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Research


I am an evolutionary biologist who is fascinated by rapid changes in biodiversity, host-microbe co-evolution, and the health implications of recent changes in the human microbiome.

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Research


I am an evolutionary biologist who is fascinated by rapid changes in biodiversity, host-microbe co-evolution, and the health implications of recent changes in the human microbiome.

 

I combine innovative ideas, large genomic data sets, and bioinformatics tools to create novel, interdisciplinary research programs.       

The Microbiome, a totally fake movie trailer, but the science is real! Microbes are important in all life and earth sciences.  I study communities of microbes using a variety of molecular approaches. Read about some of my research below!  Produced by Mike Liguori 

 

Forensics


 

One of our current research focuses has major implications for the future of of forensics investigations. Investigate for yourself below to learn more! 

Forensics


 

One of our current research focuses has major implications for the future of of forensics investigations. Investigate for yourself below to learn more! 

Microbial tools for forensic Science

Microbial stopwatch of death

Because microbes are ubiquitous, they can be tiny witnesses to the events of our lives. I have been developing a microbial stopwatch that begins at death as a novel tool for estimating the time since death, or postmortem interval (PMI). PMI is important for criminal investigations because it can lead to the identification of the deceased and validate alibis. However, establishing PMI can be very challenging with few evidentiary tools available after the first after death.  Rob Knight (UCSD), David Carter (Chaminade University), and I, along with a number of excellent collaborators, received funding from the National Institutes of Justice (NIJ 2011-DN-BX-K533, 2014-R2-CX-K01, 2015-DN-BX-K016) to support research to test and fine tune the use of microbiome tools for estimating PMI. Please read about it in our most recent publication in the journal Science.

 A PCoA plot illustrating the beta-diversity of skin bacterial samples colored by time of decomposition, with blue representing early decomposition stages and red representing later advanced stages of decomposition. We can see that the microbiota associated with decomposing skin changes progressively during decomposition (left) with no major effect of soil type (right).

A PCoA plot illustrating the beta-diversity of skin bacterial samples colored by time of decomposition, with blue representing early decomposition stages and red representing later advanced stages of decomposition. We can see that the microbiota associated with decomposing skin changes progressively during decomposition (left) with no major effect of soil type (right).

 

Solving Crimes with the Necrobiome

My lab was recently featured in a segment narrated by Ed Yong, the acclaimed science writer who authored "I Contain Multitudes", which lets us peek into the ubiquitous nature of microbes and how vital they are. Check it out below!

 

Microbes as skin trace evidence

Skin microbes also hold great potential for forensic science.  People's skin is home to an individualized and generally stable microbial community that can be transferred to objects associated with a given person, such as computer keyboards, cell phones, and other commonly touched surfaces. We also found that humans transfer clouds of our microbes to the physical spaces we inhabit and that we come to share microbes with the humans and pets that we live with. We are currently studying how well skin microbes transfer to different common material types (glass, plastic, metal, ceramic and wood). We are also studying how long a person's skin microbial signature persists after death. 

 

 Do skin microbes transfer to different material types equally well?  In this experiment we are testing whether microbes from people's hands transfer to glass, plastic, metal, ceramic and wood after just 20 touches, and whether our hands run out of microbes after 20, 40, 60, 80 or 100 touches.

Do skin microbes transfer to different material types equally well?  In this experiment we are testing whether microbes from people's hands transfer to glass, plastic, metal, ceramic and wood after just 20 touches, and whether our hands run out of microbes after 20, 40, 60, 80 or 100 touches.

 

meat science


meat science


 Meat spoilage and food waste are a major problem. We work to better understand the microbial ecology of meat with the goal of better predicting and preventing food spoilage.


Reducing food and energy waste in poultry

Along with several faculty in Animal Sciences at CSU, my lab is working with UC Davis and Foster Farms to investigate the differences between air vs water chilling of chickens with the goal of improving shelf-life and shelf-life prediction, meat quality, and energy usage. Approximately 250 chickens were cooled either via water chilling or by air chilling and fabricated into either bone-in or boneless breasts for dark storage and display. Chicken breasts were sampled at several time points throughout the process. This project includes a truly interdisciplinary approach to assessing the two cooling methods. We are characterizing the microbial ecology, sensory attributes, and nutritive value of each chicken, as well as energy and water budgets of each cooling method. This holistic assessment will provide industry with a comprehensive view of the value of these two processing approaches. This research is funded by the Innovation Institute for Food and Health.

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The Ancestral Gut Microbiome


The Ancestral Gut Microbiome


What is a healthy human gut microbiome? We are currently characterizing the human gut microbiome in cultures that have dramatically altered their microbial counterparts with intensive hygiene practices, widespread antibiotic use, high fat and protein diets, and extensive time spent indoors. We can try to understand the ancestral state of the human gut microbiome in two ways to do this – 1) study the microbiome of human populations living traditional lifestyles, particularly ones that haven’t been exposed to antibiotics and 2) by sampling ancient gut microbiomes in well preserved ancient human fecal material. I currently work on both of these types of projects. Through highly collaborative research projects, I study the gut microbiomes of people living traditional lifestyles today (e.g. hunter-gatherers). Additionally, I study gut microbiota preserved in ancient fecal material discovered in caves, Viking latrines, and naturally mummified human remains.

extracting DNA from 1000 year old viking latrine samples

 

Domestication


Domestication


The effect of domestication and captivity on the microbiome

The Przewalski horse microbiome

We are only just beginning to understand the complex and beautiful relationship between vertebrate hosts and their microbial partners. I am interested in a broad range of questions about how vertebrate microbiomes have evolved and how they may have changed through domestication and modern agriculture. Recently I worked with an international group of collaborators to study the difference between domesticated horses and Przewalski horses, which are the only group of horses left on earth not successfully domesticated by humans. I had the opportunity to work with Claudia Feh (Association pour le cheval de Przewalski: TAKH, Station biologique de la Tour du Valat) and Ludovic Orlando (Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, Université de Toulouse). Their teams collected fecal samples and important metadata from herded, domestic horses and Przewalski horses living near Seer, Mongolia and separated by a fence. 

Check out our recent paper published in Scientific Reports

We discovered Przewalski horse fecal microbiomes hosted a distinct and more diverse community of bacteria compared to domestic horses, which is likely partly explained by different plant diets as revealed by trnL maker data. Within the PH population, four individuals were born in captivity in European zoos and hosted a strikingly low diversity of fecal microbiota compared to individuals born in natural reserves in France and Mongolia. These results suggest that anthropogenic forces can dramatically reshape equid gastrointestinal microbiomes, which has broader implications for the conservation management of endangered mammals.

Here we link to an updated Supplementary Table 3, in which we added and corrected several items highlighted in red. You can find a description of the changes in the comment section of our online manuscript. 

Metcalf et al. 2017 Does domestication and captivity shape the horse gut microbiome? Scientific Reports.  Vol. 7, 1-9.

 
 photo by Ludovic Orlando

photo by Ludovic Orlando

 

rumen microbiomes

I am also very interested in rumen microbiomes and how rumen ecology of domesticated livestock may differ from their wild ancestors or close relatives. I am starting several projects along these lines.

 

Tumor Microbiome


Tumor Microbiome


LONGITUDINAL STUDY OF THE MICROBIOME OF APPENDICEAL CANCER PATIENTS

Appendix cancer is newly diagnosed in over 1,000 Americans a year. Recent research has revealed the presence, and potential role, of bacteria in tumor material of the appendiceal neoplasm Pseudomyxoma Peritonei (PMP) (1), which is a mucinous tumor type invades the peritoneal cavity. Gilbreath et al. (2013) showed that tumor/mucin microbiome was dominated by bacteria of the Phylum Proteobacteria such as Helicobacter. Helicobacter pylori has been implicated in other gastric cancers with antibiotic treatments effectively reducing tumor and improving survivorship in some cases. Similarly, a pilot study completed by the authors of this proposal demonstrated that antibiotic treatment increased survivorship for patients with the malignant form of PMP (Gilbreath et al. 2013, Semino-Mora et al. 2013), which is also associated with higher bacterial loads. 

We hypothesize that tumor-promoting species are more prevalent in the fecal flora of PMP patients at the time of diagnosis, and these species could serve as both diagnostic and therapeutic targetsWe will generate longitudinal gut microbiome data from the first 25 patients enrolled in clinical trial NCT02387203 and determine whether microbiome composition influences either carcinogenesis or post-surgical diarrheal illness, with the potential of markedly improving the quality of life of patients.

Conservation genetics


Conservation genetics


Extinctions of South American megafauna

One of my passions is the study of animals that became extinct during the late Pleistocene. What are their closest extant relatives? When did they became extinct? Were populations declining before extinction or did they became extinct suddenly? Is the timing of their extinction or population decline associated with changes in climate or human occupation of the region? A combination of radiocarbon data and DNA sequence data derived from teeth, bones, and other biological material provides clues to the answers of these questions. In collaboration with archaeologists and paleontologists, these data can be interpreted to help answer long-standing questions about the intriguing megafauna that no longer roam the earth. During my post-doc at ACAD, I worked on several projects in which we examined the late Pleistocene genetic diversity of large herbivores across a number of continents. In my focal study system of South American camelids, I uncovered previously undocumented extinction events in the Patagonia region of South America.

 Extinct South American megafauna includes camelids, felids, equids, ground sloth, and large bear.

Extinct South American megafauna includes camelids, felids, equids, ground sloth, and large bear.

Conservation genetics of Colorado's greenback cutthroat trout

In the 1930s, the greenback cutthroat trout was declared extinct in Colorado. More than 75 years later, a genetic sleuthing effort led by the University of Colorado Boulder resulted in the stocking of the official state fish back into its native range.  More on this story here.

We clarified the taxonomy and diversity of cutthroat trout subspecies in the drainages of Colorado by using early museum collections (1857 – 1890 AD) of cutthroat trout. In my PhD research, I studied the population genetics and phylgenetics of modern cutthroat trout populations in Colorado, and demonstrated that early 20th century fish propagation and stocking activities had resulted in divergent lineages of cutthroat trout mixing across major drainage systems on both the Atlantic and Pacific slopes of the Continental Divide. The results demonstrated uncertainty about whether populations of the federally protected greenback cutthroat trout still existed (Metcalf et al. 2007). Subsequently, with funding and support from a wide range of federal and state agencies as well as Trout Unlimited, I successfully sequenced DNA recovered from 30 individuals of ~150 year old cutthroat trout specimens preserved in ethanol. The results of this research revealed recent extinctions, undescribed lineages, errors in taxonomy, and dramatic range changes induced by human movement of fish (Metcalf et al. 2012). We discovered that cutthroat trout lineages native to the Arkansas River and San Juan River, respectively, had become extinct since historic times. Our biggest surprise was the discovery of a single remaining population of greenback cutthroat trout (O. c. stomias) currently located outside of its native range in Bear Creek near Pikes Peak in the Arkansas River drainage. On August 8, 2014, in an effort spearheaded by the greenback cutthroat recovery team, our state fish was reintroduced to its native range.

 
 
 Reintroducing greenback cutthroat trout to the South Platte, a win for conservation genetics.

Reintroducing greenback cutthroat trout to the South Platte, a win for conservation genetics.