PMI in the news
QIIME 2: PMI Director, Dr. Greg Caporaso and his team reengineer bioinformatic software for next generation of microbiome science Accordion Closed
In the last 20 years, rapid advances in DNA sequencing and bioinformatics technologies have significantly improved scientists’ understanding of the microbial world. Examples include increased knowledge about the vast diversity of microorganisms; how microbiota and microbiomes impact disease and medical treatment; how microorganisms impact the health of our planet; and the potential for applications of microbiome biotechnology in the medical, forensic, environmental and agricultural fields.
In 2009, Northern Arizona University associate professor Greg Caporaso of the Center for Applied Microbiome Science, part of the Pathogen and Microbiome Institute—who was at that time working as a postdoctoral scholar in Rob Knight’s laboratory, then at the University of Colorado at Boulder—led the development of the first open-source QIIME (Quantitative Insights Into Microbial Ecology) bioinformatics software platform under Knight’s guidance. An announcement of the software launch was published in Nature Methods in 2010. The software enables scientists to perform microbiome analysis from increasingly large amounts of DNA sequencing data, and was designed to take users from raw sequencing data through publication-quality graphics and statistics.
PMI’s Executive Director Dr. Paul Keim shares his experience in forensics on the Science History Podcast. Accordion Closed
Keim, a Regents professor of biology and director of the Pathogen and Microbiome Institute at Northern Arizona University, shared his experience in forensics with fellow biology professor Frank von Hippel, an ecotoxicologist who hosts the monthly Science History Podcast.
PMI Executive Director Paul Keim traveled to South Korea to speak about the growing dangers of Botox production. Accordion Closed
Professor of biological sciences and PMI Executive Director Paul Keim traveled to South Korea to meet with Wonjong Jang, head of the Korean Biological Safety Association and professor at Konkuk University, and to speak about the growing dangers of Botox production in South Korea. Keim was highlighted in Pulse, the country’s major business publication.
Crystal Hepp, assistant professor in SICCS and PMI Affiliate Researcher, published Accordion Closed
Crystal Hepp, assistant professor in the School of Informatics, Computing, and Cyber Systems, published “Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest” in the peer-reviewed journal PLOS ONE. The paper examines whether cases of West Nile Virus in Maricopa County are endemic or imported each year.
Greg Caporaso of the Pathogen and Micobiome Institute was included on the Highly Cited Researchers of 2018 list Accordion Closed
Greg Caporaso of the Pathogen and Microbiome Institute was included on the Highly Cited Researchers of 2018 list released by Clarivate Analytics. The list, drawn from the top 1 percent of scientific citations over the last decade, offers a benchmark of researchers’ influence within and across 21 scientific fields. Caporaso was recognized for his publications in microbiology.
PMI researchers Dr. Jeffrey Foster and Katy Parise found previously unknown connections can spread diseases between species Accordion Closed
Researchers have long known how diseases are spread, most of which involve contracting germs through air, feces, mucus membranes, blood or other bodily fluids. But because germs are naked to the human eye, seeing the process in which these pathogens move has remained a mystery. Until now.
A team of biologists from several institutions throughout the United States, including Northern Arizona University researchers Jeffrey Foster and Katy Parise, looked at disease transmission in bats. What they found revealed previously unknown connections can spread diseases between species and lead to large-scale outbreaks, like white-nose syndrome—responsible for killing millions of North American bats since 2006.
PMI’s Dr. David Wagner receives $2.25 million grant to study potential biological warfare agent Accordion Closed
Francisella tularensis is one of the most infectious pathogenic bacteria known to science—so virulent, in fact, that it is considered a serious potential bioterrorist threat. Humans can contract respiratory tularemia—a rare and deadly disease—by inhaling as few as 10 airborne organisms.
Northern Arizona University professor David Wagner, director of the Pathogen and Microbiome Institute’s (PMI) Biodefense and Disease Ecology Center, was recently awarded a $2.25 million grant by the U.S. Defense Threat Reduction Agency (DTRA) for a three-year project to better understand the life cycle and behavior of F. tularensis.
Wagner, who has been performing advanced DNA “fingerprinting” of this pathogen for almost 15 years, said that because some countries have developed biological warfare agents based on F. tularensis, it is imperative that the U.S. government develop the tools and knowledge to protect Americans from this potential threat.
“This project is critical to the science of countering weapons of mass destruction because F. tularensis is a potential biological warfare agent and its natural life cycle is poorly understood,” Wagner said.
Hyenas, hippos and lions joined PMI’s Dr. Faith Walker’s inaugural study abroad class in Zambia Accordion Closed
For most of us, seeing lions on an African safari would rank as the highlight of the trip, if not the year.
Seeing them defecate? Not so much. But that is the first moment Northern Arizona University wildlife geneticist Faith Walker recollects when she talks about her trip to Zambia in June.
Oh, and seeing a pride of lions take down a puku later that night was pretty cool, too. Two safari jeeps filled with NAU faculty and students sat quietly and watched the circle of life.
It wasn’t the typical study abroad or research experience, perhaps, but it was the trip of a lifetime.
PMI’s Dr. Faith Walker, along with School of Forestry professor Carol Chambers, led a group of students—four undergraduates and grad student Dan Sanchez—halfway around the world to experience what only Africa has to offer. They spent a week at Zikomo Safari Lodge near Mfuwe, outside South Luangwa National Park, exploring the park, doing non-invasive research on the wildlife and learning about Africa’s conservation history and challenges. Thanks to an NAU grant, they also got to donate school supplies to local schoolchildren and help with an unusual two-pronged economic development program in the village.
PMI’s Dr. Jason Ladner on international study reporting first known case of virus transmission from female Ebola survivor Accordion Closed
According to the Centers for Disease Control and Prevention (CDC), the 2014-2015 outbreak of Ebola virus disease in Western Africa was unprecedented, with 28,000 cases killing more than 11,000 people in Liberia, Guinea and Sierra Leone.
While Ebola virus is typically spread through the bodily fluids of symptomatic individuals, the virus can persist in some compartments of the body, such as the male reproductive system. In several cases, sexual transmission from these persistent infections has resulted in the renewed spread of Ebola virus disease in Western Africa.
A new study recently published in The Lancet Infectious Diseases, however, reports on the first known case of Ebola virus transmission from a female Ebola survivor. Northern Arizona University geneticist Jason Ladner, assistant director of The Pathogen and Microbiome Institute, is a joint first author of the study, along with colleagues on an international team of scientists from organizations including the CDC, the National Institutes of Health, the World Health Organization, the U.S. Army Medical Research Institute of Infectious Diseases and the International Rescue Committee.
“This investigation underscores the need for focused prevention efforts among survivors, as well as sustained capacity to rapidly detect new cases, in order to prevent further spread of the virus following an outbreak,” Ladner said.
NAU makes history with three students chosen as Goldwater Scholars, two from PMI Accordion Closed
For the first time in the school’s history, three Northern Arizona University students have been selected as Goldwater Scholars.
The prestigious award, given to undergraduate students studying natural sciences, mathematics or engineering, provides one- or two-year full-ride scholarships to each of the recipients.
This year, 1,280 STEM students were nominated by campus representatives from more than 2,000 colleges and universities nationwide. Among the 211 selected to receive scholarships for the 2018-19 academic year were NAU biology students Austin Dikeman and Shelby Hutton and mechanical engineering student Dan Rivera. An additional 281 nominees were named as honorable mentions.
“This says a lot about the caliber of students at NAU,” NAU President Rita Cheng said. “I could not be prouder of these Lumberjacks for I know they will continue to accomplish nothing but great things. Hurrah for NAU!”
PMI’s Dr. Emily Cope uses microbial sequencing to understand and treat respiratory diseases Accordion Closed
According to the Centers for Disease Control and Prevention, more than 16 percent of adults in the United States have been diagnosed with chronic rhinosinusitis, or CRS—commonly defined as a sinus infection and inflammation that lasts more than 12 weeks. Not only do CRS patients report a significantly worse quality of life than those with asthma, congestive heart failure and chronic back pain, but the disease results in $65 billion per year in health care costs. Yet, despite the substantial socioeconomic impact of sinonasal inflammation, its underlying cause is not well understood.
Emily Cope, an assistant professor of microbiology and assistant director of the Pathogen and Microbiome Institute at Northern Arizona University, is out to change that with her research.
“The goals of my lab are to first understand the biology of the airway and the microbiome in the context of human health and disease and then to use that knowledge to develop new therapeutics, such as microbial therapies—prebiotics or probiotics—to help treat CRS and asthma,” Cope said.