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Biogeographic Study Of Human Gut-Associated Crassphage Suggests Impacts From Industrialization And Recent Expansion, Tanvi P/ Honap, Krithivasan Sankaranarayanan, Stephanie L. Schnorr, Andrew T. Ozga, Christina Warinner, Cecil M. Lewis Jr.
Biogeographic Study Of Human Gut-Associated Crassphage Suggests Impacts From Industrialization And Recent Expansion, Tanvi P/ Honap, Krithivasan Sankaranarayanan, Stephanie L. Schnorr, Andrew T. Ozga, Christina Warinner, Cecil M. Lewis Jr.
Anthropology Faculty Research
CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as compared to …
Comparing Microbiome Sampling Methods In A Wild Mammal: Fecal And Intestinal Samples Record Different Signals Of Host Ecology, Evolution, Melissa R. Ingala, Nancy B. Simmons, Claudia Wultsch, Konstantinos Krampis, Kelly A. Speer, Susan L. Perkins
Comparing Microbiome Sampling Methods In A Wild Mammal: Fecal And Intestinal Samples Record Different Signals Of Host Ecology, Evolution, Melissa R. Ingala, Nancy B. Simmons, Claudia Wultsch, Konstantinos Krampis, Kelly A. Speer, Susan L. Perkins
Publications and Research
Processing of multimodal information is essential for an organism to respond to environmental events. However, how multimodal integration in neurons translates into behavior is far from clear. Here, we investigate integration of biologically relevant visual and auditory information in the goldfish startle escape system in which paired Mauthner-cells (M-cells) initiate the behavior. Sound pips and visual looms as well as multimodal combinations of these stimuli were tested for their effectiveness of evoking the startle response. Results showed that adding a low intensity sound early during a visual loom (low visual effectiveness) produced a supralinear increase in startle responsiveness as compared …
Quorum Sensing Signals Produced By Heterotrophic Bacteria In Black Band Disease (Bbd) Of Corals And Their Potential Role In Bbd Pathogenesis, Chinmayee D. Bhedi
Quorum Sensing Signals Produced By Heterotrophic Bacteria In Black Band Disease (Bbd) Of Corals And Their Potential Role In Bbd Pathogenesis, Chinmayee D. Bhedi
FIU Electronic Theses and Dissertations
Black band disease (BBD) of corals is a temperature dependent, highly virulent, polymicrobial disease affecting reef-building corals globally. The microbial consortium of BBD is primarily comprised of functional physiological groups that include photosynthetic cyanobacteria, sulfate reducers, sulfide oxidizers and a vast repertoire of heterotrophic bacteria. Quorum sensing (QS), the cell-density dependent communication phenomenon in bacteria, is known to induce expression of genes for a variety of virulence factors in diseases worldwide. Microbes capable of QS release signals such as acyl homoserine lactones (AHLs) and autoinducer-2 (AI-2), which coordinate microbial interaction. The focus of the present study was to investigate the …
A Global Edna Comparison Of Freshwater Bacterioplankton Assemblages Focusing On Large-River Floodplain Lakes Of Brazil, Michael Tessler, Mercer R. Brugler, Rob Desalle, Rebecca Hersch, Luiz Felipe M. Velho, Bianca T. Segovia, Fabio A. Lansac-Toha, Michael J. Lemke
A Global Edna Comparison Of Freshwater Bacterioplankton Assemblages Focusing On Large-River Floodplain Lakes Of Brazil, Michael Tessler, Mercer R. Brugler, Rob Desalle, Rebecca Hersch, Luiz Felipe M. Velho, Bianca T. Segovia, Fabio A. Lansac-Toha, Michael J. Lemke
Publications and Research
With its network of lotic and lentic habitats that shift during changes in seasonal connection, the tropical and subtropical large-river systems represent possibly the most dynamic of all aquatic environments. Pelagic water samples were collected from Brazilian floodplain lakes (total n = 58) in four floodpulsed systems (Amazon [n = 21], Araguaia [n = 14], Paraná [n = 15], and Pantanal [n = 8]) in 2011–2012 and sequenced via 454 for bacterial environmental DNA using 16S amplicons; additional abiotic field and laboratory measurements were collected for the assayed lakes.We report here a global comparison of the bacterioplankton makeup of freshwater …
18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, Catherine Putonti
18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, Catherine Putonti
Bioinformatics Faculty Publications
Despite their critical role in the aquatic food web and nutrient cycling, microeukaryotes within freshwater environments are under-studied. Herein we present the first high-throughput molecular survey of microeukaryotes within Lake Michigan. Every two weeks from May 13 to August 5, 2014, we collected surface water samples from the nearshore waters of four Chicago area beaches: Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach. Four biological replicates were collected for each sampling date and location, resulting in 112 samples. Eighty-nine of these samples were surveyed through targeted sequencing of the V7 and V8 regions of the 18S rDNA gene. …
Dissecting Biological “Dark Matter” With Single-Cell Genetic Analysis Of Rare And Uncultivated Tm7 Microbes From The Human Mouth, Yann Marcy, Cleber C. Ouverney, Elisabeth M. Bik, Tina Lösekann, Natalia Ivanova, Hector Garcia Martin, Ernest Szeto, Darren Platt, Philip Hugenholtz, David A. Relman, Stephen R. Quake
Dissecting Biological “Dark Matter” With Single-Cell Genetic Analysis Of Rare And Uncultivated Tm7 Microbes From The Human Mouth, Yann Marcy, Cleber C. Ouverney, Elisabeth M. Bik, Tina Lösekann, Natalia Ivanova, Hector Garcia Martin, Ernest Szeto, Darren Platt, Philip Hugenholtz, David A. Relman, Stephen R. Quake
Faculty Publications, Biological Sciences
We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach …