I am a plant evolutionary developmental (evo-devo) biologist interested in uncovering the molecular mechanisms underlying the evolution of plant form. As part of the Green Biome Institute (GBI), I have also engaged in efforts to profile and manage California rare and endangered plant species using molecular tools. In both cases (plant evo-devo and conservation), a solid understanding of the plant microbiome is of utmost importance, and I have recently focused on the contributions of the plant microbiome to plant development and conservation. I am committed to mentoring and supporting the development of the next generation of microbiome scientists from diverse backgrounds and experiences, particularly those interested in interdisciplinary research. RaMP has provided me with the ideal environment to do so! Areas of interest include:

• Plant microbiome in development and evolution

• Plant microbiome and management practices

More about the Almeida Lab

I am an environmental microbiologist and health engineer with a broad interest in pathogens and urban water. I am passionate about studying microbes that sustain life on Earth, understanding climate change impacts and educating students through applied research. I am especially interested in working with students from underrepresented communities and promoting inclusivity in research. I am also eager to work with indigenous communities concerning urban water use, fishing communities concerning fish health, citizens in restoration projects, and on several other evolving  human and environmental health topics. In the Anand lab, our fundamental work focuses on two broad themes. Firstly, environmental health in developed coastal cities with sandy beaches, and oyster reefs. Secondly, we are fascinated by wastewater. We work with effluent to demystify nutrient cycling in the ocean and influent for infectious disease epidemiology to protect human health. Specific areas of interest include:

• Microbes in oyster reefs and how they influence oyster restoration efforts

• Bacterial pathogens and phages in wastewater

• Carbon sequestration in sediments

More about the Anand Lab

Our team is mostly at Berkeley Lab. We work to unravel complex interactions within soil ecosystems, focusing on how microbial communities influence–and are influenced by–their environment. We develop new methods and use a range of approaches from the fields of physics, chemistry, biology, and math, to discover the mechanisms of microbial function and their impacts on nutrient cycling, carbon sequestration, and overall soil health. We do this because it matters. Soil and soil microbes are crucial for developing sustainable agricultural practices, mitigating climate change, and preserving Earth's biodiversity. My own career path was not linear, and I had key mentors along the way who provided open and inclusive environments where young scientists could be creative, take risks, and make mistakes. We are excited to be part of the RaMP program to share our passion for microbes, and what it is like to be part of a team of scientists - and because mentoring is what helps us all be successful. Areas of interest include:

• Understanding the genomic basis of microbial functional traits in soil

• Developing new approaches to restore soil biodiversity

• Measuring and predicting how climate and land-use will impact soil microbiomes and biogeochemical functions

More about the Brodie Lab

As a mentor, my goal is to remove barriers to learning and research, to make STEM disciplines welcoming and inclusive, and to support mentees in moving along their career paths and reaching their full potenial as scientists. I am excited to be part of the Bay Area RaMP network because mentoring allows. ideas, information, and enthusiasm to be shared at a rapid pace, and the potential to develop long-term collaboration exists. The Correa Lab's research bridges micro- and macroscopic realms to aid coral reef ecosystems in surviving climate change. We are working to understand the roles of microorganisms in bolstering coral health or contributing to disease on reefs. We are particularly interested in viruses that infect a key dinoflagellate symbiont of corals, and the extent to which these viral infections may contribute to some bleaching signs. We are also studying how fish that take bites out of corals may indirectly contribute to reef health by spreading live 'coral probiotics' in their feces. Areas of interest include:

• Context-dependent roles of microorganisms in host health and disease

• Trophic transmission of microbial symbionts by consumers

• Leveraging the properties of microorganisms and symbioses to mitigate global change impacts

• Coral reef biology, ecology and conservation

More about the Correa Lab

Our research group combines field work, laboratory experiments and computational (bioinformatic) approaches to address questions of microbial ecology and evolution. Much of our work has focused on understanding microbial communities in high temperature environments such as terrestrial hot springs, with a particular interest in how microorganisms drive the nitrogen cycle. Our recent work has centered on understanding how populations of microorganisms living in hot springs in the Nevada desert and in Yellowstone National Park adapt and evolve over time. Students in my lab are involved in a long-term series, collecting hot springs sediment samples monthly over the course of the year. Samples are then used to cultivate representative organisms as well as for metagenomic sequencing. These paired approaches allow us to see how natural populations evolve in response to changing environmental conditions, as well as in response to biological factors such as viral predation. Areas of interest include:

• Using metagenomes to assess genomic diversity of natural microbial populations

• Discovery of novel viruses and their hosts using cultivation-independent approaches

• Using new sequencing technologies (e.g. long-read metagenomics) to discover novel microbial lineages, sometimes referred to as microbial dark matter

• Reconstucting microbially driven geochemical cycles (e.g. nitrogen)

More about the de la Torre Lab

Our group focuses on computational tool development, research activities to uncover microbial diversity and associated functional capacity, and efforts to democratize microbiome data science to advance microbiome research. At the Joint Genome Institute or through the National Microbiome Data Collaborative, there are opportunities to tackle big questions about tiny microbes using a collaborative, team science approach. I am excited to be part of the RaMP network to support mentorship and research experiences that will get the next generation of scientists passionate about microbiomes. Areas of interest include:

• Applying genome-resolved metagenomics to characterize uncultivated microbes and viruses

• Bioinformatic tool development for comparing genes, genomes, and metagenomes

• Reconstructing metabolic properties from microbial data

More about the Eloe-Fadrosh Lab

I study tiny organisms' social behaviors, particulary as they navigate dense communities such as the gut and soil microbiomes. My team asks how bacteria recognize one other, engage in collective behaviors such as territory formation, and cause disease. I joined the RaMP network to support training and mentoring opportunities, as well as to connect with the Bay Area microbiology community. The Gibbs Lab takes an integrative approach to understanding bacteria's social behaviors, from genes to population dynamics. Our interests include:

• Self versus non-self (kin) recognition in bacteria

• Cell-cell communication and signaling pathways

• Relationships between individual agency and group structures in collective behaviors

More about the Gibbs Lab

The Koskella lab combines experimental evolution, microbial ecology approaches, and molecular biological techniques to understand how microbiomes assemble and affect their host's fitness and evolution over time. We use plant microbiomes as models to understand fundamental evolutionary and ecological principles shaping the microbiome, including the role that microbiota and phages play in shaping disease. We are thrilled to be part of the RaMP network to share our love of microbiomes and interest in using them to address important societal problems with new RaMP scholars who are equally curious about the world and interested in making a difference. Areas of interest include: 

• Co-evolution between bacteria, their hosts and their phage viruses

• Experimenetal (co)evolution of host-associated microbiomes

• Composition and function of the above ground plant microbiome

• Disease-protective effects of the plant microbiome

More about the Koskella Lab

Our group studies the role of gut and airway microbiomes in chronic inflammatory diseases. We're particularly interested in understanding microbial activities in infant microbiomes that predict childhood allergic asthma development and deciphering the mechanisms by which these activities shape immune cell function. Leveraging these observations, we build microbial-based prognostics, diagnositcs and therapeutics to improve our capacity to precision treat and prevent chronic inflammatory disease. Areas of interest include:

• Predicting disease risk from microbiome composition

• Developing synthetic microbiomes for immune training

• The role of microbiomes in the origins and chronicity of inflammatory diseases

• Microbial-derived mechanisms that promote immune function

More about the Lynch Lab

The Nayak lab studies the human gut microbiome and its impact on the treatment of autoimmune and rheumatic disease. We use cutting-edge technologies, such as next-generation sequencing, anaerobic microbiology, metabolomics, and gnotobiotics to investigate the molecular mechanisms by which microbes imapct human health and disease. I am a physician-scientist that sees patients, so we also study samples from patient cohorts. We strive to make mechanistic discoveries with strong clinical implications. I am excited to be part of the RaMP network because my love for science and research was inspired and sustained by good mentors. I would like to provide that opportunity for others now. In the Nayak lab, you will gain exposure to:

• Thinking about how drugs are metabolized by bacteria

• Thinking about how drugs act on bacteria to shape host immunity

• In vitro anaerobic microbiology

• Analysis and visualization of large datasets using programming languages such as R

• Generation and analysis of sequencing libraries, such as metagenomics, transcriptomics and transposon-sequencing libraries

• Analytical chemistry, such as HPLC

• Basic techniques in molecular biology

More about the Nayak Lab

Our lab studies populations of marine organisms with a focus on the ecological and climate interactions that shape their dynamics. To do so, we conduct experiments, fieldwork, and modeling that integrate physiology, demography, climate stressors, and trophic interactions. Core species include sea urchins, abalone, kelp, fish, and corals. We design our research to be directly relevant to communities and management, while also ensuring it is an exciting and fun platform for training students from diverse backgrounds. The latter is particularly important to us as modern careers in marine biology have historically been restricted to the privileged despite the fact that billions of people worldwide rely on the oceans for life, livelihoods, and well-being and the imminent need for conservation solutions for diverse communities. To demonstrate such a commitment, our lab has published multiple papers on the need to diversify how we conduct marine science as well as for whom and by whom. We have recently begun focusing on how microbiomes shape, and are shaped by, organismal responses to environmental stress. Two example projects where scholars may contribute are sea urchin gut microbiomes under starvation and ocean warming (located at the Bodega Marine Lab) and how coral endosymbiont communities change with climate forcing and alter coral photophysiology (located at the Smithsonian Tropical Research Institute in Panama). Areas of interest include:

• Population dynamics of marine organisms

• Bioenergetics

• Marine conservation and policy

• Biostatistics

More about the Okamoto Lab

The Razafindratsima lab is a group of ecologists interested in tropical ecology and conservation. We focus our research on primates and birds in tropical rainforests and the organisms that interact with them. One of our primary goals is to provide insights about the roles and impacts of vertebrates in terrestrial systems. Most recently, we started exploring the potential combined effects of lemur gut microbiome and seed microbiome in influencing the germination of seeds that are ingested and dispersed by lemurs. Areas of interest include:

• Species interactions

• Community ecology

• Primate ecology

More about the Razafindratsima Lab

The Viral Genomics group at the JGI focuses on characterizing the environmental diversity of viruses of microbes and their impacts on ecosystems using (mostly) fancy 'omics tools. Our current projects include the study of viral genomic diversity and virus:host interactions in soil and freshwater environments, along with the development of new bioinformatic tools to quantify and further characterize uncultivated viruses. The long-term goal of our research is to understand the ecological and evolutionary drivers of virus:host dynamics in natural microbial communities. By combining approaches on scales spanning from single molecules to entire ecosystems, we hope to eventually improve our collective understanding of fundamental questions such as: How do viruses spread and adapt across environments? How do viruses take over and reprogram microbial cells? How do viral infections alter ecosystem processes? Our current projects are purely computational and rely on large-scale anaylsis of public data along with newly generated custom datasets. Areas of interest include:

• Viral diversity across microbiomes

• Comparative genomics and functional annotation of viruses/bacteriophages

• Genetic determinants of host range in bacteriophages

• Novel bioinformatic resources to explore global viral diversity

More about the Roux Lab

I am a physicial-scientist excited about how interactions with our microbiome impact skin health. I've enjoyed hosting RaMP scholars and other post-bac trainees in my lab for several years and am proud to have a lab team commited to DEIA mentorship. Work in our lab focuses on dissecting interactions between skin bacteria and the cutaneous immune system. We use microbiome and microbiology approaches in tandem with immunology research tools, including murine models. Ongoing areas of investigation include:

• How antigen-presenting cells sense and respond to skin commensal bacteria

• How immune memory response to skin bacteria are formed

• How bacteria impact early life development of the skin immune system

More about the Scharschmidt Lab

I am excited to be part of the Bay Area RaMP network. Microbiomes are important for human health and our planet, and our lab wants to figure out how the many interactions between individual microbes act together to form complex communities. Projects in the lab span different layers of complexity, from cultured microbes and molecules to whole communities, all centered around corrinoids, a group of model nutrients related to vitamin B12. RaMP scholars, students, and other trainees in the lab learn about diverse approaches such as molecular biology, ecology, and bioinformatics while conducting their research projects. Areas of interest include:

• How bacteria share nutrients, with a focus on vitamin B12 and other corrinoids

• Molecular basis of microbe-microbe interactions

• Ecology and evolution of microbial nutritional interdependence

More about the Taga Lab

I’m excited about the potential for using knowledge about the microbiome to improve the practice of medicine. I joined the RaMP network to provide additional mentorship opportunities for our current lab members and to make microbiome research accessible to the next generation of scientists from diverse scientific and personal backgrounds. Ongoing projects in our lab are focused on understanding how the microbiome impacts the current drugs used to treat cancer, Parkinson’s, and other diseases, as well as developing new approaches to target the microbiome to better treat disease. Areas of interest include:

• Biochemical roles of bacteria in the human gut microbiome

• Lab studies, mouse models, and human cohorts

• Mechanisms of microbiome effects on small molecules and therapies

• How the diet shapes the microbiome

More about the Turnbaugh Lab

Microbiome research in the Wolf Lab encompasses two areas: bacterial metabolism of dietary ingredients and microbiota-mediated protection against infectious disease (including Mycobacterium tuberculosis and Shigella). We combine human microbiome data, laboratory models, and computational analyses to ask questions about the role of diet, microbial competition, and host factors in gut microbiome structure and function. I'm fascinated by how the gut microbiome protects us from infectious disease and helps us degrade different diet ingredients. I joined the RaMP network so recent graduates can grow as scientists and learn the techniques we use to answer questions about the gut microbiome.

• How does the gut microbiome protect against Shigella infection?

• How does bacterial metabolism of dietary sialic acids impact host physiology?

More about the Wolf Lab

We are a dynamic team of microbial ecologists with a passion for unveiling the mysteries of microbial engines that propel biogeochemical cycles, influence plant productivity, and shape soil health. Beyond their role in climate change, microorganisms harbor potential for innovative, nature-based solutions. Utilizing state-of-the-art tools in microbial genomics, metabolomics, and soil biogeochemistry, we delve into the intricate interactions among microorganisms, plants, soil metabolites, and their environment. Through this lens, we investigate how these microcosmic entities drive biogeochemical processes, influence climate dynamics, and respond to human activities. This knowledge lays the foundation for developing nature-based solutions that pave the way to a sustainable future. We are enthusiastic about our participation in the RaMP program, where we eagerly anticipate the opportunity to mentor the next generation of scientists. Areas of interest include:

• Plant-microbe and microbe-microbe interactions (microbial genes, plant exudates and microbial metabolites)

• Mechanisms of microbiome assembly in natural microbiomes and simplified model communities

• Design of synthetic communities to improve plant growth, enhance carbon sequestration, reduce nitrogen loss from soils

• The role of soil Archaea in biogeochemical cycling

More about the Zhalnina Lab