Ongoing Projects

Urban Microbial Ecology:

The Sewerage Microbiome

We are investigating the microbial communities of sewage and sewer systems. Pipe infrastructure is a relatively new habitat on this planet, and microbes have colonized these urban systems. In fact, pipe infrastructure is an ecosystem where microbes exhibit community patterns similar to those of lakes, oceans, or soils, such as: seasonal dynamics, resident and transient members, and biogeography. We are now working to more thoroughly characterize the sewage microbiome, the activities of the microbes therein, and how the unique selective pressures in these systems shape genomic content. We also collaborate Dr. Sandra McLellan's at the University of Wisconsin-Milwaukee, to develop methods to quantify microbes/genes in wastewater to serve as indicators of health in human populations.  Recent publications of this work. Roguet, A.R., A.M. Eren, R.J. Newton, & S.L. McLellan. 2022. Guts of the urban ecosystem: Microbial ecology of sewer infrastructure. mSystems e00118-22. Link LaMartina, E.L., A.L. Schmoldt, & R.J. Newton. 2022. Full-length 16S rRNA gene sequences from raw sewage spanning geographic and seasonal gradients in conveyance systems across the USA. Microbiology Resource Announcements e00319-22. Link LaMartina, E.L., A.A. Mohaimani, & R.J. Newton. 2021. Urban wastewater bacterial communities assemble into seasonal steady states. Microbiome 9(1):1-13. Link  Feng, S., A. Roguet, J.S. McClary-Gutierrez, R.J. Newton, N. Kloczko, J.G. Meiman, S.L. McLellan. 2021. Evaluation of sampling, analysis, and normalization methods for SARS-CoV-2 concentrations in wastewater to assess COVID-19 burdens in Wisconsin communities. ACS ES&T Water 1(8):1955-1965. Link Bivins, A., D. North, A. Ahmad, et al., 2020. Wastewater-based epidemiology: global collaborative to maximize contributions in the fight against COVID-19. Environmental Science & Technology 54:7754-7757. Link

Urban Microbial Ecology:
Connections between water infrastructure & natural water systems

We have begun projects to look at the impact water infrastructure-associated microorganisms have on receiving waters. Can pipe derived microbes survive in freshwaters, and if so for how long? What about the genetic content of these microorganisms; does it spread into aquatic systems? Is the human-derived pipe environment a new vector of genetic diversity to aquatic ecosystems?   In collaboration with Dr. Sandra McLellan at the University of Wisconsin-Milwaukee, we are also using these systems to identify microorganisms that are abundant and common across human populations and urban water infrastructure to develop more accurate and source-specific indicators of human fecal pollution and other urban environments. Recent publications of this work. Roguet, A., A.M. Eren, R.J. Newton, & S.L. McLellan. 2018. Fecal source identification using random forest. Microbiome 6:185. doi: 10.1186/s40168-018-0568-3.  McClary-Gutierrez, Z. Driscoll, C. Nenn, & R.J. Newton. 2021. Human fecal contamination corresponds to changes in the freshwater bacterial communities of a large river basin. Microbiology Spectrum 9(2):e01200-21. Link Roguet, A., Ö.C. Esen, A.M. Eren, R.J. Newton, & S.L. McLellan. 2020. FORENSIC: an online platform for fecal source identification. mSystems 5(2):e00869-19. Link Newton, R.J. & J.S. McClary. 2019. The flux and impact of wastewater infrastructure microorganisms on human and ecosystem health. Current Opinion in Biotechnology. 57:145-150. doi: 10.1016.j.copbio.2019.03.015. Link

Urban Microbial Ecology:

Antimicrobial resistance & urban water infrastructure

Antimicrobial resistance is growing human health problem. To combat this global issue, reservoirs of resistance and resistance transfer need to be identified. Urban water infrastructure, especially wastewater is a hot-spot of antimicrobial resistance and an ideal location for transfer of resistance among microbes. Currently we are working on understanding the distribution of antimicrobial resistance in urban sewage systems and how system dynamics impact the diversity and quantity of resistance genes. Drinking water systems are less discussed but an important environment for understanding antimicrobial resistance in urban landscapes. In collaboration with Dr. Patrick McNamara's lab at Marquette University ( we are examining the influence of pipe materials and dissenfection products on resistance.

Freshwater Microbial Communities & the Laurentian Great Lakes

For much of my career, I have studied the distribution and activities of microbes in freshwater lakes. In recent years, much of this work has focused on the microorganisms in the Laurentian Great Lakes. Our lab is located on the shores of Lake Michigan near downtown Milwaukee, WI. From this great access point, we are working to understand how the microbes in these large lake systems differ from smaller inland lakes and how large urban centers, like Milwaukee, influence coastal lake processes. Much of our work is in collaboration with the lab of Dr. Maureen Coleman at the University of Chicago. Dr. Coleman's group has collected samples over many years aboard the R/V Lake Guardian from all five of the Laurentian Great Lakes. Amplicon-based and metagenomic sequencing and analysis are ongoing so that we can better understand whether the microbial communities and populations in each lake are unique and/or differentiated from smaller inland lakes and oceans, how gene content is partitioned in these large systems, what unrecognized organisms or life traits are contributing to the nutrient cycling and population dynamics in these large systems, and much more. See the Coleman lab website for further information.  Paver, S.F., R.J. Newton, & M.L. Coleman. 2020. Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry. Environmental Microbiology 22:433-446. Link  Paver, S.F., D. Muratore, R.J. Newton, & M.L. Coleman. 2018. Reevaluating the salty divide: Phylogenetic specificity of transitions between marine and freshwater systems. mSystems 3(6): e00232-18. doi:10.1128/mSystems.00232-18. Rohwer, R.R., J.J. Hamilton, R.J. Newton, & K.D. McMahon. 2018. TaxAss: Leveraging a custom database achieves fine-scale taxonomic resolution. mSphere 3:e00327-18. doi: 10.1128/mSphere.00327-18. Link


Typical aquaculture diets differ vastly from what reared animals encounter in nature and thus likely have a large impact on the microbial gut community. It is clear, gut microbial communities have a profound impact on animal health. It is not yet clear how aquaculture diets impact animal gut microbes or more importantly whether these changes impact animal health in these systems. In collaboration with Dr. Dong-Fang Deng's lab at UW-Milwaukee, we are initiating trials to understand the interaction between diet in an aquaculture setting, gut microbial communities, and fish health. Publications on this work:  Lu, X., D-F. Deng, F. Huang, F. Casu, E. Kraco, R.J. Newton, M. Zohn, S.J. Teh, A.M. Watson, B. Sheperd, Y. Ma, M.A.O. Dawood, L.M. Rios Mendoza. 2022. Chronic exposure to high-density polyethylene microplastic through feeding alters the nutrient metabolism of juvenile yellow perch (Perca flavescens). Animal Nutrition 9: 143-158. Link Jiang, M., H. Zhao, S.-W. Zhai, R.J. Newton, B. Shepherd, J. Tain, A.G. Lofald, S. Teh, F.P. Binkowski, & D.-F. Deng. 2020. Nutritional quality of different starches in feed fed to juvenile yellow perch, Perca flavescens. Aquaculture Nutrition. doi: 10.1111/anu.13026. Link