Multi-omic analysis of the anal sac microbiome in the domestic cat
Postdoctoral Work, Eisen Lab, UC Davis 2021 - Present
Scent secretions and scent marking behaviors play critical roles in the chemical communication of carnivores. In particular, within the anal sac, bacteria are known to produce some of the volatiles that are constituents of their hosts odorous secretions. While research on the anal sac microbiome has been documented for meerkats, badgers, and hyenas, studies examining the anal sac microbiome in combination with its metabolites is more scarce. Here we use culture-dependent and -omics approaches to characterize the anal sac microbiome and its metabolites in domestic cats (Felis catus). We provide insight into the variation observed among felid anal sac microbiome compositions, profile the volatiles present in felid scent secretions, and assemble genomes of resident microbes to highlight potential gene pathways involved in the production of the volatiles.
Postdoctoral Work, Eisen Lab, UC Davis 2021 - Present
Scent secretions and scent marking behaviors play critical roles in the chemical communication of carnivores. In particular, within the anal sac, bacteria are known to produce some of the volatiles that are constituents of their hosts odorous secretions. While research on the anal sac microbiome has been documented for meerkats, badgers, and hyenas, studies examining the anal sac microbiome in combination with its metabolites is more scarce. Here we use culture-dependent and -omics approaches to characterize the anal sac microbiome and its metabolites in domestic cats (Felis catus). We provide insight into the variation observed among felid anal sac microbiome compositions, profile the volatiles present in felid scent secretions, and assemble genomes of resident microbes to highlight potential gene pathways involved in the production of the volatiles.
Microbiome responses to fecal microbiota transplantation in cats
Collaborative Project, AnimalBiome, 2021 - Present
While there is growing interest in the application of fecal microbiota transplants (FMTs) particularly to treat digestive disorders, there are few published studies that have evaluated their effectiveness, and this research is even more limited in animals. Here, we are evaluating the application and effectiveness of an oral capsule FMT treatment on the fecal microbiome of domestic cats (Felis catus) suffering from chronic digestive issues. We document the changes in fecal microbiome composition in response to FMT and evaluate the extent to which gut microbiomes of recipient animals became similar to the gut microbiomes of their donor animals or healthy animals.
Collaborative Project, AnimalBiome, 2021 - Present
While there is growing interest in the application of fecal microbiota transplants (FMTs) particularly to treat digestive disorders, there are few published studies that have evaluated their effectiveness, and this research is even more limited in animals. Here, we are evaluating the application and effectiveness of an oral capsule FMT treatment on the fecal microbiome of domestic cats (Felis catus) suffering from chronic digestive issues. We document the changes in fecal microbiome composition in response to FMT and evaluate the extent to which gut microbiomes of recipient animals became similar to the gut microbiomes of their donor animals or healthy animals.
Socioecological predictors of microbiome variation in wild African mammals
Dissertation Work, Holekamp Lab, MSU 2015 - 2021
Animal-associated microbiomes influence multiple aspects of their host’s phenotype. Over a decade of research shows that the microbiome can vary with both host factors and environmental factors. However, much of the existing literature has been limited to intestinal microbiomes and to laboratory or domesticated animals. Multi-body site and longitudinal analyses of the microbiomes of wild mammals are lacking. For my dissertation, I addressed these gaps in knowledge and used DNA sequencing to survey the microbiomes African carnivores and herbivores, with particular emphasis on spotted hyenas (Crocuta crocuta). In Chapter 1, I evaluated whether the microbiomes at six body-sites varied with host age, sex, and social rank in spotted hyenas. For Chapter 2, I conducted a longitudinal analysis of the gut microbiome across 3 generations of spotted hyenas from 4 maternal lineages, and elucidated the potential ways gut microbes may be contributing to their host’s metabolism. Chapter 3 inquired whether host social interactions and close associations between individuals shaped gut microbiota similarity and diversity in hyenas. Chapter 4 compared the gut microbiomes of 11 species of sympatric African herbivores from the MMNR and Laikipia region in Kenya, and quantified the relative influence of host diet and host phylogenetic relatedness in structuring the microbiome.
Dissertation Work, Holekamp Lab, MSU 2015 - 2021
Animal-associated microbiomes influence multiple aspects of their host’s phenotype. Over a decade of research shows that the microbiome can vary with both host factors and environmental factors. However, much of the existing literature has been limited to intestinal microbiomes and to laboratory or domesticated animals. Multi-body site and longitudinal analyses of the microbiomes of wild mammals are lacking. For my dissertation, I addressed these gaps in knowledge and used DNA sequencing to survey the microbiomes African carnivores and herbivores, with particular emphasis on spotted hyenas (Crocuta crocuta). In Chapter 1, I evaluated whether the microbiomes at six body-sites varied with host age, sex, and social rank in spotted hyenas. For Chapter 2, I conducted a longitudinal analysis of the gut microbiome across 3 generations of spotted hyenas from 4 maternal lineages, and elucidated the potential ways gut microbes may be contributing to their host’s metabolism. Chapter 3 inquired whether host social interactions and close associations between individuals shaped gut microbiota similarity and diversity in hyenas. Chapter 4 compared the gut microbiomes of 11 species of sympatric African herbivores from the MMNR and Laikipia region in Kenya, and quantified the relative influence of host diet and host phylogenetic relatedness in structuring the microbiome.
Soil microbial community composition and tolerance to contaminants in an urban brownfield site
Collaborative Project, UC Davis and UCLA, 2020 - Present
Brownfields are unused sites that likely contain hazardous substances due to previous commercial or industrial use. Bioremediation of brownfield sites can be facilitated by in situ microbial communities, but little research exists that characterizes microbial communities at these sites or understands which microbial taxa may play a role in successful bioremediation at Brownfields. We sequenced three gene markers (16S ribosomal RNA, 18S ribosomal RNA and Fungal Internal Transcribed Spacer) in 36 soil samples collected at five depths from a defunct urban rail yard in Los Angeles to: (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants.
Collaborative Project, UC Davis and UCLA, 2020 - Present
Brownfields are unused sites that likely contain hazardous substances due to previous commercial or industrial use. Bioremediation of brownfield sites can be facilitated by in situ microbial communities, but little research exists that characterizes microbial communities at these sites or understands which microbial taxa may play a role in successful bioremediation at Brownfields. We sequenced three gene markers (16S ribosomal RNA, 18S ribosomal RNA and Fungal Internal Transcribed Spacer) in 36 soil samples collected at five depths from a defunct urban rail yard in Los Angeles to: (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants.
Anaerobic Microbial Communities and Interactions in a Permanently Stratified Sulfidic Lake
Collaborative Project, Klepac-Ceraj Lab, MSU & Wellesley College, 2013 - 2020
The structure of microbial communities in several meromictic lakes has been described, but much less is known about the biotic and abiotic factors that govern the assembly of these communities and the biologically mediated coupling of elemental cycles. Here, we sought to identify relationships between the structure of microbial communities and biogeochemical cycling in Fayetteville Green Lake. We used a combination of 16S rRNA gene sequencing, enrichment cultures and network analyses to: (1) characterize the composition and diversity of bacterial communities below the chemocline in FGL; (2) determine how organic electron donors and terminal electron acceptors drive microbial community structure and function below the photic zone; and (3) elucidate key microbial interactions potentially involved in nutrient cycling. Comparisons of the 16S rRNA gene surveys of microbial communities sampled from different depths of the lake along with those obtained under a range of culturing conditions revealed specific microbe-microbe interactions mediating the biogeochemical cycling of elements in meromictic lakes.
Collaborative Project, Klepac-Ceraj Lab, MSU & Wellesley College, 2013 - 2020
The structure of microbial communities in several meromictic lakes has been described, but much less is known about the biotic and abiotic factors that govern the assembly of these communities and the biologically mediated coupling of elemental cycles. Here, we sought to identify relationships between the structure of microbial communities and biogeochemical cycling in Fayetteville Green Lake. We used a combination of 16S rRNA gene sequencing, enrichment cultures and network analyses to: (1) characterize the composition and diversity of bacterial communities below the chemocline in FGL; (2) determine how organic electron donors and terminal electron acceptors drive microbial community structure and function below the photic zone; and (3) elucidate key microbial interactions potentially involved in nutrient cycling. Comparisons of the 16S rRNA gene surveys of microbial communities sampled from different depths of the lake along with those obtained under a range of culturing conditions revealed specific microbe-microbe interactions mediating the biogeochemical cycling of elements in meromictic lakes.