NMDC Snapshots

Intro

Alejandro De Santiago is a bioinformatician in the Bik Lab at the University of Georgia where he uses long-read and short-read metagenomic sequencing to study the biodiversity of nematodes and the functional profiles of their host-associated microbiome. We recently spoke with Alejandro about his research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

As an undergraduate student, I took a Course-based Undergraduate Research Experience (CURE) on plant genetics. CURE gives undergraduate students the opportunity to spend a semester or quarter working on a research project. Even though my research project wasn’t related to microbiomes, my CURE experience introduced me to science and inspired me to look for research opportunities as an undergrad. Soon after CURE, I began working in a research lab that studies marine microbiomes and microbial eukaryotes, such as nematodes. I never would have thought I would end up studying worms and bacteria, but I discovered that I enjoy working at the intersection of biology and computer science. I liked the research so much that I decided to continue my graduate studies in bioinformatics while working in the same lab. 

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

Nematodes are round microscopic worms that are found everywhere on Earth. Even though these worms are invisible to the naked eye, they have a community of bacteria that live in their guts and on their cuticle (exoskeleton). Most people probably remember watching marine nematodes on SpongeBob devouring everything they encountered in Bikini Bottom. However, nematodes are usually harmless and transparent. There are a few parasitic nematodes, but amazingly, the majority of these tiny worms play an important role in maintaining healthy oceans. I am studying how bacteria living in the gut and on the cuticle of marine nematodes interact with their host and how they might affect the ability of these worms to survive across vastly different environments. As human activities continue to impact ocean ecosystems, the microbiome of marine nematodes may help them adapt to rapidly changing environments.

How does your work contribute to researchers’ understanding of the microbiome?

Even though nematodes are found everywhere, their tiny size makes them very difficult to study. Most studies on the microbiome of nematodes have focused primarily on model species or agricultural pests. My work will help expand our knowledge of the microbiomes of free-living marine nematodes and how these bacteria interact with the host and the environment. 

What song do you currently have on repeat?

You will probably catch me listening to Bad Bunny. But currently, “Not Like Us” by Kendrick Lamar.

Intro

Andrian Gajigan is a PhD candidate working in Grieg Steward’s Lab at the University of Hawai’i at Mānoa. His research interests include microbial oceanography, marine virology, genomics, and gene regulation. We recently spoke with Andrian about his research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

I got interested in microbiome research through marine science. My first introduction to microbiome research aside from college level classes, is through a project understanding the impact of ocean warming to coral microbiome as well as a project looking at microbial community structuring across an open ocean water column. Microbes are literally the unseen chemists and sentinels of earth’s climate and biogeochemical cycles. They are the most abundant organisms in the ocean forming the base of the food web. Because of their importance, and my fascination towards microscopic life forms and molecular biology, I am now deep in microbiome research.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

All organisms on the planet are infected by some kind of virus. This is the case for phytoplankton, the microscopic plants living in the ocean. My project tries to understand the mechanism of phytoplankton-virus infection, how they cause mortality, and at the same time, how they sustain diversity through shuffling genetic material around. 

How does your work contribute to researchers’ understanding of the microbiome?

In my work, we are developing phytoplankton-giant virus systems in the lab for us to better understand their dynamics and interaction. In addition to lab-based systems that we can easily interrogate in the lab, we are doing field investigations on how viruses impact algal bloom demise and phytoplankton succession. 

What song do you currently have on repeat?

“That Life” by Unknown Mortal Orchestra

Intro

Becca Maher is the Marine Genomics Postdoc at Friday Harbor Laboratories on San Juan Island in Washington State. She is interested in the contribution of the microbiome to host resistance to disturbances such as climate change and disease in several systems including corals, zebrafish, and most recently, seagrass. We recently spoke with Becca about her research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

As a graduate student, I joined a coral reef microbiology lab because I wanted to earn a PhD while SCUBA diving in Mo’orea, French Polynesia. I had no previous coursework (or interest) in microbiology. Little did I know, I would spend most of my PhD on my computer analyzing coral microbiome data. Even more surprisingly, I discovered I loved bioinformatics just as much as SCUBA diving! I love trouble-shooting bioinformatic pipelines and using code to make sense of the vast, hidden world of microbes that is all around us.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

Seagrasses are plants that live in the coastal ocean. They are really important to the health of the ocean and all ocean animals, like fish. They are found all around the world, and in some places, they are getting sick from a disease. I’m trying to understand if the tiny, microscopic bugs (aka bacteria) that live on the seagrass can protect the plant from the disease. So far, we think that some bacteria on the plants can actually make the disease worse. I’m excited about this project because we know very little about the bacteria on these marine plants. My work can add a lot of new knowledge to the world.

How does your work contribute to researchers’ understanding of the microbiome?

I hope to characterize the microbiome of seagrass over the course of a year. This will add to our understanding of the stability of host-associated microbiomes over time. Additionally, seagrasses are experiencing more frequent and severe heat stress events, like most marine ecosystems. My work will provide another data point on how environmental microbes are responding to climate change. I also hope to demonstrate the importance of including the host microbiome in disease ecology studies that aim to understand the dynamics of host, pathogen, and environment.

What song do you currently have on repeat?

“Latinoamérica” by Calle 13.

Intro

Buck Hanson is a microbial ecologist at Los Alamos National Laboratory where his work centers on understanding the roles of soil and root-associated microbiomes in biogeochemical cycling and ecosystem resilience. We recently spoke with Buck about his research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

My first exposure to microbiome research was as a postdoc at the University of Vienna. At the time, my perspective of what a microbiome was limited to gut and other human-associated microbiomes (e.g., skin). However, I realize now that microbiomes exist across a wide range of environments and time scales. One of the things I love about studying microbes is how translatable concepts and processes are. 

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

My work aims to develop novel approaches using microbes to mitigate the harmful risks of climate change on natural resources (clean water, crops production, alternative fuels, etc.)

How does your work contribute to researchers’ understanding of the microbiome?

My work contributes to understanding the relationships between soil microbiomes and their influences on plant growth and stress resilience.

What song do you currently have on repeat?

I don’t listen to music that often, but there are three songs that I could hear anytime, anywhere:

1. “Celebration”, Kool & the Gang
2. “Red Red Wine”, UB40 (version), although you can never go wrong with Neil Diamond
3. “Love Shack”, The B-52’s

Intro

Chris Robinson is a 3rd year PhD student with Dr. Irene Newton at Indiana University and studies the interactions of bacteria and mobile genetic elements within honey bee colonies. His current research explores how accessory genes of bacterial pangenomes are distributed across honey bee microbiomes. We recently spoke with Chris about their research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

When I was 13, I was diagnosed with Crohn’s Disease – which I later learned is often caused by dysbiosis, or a change in the microbiota that can have negative effects. I thought that this was so cool! The species were the same, but their composition was abnormal. How could that be important?  I really didn’t commit to studying this until my PhD, but this initial mingling of curiosity and my disease laid a pretty strong foundation for the questions I’d later become interested in.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

So, I’m really interested in genes that move around. Historically, we have focused on genes that move between generations (grandma passes some genes to my mother, who then passes some genes onto me). But there are genes that move within generations too. In this case, grandma could pass on some genes to grandpa, or another grandma, or another entirely unrelated person. It’s unlinked to how we normally think of genes. 

These genes tend to be found on these strange entities known as plasmids or viruses,  which infect bacteria and can cause all sorts of effects on the bacterial host, such as antibiotic resistance or the ability to digest new food.

Now, we have a pretty good understanding of how genes that move between generations evolve or change over time. But how evolution modifies these genes that move within generations is not well understood at all. And these genes are everywhere – especially in your microbiome, where they can cause diseases and affect digestion and metabolism.

In my project, I use the honey bee as a model system, because its microbiome is very simple compared to humans. I use this model to identify mobile genes and to investigate which kind of genes tend to be mobile and which bacterial hosts they like to be in. I love this project because I get to use known methods in population genetics, which allows me to measure rates of molecular evolution in addition to applying new methods, such as proximity ligation, which allows me to identify which bacteria is with virus or plasmid. On top of it all, I get to be a beekeeper and play with bees, which makes doing and talking about my science very easy.

How does your work contribute to researchers’ understanding of the microbiome?

Currently, our field knows a lot about who is in the microbiome – especially bacteria. But we don’t have a good grasp on what those microbiome members are doing, and how the genes they associate with might be evolving. And the microbiome has a whole microbiome of its own in terms of mobile genetic elements such as viruses and plasmids. This is only beginning to really get studied.

My hope is that my work contributes to ways to better compare microbiomes across different systems. Every microbiome, whether it’s between individual people or individual species, differs in terms of its species, composition, ecology, etc. But each of these microbiomes encode genes. If we can better understand how these genes evolve and identify characteristic patterns, then we can begin figuring out what evolutionary and ecological forces are important in creating that pattern and go before testing it out on other microbiome communities. 

What song do you currently have on repeat?

This is by far the hardest question. I usually listen to some pretty disgusting metal (lyrically at least), but I love any song with really good basslines. I have to pick three – sorry.

The first is just a really brilliant, grungy cover of The Stone Roses’ classic. 

The second song comes from a cool band from Australia and reminds me of Joy Division in a haze of dream pop. 

The third song comes from Cindy Lee, who I was lucky to see last year in Detroit and is easily the most brilliant musician right now. This one’s off an earlier album, Model Express, which I first heard while stuck in Bosnia and deathly sick with Covid. The song’s always in my head.

#1 King Woman – I Wanna Be Adored

#2 Eternal Dust – Salome

#3 Cindy Lee – Left Hand Path

Intro

Daniela Betacurt-Anzola is a PhD student in the BMMB program at Penn State. Her research interests focus on the ecology of the gut microbiome and how it affects the host’s physiology and health. We recently spoke with Daniela about her research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

My interest in the gut microbiome began when I discovered the vast number of microorganisms residing there and the significant impact of their encoded proteins on our health. Unraveling the potential to prevent diseases through the complex interactions between the microbiome and its host is fascinating to me.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

You know how our bodies have tiny bacteria living in our intestines? Well, these little bacteria can actually change how our bodies use different metals from the food we eat. Some metals, like mercury, can be harmful, but these bacteria have a way to make it safer for us. I’ve been studying bacterial enzymes that help these bacteria break down harmful mercury into a form that’s not as dangerous. By understanding how these bacteria work with metals, we hope to find ways to help people stay healthier by improving how their bodies use nutrients from food. This discovery not only sheds light on how our bodies interact with these substances but also opens doors to potentially improving human health through microbiome-based interventions. It’s thrilling to think that our work could eventually help people better absorb nutrients and avoid the harmful absorption of detrimental metals in their diets.

How does your work contribute to researchers’ understanding of the microbiome?

My work contributes to researchers’ understanding of the microbiome by focusing on how gut microbes interact with dietary metals, particularly mercury, and their implications for human health. By investigating microbial mechanisms like metal biotransformation, we are expanding knowledge of how these organisms influence nutrient bioavailability and detoxification processes within the body. Additionally, our study of the gut microbiome’s metal resistomes provides insights into microbial diversity and functional capabilities in different populations. This research not only deepens our understanding of microbiome dynamics but also suggests new avenues for microbiome-targeted therapies to enhance nutrition and health outcomes.

What song do you currently have on repeat?

“Pajarito colibrí” – Natalia Lafourcade

Intro

Emilie Skoog is a postdoctoral scholar at the Scripps Institution of Oceanography. She uses multi-omic approaches to study microbial and viral ecology in extreme environments in order to better understand the limits of life on Earth and potential for life beyond this planet. We recently spoke with Emilie about her research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

My work in microbiomes began during my undergraduate career when I took a class on astrobiology and geobiology and learned about microbial communities persisting in extreme environments. I then joined a lab where I characterized microbial communities inhabiting subglacial lakes in Iceland. This began my ongoing passion for studying microbial communities living at the limits of life.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

I am working on deciphering dynamics between microbial hosts and their viral counterparts in some of these most extreme places on Earth including anoxic basins at the bottom of the ocean that are 13 times the salinity of seawater and these salty, acidic ephemeral lakes in Western Australia. Understanding the ability for life to exist in some of the most extreme environments on Earth is both exciting and gives us a sense for the potential for life to persist in similar environments beyond Earth.

How does your work contribute to researchers’ understanding of the microbiome?

A key aspect to understanding microbiomes is understanding the role that viruses play in influencing their microbial hosts, especially when these microbial communities undergo stress. They can do this via horizontal gene transfer or even expressing auxiliary metabolic genes that can enable certain microbes to survive in extreme environments. My work will shed light on the role that viruses residing in saline, anoxic, and acidic environments may have on influencing microbial host adaptation and evolution in these environments. 

What song do you currently have on repeat?

“End of Beginning” by Djo

Intro

Heather Skeen is a Research and Teaching Scholar at University of Connecticut and received her PhD from the University of Chicago. Her research focuses on understanding how ecological and evolutionary forces influence host-associated symbionts, with an emphasis on gut microbiota and disease ecology in migratory birds. We recently spoke with Heather about her research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

As a research technician, I was tasked with processing a large batch of samples for downstream microbiome characterization.  Through this project I became interested in the vast diversity and complexity of host-associated microbiota, especially in wild birds.  

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

My current work focuses on seeing if and how gut bacteria differ depending on what host bird species they come from. This is exciting because this is the most in depth look I have taken at microbiota within individual host species. 

How does your work contribute to researchers’ understanding of the microbiome?

Migratory birds travel vast distances twice a year. This feat has substantial impacts on their physiological condition. Additionally, these birds experience variation in diet and environment over the course of a migratory cycle.  I look at temporal and geographic variation in migratory bird microbiota, which contributes to the overall understanding of if and how microbiota change depending on when and where the host is sampled.  

What song do you currently have on repeat?

Ramin Djawadi soundtracks – they’re good for writing. 

Intro

Iyanu Mumeen Oduwole is a PhD candidate in the Genomics Science and Technology program at Bredesen Center, UT-Oak Ridge Innovation Institute. His research focuses on leveraging bioinformatics, metadata analysis, and applied machine learning techniques to enhance the cultivation and elucidate the adaptation mechanism of uncultured microbes, particularly those found in permafrost and deep cold subsurface environments. We recently spoke with Iyanu about his research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

I became interested in microbiome research when I joined the Environmental Microbiology Group at the American University in Cairo (AUC) for my master’s program. There, I worked on identifying novel thermostable DNA ligases from the Red Sea brine pools. This experience ignited my fascination with the potential of microbial dark matter, particularly from underexplored environments, and how these novel microbial products can benefit both humans and the environment.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

My project involves studying tiny microbes that we can’t easily grow in the laboratory. I use computers to examine their genomes, which are like their instruction manuals. By doing this, I find clues that might help us understand how to grow and study them better in the lab. Additionally, I discover how these microbes survive, particularly in the cold and deep underground environments that interest me. 

What excites me most about my research is the opportunity to uncover the hidden secrets of these fascinating microbes. Understanding how they adapt to extreme conditions could lead to new discoveries that benefit science and society, such as new medicines or environmental solutions.

How does your work contribute to researchers’ understanding of the microbiome?

My work addresses a significant challenge in microbiology: the fact that over 80% of microbes remain uncultured. By studying these elusive microorganisms, my research provides valuable insights that can help the broader scientific community better understand microbial adaptation and the factors that lead to their successful cultivation in the laboratory. For instance, our observations indicate that growth rate and the ability to synthesize certain co-factors play crucial roles in determining whether a microbe can be cultured. These findings contribute to advancing the field by offering new strategies and methods for cultivating previously unculturable microbes, thereby enhancing our overall understanding of the microbiome.

What song do you currently have on repeat?

I love to listen to the Quranic recitation from Mishary Rashid Alafasy

Intro

Kacie Kajihara is a graduate student at the University of Hawaiʻi at Mānoa. Her research combines microbial ecology and data science to uncover indicators of microbiome stability across a Hawaiian watershed. We recently spoke with Kacie about her research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

Once upon a time, I was a pre-medical student interested in gaining general research experience, and I very luckily landed in a fungal ecology lab. It was here that I lived out the entirety of my undergraduate career long after deciding not to pursue medicine, assisting in wet-lab tasks surrounding mycorrhizal fungi in restored forests and whole-watershed microbiome characterization. I really came to enjoy conducting microbiome research itself when the pandemic hit, and my capstone research project shifted towards bioinformatics. I love that by using code, we can mold data into different shapes that help us answer different questions and better understand the activities of microbes, who play such integral roles in our ecosystems. 

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

Waimea Valley, over on the north shore of our Hawaiian island Oʻahu, houses a huge diversity of environments, plants, animals, within a pretty small pie-shaped area. Every single one of the inhabitants of this valley (for example, a tree, bug, bird, rock, or river) has a collection of microbes that they associate with and many times rely on for their well-being, just like how we humans have a collection of microbes in our guts that helps us digest food and stay healthy. These microbes can interact or coexist with other microbes too, creating a sort of social network of fungi and bacteria. I study these networks across the entirety of the Waimea Valley watershed to better understand what makes microbiome networks stable, or less sensitive to disturbance.   

What’s exciting about this project lies in the richness of the dataset: with over a thousand samples involving 13 distinct sample types across land, stream, and sea habitats, and representing continental-scale environmental diversity, we are able to unearth more “universal” properties of microbiome stability with networks that more closely represent real life ecosystems.

How does your work contribute to researchers’ understanding of the microbiome?

Stability has been positioned as an aspirational state for microbiome engineering efforts, as we want our introduced communities to successfully establish and persist. This research has distilled a “recipe” for what network properties we found to describe the most stable microbiomes, but we also found that the most pristine sites had the least stable networks, emphasizing the consideration that stability may not always be desirable (think stubborn invasive species). 

What song do you currently have on repeat?

“Naturally” by Kalapana

Intro

Kent Pham is a PhD candidate in the Department of Plant and Soil Sciences at the University of Kentucky. He is studying the ecological impact that hemp has on conventional cropping systems and its associated microbes. We recently spoke with Kent about his research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

I got my start in microbiology during my undergraduate studies looking at the role of yeast in fermented beverages like beer and kombucha. I noticed that while a pure culture would create the same product every time, introducing a mixed community of microbes would often lead to varied and more interesting final product. I became fascinated with how microbes interacted with one another and could create a product greater than the sum of their parts.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

There are trillions of bacteria and fungi in the soil beneath our feet, all influencing their surroundings and changing the environment. My goal is to not only find out who is there, but to see if we can find out what everybody’s job is. This is fascinating to me as knowing everyone’s job might let us choose the best bacteria to solve different challenges. This is especially vital now as creating the best soil for farming becomes more and more important as the population increases and arable land decreases.

How does your work contribute to researchers’ understanding of the microbiome?

I’m currently looking at the microbiome associated with hemp, a crop that was only legalized in America in 2014 and doesn’t have much in the way of microbiome research. My research provides insight into the rhizosphere and phyllosphere communities and their interactions with the plant, specifically during its harvest and processing stage. I hope my work will inspire further microbiome research on this new crop and increase its adoption in not only the scientific community but throughout all of society.

What song do you currently have on repeat?

I’ve gotten into country music since coming to Kentucky for my PhD so recently it’s been “Feathered Indians” by Tyler Childers.

Intro 

Lennel Camuy-Velez is a Puerto Rican microbiologist studying invasive plant-microbe interactions. He works in Samiran Banerjee’s Microbial Ecology Lab, where his main focus is on understanding the mechanisms by which invasive plants recruit key microbes to establish themselves in a native ecosystem. We recently spoke with Lennel about his research. (Answers have been lightly edited.)

How did you become interested in microbiome research? 

I think everything started when I took my first microbiology course during my undergraduate studies, and I had my first experience in research. I went to undergrad thinking about going to medical school, but this first experience changed all of that. After this first encounter, I continued to feel more and more fascinated by microbiology and amazed by how much impact they have on our lives. It has been an interesting journey since then, following a post-bac, a master’s degree, and now soon to becoming a PhD in Microbiology. Looking back now, it is amazing how everything that I’ve done has been intertwined and built upon to help me better understand microbiomes. Moving from researching quorum sensing in bacteria to learning from insect-microbe interactions, continuing to study microbial ecology and plant-microbe interactions. Now, in the present, I find microbiome research even more fascinating with the implementation of new technology and analysis making understanding this world a bit easier. 

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project?  

Native grasslands are impacted by invasive plants that affect their community above ground and below ground. I am currently involved in trying to understand what microorganisms like bacteria or fungi do to help these invasive plants establish and see how I can find answers to help the native species outcompete invasive ones. And find ways in the future to help restore invaded locations. 

What excites me about this project is the use of non-model plants in understanding plant-microbe interactions. I think looking into these invasive plants will help get better insights into how microbes work with other organisms. Studying invasion can lead to better development of management and restoration efforts in affected native ecosystems. In addition, in another project I am involved in, I have seen firsthand how different management practices that have been implemented impact the soil microbes and directly seen the impact on ranchers and farmers. 

How does your work contribute to researchers’ understanding of the microbiome?

My work focuses on understanding and trying to elucidate the mechanisms by which invasive plants recruit microbes and how these microbes help establish plants in new environments. The combination of field and greenhouse experiments, amplicon, and multi-omics approaches contributes to dissecting the microbiome’s impact on these hosts and its implications for larger communities. The results and data generated from this will help researchers understand the microbiome from an invasion biology perspective. 

What song do you currently have on repeat?

I think I would have to say “Rollercoaster” by Bleachers.

Intro

Lílian Caesar is a postdoctoral fellow in the Department of Biology at Indiana University, Bloomington, where she investigates host-microbiome ecology and evolution. Her current research focuses on characterizing the assembly and maintenance of multi-kingdom microbiomes in eusocial bees. We recently spoke with Lílian about her research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

I became interested in microbiome research during my undergraduate studies while investigating the symbiotic relationship between Wolbachia and drosophilids. In my final experiments, I used antibiotics to cure the Wolbachia infection and observed changes in fly fitness. Although the fly microbiome field was still growing at the time, I realized that my treatments were likely affecting other fly-associated microbes as well, sparking my curiosity to investigate this further. To explore this, I decided to pursue a PhD to study the role of the gut microbial community in host health and fitness, using stingless bees as my novel model system.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

Bees, like us, have a community of tiny living things in their guts and hives that keep them healthy. This community, called the microbiome, is crucial for their well-being. If it’s missing or different, bees can get very sick. Healthy bees are important because they make products such as honey and help plants like coffee and orange trees grow. My research looks at how these tiny living things interact in the bee’s gut and hives, and how they impact bee health. I’m excited because this project explores the complex world of the bee microbiome and its multi-kingdom interactions.

How does your work contribute to researchers’ understanding of the microbiome?

My research contributes to understanding the ecology and evolution of microbiomes in different ways. First, by studying the microbiome of eusocial bees, I can investigate microbiome dynamics in the context of social interactions within the hive, such as comparing bee castes and observing microbes’ transmission. Second, since bees are holometabolous insects, I can observe how development (egg, larva, pupa, adult) and associated behavioral, physiological, or morphological changes affect microbiome establishment. Third, the bee species I study have microbiomes composed of bacteria, phages, and fungi, allowing me to explore multi-kingdom interactions and their impact on microbiome assembly and maintenance.

What song do you currently have on repeat?

Several songs from Emma Ruth Rundle, to mention one: “Protection“.

Intro

Maria A. Sierra is a PhD candidate within the Tri-Institutional Computational Biology & Medicine program at the Rockefeller University and Weill Cornell Medicine. Maria’s research delves into the intricate world of microbiomes across diverse hosts and environments, from terrestrial to extraterrestrial realms such as extreme environments and the International Space Station (ISS). We recently spoke with Maria about her research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

I became interested in microbiome research during college when I volunteered for the MetaSUB project, taking swabs from the city’s transportation system. I was awed by the thought of all the undiscovered microorganisms we come into contact with every day, not knowing who they are or what they do.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project?

My research is like being a detective for tiny germs, especially viruses. I study how these germs live in different places, including really extreme ones like outer space. I use computers to help me understand how these germs can sometimes make people sick, especially by affecting their brains. I also create big lists that help other scientists learn about these germs. My work helps us understand more about how these tiny creatures live and how we can stay healthy, both on Earth and in space.

What excites me about my projects is that I can contribute to knowledge of biological science to humanity, and potentially my contributions can make an impact in people’s lives and the environment.

How does your work contribute to researchers’ understanding of the microbiome?

My work contributes to researchers’ understanding of the microbiome by providing detailed insights into the interactions between microorganisms and their hosts across diverse environments, including extreme and extraterrestrial settings. Utilizing advanced bioinformatics and multiomics approaches, I analyze the genomic, transcriptomic, and proteomic profiles of these microbes to uncover their roles in health and disease. By developing and curating comprehensive genomic databases, I facilitate the characterization and classification of microbial communities, enhancing the ability to identify novel pathogens and understand their mechanisms of host invasion and CNS involvement. This research advances our knowledge of microbial ecology, pathogenicity, and the impact of microbiomes on both terrestrial and space environments, ultimately contributing to the development of targeted therapeutic strategies and improving our overall understanding of microbial dynamics.

What song do you currently have on repeat?

“Que chimba de vida” by Karol G. This song is about exploring and celebrating diverse experiences in life. Just as the song celebrates the richness and vibrancy of life, my research delves into the diverse and complex world of microbiomes, uncovering the myriad ways these microorganisms interact with their environments. Both the song and my research highlight the beauty and intricacy of life’s different facets, whether it’s through music or scientific discovery. This connection reflects a passion for understanding and appreciating the complexity and diversity of the world around us.

Intro

Mark McCauley is a biological researcher at the United States Geological Survey focusing on mesophotic and deep-sea coral restoration. He is currently engaged in unifying over a decades’ worth of marine microbiome data, to help further ecosystem restoration and understanding ocean biodiversity before it is irreparably impacted by anthropogenic disturbances. We recently spoke with Mark about his research. (Answers have been lightly edited). 

How did you get interested in microbiome research?

I came to microbiome research from an ecological, coral host perspective. I was observing significantly different responses of hard and soft corals to environmental stressors that I couldn’t explain. Characterizing the microbiome offered a potential explanation, which got me very interested in microbial function and their role of coral health and resilience.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

“Hey Gran, did you know that I am reanalyzing 25 years worth of marine DNA sequences? From microbes to mammals, I am unifying global DNA sequencing into a single database, so that we have a multi-decadal baseline for marine conservation and ocean management.”

I am most excited about the prospect of taking hundreds of thousands of highly informative metabarcoding samples that are languishing in data repositories and making them useful and accessible for everybody.

How does your work contribute to researchers’ understanding of the microbiome?

It helps to provide a baseline for corals, this is particularly important for bleaching, unhealthy, or diseased corals. Current work is combining microbial sequences with eDNA sequences from larger organisms to create a unified understanding of large-scale and multi-trophic marine systems.

What song do you currently have on repeat?

“Electric Energy”, by Ariana DeBose, Boy George, and Nile Rogers. Such a fun and energetic song, and better than its movie.

Intro

Michael Sieler is a 4th year PhD candidate at Oregon State University. His research investigates how environmental factors interact to impact gut microbiome stability and resilience to influence host health. We recently spoke with Michael about his research. (Answers have been lightly edited). 

How did you get interested in microbiome research?

I became interested in microbiome research in 2018 when I joined the Sharpton Lab as an undergraduate student researcher at Oregon State University. There, I worked on an independent research project studying how the environmental pollutant Benzo[a]Pyrene impacts juvenile zebrafish, their gut microbiome and neurobehavioral development. I remain fascinated by how many different ways our gut microbiome interacts with us and our environment to influence our health.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

Our gut microbiomes, the community of microorganisms living along our digestive tract, play an important role in supporting our health. They support our health by keeping our bodily systems in a homeostatic, stable state. We can think of our gut microbiome like a spring. Imagine holding a spring on one end while the other end dangles towards the ground. If no outside force pushes or pulls on the spring while you’re holding it, the spring will remain at rest. However, if you were to pull the other end of the spring towards the ground and then let go, the spring would bounce up and down many times until it finally returned to its resting position. Similarly, our gut microbiomes are relatively stable unless something disrupts it, causing it to become unstable like the spring. I study how different forces in our environment (diet, pollutants, parasites, climate change) impact our gut microbiome’s stability to influence our health. I’m excited about my current research because I’m discovering ways that we can support our microbiome’s stability to maintain or improve our health.

How does your work contribute to researchers’ understanding of the microbiome?

My work clarifies the ecological context of how environmental conditions and -stressors differentially interact with the gut microbiomes to influence host health using the zebrafish (Danio rerio) model organism, with important implications to plants, animals and humans. By understanding the contextual landscape that our microbiomes exist within allows researchers to better prepare and manage the effects of climate change on human and ecosystem health.

What song do you currently have on repeat?

“Summer Dreams” by Skream

Intro

Nicola received her PhD from Boston University, where she examined the role of the environment in structuring bacterial communities within corals. Now she is conducting postdoctoral research at the University of Hawai‘i at Mānoa manipulating bacterial community composition in the water column to examine the impact on mosquito larval fitness. We recently spoke with Nicola about her research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

I knew I wanted to spend my PhD studying corals because of how important they are to supporting life in the ocean. I then learned about the single-celled algae that tropical corals can’t live without. More recent discoveries also indicate that many other types of microorganisms (bacteria, viruses, fungi, etc.) may underpin coral health. So these biodiversity hotspots, coral reefs, can grow so extensively that you can see them from satellites in outer space, yet they only exist thanks to symbioses with microorganisms. That blew my mind. 

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

Because I became so interested in microorganisms during my PhD, I moved on from corals to a completely different system during my postdoctoral research–the effects of bacteria on mosquitoes. Mosquitoes hatch in small freshwater pools; they love laying eggs in any buckets or flower pots left out around the garden. In the lab, we can raise newly hatched mosquitoes almost completely bacteria-free. I then give the hatchlings different types of bacteria to figure out whether specific types have good, bad, or neutral impacts on mosquitoes. What excites me about my current research project is seeing the really stark differences between a ‘good’ bacterial partner and a bad or neutral one. It’s like night and day when 0 out of 20 mosquitoes live past a few days when I give them the wrong bacteria as compared to 20 out of 20 mosquitoes completing their life cycle when I give them the right bacteria. It just goes to show how important these largely invisible organisms are to bigger organisms. 

How does your work contribute to researchers’ understanding of the microbiome?

Gathering more information on what helps or harms mosquitoes through their microbiome holds a ton of potential for figuring out how to eradicate them where they are spreading disease or causing environmental harm. For instance, they are currently spreading avian malaria throughout the Hawaiian islands (where I live), which is decimating the native bird populations. More generally, it is very complicated to study host-microbe interactions when you are dealing with more complicated organisms, like humans, so mosquitoes provide a very easy system to explore in the lab. 

What song do you currently have on repeat?

Too Sweet by Hozier

Intro

Patrick is a microbial biogeochemist studying how soil microbiomes assemble in high-elevation watersheds. He is currently a Project Scientist at Lawrence Berkeley National Lab. We recently spoke with Patrick about his research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

Two formative experiences sparked my interest in microbiome research. The first experience was in my undergraduate introductory biology class. We were doing a unit on microbiology and our lecturer told us that there were millions of ‘invisible’ microbes all over the classroom and on our skin at that very moment. That assertion blew my mind and made me resolved to invent ‘glasses’ to someday be able to see all those tiny creatures. My first research experience then was working in a microbial ecology lab on a project isolating microbes from the environment to be used for cleaning up agricultural wastewater and producing hydrogen at the same time. The big idea was – that at larger scales – these reactors could use the hydrogen to make electricity for the wastewater treatment plants. I loved the idea of using environmental microbes to solve a technology problem and that had me hooked on studying microbiomes.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

Most animals and plants have life cycle stages that can change seasonally. For example, many trees lose their leaves in autumn and then their leaves grow back in the spring. Also, many different animals seem to have a ‘rest’ when it is cold during winter – think hibernating bears – especially in places where there is a lot of winter snow. Similar to plants and animals, my research project is studying whether or not microbes living in the soil also have distinct characteristics that change seasonally. It turns out that tiny microorganisms living in the soil are actually very active during winter under the snow. We think this is because the snow acts like a blanket to keep the soil warm even when the air temperature is freezing during winter. These winter-loving microbes decompose organic material which releases nutrients that plants use when the plants get more active in spring. The activity of winter-loving microbes also releases planet-warming greenhouse gasses, like carbon dioxide and methane. Winter snowpacks are shrinking globally because of higher air temperatures, so I am also studying how less snow in a warmer world might affect soil microbes in the future.

How does your work contribute to researchers’ understanding of the microbiome?

My research is showing that specific soil bacteria, archaea and fungi have different genomic, metabolic and physiological traits that allow them to occupy distinct environmental niches in the soil that are created by winter snow accumulation, the snowmelt period, and then the complete loss of snowpack. These organisms and their traits affect the molecular properties and turnover of organic matter during winter. This information can be used to inform reactive-transport or trait-based models to predict how carbon and nitrogen cycling might be affected by less snow in a warmer world in the future.

What song do you currently have on repeat? 

I’ve been listening to a lot of Holly Bowling’s Wilderness Sessions albums lately. 

Intro

Shane Roesemann is a graduate student at University of Wisconsin-Madison in the lab of Dr. Jason Kwan. He is interested in improving our ability to bin metagenomes by using more comprehensive marker gene sets, microbial ecology in general, and searching for novel secondary metabolites. We recently spoke with Shane about his research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

In undergrad, I spent a semester studying abroad in Costa Rica with a curriculum of Tropical Ecology. This started my mind thinking about the high degree of interconnectivity in community scale interactions. When I graduated, I worked in a microbiome lab and found a direct parallel with macroecological concepts. This allowed microbiome research to really resonate with me and spark a similar sense of passion.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

Sometimes bacteria are able to make new drugs that are useful for society like anti-cancer drugs or antibiotics. To search for these new drugs, we need to be able to look at their genes. To be able to inspect their genes correctly, we need specialized software to rearrange their genomes. I am developing software to do this rearrangement (a process called metagenomic binning) so we might get useful information from the genomes.

How does your work contribute to researchers’ understanding of the microbiome?

Developing metagenomic binning software is a fundamental aspect of microbiome research which could affect the fidelity of all downstream metagenomics-based outcomes such as those related to drug discovery, taxonomy classification, or functional profiling of novel and unculturable bacteria.

What song do you currently have on repeat?

“Holiday” – Weezer 

Intro

Viviana Alban is an Ecuadorian PhD student from Levy’s lab at the University of Washington. She is interested in understanding how environmental exposures, such as contact with animals and their feces, impact the gut microbiome of children living in Low and Middle-Income countries. We recently spoke with Viviana about her research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

I became interested in microbiome research during my master’s program. I had the opportunity to get involved in a local research project in my country, Ecuador, and attended multiple presentations related to the human gut microbiome. It was fascinating to me to understand how the gut microbiome coevolves with the host from birth onward in a symbiotic relationship, where the microbial community promotes immune system development and acts as a defense barrier against enteric infections. In contrast, the human host provides nutrition and protection to the microbes. This exposure sparked my fascination with the field and motivated me to pursue further research in human gut microbiome studies.

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

My project is about understanding how animals and their feces can bring harmful microorganisms and antibiotic-resistant bacteria into our homes. This is particularly risky for young children, who can easily get enteric infections. While we know a lot about how animals affect the gut health of children in rich countries, we don’t know much about this in poorer countries like Ecuador, where clean water and proper toilets might not be available. 

In places like these, having animals close to where people live can make it easier for children to get sick with diarrhea and other health problems. Also, if animals pass on antibiotic-resistant bacteria to humans, it can make treating diseases much harder. To tackle this, my research in Ecuador will look at where the fecal contamination comes from and how being around animals affects children’s gut health and antibiotic resistance over time. This will help us understand how to keep children healthier in places where they live close to animals.

What excites me about my current research project is the opportunity to work closely with communities from my own country. This motivates me to continue contributing to the advancement of knowledge originating from my homeland, making a positive impact on the health and well-being of my people.

How does your work contribute to researchers’ understanding of the microbiome?

My work enhances researchers’ understanding of the microbiome by examining the crucial role that environmental factors, such as exposure to animals and their feces, play in shaping the gut microbiome from an early age. By focusing on these dynamics in the unique context of Ecuador, my study addresses a significant knowledge gap regarding the infant gut microbiome in low- and middle-income countries (LMICs).

What song do you currently have on repeat? 

“Limón y Sal” – Julieta Venegas

Intro

Winston Anthony is a Post-Doctoral Research Associate at the Pacific Northwest National Laboratory. He is fascinated by the microbiome and how we can use multi-omic approaches to increase knowledge gained through microbiome sampling. We recently spoke with Winston about his research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

I started my career in biological research in ecology, studying the complex interactions between flowering plants, bumble bees, and a parasite that uses plant nectar as a vector to infect bee hives. We would look for these parasites by studying the gut contents of infected bumblebees, and the complexity of the gut microbiome fascinated me. Even though I took detours to study marine biology, and later the aging process, I never forgot how studying the microbiome always felt like going into a cave to prospect for gold; you never knew what you were going to find. I finally got my chance to return to microbiome research in grad school at the Washington University in St. Louis School of Medicine when I joined a laboratory studying the effect of antibiotics on the human gut microbiome. It was there that I was finally able to connect the two aspects of my previous areas of research that exited me: the ecology of a dynamic community and a direct connection to the human experience. 

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

I work for the Department of Energy in a National Laboratory, using computer science to model biology at different levels, from the individual cell to entire communities. I am trying to understand and identify the community level interactions that decide whether an engineered microbe will be able to live and thrive. These can be microbe to microbe, microbe to plant, or microbe to environment relationships, and they can have a direct effect on the ability of a plant to grow. At the cell level, we are trying to find ways to predict the function of the many, many genes within bacteria that we know very little about. This all ends up being important because the microbiome in a field can directly affect the growth of a crop used for producing bioenergy-based fuel, reducing the national reliance on fossil fuels.

How does your work contribute to researchers’ understanding of the microbiome?

Our work pushes the boundary on some important aspects of both basic ecology as well as microbiome engineering. At an ecological level, we are uncovering the spatial dependency within soil microbiomes, an aspect of microbiome science which is often hidden due to the homogenization process that most soil samples undergo when they are collected for research. At an engineering level, we are trying to establish some of the first standards and protocols for the safe and controlled introduction of synthetically engineered organisms into active soil microbiomes. Finally, we are also attempting to bridge the divide between domain science (in this case microbiome science) and computer science and machine learning engineering by applying machine learning and artificial intelligence to the study of microbial communities. 

What song do you currently have on repeat?

“Show Me how” by Men I Trust 

Intro

Zach Burcham is a Research Assistant Professor at the University of Tennessee-Knoxville. He has a passion for the integration of multi-omics microbiome data and a particular interest in the microbes involved in host decomposition. We recently spoke with Zach about his research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

My journey into microbiome research began while completing my PhD. I jumped headfirst into a project that incorporated molecular biology and microbiology with metagenomics and metatranscriptomics. The problem was, I had zero experience in microbiome data analysis. Therefore, I began searching for online tutorials, workshops, and classes on campus to learn. The more I learned about microbiome data the more interested I became. The thrill of solving complex problems, troubleshooting pipelines, and getting community-level insight in microbiomes became addicting. I had discovered my passion for microbiome research and data analysis and have now built my research focus in the field. 

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

Currently, I study how microbes, specifically bacteria, cooperate and compete to break down complex materials. We can predict how some of these bacteria will behave when growing together and use this information to understand their role in the community. By understanding these roles, we hope to be able to manipulate these bacteria or communities to be more efficient at breaking down complex materials in a way that is beneficial to humans. 

How does your work contribute to researchers’ understanding of the microbiome?

Our work takes microbiome research one step further than just profiling “what” microbes are present within an environment. We are beginning to answer questions about the “how” and “why” microbiomes do what they do. 

What song do you currently have on repeat?

“Brain Stew” by Green Day

Intro

Zoe Hansen is a postdoctoral researcher at the University of Minnesota – Twin Cities and is currently investigating the ecology of microbial interactions among plant-associated microbes. She has explored multiple facets of microbiomes in her doctoral and postdoctoral work, ranging from metagenomics analysis of the human gut to characterizing competitive interactions within soil communities. We recently spoke with Zoe about her research. (Answers have been lightly edited.)

How did you get interested in microbiome research?

I first encountered the term “microbiome” as an undergraduate student at St. Olaf College. I was fascinated by the concept and technologies that were being developed to explore the diversity and functionality of microbial communities. When I decided to pursue a PhD in microbiology at Michigan State University, I knew that I wanted to continue learning about how microbes interact, coexist, and coevolve in different environments. As a graduate student, I explored the impacts of foodborne infection on the human gut microbiome. Now, as a postdoc at the University of Minnesota, I’m working to understand how bacteria and fungi from soil environments interact with one another. 

Briefly describe your project as if you were talking to your grandmother. What excites you about your current research project? 

Soil is teeming with microscopic organisms that play really important roles like providing nutrients to plants. I’m really interested in how some of these organisms, such as bacteria and fungi, interact with each other in the soil. We are trying to answer questions like, “Do bacteria and fungi compete for the same nutrients?” or “Do these microbes behave the same way when they are alone versus together?” Answering these questions may give us insight into how bacteria and fungi contribute to the soil environments in which they live. 

How does your work contribute to researchers’ understanding of the microbiome?

My current work explores interactions between soilborne Streptomyces (bacteria) and Fusarium (fungi). We are trying to capture how inter- or intra-kingdom interactions among these microbes alter transcription, and whether these changes are distinct for sympatric microbes (originating from the same place) versus allopatric microbes (originating from different places). Our overarching goal is to better understand which factors contribute to the development of soil microbial communities that support plant productivity in agricultural and natural environments. 

What song do you currently have on repeat?

“Cinderella” by Remi Wolf