A study on the effect of diet particle size got published!

I’m pleased to announce that the “particle size” project is officially published!  I inherited this dataset of bacterial 16S rRNA sequences in 2015, while working for the Yeoman Lab.  This collaborative project combined nutrition, animal production, and microbial ecology to look at the effect of diet particle size on lambs and their rumen bacteria. While small in size, the project was large in scope – despite everything we know about how different diet components encourage different microbial communities to survive in the digestive tract, we know practically nothing about how the size of the particles in that diet might contribute.

Ruminants, like sheep, goats, cows, deer, moose, etc.,  have a four-chambered stomach, the largest of which is called the rumen.  The rumen houses symbiotic microorganisms which break down plant fibers that the animal can’t digest on its own.  It’s estimated that up to 80% of a ruminant’s energy need is met from the volatile fatty acids (also called short-chain fatty acids) that bacteria produce from digesting fiber, and that up to 85% of a ruminant’s protein need is met from microbial proteins.

A lot of factors can be manipulated to help get the most out of one’s diet, including adjusting ingredients for water content, palatability, ease of chewing, and how easy the ingredients are to digest.  For example, highly fibrous foods with larger particles/pieces require more chewing, as well as a longer time spent in the rumen digesting so that microorganisms have plenty of time to break the chemical bonds of large molecules.  Smaller food particles can reduce the time and effort spent chewing, allow for more surface area on plant fibers for microorganisms to attach to and digest faster, and speed up the movement of food through the digestive tract.  On the other hand, moving food too quickly could reduce the amount of time microorganisms can spend digesting, or time the ruminant can absorb nutrients across their GI tract lumen, or cause slow-growing microbial species to wash out.

Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed.

Suzanne L. Ishaq1, Medora M. Lachman2, Benjamin A. Wenner3, Amy Baeza2, Molly Butler2, Emily Gates2, Sarah Olivo1, Julie Buono Geddes2, Patrick Hatfield2, Carl J. Yeoman2

  1. Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
  2. Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, United States of America
  3. Department of Animal Sciences, The Ohio State University, Columbus, Ohio, United States of America


Diet composed of smaller particles can improve feed intake, digestibility, and animal growth or health, but in ruminant species can reduce rumination and buffering – the loss of which may inhibit fermentation and digestibility.  However, the explicit effect of particle size on the rumen microbiota remains untested, despite their crucial role in digestion.  We evaluated the effects of reduced particle size on rumen microbiota by feeding long-stem (loose) alfalfa hay compared to a ground and pelleted version of the same alfalfa in yearling sheep wethers during a two-week experimental period.  In situ digestibility of the pelleted diet was greater at 48 h compared with loose hay; however, distribution of residual fecal particle sizes in sheep did not differ between the dietary treatments at any time point (day 7 or 14).  Both average daily gain and feed efficiency were greater for the wethers consuming the pelleted diet.  Observed bacterial richness was very low at the end of the adaptation period and increased over the course of the study, suggesting the rumen bacterial community was still in flux after two weeks of adaptation.  The pelleted-hay diet group had a greater increase in bacterial richness, including common fibrolytic rumen inhabitants. The pelleted diet was positively associated with several Succiniclasticum, a Prevotella, and uncultured taxa in the Ruminococcaceae and Rickenellaceae families and Bacteroidales order. Pelleting an alfalfa hay diet for sheep does shift the rumen microbiome, though the interplay of diet particle size, retention and gastrointestinal transit time, microbial fermentative and hydrolytic activity, and host growth or health is still largely unexplored.

Symposium presentation at 2019 Joint AFS-TWS Meeting

I’m excited to announce that I’ll be giving a presentation at the American Fisheries Society and The Wildlife Society 2019 Joint Annual Conference this September. I was invited to participate in a symposium: Utility of Microbiomes for Population Management. I’ll be returning to my roots and presenting on moose microbes. See you in Reno!

Abstract 36407 – “Moose Rumen Microbes and Their Relevance to Agriculture and Health”

Spring Updates

Continuously in science, you find yourself with more ideas than you can possibly put into action, and more tasks on your daily to-do list than you can possibly complete in one day. Spring has been, predictably, busier than anticipated – so much so that I haven’t posted in over a month! Here are some of the highlights, and I hope to be posting more over the summer as papers get published and courses get taught.

Over the past few months I’ve been focusing on wrapping old projects; those large and small things that carry over even after a scientific position has run out of funds to pay you. Scientific research, and especially the interpretation and writing of results, takes a long time and often outlives short-term student, post-doc, or non-tenured faculty postings. Eventually everyone who collaborated on a project has moved on and it is increasingly more difficult to finalize and publish that work. And, most of the undergraduate students I’ve been working with at BioBE are graduating in June and need to finish their projects so they can cleanly begin the next phase of their life.

For the most part, wrapping these projects has involved writing up manuscripts, getting the authors to agree on a final draft (which can take weeks or years), and submitting it to a scientific journal for review. I currently have seven manuscripts in review; 4 scientific articles and 3 scientific reviews, some of which have been in review for months. And I still have at least four more papers that need to get finished and written up. I’m also a guest editor on a special call for papers through PloS One on the Microbiome Across Biological Systems, which to date has required communication and brainstorming from me but which will soon include quite a bit of editing and oversight.

February was generally absorbed by grant proposal writing, and it looks like May is shaping up similarly. Grant proposal writing is an arduous process requiring a lot of planning and coordination between contributing parties. The majority of proposals don’t get funded on their first round, which means you may sink a lot of time into developing something with a very delayed payoff. I am in the process of developing several highly-collaborative proposals which have been maturing into increasingly-finer wine.

Equity is not a term that’s typically associated with microbes, yet. The work this spring that I’ve been (happily) most absorbed in has been development of the summer course I’m teaching for the UO Clarks Honors College, Microbes and Social Equity. It’s only four weeks long, but will be four days a week, and I’m hoping to cover a number of different topics and coordinate several guest speakers, so there are a lot of lectures to make and emails to send.

Engagement on social media from me has been slim the past few months, but other science communications have been thriving. I gave a print interview with the UO College of Design and a radio interview with Jefferson Exchange. Most recently, I presented at the Institute for Health in the Built Environment 2019 Build Health event, where I connected with a dozen or so of my ongoing and future collaborators.

PLoS “Microbiome Across Biological Systems” Call for Papers!

I am pleased to announce that several PLoS journals are teaming up for a special issue, titled “Microbiome Across Biological Systems”, and the call for submissions is open!

PLoS (Public Library of Science) is a non-profit publisher that fosters open-access and accessibility in science, with a variety of subject-specific journals, as well as the interdisciplinary journal, PLoS ONE. I spend a lot of my time with interdisciplinary science which doesn’t quite fit with any one field, and I appreciate journals which are interested in that intersectionality. In fact, that’s what this call is about: looking at whole microbial communities at the intersection of ecosystems, at multiple trophic levels, and where the science is interdisciplinary.

I am currently an Academic Editor at PLoS One. I’m acting as a guest editor on this open call, and I look forward to curating this exciting upcoming issue! Submit online by August 6th.

What is a microbiome? Asking for a friend.

If you find that the word ‘microbiome’ has crept into your lexicon but you don’t really know what it means or how to use it – fear not, you’re not alone. Microbiome is a new-ish term to describe something that has been studied for almost a century: the collection of microorganisms in a dynamic ecosystem, including who they are and what they are doing.

Picture a crowd of humans. Maybe this one:

Image result for crowd oregon
Image Source: Wikimedia Commons, 2017-09-09 Oregon Ducks vs. Nebraska Cornhuskers

The picture is just one instant in an event involving hundreds or thousands of organisms that were all doing a lot of different things, sometimes for just a few seconds. How would you describe it?

Maybe using the number of members present in this community? Or a list of names of attendees? The 16S rRNA gene for prokaryotes, or the 18S rRNA or ITS genes for eukaryotes, for examples, would tell us that. Those genes are found in all types of those organisms, and is a pretty effective means of basic identification. But, it’s only as good as how often that gene is found in the organisms you are looking for. There is no one gene that’s found exactly the same in all organisms, so you might need to target multiple different identification genes to look at all the different types of microorganisms, such as bacteria, fungi, protozoa, or archaea. Viruses don’t share a common gene across types, to look at viruses you’d need something else.

From our identification genes we could identify all the organisms wearing yellow; ex. phylogenetic Family = Ducks. That wouldn’t tell us if they were always found in this ecosystem (native Eugene population) or just passing through (transient population), but we could figure that out if we looked at every home game of the season and found certain community members there time and again.

But knowing they are Ducks doesn’t tell us anything else about that community member. What will they do if it starts raining? Are they able to go mountain biking? Perhaps we could identify their potential for activity by looking at the objects they are carrying? That would be akin to metagenomics, identifying all the DNA present from all the organisms, which tells us what genes are present, but not if they are currently or ever used. It can be challenging to interpret: think of sequencing data from one organism’s genome as one 1,000,000-piece puzzle and all the genomes in a community as 1,000 1,000,000-piece puzzles all dumped in a pile. In the crowd, metagenomics would tell us who had a credit card that was specifically used to buy umbrellas, but not whether they’d actually use the umbrella if it rains (ex. Eugeneans would not).

We could describe what everyone is doing at this moment. That would be transcriptomics, identifying all the RNA to determine which genes were actively being transcribed into proteins for use in some cellular function. If we see someone in the crowd using that credit card for an umbrella (DNA), the receipt would be the RNA. RNA is a working copy you make of the DNA to take to another part of the cell and use as a blueprint to make a protein. You don’t want your entire genome moving around, or need it to make one protein, so you make a small piece of RNA that will only hang around for a short period before degrading (i.e. you crumpling that RNA receipt and throwing it away because who keeps receipts anymore).

Using transcriptomics, we’d see you were activating your money to get that umbrella, but we wouldn’t see the umbrella itself. For that, we’d need metabolomics, which uses chemistry and physics instead of genomics, in order to identify chemicals (most often proteins). Think of metabolomics as describing this crowd by all the trash and crumbs and miscellaneous items they left behind. It’s one way to know what biological processes occurred (popcorn consumption and digestion).

Image result for metabolomics
Image Source: Wikimedia Commons, Metabolomics

From a technical standpoint, researching a microbiome might mean looking at all the DNA from all the organisms present to know who they are and of what they are capable. It might also mean looking at all the RNA present, which would tell you what genes were being used by “everyone” for whatever they were doing at a particular moment. Or you might also add metabolomics to identify all the chemical metabolites, which would be all the end products of what those cells were doing, and which are more stable than RNA so they could give you data about a longer frame of time. Collectively, -omics are technology that looks at all of a certain biological substance to help you understand a dynamic community. However, it’s important to remember that each technology gives a particular view of the community and comes with its own limitations.

“Microbes and social equity”: I’m teaching a new UO Honors College summer course!

I’ll be teaching a new course for the UO Clark Honor’s College this summer!

Course Description: Microbes and social equity

This colloquium course introduces students to current knowledge on selected host-associated or human-associated microbiomes, and uses that base knowledge to discuss their relevance to human health in the context of social equity.  Example topics include the effect of diet on the microbial community in the gut and the importance of nutrient composition of free school lunches; maternal stress and the effect on offspring physiology, immune development, and host-microbial interactions; microbial communities in air, air quality, and income-based housing; building quality, indoor microbiology, and enforced occupancy (ex. prisons or public schools); and more. Guest lectures from relevant experts will be included as possible.

Some background in microbial ecology, genetics, anatomy, immunology, or sociology would be helpful, but is not required.  While difficult concepts will be discussed, the course is intended to teach students about the basic principles and how to apply them to contemporary social issues: what is a microbiome? How does host anatomy and health drive microbial ecology?  How does environmental microbiology and building microbiology contribute to or impinge on health? When we read about host-associated microbiomes in the news, especially regarding health, how can we assess if the study is rigorous and how should we interpret the scope of the findings?  The skill-set objectives include learning to review scientific journal articles, distilling their findings while understanding their limitations, and developing science communication skills via written assignments and in-class discussions.

Microbes in the built environment; interview with Jefferson Exchange

In case you missed it live, you can stream my interview with Geoffrey Riley at the Jefferson Exchange.

We talk about how to go from researching microbes in the rumen stomach of moose to researching the effect of building surface materials on microbes living in your dust, sharing microbes and knowledge through science communication, and the importance of diversity and inclusion in science!

Upcoming interview on Jefferson Exchange!

I’ll be speaking with the Jefferson Exchange crew on their live radio show about my work on microbiology in the built environment! I’ll be on March 11th, at about 8:30 am PST.

If you are local to the west coast, you can find a station to tune into. Otherwise, you can stream the segment live on jeffexchange.org.

Have a question? Call into the show at 800-838-3760 or email JX@jeffnet.org. Jefferson Exchange is also on Facebook and Twitter @JeffExchange.

Reblog: Stop Motion Science

Over the fall 2018 term, BioBE and ESBL undergrads made a project video explaining a recent publication on the effect of different daylight treatments on bacteria in dust. The post and video can be found here!

Interview on Indoor Microbiology

I sat down with UO College of Design’s Alex Notman to chat about my work on microbes in buildings and the intersection of biology and buildings: “The Great Indoors: Interior Ecology Under the Looking Glass.”