Update: on the very last day of June, I received word that two more papers had been accepted for publication, bringing the tally to five in the month of June alone!
I’ve previously discussed how many researchers end up with partially-completed projects in their wake, and I’ve made a concerted effort in the last 6-ish months to get mine across the finish line. I have five new publications which were accepted in June alone, with one reviews and one manuscript currently in review, and another three manuscripts in preparation. On top of that, I have a number of publications that are looming in the second half of 2019.
Ishaq, S.L., Lachman, M.M., Wenner, B.A., Baeza, A., Butler, M., Gates, E., Olivo, S., Buono Geddes, J., Hatfield, P., Yeoman, C.J. 2019. Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed. PLoS ONE 14(6): e0215797. Article.
Stenson, J., Ishaq, S.L., Laguerre, A., Loia, A., MacCrone, G., Mugabo, I., Northcutt, D., Riggio, M., Barbosa, A., Gall, E.T., Van Den Wymelenberg, K. 2019. Monitored Indoor Environmental Quality of a Mass Timber Office Building: A Case Study. Buildings 9:142. Article.
This was a case study on a newly (at the time of sample collection) constructed building in Portland, OR which was made using mass timber framing. Since building materials alter the sound, vibration, smell, and air quality of a building, the primary goals of the study were to evaluate occupant experience and indoor air quality. Dust samples were also collected to investigate the indoor bacterial community, as the effect of building materials on the whole microbial community indoors is unknown. For this project, I assisted with microbial sample processing and analysis, for which I taught Georgia MacCrone, an undergraduate Biology/Ecology junior at UO, bioinformatics and DNA sequence analysis.
Garcia-Mazcorro, J.F., Ishaq, S.L., Rodriguez-Herrera, M.V., Garcia-Hernandez, C.A., Kawas, J.R., Nagaraja, T.G. 2019. Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits. Animal. Accepted.
This review was a pleasure to work on. Last year, Dr. Jose Garcia-Mazcorro emailed me, as I am the corresponding author on a paper investigating protozoa and fungi in cows with acidosis. We corresponded about fungi in the rumen, probiotics, and diet, and Jose graciously invited me to contribute to the review. Last August, after having worked with Jose for months, we finally met in person in Leipzig, Germany at ISME. Since then, we’ve been discussion possible collaborations on diet, probiotics, and the gut microbiome.
Horve, P.F., Lloyd, S., Mhuireach, G.A., Dietz, L., Fretz, M., MacCrone, G., Van Den Wymelenberg, K., Ishaq, S.L. Building Upon Current Knowledge of Indoor Microbiology to Construct the Next Era of Research into Microorganisms, Health, and the Built Environment. Journal of Exposure Science and Environmental Epidemiology. Accepted.
Seipel, T., Ishaq, S.L., Menalled, F.D. Agroecosystem resilience is modified by management system via plant–soil feedbacks. Basic and Applied Ecology. Accepted.
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.
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.
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
Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, United States of America
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.
No one is sorry to say goodbye to 2018, yet it still seems like the 2018 Year in Review has arrived too soon. As usual, I’ve been keeping busy; you can find my reviews for 2017 and 2016 in the archives. For the first year in the three years since I started this blog, I’m not starting a new job! I’ve been at BioBE for a year and a half, and it’s a relief to be in an academic position long enough to finish the projects you started (I’m only just starting to submit some manuscripts for work I did back in Montana).
Two papers of mine were published this year, including one on the bacteria along the GI tract of calves, one on the effect of dietary zinc on bacteria in sheep. A comprehensive culturing initiative of rumen microorganisms, called the Hungate 1000 Project, an international initiative to which I contributed data, was also published. That puts me up to 17 scientific articles, of which 9 are first-authored, as well as 5 scientific reviews. I have three manuscripts in review right now, and another five being prepared – 2019 will be a busy year.
I joined two journal editorial boards this year, PloS One and Applied and Environmental Microbiology. Both positions are as an Academic (or handling) Editor; I will oversee manuscript review by soliciting reviewers, assessing their recommendations, and interfacing with authors. In recent years, the gender discrepancy in science has received more attention, and some journals are making efforts towards increasing the number of female editors, reviewers, and contributors to reduce implicit bias in science publishing. I am pleased to be in a position where I can help change that!
I’ve been spending a lot of time writing grants and developing potential projects on microbiology and health in the built environment, many of which should be moving forward in 2019. I’ve also been spending time training the 9 undergraduate students I hired over the summer and fall to work at BioBE. In addition to microbiology and molecular biology laboratory skills, I have been training them on DNA sequence analysis and coding, scientific literature review, and science writing and communications.
This fall term, I taught Introduction to Mammalian Microbiomes for the University of Oregon Clark Honor’s College. I proposed this new course last year, and developed the curricula largely from scratch. I’d previously taught some of the subject material at Montana State University in Carl Yeoman and Seth Walk’s Host-Associated Microbiomes course; however in IMM I was teaching to non-science majors. The course went well, and I’ll be diving into it in detail with a full blog post in a few weeks. I proposed the course again for next year, as well as another new course; Microbiology of the Built Environment.
Presentations and travel
Early in the year, I gave two public talks on the gut microbiome for Oregon Museum of Science and Industry; one in Eugene and one in Portland. Both were a lot of fun, and I really enjoyed getting to share my work with the public.
At the end of the spring term, I also presented at the University of Oregon IDEAL Framework Showcase. Over the 2017/2018 academic year I served on the Implicit Bias working group, tasked with assessing the need for campus-wide training and making recommendations to the college.
In June, I attended the HOMEChem Open House at the UT Austin Test House, University of Texas at Austin’s J.J. Pickle Research Campus. I got to tour the amazing indoor chemistry labs there, and met with BioBE collaborators to discuss pilot projects exploring the link between indoor chemistry and indoor microbiology.
MoBE 2018 was an intensive meeting that brought together the top names and the rising stars of MoBE research. Gordon conferences are closed-session to encourage the presentation of unpublished data and ideas, and to facilitate discussion and theoretical contemplation. While in Biddeford, I had the opportunity to eat seafood, visit friends, and check out Mug Buddy Cookies!!
Immediately after MoBE, I flew to Philadelphia for the Indoor Air 2018 conference. I again presented some of the work I’ve been part of, exploring the effect of weatherization and lifestyle on bacteria indoors. I also found some incredible shoes.
I spent a great deal of 2018 participating in activities for 500 Women Scientists. I am a Pod Coordinator for the Eugene Pod, and as such I meet regularly with other Coordinators to plan events. The majority of our 2018 events were Science Salons: science talks by local female researchers around a particular theme, with a hands-on activity to match, and a Q&A session about life as a (female) scientist. We heard about some awesome research, raised $1300 for local science non-profits, and learned how to be better community members by sharing personal stories about the triumphs and troughs of being a woman in science.
We also hosted a film screening of My Love Affair with the Brain, generously lent to 500WS by Luna Productions, followed by a panel discussion of women neuroscientists here in Eugene.
Along with two other Eugene Pod Coordinators, I wrote a small proposal which was funded, to coordinate workshops at UO: “Amplifying diverse voices: training and support for managing identity-based harassment in science communication”. Those workshops will take place in 2019.
I again participated in citizen science through Adventure Scientists, as part of their wood crews for the Timber Tracking 2018 campaign. Lee and I drove around a 20,000 sq mi section of southwestern Oregon to collect samples from big leaf maple trees at 10 locations which adhered to certain sampling parameters. Despite the large number of big leafs in Oregon, the sampling criteria made it difficult to find the perfect tree in an entire forest, and we logged a lot of mileage. Lee and I also volunteered for their Gallatin County Microplastics Initiative while we lived in Bozeman, MT.
As of today, my site received 4,447 view from 97 countries and 3,101 visitors in 2018. So far, I’ve published 109 posts, and received 6,147 visitors who viewed the site 9,481 times.
It’s easy to forget how many life events go by in a year, unless your social media is making you a video about them. But they were all important parts of my life and had some impact, however negligible, on my work. The one I’m most proud of was officiating the wedding of two dear friends, in Vermont.
I tried to spend more time on creative projects, including getting back into art after more-or-less tabling it for several years.
As usual, 2019 promises an abundance of opportunities. Already, I am planning out my conference schedule, seeking speakers for upcoming 500WS Science Salons, and writing, writing, writing. But through all of it, I will be trying to cultivate a more open, inclusive, and supportive work environment. In 2018, after more than a decade of trying to convince doctors that I should have agency over my own organs, I was finally approved for the hysterectomy that I’d wanted for so long, and the medical diagnostics to show that I’d actually needed it for probably just as long.
The surgery has dramatically improved my quality of life, and the scars are a constant reminder that you never know who is dealing with something in their life that isn’t visible to you, who is trying to pretend they aren’t in pain because they can’t afford to take time off to resolve their situation. At first, I kept the details to myself and I kept it off my professional social media. I did share, in exquisite detail, on my personal social media, and was flooded with similar stories from other women. It encouraged me to share a little more, after all, if I’d had surgery on a knee or a kidney I would talk about it openly, why not a uterus?
In a typical semester, one to two-thirds of the students that I teach or mentor will disclose that they experienced a serious life event, most often while at school. They may casually joke about how they couldn’t get time off or almost failed out that semester, or recall how receiving help saved them. I take my role as an educator, mentor, or supervisor seriously – the competition in academia forces students to work long or odd hours, to prioritize other things over study, to accept positions of low or no pay “for the experience”, or to accept professional relationships where they are not respected or may be taken advantage of. I have always tried to be a supportive mentor to students, but the higher up the ladder I climb the more important it is for me to set a good example for these students who will one day mentor people of their own.
In addition to listening to them, and having frank conversations, my response this year has been to get rid of student employee deadlines whenever possible. We are asked to do so much with our time in school, or in academia, but there are so many hours in the day. Sure, I routinely wish things were accomplished more promptly, but I have never once regretted not causing someone to have a breakdown. And constantly telling my students to take care of themselves first and work second reminds me to do the same, it benefits my work , and it’s made a certain furball very happy. Happy New Year!
Zinc is an important mineral in your diet; it’s required by many of your enzymes and having too much or too little can cause health problems. We know quite a bit about how important zinc is to sheep, in particular for their growth, immune system, and fertility. We also know that organically- versus inorganically-sourced zinc differs in its bio-availability, or how easy it is for cells to access and use it. Surprisingly, we know nothing about how different zinc formulations might affect gut microbiota, despite the knowledge that microorganisms may also need zinc.
This collaborative study was led by Dr. Whit Stewart and his then-graduate student, Chad Page, while they were at Montana State University (they are now both at the University of Wyoming). Chad’s work focused on how different sources of zinc affected sheep growth and performance (previously presented, publication forthcoming), and I put together this companion paper examining the effects on rumen bacteria.
The pre-print is available now for Journal of Animal Science members, and the finished proof should be available soon. JAS is the main publication for the American Society of Animal Science, and one of the flagship journals in the field.
Zinc amino acid supplementation alters yearling ram rumen bacterial communities but zinc sulfate supplementation does not.
Ishaq, S.L., Page, C.M., Yeoman, C.J., Murphy, T.W., Van Emon, M.L., Stewart, W.C. 2018. Journal of Animal Science. Accepted.Article.
Despite the body of research into Zn for human and animal health and productivity, very little work has been done to discern whether this benefit is exerted solely on the host organism, or whether there is some effect of dietary Zn upon the gastrointestinal microbiota, particularly in ruminants. We hypothesized that 1) supplementation with Zn would alter the rumen bacterial community in yearling rams, but that 2) supplementation with either inorganically-sourced ZnSO4, or a chelated Zn amino acid complex, which was more bioavailable, would affect the rumen bacterial community differently. Sixteen purebred Targhee yearling rams were utilized in an 84 d completely-randomized design, and allocated to one of three pelleted dietary treatments: control diet without fortified Zn (~1 x NRC), a diet fortified with a Zn amino acid complex (~2 x NRC), and a diet fortified with ZnSO4 (~2 x NRC). Rumen bacterial community was assessed using Illumina MiSeq of the V4-V6 region of the 16S rRNA gene. One hundred and eleven OTUs were found with > 1% abundance across all samples. The genera Prevotella, Solobacterium, Ruminococcus, Butyrivibrio, Olsenella, Atopobium, and the candidate genus Saccharimonas were abundant in all samples. Total rumen bacterial evenness and diversity in rams were reduced by supplementation with a Zn-amino-acid complex, but not in rams supplemented with an equal concentration of ZnSO4, likely due to differences in bioavailability between organic and inorganically-sourced supplement formulations. A number of bacterial genera were altered by Zn supplementation, but only the phylum Tenericutes was significantly reduced by ZnSO4 supplementation, suggesting that either Zn supplementation formulation could be utilized without causing a high-level shift in the rumen bacterial community which could have negative consequences for digestion and animal health.
Not a day goes by that I don’t search for information, and whether that information is a movie showtime or the mechanism by which a bacterial species is resistant to zinc toxicity, I need that information to be accurate. In the era of real fake-news and fake real-news, mockumentaries, and misinformation campaigns, the ability to find accurate and unbiased information is more important than ever.
Thanks to the massive shift towards digital archiving and open-access online journals, nearly all of my information hunting is done online (and an excellent reason why Net Neutrality is vital to researchers). Most of the time, this information is in the form of scientific journal articles or books online, and finding this information can be accomplished by using regular search engines. In particular, Google has really pushed to improve its ability to index scientific publications (critical to Google Scholar and Paperpile).
However, it takes skill to compose your search request to find accurate results. I nearly always add “journal article” or “scientific study” to the end of my query because I need the original sources of information, not popular media reports on it. This cuts out A LOT of inaccuracy in search results. If I’m looking for more general information, I might add “review” to find scientific papers which broadly summarize the results of dozens to hundreds of smaller studies on a particular topic. If I have no idea where to begin and need basic information on what I’m trying to look for, I will try my luck with a general search online or even Wikipedia (scientists have made a concerted effort to improve many science-related entries). This can help me figure out the right terminology to phrase my question.
How do I know if it’s accurate?
One of the things I’m searching for when looking for accurate sources is peer-review. Typically, scientific manuscripts submitted to reputable journals are reviewed by 1 – 3 other authorities in that field, more if the paper goes through several journal submissions. The reviewers may know who the authors are, but the authors don’t know their reviewers until at least after publication, and sometimes never. This single-blind (or double-blind if the reviewers can’t see the authors’ names) process allows for manuscripts to be reviewed, edited, and challenged before they are published. Note that perspective or opinion pieces in journals are typically not peer-reviewed, as they don’t contain new data, just interpretation. The demand for rapid publishing rates and the rise of predatory journals has led some outlets to publish without peer-review, and I avoid those sources. The reason is that scientists might not see the flaws or errors in their own study, and having a third party question your results improves your ability to communicate those results accurately.
Another way to assess the validity of an article is the inclusion of correct control groups. The control group acts a baseline against which you can measure your treatment effects, those which go through the same experimental parameters except they don’t receive an active treatment. Instead, the group receives a placebo, because you want to make sure that the acts of experimentation and observation themselves do not lead to a reaction – The Placebo Effect. The Placebo Effect is a very real thing and can really throw off your results when working with humans.
Similarly, one study does not a scientific law make. Scientific results can be situational, or particular to the parameters in that study, and might not be generalizable (applicable to a broader audience or circumstances). It often takes dozens if not a hundred studies to get at the underlying mechanisms of an experimental effect, or to show that the effect is reliably recreated across experiments.
Data or it didn’t happen. I can’t stress this one enough. Making a claim, statement, or conclusion is hollow until you have supplied observations to prove it. This a really common problem in internet-based arguments, as people put forth references as fact when they are actually opinionated speeches or videos that don’t list their sources. These opinionated speeches have their place, I post a lot of them myself. They often say what I want to say in a much more eloquent manner. Unfortunately, they are not data and can’t prove your point.
The other reason you need data to match your statements is that in almost all scientific articles, the authors include speculation and theory of thought in the Discussion section. This is meant to provide context to the study, or ponder over the broader meaning, or identify things which need to be verified in future studies. But often these statements are repeated in other articles as if they were facts which were evaluated in the first article, and the ideas get perpetuated as proven facts instead of as theories to be tested. This often happens when the Discussion section of an article is hidden behind a pay wall and you end up taking that second paper’s word for it about what happened in the first paper. It’s only when the claim is traced all the way back to the original article that you find that someone mistook thought supposition for data exposition.
The “Echo Chamber Effect” is also prominent when it comes to translating scientific articles into news publications, a great example of which is discussed by 538. Researchers mapped the genome of about 30 transgender individuals – about half and half of male to female and female to male, to get an idea of whether gender identity could be described with a nuanced genetic fingerprint rather than a binary category. This is an extremely small sample group, and the paper was more about testing the idea and suggesting some genes which would be used for the fingerprint. In the mix-up, comments about the research were attributed to a journalist at 538 – comments that the journalist had not made, and this error was perpetuated when further news organizations used other news publications as the source instead of conducting their own interview or referencing the publication. In addition, the findings and impact of the study were wrongly reported – it was stated that 7 genes had been identified by researchers as your gender fingerprint, which is a gross exaggeration of what the original research article was really about. When possible, try to trace information back to its origin, and get comments straight from the source.
How do I know if it’s unbiased?
This can be tricky, as there are a number of ways someone can have a conflict of interest. One giveaway is tone, as scientific texts are supposed to remain neutral. You can also check the author affiliations (who they are and what institution they are at), the conflict of interest section, and the disclosure of funding source or acknowledgements sections, all of which are common inclusions on scientific papers. “Following the money” is a particularly good way of determining if there is biased involved, depending on the reputation of the publisher.
When in doubt, try asking a librarian
There are a lot of resources online and in-person to help you find accurate information, and public libraries and databases are free to use!
Most studies that examine the microbial diversity of the gastrointestinal tract only look at one or two sample sites, usually the mouth, the rumen in ruminant animals, or the feces. It can be difficult, expensive, invasive, or fatal to get samples from deep inside the intestinal tract; however many studies have pointed out that anatomical location and local environmental factors (like temperature, pH, host cells, nutrient availability, and exposure to UV light) can dramatically change a microbial community. Thus, the microbes that we find in feces aren’t always what we would find in the stomach or along the intestines. On top of that, certain microorganisms have been shown to closely associate with or attach to host cells, and the diversity of microbes next to host tissues can be different from what’s at the center of the intestines (the digesta).
This large, collaborative project took samples from nine different sites along the digestive tract of calves over the first 21 days of life to determine how body sites differed from each other, how sites changed over time as the calf matured, and how the lumen-associated bacteria would differ from the digesta-associated bacteria. Samples from the mothers were also taken to understand how maternal microbial influence would affect body sites over time.
This paper was just published in Scientific Reports, and was something I had previously presented on at the Joint Annual Meeting of the American Society for Animal Science, the American Dairy Science Association, and the Canadian Society for Animal Science in Salt Lake City, UT in 2016.
The impact of maternal microbial influences on the early choreography of the neonatal calf microbiome were investigated. Luminal content and mucosal scraping samples were collected from ten locations in the calf gastrointestinal tract (GIT) over the first 21 days of life, along with postpartum maternal colostrum, udder skin, and vaginal scrapings. Microbiota were found to vary by anatomical location, between the lumen and mucosa at each GIT location, and differentially enriched for maternal vaginal, skin, and colostral microbiota. Most calf sample sites exhibited a gradual increase in α-diversity over the 21 days beginning the first few days after birth. The relative abundance of Firmicutes was greater in the proximal GIT, while Bacteroidetes were greater in the distal GIT. Proteobacteria exhibited greater relative abundances in mucosal scrapings relative to luminal content. Forty-six percent of calf luminal microbes and 41% of mucosal microbes were observed in at-least one maternal source, with the majority being shared with microbes on the skin of the udder. The vaginal microbiota were found to harbor and uniquely share many common and well-described fibrolytic rumen bacteria, as well as methanogenic archaea, potentially indicating a role for the vagina in populating the developing rumen and reticulum with microbes important to the nutrition of the adult animal.
The end of 2017 marks the second year of my website, as well as another year of life-changing events, and reflecting on the past year’s milestones help put all those long hours into perspective. I reviewed my year last year, and found it particularly helpful in focusing my goals for the year ahead.
This involved another large move, not only from Montana to Oregon, which has led to some awesome new adventures, but also from agriculture and animal science to indoor microbiomes and building science. So far, it has been a wonderful learning experience for incorporating research techniques and perspectives from other fields into my work.
This year, I added fournewresearchpublications and one review publication to my C.V., and received word that a massive collaborative study that I contributed to was accepted for publication- more on that once it’s available. In April, I hosted a day of workshops on soil microbes for the Expanding Your Horizons for Girls program at MSU, and I gave a seminar at UO on host-associated microbiomes while dressed up as a dissected cat on Halloween. In November, I participated in a Design Champs webinar; a pilot series from BioBE which provides informational discussions to small groups of building designers on aspects of how architecture and biology interact.
I published 34 posts in 2017, including this one, which is significantly fewer than the 45 I published in 2016. However, I have doubled my visitor traffic and views over last year’s totals: over 2,000 visitors with over 3,200 page views in 2017! My highest-traffic day was April 27th, 2017. While I am most popular in the United States, I have had visitors from 92 countries this year!
I also added some “life” to my work-life balance; in November, I married my best friend and “chief contributor“, Lee Warren, in a small, stress-free ceremony with some local friends in Eugene, Oregon!!
I have high hopes for 2018, notably, I’d like to finish more of the projects that have been in development over the last two years during my post-docs. Nearly all academics carry forward old projects: some need additional time for experimentation or writing, some get shelved temporarily due to funding or time constraints, some datasets get forgotten and gather dust, and some which got cut short because of the need to move to a new job. This is a particular concern as grant funding and length of job postings become shorter, forcing researchers to cut multi-year projects short or finish them on their own time. After defending in early 2015, I had two one-year postings and started at UO in June 2017, making this my fourth job in three years. I’m looking forward to roosting for a bit, not only to clear out unfinished business, but also to settle into my new job at BioBE. This fall, I have been analyzing data on a weatherization project, writing a handful of grants, and developing pilot projects with collaborators. I have really enjoyed my first six months at BioBE, and Lee and I have taken a shine to Eugene. In the next few months, I hope to have more posts about my work there, exciting new developments in BioBE and ESBL, and more insights into the work life of an academic. Happy New Year!
I’m pleased to announce that one of my collaborators, Dr. Huawei Zeng of the USDA Agricultural Research Service, recently published another study of his, to which I contributed some analysis of bacterial communities from mice. Several years ago, during my Ph.D. at the University of Vermont, I provided wet-lab and DNA sequence analysis work for a previous project of Dr. Zeng, investigating the health effects of a low or high fat diet on mice, which can be found here.
Zeng, H., Ishaq, S.L., Liu, Z., Bukowski, M.R. 2017. Journal of Nutritional Biochemistry. In press, doi.org/10.1016/j.jnutbio.2017.11.001.
The increasing worldwide incidence of colon cancer has been linked to obesity and consumption of a high-fat western diet. To test the hypothesis that a high fat diet (HFD) promotes colonic aberrant crypt (AC) formation in a manner associated with gut bacterial dysbiosis, we examined the susceptibility to azoxymethane (AOM)-induced colonic AC and microbiome composition in C57/BL6 mice fed a modified AIN93G diet (AIN, 16% fat, energy) or a HFD (45% fat, energy) for 14 weeks. Mice receiving the HFD exhibited increased plasma leptin, body weight, body fat composition and inflammatory cell infiltration in the ileum compared with those in the AIN group. Consistent with the gut inflammatory phenotype, we observed an increase in colonic AC, plasma interleukin 6 (IL6), tumor necrosis factor α (TNF α), monocyte chemoattractant protein 1 (MCP1), and inducible nitric oxide synthase (iNOS) in the ileum of the HFD-AOM group compared with the AIN-AOM group. Although the HFD and AIN groups did not differ in bacterial species number, the HFD and AIN diets resulted in different bacterial community structures in the colon. The abundance of certain short chain fatty acid (SCFA) producing bacteria (e.g., Barnesiella) and fecal SCFA (e.g., acetic acid) content were lower in the HFD-AOM group compared with the AIN and AIN-AOM groups. Furthermore, we identified a high abundance of Anaeroplasma bacteria, an opportunistic pathogen in the HFD-AOM group. Collectively, we demonstrate that a HFD promotes AC formation concurrent with an increase of opportunistic pathogenic bacteria in the colon of C57BL/6 mice.
Ruminal acidosis is a condition in which the pH of the rumen is considerably lower than normal, and if severe enough can cause damage to the stomach and localized symptoms, or systemic illness in cows. Often, these symptoms result from the low pH reducing the ability of microorganisms to ferment fiber, or by killing them outright. Since the cow can’t break down most of its plant-based diet without these microorganisms, this disruption can cause all sorts of downstream health problems. Negative health effects can also occur when the pH is somewhat lowered, or is lowered briefly but repeatedly, even if the cow isn’t showing outward clinical symptoms. This is known as sub-acute ruminal acidosis (SARA), and can also cause serious side effects for cows and an economic loss for producers.
In livestock, acidosis usually occurs when ruminants are abruptly switched to a highly-fermentable diet- something with a lot of grain/starch that causes a dramatic increase in bacterial fermentation and a buildup of lactate in the rumen. To prevent this, animals are transitioned incrementally from one diet to the next over a period of days or weeks. Another strategy is to add something to the diet to help buffer rumen pH, such as a probiotic. One of the most common species used to help treat or prevent acidosis is a yeast; Saccharomyces cerevisiae.
This paper was part of a larger study on S. cerevisiae use in cattle to treat SARA, the effects of which on animal production as well as bacterial diversity and functionality have already been published by an old friend and colleague of mine, Dr. Ousama AlZahal, and several others. In total, very little work has been done on the effect of SARA or S. cerevisiae treatment on the fungal or protozoal diversity in the rumen, which is what I added to this study. I was very pleased to be invited to analyze and interpret some of the data, as well as to present the results at a conference in Chicago earlier this year. The article itself has just been published in Frontiers in Microbiology!
An investigation into rumen fungal and protozoal diversity in three rumen fractions, during high-fiber or grain-induced sub-acute ruminal acidosis conditions, with or without active dry yeast supplementation.
Sub-acute ruminal acidosis (SARA) is a gastrointestinal functional disorder in livestock characterized by low rumen pH, which reduces rumen function, microbial diversity, host performance, and host immune function. Dietary management is used to prevent SARA, often with yeast supplementation as a pH buffer. Almost nothing is known about the effect of SARA or yeast supplementation on ruminal protozoal and fungal diversity, despite their roles in fiber degradation. Dairy cows were switched from a high-fiber to high-grain diet abruptly to induce SARA, with and without active dry yeast (ADY, Saccharomyces cerevisiae) supplementation, and sampled from the rumen fluid, solids, and epimural fractions to determine microbial diversity using the protozoal 18S rRNA and the fungal ITS1 genes via Illumina MiSeq sequencing. Diet-induced SARA dramatically increased the number and abundance of rare fungal taxa, even in fluid fractions where total reads were very low, and reduced protozoal diversity. SARA selected for more lactic-acid utilizing taxa, and fewer fiber-degrading taxa. ADY treatment increased fungal richness (OTUs) but not diversity (Inverse Simpson, Shannon), but increased protozoal richness and diversity in some fractions. ADY treatment itself significantly (P < 0.05) affected the abundance of numerous fungal genera as seen in the high-fiber diet: Lewia, Neocallimastix, and Phoma were increased, while Alternaria, Candida Orpinomyces, and Piromyces spp. were decreased. Likewise, for protozoa, ADY itself increased Isotricha intestinalis but decreased Entodinium furca spp. Multivariate analyses showed diet type was most significant in driving diversity, followed by yeast treatment, for AMOVA, ANOSIM, and weighted UniFrac. Diet, ADY, and location were all significant factors for fungi (PERMANOVA, P = 0.0001, P = 0.0452, P = 0.0068, Monte Carlo correction, respectively, and location was a significant factor (P = 0.001, Monte Carlo correction) for protozoa. Diet-induced SARA shifts diversity of rumen fungi and protozoa and selects against fiber-degrading species. Supplementation with ADY mitigated this reduction in protozoa, presumptively by triggering microbial diversity shifts (as seen even in the high-fiber diet) that resulted in pH stabilization. ADY did not recover the initial community structure that was seen in pre-SARA conditions.
In 2015, while working in the Yeoman Lab, I was invited to perform the sequence analysis on some samples from a previously-run diet study. The study was part of ongoing research by Dr. Travis Whitney at Texas A & M on the use of juniper as a feed additive for sheep. The three main juniper species in Texas can pose a problem- while they are native, they have significantly increased the number of acres they occupy due to changes in climate, water availability, and human-related land use. And, juniper can out-compete other rangeland species, which can make forage less palatable, less nutritious, or unhealthy for livestock. Juniper contains essential oils and compounds which can affect some microorganisms living in their gut. We wanted to know how the bacterial community in the rumen might restructure while on different concentrations of juniper and urea.
Coupled with the animal health and physiology aspect led by Travis, we published two companion papers in the Journal of Animal Science. We had also previously presented these results at the Joint Annual Meeting of the American Society for Animal Science, the American Dairy Science Association, and the Canadian Society for Animal Science in Salt Lake City, UT in 2016. Travis’ presentation can be found here, and mine can be found here. The article can be found here.
Ground redberry juniper and urea in supplements fed to Rambouillet ewe lambs.
Part 1: Growth, blood serum and fecal characteristics, T.R. Whitney
This study evaluated effects of ground redberry juniper (Juniperus pinchotii) and urea in dried distillers grains with solubles-based supplements fed to Rambouillet ewe lambs (n = 48) on rumen physiological parameters and bacterial diversity. In a randomized study (40 d), individually-penned lambs were fed ad libitum ground sorghum-sudangrass hay and of 1 of 8 supplements (6 lambs/treatment; 533 g/d; as-fed basis) in a 4 × 2 factorial design with 4 concentrations of ground juniper (15%, 30%, 45%, or 60% of DM) and 2 levels of urea (1% or 3% of DM). Increasing juniper resulted in minor changes in microbial β-diversity (PERMANOVA, pseudo F = 1.33, P = 0.04); however, concentrations of urea did not show detectable broad-scale differences at phylum, family, or genus levels according to ANOSIM (P> 0.05), AMOVA (P > 0.10), and PERMANOVA (P > 0.05). Linear discriminant analysis indicated some genera were specific to certain dietary treatments (P < 0.05), though none of these genera were present in high abundance; high concentrations of juniper were associated with Moraxella and Streptococcus, low concentrations of urea were associated with Fretibacterium, and high concentrations of urea were associated with Oribacterium and Pyramidobacter. Prevotella were decreased by juniper and urea. Ruminococcus, Butyrivibrio, and Succiniclasticum increased with juniper and were positively correlated (Spearman’s, P < 0.05) with each other but not to rumen factors, suggesting a symbiotic interaction. Overall, there was not a juniper × urea interaction for total VFA, VFA by concentration or percent total, pH, or ammonia (P > 0.29). When considering only percent inclusion of juniper, ruminal pH and proportion of acetic acid linearly increased (P < 0.001) and percentage of butyric acid linearly decreased (P = 0.009). Lamb ADG and G:F were positively correlated with Prevotella(Spearman’s, P < 0.05) and negatively correlated with Synergistaceae, the BS5 group, and Lentisphaerae. Firmicutes were negatively correlated with serum urea nitrogen, ammonia, total VFA, total acetate, and total propionate. Overall, modest differences in bacterial diversity among treatments occurred in the abundance or evenness of several OTUs, but there was not a significant difference in OTU richness. As diversity was largely unchanged, the reduction in ADG and lower-end BW was likely due to reduced DMI rather than a reduction in microbial fermentative ability.