Research Interests
Microorganisms thrive in every hospitable environment on (and in) Earth where they drive biogeochemical cycles. Many also form symbiotic associations with diverse plants and animals (including humans) that span the spectrum from mutualistic to parasitic. In short, life as we know it is dependent on microorganisms in one way or another, and thus, understanding the ecology and evolution of microorganism is vital in maintaining a healthy planet. With my research, I am to understand the factors that control the diversity, distribution, and function of microorganisms in a variety of environments. I am particularity interested in understanding how microorganisms interact with and shape their environments, including interactions with other microorganisms and with their hosts in symbiotic associations. To carry out this research, I take a systems biology approach that includes incorporation of traditional cultivation-dependent and multi-omic techniques with ecological theory, biochemistry, and mathematical modeling. I continue to collaborate with scientists from a number of disciplines including, geology, nutrition, math, and chemistry.
Microorganisms thrive in every hospitable environment on (and in) Earth where they drive biogeochemical cycles. Many also form symbiotic associations with diverse plants and animals (including humans) that span the spectrum from mutualistic to parasitic. In short, life as we know it is dependent on microorganisms in one way or another, and thus, understanding the ecology and evolution of microorganism is vital in maintaining a healthy planet. With my research, I am to understand the factors that control the diversity, distribution, and function of microorganisms in a variety of environments. I am particularity interested in understanding how microorganisms interact with and shape their environments, including interactions with other microorganisms and with their hosts in symbiotic associations. To carry out this research, I take a systems biology approach that includes incorporation of traditional cultivation-dependent and multi-omic techniques with ecological theory, biochemistry, and mathematical modeling. I continue to collaborate with scientists from a number of disciplines including, geology, nutrition, math, and chemistry.
Ongoing Projects
Mechanisms and Consequences of Human Milk Oligosaccharide Growth and Bile Stress Across Diverse Strains of the Potential Therapeutic Bacterium, Akkermansia muciniphila.
The current paradigm that Akkermansia muciniphila is a beneficial member of the human gut microbiome is based on an incomplete understanding of the physiological diversity and mechanistic activity across the lineage, as all previous work has focused on one described strain. The long-term goal of our work is to help develop targeted, therapeutic uses of Akkermansia, either through stimulating endogenous strains with prebiotics or by administering specific strains as probiotics. The overall objectives of this project are to characterize the molecular mechanisms and immunogenic properties of genomically diverse strains of human-associated Akkermansia grown (i) on human milk oligosaccharides (HMO) and (ii) in the presence of bile. The rationale for this work is that if we are to use Akkermansia for the therapeutic treatment of metabolic disorders or other gastrointestinal diseases, then we need to design biologically informed treatment strategies that promote or introduce select strains for optimal health outcomes. This work is supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number SC1GM136546.
Integrated Studies Into the Genomic, Metabolic, and Cultivable Diversity of the Human Gut Symbiont Akkermansia muciniphila
Akkermansia muciniphila is a mucin-degrading specialist found in the gut of most healthy humans, typically at 1 to 4% relative abundance. A number of studies in humans and model organisms have found positive associations between the abundance of this organism and intestinal health, suggesting that Akkermansia may be a beneficial member of the gut microbiome that could be used as a biomarker of a healthy gut. However, compared to other gut mucin degraders, A. muciniphila is understudied as only one species has been formally described and a mechanistic understanding of its mucin-degrading capabilities is lacking. The overall objective of this study is to fill this void by providing specific details about the genomics content, metabolic mechanisms, and cultivable diversity of this mucin-degrading specialist through complementary genomic- and cultivation-based approaches. This work was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number SC2GM122620.
Dietary Drivers of the Human Gut Microbiome
Literature on the importance of the gut microbiome to health promotion and disease prevention is burgeoning. In the past few years, studies have advanced from characterizing a broad community of microbes to identifying functional elements, individual groups of organisms, and particular properties of the gut microbiome that may be important for human health. Much work has addressed the role that gut microbiota has in obesity, and several studies have found associations between the gut microbiome and weight gain. Dietary data have been explored in relation to the gut microbiome, but only at a cursory level examining the associations of macronutrients (e.g., carbohydrates, proteins and fats), with a particular focus on carbohydrates, with community composition. However, little information exists on the quantitative relationships between diet and gut microbial community taxonomy and function, particularly in post-weaned children. Recent advances in DNA sequencing technologies coupled with bioinformatic tools now allow for more in-depth analyses of gut microbial communities to better understand not only community composition but also community function. Therefore, a gap in our understanding exists to explain how diet affects community function and whether particular elements of the diet beyond macronutrients (e.g., micronutrients) have the potential to structure the gut microbiome that ultimately affects human health. In collaboration with Dena Herman in the Department of Family and Consumer Sciences at CSUN, we are characterizing the taxonomic and functional diversity of gut microbial communities in a diverse population of children within the greater Los Angeles area.
Temporal Dynamics of Salt Marsh Microbial Communities
Coastal salt marshes are highly productive marine ecosystems found along protected shorelines in temperate regions of the world. They are important environments because of the numerous ecosystem services they provide. For example, salt marshes remove excess nutrients from coastal waters, sequester carbon, and provide breeding and feeding grounds for a number of commercially important vertebrate and invertebrate animals. Unfortunately, a number of historical and contemporary human activities like land reclamation, pollution, and sea level rise resulting from global climate change, continue to threaten salt marshes and the ecosystem services they provide.
Many of the ecosystem services provided by salt marshes are directly linked to the activity of diverse microorganisms. For example, excess nitrogen entering in run-off is cycled and removed by the combined activities of Archaea and Bacteria. Within salt marshes, a number of distinct microbial habitats can be found including tidal creeks, hypersaline pools, and photosynthetic microbial mats. Since 2014, we have been characterizing the taxonomic diversity of sediment microbial communities from each of these these communities seasonally within a local salt marsh ecosystem. The overall objective of this study is to understand how these salt marsh communities change through space and time and how these changes influence the ecosystem services of salt marshes on the west coast of the US.
Mechanisms and Consequences of Human Milk Oligosaccharide Growth and Bile Stress Across Diverse Strains of the Potential Therapeutic Bacterium, Akkermansia muciniphila.
The current paradigm that Akkermansia muciniphila is a beneficial member of the human gut microbiome is based on an incomplete understanding of the physiological diversity and mechanistic activity across the lineage, as all previous work has focused on one described strain. The long-term goal of our work is to help develop targeted, therapeutic uses of Akkermansia, either through stimulating endogenous strains with prebiotics or by administering specific strains as probiotics. The overall objectives of this project are to characterize the molecular mechanisms and immunogenic properties of genomically diverse strains of human-associated Akkermansia grown (i) on human milk oligosaccharides (HMO) and (ii) in the presence of bile. The rationale for this work is that if we are to use Akkermansia for the therapeutic treatment of metabolic disorders or other gastrointestinal diseases, then we need to design biologically informed treatment strategies that promote or introduce select strains for optimal health outcomes. This work is supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number SC1GM136546.
Integrated Studies Into the Genomic, Metabolic, and Cultivable Diversity of the Human Gut Symbiont Akkermansia muciniphila
Akkermansia muciniphila is a mucin-degrading specialist found in the gut of most healthy humans, typically at 1 to 4% relative abundance. A number of studies in humans and model organisms have found positive associations between the abundance of this organism and intestinal health, suggesting that Akkermansia may be a beneficial member of the gut microbiome that could be used as a biomarker of a healthy gut. However, compared to other gut mucin degraders, A. muciniphila is understudied as only one species has been formally described and a mechanistic understanding of its mucin-degrading capabilities is lacking. The overall objective of this study is to fill this void by providing specific details about the genomics content, metabolic mechanisms, and cultivable diversity of this mucin-degrading specialist through complementary genomic- and cultivation-based approaches. This work was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number SC2GM122620.
Dietary Drivers of the Human Gut Microbiome
Literature on the importance of the gut microbiome to health promotion and disease prevention is burgeoning. In the past few years, studies have advanced from characterizing a broad community of microbes to identifying functional elements, individual groups of organisms, and particular properties of the gut microbiome that may be important for human health. Much work has addressed the role that gut microbiota has in obesity, and several studies have found associations between the gut microbiome and weight gain. Dietary data have been explored in relation to the gut microbiome, but only at a cursory level examining the associations of macronutrients (e.g., carbohydrates, proteins and fats), with a particular focus on carbohydrates, with community composition. However, little information exists on the quantitative relationships between diet and gut microbial community taxonomy and function, particularly in post-weaned children. Recent advances in DNA sequencing technologies coupled with bioinformatic tools now allow for more in-depth analyses of gut microbial communities to better understand not only community composition but also community function. Therefore, a gap in our understanding exists to explain how diet affects community function and whether particular elements of the diet beyond macronutrients (e.g., micronutrients) have the potential to structure the gut microbiome that ultimately affects human health. In collaboration with Dena Herman in the Department of Family and Consumer Sciences at CSUN, we are characterizing the taxonomic and functional diversity of gut microbial communities in a diverse population of children within the greater Los Angeles area.
Temporal Dynamics of Salt Marsh Microbial Communities
Coastal salt marshes are highly productive marine ecosystems found along protected shorelines in temperate regions of the world. They are important environments because of the numerous ecosystem services they provide. For example, salt marshes remove excess nutrients from coastal waters, sequester carbon, and provide breeding and feeding grounds for a number of commercially important vertebrate and invertebrate animals. Unfortunately, a number of historical and contemporary human activities like land reclamation, pollution, and sea level rise resulting from global climate change, continue to threaten salt marshes and the ecosystem services they provide.
Many of the ecosystem services provided by salt marshes are directly linked to the activity of diverse microorganisms. For example, excess nitrogen entering in run-off is cycled and removed by the combined activities of Archaea and Bacteria. Within salt marshes, a number of distinct microbial habitats can be found including tidal creeks, hypersaline pools, and photosynthetic microbial mats. Since 2014, we have been characterizing the taxonomic diversity of sediment microbial communities from each of these these communities seasonally within a local salt marsh ecosystem. The overall objective of this study is to understand how these salt marsh communities change through space and time and how these changes influence the ecosystem services of salt marshes on the west coast of the US.
