A5003633580- Microbial Community Ecology and Physiology
- Aquatic Ecosystems and Phytoplankton Dynamics
- Marine and coastal ecosystems
- Environmental DNA in Biodiversity Studies
- Genomics and Phylogenetic Studies
- Enterobacteriaceae and Cronobacter Research
- Gut microbiota and health
- Microbial Applications in Construction Materials
- Hematopoietic Stem Cell Transplantation
- Bacterial biofilms and quorum sensing
- Myxozoan Parasites in Aquatic Species
- Pharmaceutical and Antibiotic Environmental Impacts
- Aquatic Ecosystems and Biodiversity
- Building materials and conservation
- Protist diversity and phylogeny
- Nutrition and Health in Aging
- Diet and metabolism studies
- Hydrology and Watershed Management Studies
- Microbial metabolism and enzyme function
- Infections and bacterial resistance
- Bacteriophages and microbial interactions
- Biocrusts and Microbial Ecology
- Oral health in cancer treatment
- Clinical Nutrition and Gastroenterology
- Constructed Wetlands for Wastewater Treatment
University of Michigan–Ann Arbor
2022-2025
Bowling Green State University
2025
Michigan United
2025
University of Delaware
2021-2024
Concrete is the most-used building material in world and a biologically extreme environment, with microbiome composed of bacteria that likely come from concrete precursor materials, aerosols, environmental deposition. These microbes, though seeded variety are all subject to desiccation, heating, starvation, high salinity, very pH.
ABSTRACT The Winam Gulf in the Kenyan region of Lake Victoria experiences prolific, year-round cyanobacterial harmful algal blooms (cyanoHABs) which pose threats to human, livestock, and ecosystem health. To our knowledge, there is limited molecular research on gulf’s cyanoHABs, thus, strategies employed for survival proliferation by toxigenic cyanobacteria this remain largely unexplored. Here, we used metagenomics analyze Gulf’s composition, function, biosynthetic potential. Dolichospermum...
The field of microbiome research continues to grow at a rapid pace, with multi-omics approaches becoming widely used interrogate diverse samples. However, due lagging awareness and implementation standards data stewardship, many datasets are produced that not comparable, reproducible, or reusable. In 2021, the National Microbiome Data Collaborative launched its Ambassador Program, which utilizes community-learning model annually train cohort early-career researchers in stewardship best...
Abstract Nutrient-induced blooms of the globally abundant freshwater toxic cyanobacterium Microcystis cause worldwide public and ecosystem health concerns. The response growth toxin production to new recycled nitrogen (N) inputs impact heterotrophic bacteria in phycosphere on these processes are not well understood. Here, using microbiome transplant experiments, cyanotoxin analysis, nanometer-scale stable isotope probing measure N incorporation exchange at single cell resolution, we...
ABSTRACT Methylobacterium fujisawaense strain C14 was isolated from a weathered concrete cylinder. Using PacBio sequencing, we generated complete genome for C14, which includes one circular chromosome (6,656,731 bp) and six putative plasmids (35,452 to 85,428 bp).
Extraction of high-molecular-weight DNA from Gram-positive bacterial species, with optional steps for removing surfactants. This is suitable sequencing and the protocol can be scaled up at least 5-fold. Modified a by Tina Wecke, LMU-Munich.
Antibiotic resistance and metal toxicity in freshwater bodies have human health impacts carry economic implications worldwide. The presence of antibiotic genes within microbial communities can be informative about both issues. Laurentian Great Lakes contain nearly 20% the world's supply freshwater; however, it is unclear how these are changing over time this system. In study, we characterized two hundred metagenomes collected from multiple sites western Lake Erie at a five-year interval:...
ABSTRACT Here, we report on the raw and coassembled metatranscriptomes of 39 Lake Erie surface (1.0 m) water samples collected over a 2-day diel period encompassing episodic weather bloom events. Preliminary taxonomic annotations read mappings revealed that Microcystis spp. accounted for up to ~47% transcriptionally active community.
Despite the global expansion of cyanobacterial harmful algal blooms (cHABs), research is biased to temperate systems within north, such as Laurentian Great Lakes. This lack diversity represents a significant gap in field and jeopardizes health those who reside along at-risk watersheds south. The African Lake, Lake Victoria, understudied despite serving second largest lake by surface area demonstrating year-round cHABs. Here, we address this knowledge performing molecular survey cHAB...
Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both the diversity and function microbial community in concrete, number unique challenges make this difficult for concrete samples. The high concentration divalent cations interferes with nucleic acid extraction, extremely low biomass means DNA from laboratory contamination may be large fraction sequence data. Here, we develop an improved method extraction higher...
Abstract Cyanobacteria harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These are capable of producing a variety cyanotoxins, including microcystins, that affect fishing tourism industries, human environmental health, access to drinking water. In this study, we isolated sequenced genomes 21 unialgal cultures collected from western Lake Erie between 2017-2019. While some different...
This is a protocol for extracting DNA from concrete, based on the developed by L. S. Weyrich, et al. extraction of ancient calcified dental plaque. We have scaled it up larger sample sizes and made some additional modifications chemistry concrete. extracted using this method suitable metagenomic sequencing Illumina MiSeq NextSeq, as well amplicon sequencing. should yield 10 ng to 5 μg per g depending age integrity sample. Reference: Weyrich al., Laboratory contamination over time during...
Abstract Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both diversity and function the microbial community in concrete, because biomass concrete is so low, this analysis highly affected by laboratory contamination. Here, we demonstrate improved DNA extraction from show method provides sufficient quality quantity to do shotgun sequencing. was extracted sample obtained road bridge sequenced with Illumina MiSeq....
Extraction of high-molecular-weight DNA from Gram-positive bacterial species, with optional steps for removing surfactants. This is suitable sequencing and the protocol can be scaled up at least 5-fold. Modified a by Tina Wecke, LMU-Munich.
Abstract Nutrient-induced blooms of the globally abundant freshwater toxic cyanobacterium Microcystis are cause worldwide public and ecosystem health concerns. The response growth toxin production to new recycled nitrogen (N) inputs, impact heterotrophic bacteria in phycosphere on these processes not well understood. Here, using microbiome transplant experiments, cyanotoxin analysis, stable isotope tracing measure N incorporation exchange at single cell resolution, we monitored growth,...
Extraction of high-molecular-weight DNA from Gram-positive bacterial species, with optional steps for removing surfactants. This is suitable sequencing and the protocol can be scaled up at least 5-fold. Modified a by Tina Wecke, LMU-Munich.