ORISE Research Fellow

• Provides scientific support for chicken microbiome research projects performing bioinformatics analyses with specialized software such as QIIME 2, R, LEfSe, and PICRUSt2. Published journal articles researching 1) the effects of Eimeria tenella infection on the cecal microbiota of broiler chickens and 2) the effects of E. acervulina infection on duodenal and jejunal microbiota. Manuscript in peer review on the effects of heat stress on cecal microbiota in four broiler genetic lines. Manuscript in progress on the effects of E. acervulina infection on cecal and ileal microbiota. PI: Dr. Monika Proszkowiec-Weglarz.
• Published Research Note demonstrating how choice of taxonomic database (Greengenes, RDP, and SILVA) may affect interpretation of QIIME 2 and LEfSe results in chicken microbiota studies.
• independently wrote manuscripts for the above publications, responded to peer reviewer comments, and used R packages such as ggplot2 and dplyr to prepare publication-ready graphics.
• Performs bioinformatics activities in a Linux environment daily, utilizes high performance computing (HPC) clusters on USDA-ARS SciNet, and troubleshoots program errors under guidance of Computational Biologist Jonathan Shao.
• Provides bioinformatics support to fungal genome projects working with Dr. Stephen Rehner. Performs sequence assembly and annotation in genomes of fungal genera Beauveria, Colletotrichum, Leucocoprinus, and Metarhizium. Utilizes programs such as SPAdes, Funannotate, Augustus, BUSCO, and BLAST. Used the Phyluce program to extract and align ultra-conserved element (UCE) loci. Wrote custom Python script to parse fasta sequences and distribute sequences to hundreds of new folders and files based on loci IDs.
• Prepared annotation of yeast genome and assisted in submission to NCBI for publication lead by Dr. Joseph Msanne. Used gene finding tools, including Fgenesh and HMMER, to annotate mitochondrial portions of the genome. Created a phylogeny with MEGA to find related species.
• Prepares user manuals using R Markdown documenting workflows for 1) QIIME 2 complete workflow, 2) producing publication-ready graphics with ggplot2 for microbiome studies, 3) LEfSe workflows for formatting files, running analyses, and producing graphics, and 4) Funannotate workflow for submission of fungal genome annotation to NCBI.
• Participated as a helper to instructors during two online USDA Data Carpentry training workshops on Linux, R, and Git for Reproducible Scientific Analysis (Mar 2021, Mar 2022, May 2023).
• Trained two interns to support funannotate project, doubling the project efficiency. Assisted scientists (e.g. Dr. Asis Khan) in troubleshooting issues on the USDA-ARS SciNet.

Research Technician

• Assisted with a National Science Foundation funded project investigating interactions between honey bees, their gut microbiome, and pesticides by performing bioinformatic and statistical data analyses.
• Assisted in manuscript preparation for publication.

Thesis Research

• Focus: Relationships between the chytrid fungus pathogen Batrachochytrium dendrobatidis and the skin microbiome of amphibians.
• Collaborated with the Idaho Department of Fish and Game to analyze skin microbiomes of Columbia spotted frogs from surveys in 2013-2014 impacted by chytrid fungus.
• Demonstrated differences between microbiomes of infected and uninfected frogs using bioinformatic and statistical data analyses.
• Performed field survey of frogs at wetlands in Turnbull National Wildlife Refuge in Cheney, WA to measure chytridiomycosis disease prevalence and infection intensity.

Inventory and Monitoring Intern

• Contributed to workplan for the San Francisco Bay National Wildlife Refuge Complex with reports on threats to species in the complex.
• To understand the population decline of the endangered Lange's Metalmark Butterfly in Antioch Dunes National Wildlife Refuge, completed data analysis and literature search to demonstrate the effects of temperature and wildfires on survey counts.
• Delivered oral presentation with findings to regional refuge staff.
• Attended workshops with refuge staff observing planning process for conservation management.

Field Ecology Intern

• Worked at Sagehen Creek Field Station in a team of five on experiment researching the effects of insect pollination on floral microbe communities.
• 1 month of daily, full-time fieldwork in a meadow setting.
• Collected data on plant physiological traits, collected plant samples, assisted in identification of plants and insects, collected insect samples, and pinned insects.

Research Project

• Two-quarter EVE 180 class project researching the effects of oak apple gall on fungal growth and arthropod abundance.
• Field experiments included 1) Plant and fungal survey, 2) Randomized plotting of Agaricus samples, and 3) Arthropod survey.
• Lab experiments included 1) Agaricus cultivation and 2) Plating of multiple fungal species on agar media.
• Statistical analysis performed using R.
• Completed full biological report.

Graduate Assistant

• Teaching Assistant for Introductory Biology courses (BIOL 171, 172, 173), Biological Investigation course (BIOL 270), and Senior Capstone Environmental Microbiology course (BIOL 490).

GIS Intern

• Used ESRI web GIS software to confirm address points for Local Update of Census Addresses Operation (LUCA), address points for the Sheriff Department, and fire hydrant locations for the Fire Department.
• Researched and tested open source options and web mapping options for GIS. Examples include QGIS, OSGeo4W, PostGIS/PostgreSQL, Geoserver, Leaflet, and MapHub.

Field Biology Intern (Volunteer)

• Herbicide application and safety training completed.
• Participated in field removal of invasive plant species inside National Park land using spray methods.

Assistant Producer

• Full-time job overseas. Responsible for data collection and quality control for three countries represented in FIFA soccer video game series: Australia, Chile, and Mexico.
• Project management: worked with others as a team to meet data collection goals.
• Leadership: supervised online seasonal workers through e-mail communication.

Campos PM, Lucid MK, Ehlers S, Walke JB. Low-level Pathogen Infection and Geographic Location Correlate with the Skin Microbiomes of Columbia Spotted Frogs (Rana luteiventris) in a Montane Landscape. Current Research in Microbial Sciences. 2023 (submitted).

Campos PM, Schreier LL, Proszkowiec-Weglarz M, Dridi S. Cecal microbiota composition differs under normal and high ambient temperatures in genetically distinct chicken lines. Scientific Reports. 2023 (in review).

Jenkins MC, Parker C, O’Brien C, Campos PM, Proszkowiec-Weglarz M, Miska KB. Effects of codon optimization on expression in Escherichia coli of protein-coding DNA sequences from the protozoan Eimeria. Journal of Microbiological Methods. 2023 Jun 2:106750.

Rehner SA, Gazis R, Doyle VP, Vieira WA, Campos PM, Shao J. Genome Resources for the Colletotrichum gloeosporioides Species Complex: 13 Tree Endophytes from the Neotropics and Paleotropics. Microbiology Resource Announcements. 2023 Apr 18;12(4):e01040-22.

Campos PM, Miska KB, Jenkins MC, Yan X, Proszkowiec-Weglarz M. Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the duodenum and jejunum in broiler chickens. Frontiers in Microbiology. 2023 Mar 20;14:1147579.

Msanne J, Shao J, Ashby R, Campos P, Liu Y, Solaiman D. Draft Genome Sequence of the Sophorolipid-Producing Yeast Pseudohyphozyma bogoriensis ATCC 18809. Microbiology Resource Announcements. 2022 Nov 30;12(1):e00566-22.

Proszkowiec-Weglarz M, Miska KB, Ellestad LE, Schreier LL, Kahl S, Darwish N, Campos P, Shao J. Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens. BMC microbiology. 2022 Aug;22(1):1-20.

Campos PM, Darwish N, Shao J, Proszkowiec-Weglarz M. Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota. Poultry Science. 2022 May 21:101971.

Campos PM, Miska KB, Kahl S, Jenkins MC, Shao J, Proszkowiec-Weglarz M. Effects of Eimeria tenella on cecal luminal and mucosal microbiota in broiler chickens. Avian Diseases. 2022 Jan;66(1):39-52.

NIST-Hosted Workshop on Standards for Microbiome and Multi'Omics Measurements

• Attendee at conference held by International Microbiome and Multi’Omics Standards Alliance (IMMSA)

Poultry Science Association 110th Annual Meeting 2021

• Campos, P.M., Miska K.B., Kahl S., Jenkins M.C., Shao J., Proszkowiec-Weglarz, M. (2021, Jul). Effects of Eimeria tenella on cecal luminal and mucosal microbiota in broiler chickens. Virtual oral presentation at the 110th annual meeting of the Poultry Science Association.

Student Research & Creative Works Symposium

• Oral presentation on thesis research

Idaho Chapter of The Wildlife Society 2020 Annual Meeting

• Campos, P.M., Lucid, M.K., & Walke, J.B. (2020, Mar). Impact of Chytrid Fungus Pathogen on Skin Microbiome of Columbia Spotted Frogs in Northern Idaho. Oral presentation at the annual meeting of the Idaho Chapter of The Wildlife Society, Moscow, ID.

American Fisheries Society & The Wildlife Society 2019 Joint Annual Conference

• Campos, P.M., Lucid, M.K., & Walke, J.B. (2019, Oct). Impact of Chytrid Fungus Pathogen on Skin Microbiome of Columbia Spotted Frogs in Northern Idaho. Poster session presented at the annual meeting of the American Fisheries Society & The Wildlife Society, Reno, NV.

Student Research & Creative Works Symposium

• Poster presentation on thesis research