public pools and water supplies.
Our newest publication is a collaborative research paper that found a new species of non-tuberculosis Mycobacterium in a public swimming pool in Omaha, Nebraska. Although these species do not cause tuberculosis, they can cause pulmonary diseases that resemble tuberculosis and are an emerging healthcare and community acquired infection. The CDC and FDA have an ongoing warning for NTMs and their potential harmful effects to individuals that are older, immunocompromised or have other medical conditions like open wounds, which makes this a timely and relevant discovery.
This research was a collaboration between a student from our Delfin summer research program, Daniela Hernandez-Velazquez from the Universidad Veracruzana (Mexico), a visiting student Rana Petre from the Erasmus University Brussels (Belgium), and one of own Bellevue University students, Maddy Vasquez, under the guidance of Dr. John Kyndt.
Maddy Vasquez initiated the study when she proposed to sequence the pool water for potential algal bloom contaminations. After sequencing and analysis of the samples, the team identified the new Mycobacterium species as the prominent bacterial species present in the samples. The presence of Mycobacterium in the pool itself is maybe not that surprising since it is known to be resistant to chlorine treatments, however the team also found that it contains multiple antibiotic resistance genes and the samples contained a unique bacteriophage, which makes it a unique system for further studies on phage-bacterial systems.
The study is published in the journal Microbiology Resource Announcements:
https://journals.asm.org/doi/10.1128/mra.00896-24
If you are interested in joining projects like these, there are more student opportunities to join in this type of research. For more information contact Dr. John Kyndt (jkyndt@bellevue.edu).
This week our senior science student Maddy Vasquez is in the spotlight. Maddy is graduating this Spring with her Biology bachelor’s degree with a minor in Chemistry and Natural Resource Management!
Maddy is originally from Omaha and joined Bellevue University four years ago to study Biology and play for the BU Bruins soccer team. She is currently completing her senior thesis with research on how corporate partnerships can enhance conservation efforts!
In 2018 OPPD began converting 325 acres of its property into natural pollinator habitats to foster biodiversity, prevent erosion, and beautify areas surrounding substations. Maddy helped to develop a new structured plant sampling with drones to minimize time spent on field surveys. The results of this study demonstrate how drones can be used to more efficiently (and painlessly!) to assess plant biodiversity. These results provide OPPD with a strategy to continue to enhance their biodiversity efforts through their Prairies in Progress program.
Maddy recently presented her results at the Nebraska Academy of Sciences Annual Meeting on April 19 in Lincoln.
Besides her thesis project, Maddy also served as a student representative on the Board of Directors for Green Bellevue. In addition to her academic efforts, Maddy also has had 4 successful years playing for the BU Women’s soccer team! She was also recently selected to the student commencement speaker at the spring graduation on June 1st, 2024.
Maddy is continuing her academic efforts in conservation by pursuing a Masters degree in Natural Resource Management from UNL! We’re so proud of you Maddy!
This week we have a special edition of our senior science student spotlight, highlighting our visiting international student, Rana Petre from Erasmus University College (EhB) in Brussels (Belgium).
Thanks to a recent student exchange program between their college and Bellevue University, Rana worked at Bellevue University as Science Lab Assistants for 12 weeks and gained practical experience aligned with her Erasmus studies in the area of biomedical and pharmaceutical lab technology.
EhB each year has ‘international days’ and for the past three years Dr. John Kyndt yearly gives a presentation to the second-year students about the ongoing research at BU, as an invitation for students from EhB to join for an internship. Dr. Kyndt is originally from Belgium and earned his Ph.D. in Biochemistry at the University of Ghent and build the connections with EhB through former colleagues that are Faculty at that University.
Rana is graduating this Spring with her Bachelor’s degree in Pharmaceutical Biological Lab Technologies!
Rana has been involved in several projects during her research stay at BU and spent countless hours performing DNA extractions and completed over a hundred library preparations for Illumina and Oxford Nanopore sequencing. In particular, she has played a crucial role in helping complete the skin microbiome sequencing project with one of our senior students Kaziah Terrell (featured last week!).
The results of this study provide further insight into the ability to alter or manipulate one’s skin microbiome and has potential applications in clinical and forensic microbiome studies. Rana will be presenting her final thesis on this topic in Belgium in June this year!
Rana is continuing her education in the next two months with an additional internship at AB InBev, which is global brewing company with approximately 400 beer brands produced and sold throughout the world. Their flagship brands are Stella Artois, Brahma, Beck’s, Corona, and Leffe. Rana is looking to continue her career with a position in a chemical or pharmaceutical company after graduation.
We wish you the best of luck Rana, we are thankful for all the hard work you put in and for the scientific and culinary knowledge you shared with our local students!
Dr. John Kyndt, Professor of Microbiology and Sustainability is one of this year’s recipients of the Nebraska EPSCoR grants for Undergraduate Research Experience in Small Colleges and Universities.
His proposal entitled: ‘Nebraska Salt Marsh Microbiome: an exploration of spatial and temporal microbial diversity’, will allow BU students to delve deeper into the largely unexplored world of microbes in these distinctive environments. The Nebraska Salt Marsh areas are a relic of ancient oceans that once covered the middle of North America. This project is focused on the conservation of this unique area, and aimed to identify the presence of any potentially harmful viral contaminants that might impact plant, animal, and human disease development.
“With our preliminary studies we had already shown that the microbial composition of the Nebraska Salt Marshes is quite unique and contains some potentially very interesting new species” says Dr. Kyndt. That study was published in 2021: https://doi.org/10.3390/life11050446. “Now, thanks to the EPSCoR funding, we can explore this further and study the spatial and temporal variations of these environments over an entire year”
Not only will this project address broader questions about long-term habitat and groundwater conservation, and potential disease prevention from environmental pathogens, but it is also an excellent opportunity for undergraduate students to gain real-life field sampling experience and learn specialized lab techniques like genome sequencing and metagenomic data analysis.
The Undergraduate Research Experience grant program was established by EPSCoR to provide research experience for selected students interested in research projects, and the program is funded by an NSF infrastructure grant to Nebraska EPSCoR. If you are a student interesting in working on this project, feel free to contact Dr Kyndt at jkyndt@bellevue.edu.
This week our senior science student Kaziah Terrell is in the spotlight. Kaziah is graduating this Spring with her Biology bachelor’s degree with a minor in Chemistry!
Kaziah is originally from Atlanta and joined Bellevue University four years ago to study Biology and play for the BU Bruins basketball team. She is currently completing her senior thesis with research on the resilience and diversity of the human skin microbiome.
Not often do students have a chance to combine their science and sports the way Kaziah did. She took her science to the next level when she recruited six of her basketball teammates as participants to test the skin microbiome of their hands and their basketballs over several weeks (shoutout to the Sensational Six!).
As part of the study, participants applied several cleaning methods to the skin to test their effectiveness in altering the skin microbiome, and tested the transmissibility of the microbiome to the basketball during practice. She collected about a hundred samples and sequenced them with our in-house Illumina genome sequencer. As it turns out, the skin microbiome is very resilient and very specific for each individual, even over longer periods of time!
The results of this study provide further insight into the ability to alter or manipulate one’s skin microbiome and has potential applications in clinical and forensic microbiome studies. If you want to find out more about these exciting results: Kaziah will be presenting the results of her research at the American Society of Microbiology (ASM) meeting in Atlanta in June!
Besides her thesis project, Kaziah has also been working the past two years as a lab research assistant on various sequencing projects in the BU Science Labs. She has spent many long evenings extracting DNA from soil samples or analyzing plant phylogeny plots. Even though she’s in the lab often, you probably have seen her around campus as she has helped with organizing and planning many of the residential on campus student activities during the past four years. As if that’s not enough, she is also the Vice President of BOSA (Board of Student Athletes) for the NSAA conference.
In addition to her academic efforts, Kaziah also has had 4 successful years playing for the BU Women’s basketball team! Kaziah is a busy bee, but she has done a fantastic job of achieving success in both her academic, social, and athletic life!
Kaziah is planning to continuing her education and her basketball passion in grad school and will be pursuing a Masters in forensics and criminal justice.
We wish you the best of luck Kaziah, keep making the BRUINs proud and keep exploring in science!
This week we highlight our senior science student Emma Stock, who’s about to graduate this Spring with her Biology bachelor’s degree with a minor in chemistry!
Emma is currently finishing up her thesis with research on the genetics and genomics of endangered Shoal Chub (Macrhybopsis). She has been sequencing DNA from environmentally collected fish samples that have been preserved, with the purpose of performing a detailed phylogenetic and ecological study of these species. Since these samples have been preserved for several years, it is certainly a challenging task to obtain sufficient intact genomic DNA for Illumina high-throughput sequencing, but according to Emma, taking on these challenging subjects “helps build character”.
After many lengthy hours of DNA extraction from preserved native fish samples and library preps for genome sequencing, she successfully sequenced the complete mitochondrial genomes for three endangered Nebraska fish species. This will help with further preservation efforts and provide a better understanding of the evolution of these species. Besides her thesis project, Emma has also been working this past year as a lab research assistant on various soil and plant sequencing projects in the BU Science Labs. Emma is planning to present the results from her research at the Nebraska Academy of Sciences conference in April.
In addition to her academic efforts, Emma also has had 4 successful years playing for the BU Women’s soccer team, where she functioned as team captain for the last year two years. Balancing academics and athletics can be challenging, but Emma has done a fantastic job of excelling in both!
Emma is continuing her education and passion for environmental science and has been accepted to the Master program in Environmental Studies at Evergreen State College. Good luck Emma, we know you will go on to do great things!
It’s never too late to be a continuous learner, especially when it comes to sustainable development which is concerned with providing present solutions, but taking into account the needs of future generations.
No one knows that better than Dr. Lance Stokes, who is in his 80s, and came to Bellevue University for another degree, this time in sustainability studies. With multiple degrees from other institutions already, he’s driven by a passion for lifelong learning and believes education is key to unlocking greatness.
Dr. Stokes graduated with his new degree in Sustainability Management (SUST) and reflects on his learning experiences and the program:
The Kaizen-based process of continuous improvement is also a concept that we teach in the SUST program in the broader concept of sustainable long-term improvement of processes and projects, but as indicated by Dr. Stokes testimonial, this is certainly also relatable on a personal level.
If you want to learn more about the Sustainability program, or other science opportunities at BU, feel free to contact the Program Director, Dr. John Kyndt: jkyndt@bellevue.edu.
Bellevue University professor John Kyndt, will be one of nine speakers to take the stage and present his ideas that push the boundaries of the unknown at the TEDx Omaha event, “EDGE,” set for Saturday, Nov. 18 at Creighton University.
Dr. Kyndt, who is a Professor of Microbiology and Sustainability at Bellevue University, will talk about his focused research on the genomics and biochemistry of bacteria and viruses from extreme environments, to better understand life’s adaptations to extreme conditions.
“These explorations and discoveries at the extreme edges of life teach us more about the diversity of life and how cells can adapt, and possibly even how there can be life on other planets with extremely different environments,” said Kyndt.
Dr. Kyndt specializes in microbial genomics, metabolomics and bacterial photosynthesis.
TEDx Omaha is an independently organized TED event. As part of the global TED community, TEDx Omaha connects locally to explore ideas and situations that affect our culture, our environment and our minds.
Tickets for TEDx Omaha are available now and can be purchased online.
Don’t Miss Out on the Annual Event Taking Place on Saturday, Nov. 18
Repost from BU Newsroom https://news.bellevue.edu/bellevue-universitys-john-kyndt-will-discuss-work-in-genomics–biochemistry-at-tedx-omaha/
In case you wonder what the biggest breakthroughs in biology and neuroscience were in 2024, here is the top 3 list, composed by Quanta Magazine. You might be surprised that this includes research studies that answer basic, but nevertheless important science questions such as: where do all cells originate from, and does the brain control your immune system, or how does AI from Google DeepMind help to solve the enigma of how proteins form inside your cells?
The study of life’s ancient ancestor:
The idea that all life originates from a common ancestor is certainly not new but using advanced evolutionary genomic and taxonomic analysis, a team of interdisciplinary scientists was able reconstruct a model of what this ancient cell type (or population of cells) might have looked like and how it metabolized and survived. The study suggests the existence of surprisingly complex cells some 4.2 billion years ago!
A brain-body connection that links the brain and immune system:
In the last few years, we have learned more about the gut-brain connection, which is leading to novel treatments and medications. However, little was known about any possible connection between the immune system and the brain until last year’s study. Up until recently it was thought that the immune system is mainly self-regulating when it comes to things like inflammation. However, this recent study shows an unexpected brain-immune system connection where the brain contains a specific area that can regulate inflammation. Chronic inflammation is involved in many diseases, from diabetes, obesity, atherosclerosis, arthritis, and even cancer. This newly discovered connection will certainly lead to new treatment avenues.
AI transforms protein structure science:
AI is a hot topic everywhere these days, and certainly in science its use has been expanding. You may remember that proteins fold into a specific 3-dimensional structure that is important for their function. However, for decades scientists have been trying to predict and model how this folding actually works. With the help of Google DeepMind AlphaFold2, we can now accurately predict the three-dimensional structure from a one-dimensional string of amino acids. This has many applications, from predicting viral evolution to also designing new protein-based drugs. In November 2024 the Nobel Prize in Chemistry was awarded to the creators of AlphaFold2.
Here is a video summary of these discoveries:
All of these are topics that have roots in basic science research, and if you are curious to learn more, we discuss all these in our science Gen Ed courses (like BI142 ’12 ways biology will change the way you think’) and in more detail in our advanced microbiology, molecular biology, immunology and biochemistry courses.
Native plants don’t get nearly enough research attention and the representation of genome information for native plants is substantially lower than the database information available for crop plants or popular ornamental plants.
The new student-led research at Bellevue University is trying to change some of that paradigm, and students from our research classes, visiting student programs and student worker positions have been sequencing a variety of plants from our native plant garden on campus to gain more insight into the genetic wonders these plants might contain.
Our newest publication in the International Journal of Plant Biology, presents the work of BU students Maddy Vasquez, Emma Stock and Kaziah Terrell, together with our greenhouse manager Julian Ramirez and Professor John Kyndt. The work was focused on sequencing the chloroplast genome of the native plant Cleomella serrulata (also known as Rocky Mountain bee plant or stinking clover). The chloroplast was sequenced in house and the genome was analyzed to determine the evolutionary origin of this plant and compare its genetic differences with other plant families. This is a first step to determine how native plants have evolved and adapted to certain environments over many years.
Cleomella has the ability to adapt to harsh environmental conditions and is of ecological importance in maintaining biodiversity within arid ecosystem. Historically, Native American tribes utilized various parts of the plant for medicinal purposes, from treating skin ailments to alleviating respiratory issues. Here is the link to the full publication:
https://www.mdpi.com/2037-0164/15/3/65
Obtaining plant genomic data is still a challenging endeavor. Both Emma and Kaziah spend many hours of their student research work trying to optimize the DNA extraction and sequencing methods for Cleomella and other plants. Maddy took the lead on the write up of the publication as part of her BI 305 Biological Investigations class. Under the guidance of Dr. John Kyndt and Julian Ramirez, the team was able to uncover some interesting features of the evolution of this native plant within its family. This now opens the doors for future evolutionary studies of these plant families.
Cleomella serrulata was also one of the plants that was highlighted last year in our Art + Science presentation at the Benson Theatre for its unique color pigmentation. More information and a link to that presentation can be found here:
The sequencing of native plants, soil and mushrooms is an ongoing project and there are more student opportunities to join in this research. For more information contact Dr. John Kyndt (jkyndt@bellevue.edu).
| Join us for TEDxOMAHA Salon: Your microbes and you! |
| 5 September 2024 at 6:00 PM. Fun facts. Did you know that the microbes that live in you, on you, and around you have a large impact on your health and the health of the environment? A healthy gut microbiome is important to help prevent conditions like obesity, diabetes, heart health and even mental health conditions like depression and anxiety. The microbes that live on your skin are as unique to you as your fingerprints, and they closely work with your immune system to keep you healthy. Just like the microbes living on you and in you, the ones living in your garden soil can help create a healthier environment for the plants to grow and insects to thrive. Dr. John Kyndt is inviting you to come explore the wonderful world of microbes and see some of the research he and the team have done on skin microbiomes and soil microbiomes, and learn to appreciate the importance of the microbial world that we all live in. TEDxOmaha Salon Thursday September 5th starting at 6.00 p.m. at Kaneko, located at 1111 Jones Street, Omaha, NE 68102 – please enter via the library entrance door, which is on 12th St Street Register soon because space is limited.  Thursday, 5 September 2024 18:00TEDxOMAHA Salon: Your microbes and you! Register here We hope you’re able to join us! |
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