Last June, I started a position as a Research Assistant Professor of Microbial Ecology at the Biology and the Built Environment Center at the University of Oregon. The BioBE Center is a collaborative, interdisciplinary research team investigating the built environment – the ecosystem that humans have created for themselves in buildings, vehicles, roadways, cities, etc. With my background in host-associated microbiology, I am concerned with how the built environment interacts with biology.
In addition to knowing how our presence, our behaviors (ex. cleaning), and how we run our buildings (ex. ventilation) creates the indoor microbiome, I want to know how the indoor microbiome affects us back. Not only can “sick buildings” negatively affect air quality, but they can harbor more microorganisms, especially fungi, or pathogenic species which are detrimental to our health.
My first indoor microbiome data is one that I have inherited from an ongoing project on weatherization in homes, and hope to present some of that work at conferences this summer. Since June, a large amount of my time has gone into project development and grant writing, most of which is still pending, so stay tuned for details. It has involved read lots of articles, going to seminars, networking, and brainstorming with some brilliant researchers.
As research faculty, I am not required to teach, although I have the option to propose and teach courses by adjusting my percent effort (I would use the teaching salary to “buy back” some research salary). As I am not currently tenure-track, I am also limited in my ability to hire and formally mentor students. However, I have been teaching bioinformatics to a student who recently graduated with his bachelor’s and is pursuing a masters in bioinformatics later this year.
I’ve also been keeping up with my science outreach. I gave a presentation on my host-associated microbiome work, I marched, I volunteered for a few hours at Meet A Scientist day at the Eugene Science Center, and I’m hosting a Science Pub on “A crash course in the microbiome of the digestive tract” at Whirled Pies in Eugene this Thursday, February 8th!
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.
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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, in a small, stress-free ceremony with some local friends in Eugene, Oregon!!
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Looking Ahead
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.
Abstract
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.
Service can be a vaguely defined expectation in academia, but it’s an expectation to give back to our community; this can be accomplished in different ways and is valued differently by institutions and departments. Outreach is an easily neglected part of science, because so often it is considered non-essential to your research. It can be difficult to measure the effectiveness or direct benefit of outreach as a deliverable, and when you are trying to hoard merit badges to make tenure and your time is dominated by other responsibilities, you often need to prioritize research, teaching, advising, or grant writing over extension and service activities. Nevertheless, public outreach is a vital part to fulfilling our roles as researchers. Academic work is supported by public funding in one way or another, and much of our research is determined by the needs of stakeholders, who in this sense are anyone who has a direct interest in the problem you are trying to solve.
Depending on your research field, you may work very closely with stakeholders (especially with applied research), or not at all (with theoretical or basic research). If you are anywhere in agriculture, having a relationship with your community is vital. More importantly, working closely with the public can bring your results directly to the people out in the real world who will benefit from it.
A common way to fulfill your outreach requirement is to give public presentations. These can be general presentations that educate on a broad subject, or can be specifically to present your work. Many departments have extension specialists, who might do some research or teaching but whose primary function is to connect researchers at the institution with members of the public. In addition to presentations, extension agents generate newsletters or other short publications which summarize one or more studies on a specific subject. They are also a great resource for networking if you are looking for resources or collaborations, for example if you are specifically looking for farms in Montana that grow wheat organically and are infested with field bindweed.
For my new job, I’m shifting gears from agricultural extension to building science and health extension. In fact, the ESBL and BioBE teams at the University of Oregon have recently created a Health + Energy Research Consortium to bring university researchers and industry professionals together to foster collaborations and better disseminate information. The goals of the group at large are to improve building sustainability for energy and materials, building design to serve human use better, and building microbiology and its impact on human health. I have a few public presentations coming up on my work, including one on campus at UO on Halloween, and one in February for the Oregon Museum of Science and Industry Science Pub series in February. Be sure to check my events section in the side bar for details.
Even when outreach or extension is not specified in your job title, most academics have some level of engagement with the public. Many use social media outlets to openly share their current work, what their day-to-day is like, and how often silly things go wrong in science. Not only does this make us more approachable, but it’s humanizing. As hard as scientists work to reach out to the public, we need you to reach back. So go ahead, email us (please don’t call because the stereotype is true: we really do hate talking on the phone), tweet, post, ping, comment, and engage with us!!
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.
From iDigBioA couple of weeks ago, I attended my first Ecological Society of America meeting in Portland, which assembles a diverse community of researchers looking at system-wide processes. It was an excellent learning experience for me, as scientific fields each have a particular set of tools to look at different problems and our collective perspectives can solve research problems in more creative ways.
In particular, it was intriguing to attend talks on the ecology of the human microbiome. Due to the complexity of host-associated microbial communities, and the limitations of technology, the majority of studies to date have been somewhat observational. We have mapped what is present in different animals, in different areas of the body, under different diet conditions, in different parts of the world, and in comparison between healthy and disease states. But given the complexity of the day-to-day life of people, and ethics or technical difficulty of doing experimental studies in humans, many of the broader ecological questions have yet to be answered.
For example, how quickly do microbial communities assemble in humans? When you disturb them or change something (like adding a medication or removing a food from your diet) how quickly does this manifest in the community structure and do those changes last? How does dysbiosis or dysfunction in the body specifically contribute to changes in the microbial community, or do seemingly harmless events trigger a change in the microbial community which then causes disease in humans? Some of the presentations I attended have begun teasing out these problems with a combination of observational in situ biological studies, in vitro laboratory studies, and in silico mathematical modeling. The abstracts from all the meeting presentations can be found on the meeting website under Program. I have also summarized several of the talks I went to on Give Me The Short Version.
One of my favorite parts was attending an open lunch with 500 Women Scientists, a recently-formed organization which promotes diversity and equality in science, and supports local activists to help change policy and preconceived notions about diversity in STEM. The lunch meeting introduced the organization to the conference participants in attendance, asked us to voice our concerns or difficulties we had faced, encouraged us to reach out to others in our work network to seek advice and provide mentoring, and walked us through exercises designed to educate on how to build a more inclusive society.
500 Women Scientists at ESA, August 2017
My poster presentation was on Wednesday, halfway through the meeting week, which gave me plenty of time to prepare. You never know who might show up at your poster and what questions they’ll have. In the past, I’ve always had a steady stream of people to chat with at my poster which has led to a number of scientific friendships and networking, and this year was no different. The rather large (but detailed) poster file can be found here: Ishaq et al ESA 2017 poster . Keep in mind that this is preliminary work, and many statistical tests have not yet been applied or verified. I’ve been working to complete the analysis on the large study, which also encompasses a great deal of environmental data. We hope to have manuscript drafted by this fall on this part of the project, and several more over the next year from the research team as this is part of a larger study; stay tuned!
The video presentation of my work on the effects of juniper diets on rumen bacteria is finally available for public use! I apologize for any side comments in the audio, the projector in the room kept flicking off! Stay tuned, our publication was just accepted and will be in press soon…
Abstract 1768. Ground redberry juniper and urea in DDGS-based supplements do not adversely affect ewe lamb rumen microbial communities.
![IMG_20170808_083850[4637].jpg](https://sueishaqlab.org/wp-content/uploads/2017/08/img_20170808_0838504637.jpg?w=162&h=218)
The Ishaq Lab 