JohnsonResearchProgram

Animal Microbiome Laboratory

The complex community of microbes that inhabit the gastrointestinal tract (microbiota) has gained appreciation by scientists, physicians, and the general population in recent decades. The microbiome exhibits broad reaching impacts and plays a role in host nutrition, pathogen colonization resistance, gastrointestinal disease, immune and digestive system regulation, even cardiovascular disease and neurological development and disease. Animal agriculture is about to undergo a transformation following the new Veterinary Feed Directive, which will disallow the growth promotion use of antibiotics that are important for human health. Animal producers will need to look for alternatives to the antibiotics to maintain healthy, disease resistant animals and a safe food supply to the public. Continual antibiotic use has disrupted natural microbial community structure. By understanding and promoting the microbiome, we utilize biological controls of unwanted microbiome invaders and promote benefits host-microbe interactions, while minimizing undesirable collateral effects, like antibiotic resistance.

Research Focus 1. Identify the complete picture on antibiotic resistance by selection and genetic context of antibiotic resistance. 2. Disentangle the interactions between the microbiota, the host, and gut metabolites and their role in host nutrition and their role in pathogen colonization.

Research Focus 1: Antibiotic resistance in the microbiome Antibiotic resistance is a growing barrier to the cure of infectious diseases. The Centers for Disease Control, the World Health Organization and other organizations worldwide have all initiated action to combat antibiotic resistance and have initiated a One-Health approach. This is most apparent in the issue of antibiotic resistance due to the interconnections between farms, the environment and the public, horizontal gene transfer between bacteria and the use of antibiotics in all three sectors. As animal production practices evolve, we must continually assess those practices impacts on antibiotic resistance to maintain the long-term efficacy of antibiotics in the treatment of disease.

There are two important distinctions in the development of antibiotic resistance in microbial communities: abundance of the genes and the genomic context of those resistance genes. I have shown that agricultural use of antibiotics can increase the abundance of resistance genes hundreds and thousands of times compared to a sample without antibiotics and that the co-selection of large clusters of resistance genes and mobile genetic elements occurs in Chinese swine agriculture. I am continuing this work in farms worldwide to identify the biogeography of resistance gene clusters. Mobile genetic clusters of antibiotic resistance genes represents a major problem in controlling antibiotic resistance because the resistance genes are primed to be transferred throughout bacterial communities or to pathogens. While my data are so far only associations, we are going to follow up with metagenomics approaches and isolation and sequencing of multidrug resistant bacterial isolates to identify the exact genomic context of the associations. Genomic context of antibiotic resistance genes is critical to the evolution of multidrug resistant bacteria and their horizontal gene transfer.

Research Focus 2: The microbiota-host-metabolite axis The gut microbiome significantly affects the nutrition of the host and host feed efficiency, likely due to drastically altering the chemical landscape of the gut. The chemical composition of the gut can be determined through metabolomics, the process of quantifying the metabolites in a sample. The host absorbs these metabolites from the gut into the portal bloodstream, some of which are microbially derived. The portal blood is detoxified in the liver and then delivered to the body through the peripheral blood stream. Thus we have the opportunity to identify the microbiota’s influence on the metabolites in the gut, metabolites absorbed by the host in the portal blood, and the metabolites that are distributed throughout the body. We are currently analyzing data in turkeys and identifying these interactions also with the transcriptome of the turkey cecal tonsil, a major immune organ in the avian gut. With this combined dataset, we can identify key metabolites indicative of metabolic states, microbial populations correlated with their occurrence, metabolite uptake and utilization by the host. This analysis could lead to novel probiotics or feed additives to promote growth or disease suppression, generating new hypothesis driven research. These tools could be applied to antibiotic (growth-promoting) feed trials, host-stress studies, probiotic or prebiotic trials, antibiotic-reconstituted microbiomes, or animal feed trials.

The microbiome also may potentially aid in keeping animals pathogen free. The microbiome may act directly on the pathogen to inhibit its growth or to occupy its niche environment in the host. The microbiome also might trigger the host to inhibit the pathogen. Following the lead of research in humans, probiotics (Clostridium scindens) and fecal transplantation have proven efficient in eliminating Clostridium difficile. In similar fashion, it seems feasible to decrease colonization of animal pathogens by means of competitive exclusion by other bacteria occupying the mucosal niche that the pathogen customarily occupies, or by producing molecules that prohibit its growth or colonization. The success of probiotics can be accessed by pathogen colonization rates, community profiling (to identify community interactions with the probiotic and with the pathogen), and metabolomics (to identify chemical conditions that favor pathogen colonization). Go to top

Lab Members

Tim Johnson

Assistant Professor of Food Animal Microbiome. He is originally from Missouri. Tim’s education started at Brigham Young University; he focused on soil microbiology and the role bacteria play in nutrient cycling (carbon and nitrogen) in the environment. His PhD research focused on microbial ecology in soil, animals and manure. His PhD work provided a quantitative measure of diverse impacts of in-feed antibiotics on bacterial community membership and antimicrobial resistance genes. After earning his degree, he set out on a quest for solutions to the mounting problem of antibiotic resistance. Tim found his first postdoc position at McMaster University in Ontario, Canada where he investigated antimicrobial resistance and drug discovery. In a second postdoc at the National Animal Disease Center, he used multi ’omics (metagenomics, metabolomics, metatranscriptomics, and 16S community profiling) approaches to studying the swine and turkey microbiome in efforts to find alternatives to antibiotics in animal agriculture.

Tim and Angela Johnson have 5 children – Zach, Grant, Bennett, James and Mary. As a family, they enjoy soccer, basketball, hiking, camping, swimming and running. Angela is a “semi-retired” music teacher (voice and piano). They enjoy family time outside and DIY projects.

Carmen Wickware

Carmen is a PhD student. She has a B.S. from Purdue University where she studied Food Science. As a Masters student in Food Science at Cornell University, her focus was food microbiology and safety; her thesis research was finding critical processing parameters (pH and time) for the production of safe soybean tempeh. She also has an M.S. in Bioinformatics from New York University. Follower her graduation from NYU, she worked at Virginia Tech analyzing whole genome sequences for antibiotic resistance genes from raw manure and small-scale composted manure. This was part of a much larger study looking at tracing antibiotic resistance genes and bacteria from farm-to-fork. Now as a PhD student, she would like to focus on the epidemiology of antibiotic resistance as it pertains to agriculture and finding ways to increase the disease resistance of our feed animals.

Carmen is the daughter of Marvin, Sr. and Jenifer and the younger of two children; her older brother Marvin, Jr. and his wife Beth have two children, Nathaniel and Gabriel. She enjoys biking, hiking, playing with her dog Ein, cooking, baking, going to concerts, and all types of games (video, card, board, tabletop, etc.).

Ruth Eunice Centeno

Ruth is an intern student in the Animal Sciences Department. She is originally from San Salvador, El Salvador. Ruth is a senior year student of the Agronomic Engineering Major at Zamorano University in Honduras. During her studies at Zamorano University, she worked in the areas of zootechnology, animal science, animal reproduction biotechnology, phytotechnology, horticulture, molecular diagnostic, soil management and conservation, environment and development, processing and product commercialization. Before studying at Zamorano, Ruth did a semester of Veterinary Medicine in the Alberto Masferrer University in El Salvador.

As part of her study plan from Zamorano University, she is doing an internship here at Purdue Animal Sciences in the area of food animal microbiome. She is working with chicken and swine microbiomes. She is using molecular techniques that allow her to view the changes and effects in the intestinal microbiome by the incorporation of enzymes, amino acids and other components into animal diets and how these changes affect the feed efficiency and growth performance.

After Ruth finishes her internship, she will return to Zamorano University and finish her studies.

Johanna Muurinen

Johanna is a postdoc from Finland and she is especially interested in finding links between environmental resistome and "superbugs". Her scientific career path has not been the straightest but as the result she has a broad perspective in antimicrobial resistance. From 2001 to 2007 she worked as a laboratory technician at the Faculty of Veterinary Medicine, University of Helsinki, Finland. She wanted to be a researcher herself and she almost started her studies at the Faculty of Pharmacy, but felt more like home in Environmental Soil Science, Faculty of Agriculture and Forestry, University of Helsinki. She studied agricultural properties of Biochar in her master's thesis and graduated in 2012. In 2013 she started her PhD studies in Microbiology and in the laboratory of Professor Marko Virta, Faculty of Agriculture and Forestry, University of Helsinki. The original idea for her PhD project was her own and she was the first researcher studying antibiotic resistance in Finnish agroecosystems. She defended her thesis in October 2017. From April 2017 to May 2018 she worked as a researcher at the Risk Assessment Research Unit, Finnish Food Safety Authority Evira. Her task was to study the associations between antimicrobial use, farm management and observed antimicrobial resistance in the pork production chain. Johanna joined Dr. Johnson's laboratory in July 2018 and will be continuing her research on antimicrobial resistance in production animals and agroecosystems.

Johanna is also the chairperson of One Health Finland, an NGO advancing One Health approach and science communication. She has two cats and a horse in Finland. During her free time she loves to ride dressage and reading blogs about advanced statistics and artificial intelligence.

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Join the Lab

We are interested in hiring excellent graduate students and postdocs pending available funding. Please contact Tim directly with your research interests.