A collaborative paper on zinc and rumen bacteria in sheep got published!

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.

Abstract

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 PrevotellaSolobacteriumRuminococcusButyrivibrioOlsenellaAtopobium, 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.

Featured Image Source: Wikimedia Commons

The Fine Art of Finding Scientific Information

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.

Yet, assessing the validity of information and verifying sources is an under-appreciated and under-taught skill. There are some great resources available for determining the reliability (if the same results are achieved each time), and validity (is it a real effect), of a dataset, as well as of the authors. Even with fact-evaluation resources available through The National Center for Complementary and Integrated Health (NCCIS), The University of EdinburghThe Georgetown University Library, or Michigan State University, like any skill, finding information takes practice.

Where do I go for Science Information?

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.

image description
Kriegeskorte, 2012

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!

Figure 7; Guadamillas Gómez, 2017.

 

A collaborative project got published on the biogeography of the calf digestive tract!

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.

Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract. Carl J. Yeoman, Suzanne L. Ishaq, Elena Bichi, Sarah K. Olivo, James Lowe, Brian M. Aldridge. 2018. Scientific Reports.

Abstract

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.

2017 Year in Review

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.

Looking Back

In the first half of 2017, I was working as a post-doctoral researcher in the Menalled lab at Montana State University, researching the interaction of climate change, farm management (cropping) system, and disease on soil bacteria in wheat fields, as well as the legacy effects on subsequent crops.  I am still working to analyze, interpret, and publish those results, and hope to submit several manuscripts from that project in early 2018.  In June, I began a position as a research assistant professor in the Biology and the Built Environment Center at the University of Oregon.

This slideshow requires JavaScript.

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 slideshow requires JavaScript.

2017 has been another extremely productive year for me.  I presented some work at two conferences, the Congress on Gastrointestinal Function and the Ecological Society of America meeting (additional ESA posts here and here).  While at ESA, I was able to attend the 500 Women Scientists luncheon to discuss inequality in academia as well as recommendations we could make to improve ESA and other conferences ,such as offering affordable on-site child care, and action items we could take ourselves, such as attending training workshops to combat implicit bias or making sure job searches recruit a diverse candidate pool.

500womensci
500 Women Scientist group at ESA 2017

This year, I added four new research publications 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.

This slideshow requires JavaScript.

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!

visitor_map_webpage
Map of home countries for 2017 website visitors.

My most popular post is currently “Work-life balance: what do professors do?”, with over 610 views! My least popular is “Presentation on juniper diets and rumen bacteria from JAM 2016 available!” with just 2 views, granted, that one appeals to a much narrower audience.  This year, in addition to updates on publications, projects, and positions, I wrote about writing; including theses and grants. I wrote about getting involved in science, be it through education, participation, or legislation.  I described outreach in academia, and the process of interviewing.  I gave some perspective on the effect of climate change and anthropological influence on agriculture and ecology, as well as on the debate surrounding metrics of success in graduate study.

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!!

This slideshow requires JavaScript.

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!

A study to which I contributed got published!

 

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.

 

Colonic aberrant crypt formation accompanies an increase of opportunistic pathogenic bacteria in C57BL/6 mice fed a high-fat diet.

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.

A collaborative paper on how rumen acidosis affects fungi and protozoa got published!

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.

Authors: Suzanne L. Ishaq, Ousama AlZahal, Nicola Walker, Brian McBride

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.

A collaborative project on juniper diets in lambs was published!

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

Part 2: Ewe lamb rumen microbial communities, S. L. Ishaq, C. J. Yeoman, and 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 PyramidobacterPrevotella were decreased by juniper and urea. RuminococcusButyrivibrio, 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.

My review on Plant-Microbial Interactions in Agriculture got published!

A few months ago, I was invited to submit an article to the special issue “Plant Probiotic Bacteria: solutions to feed the World” in AIMS Microbiology on the interactions between agricultural plants and microorganisms.  As my relevant projects are still being processed, I chose to write a review of the current literature regarding these interactions, and how they may be altered by different farming practices.  The review is available as open-access here!

“Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity”

A thorough understanding of the services provided by microorganisms to the agricultural ecosystem is integral to understanding how management systems can improve or deteriorate soil health and production over the long term. Yet it is hampered by the difficulty in measuring the intersection of plant, microbe, and environment, in no small part because of the situational specificity to some plant-microbial interactions, related to soil moisture, nutrient content, climate, and local diversity. Despite this, perspective on soil microbiota in agricultural settings can inform management practices to improve the sustainability of agricultural production.

Keywords bacteria; climate change; farming system; fungi; nutrient exchange; pathogens; phytohormones

Citation: Suzanne L. Ishaq. Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity. AIMS Microbiology, 2017, 3(2): 335-353. doi: 10.3934/microbiol.2017.2.335

A collaborative project on sheep feed efficiency and gut bacteria was published!

I’m pleased to announce that a paper that I contributed to was recently accepted for publication in the Journal of Animal Science!

“Feed efficiency phenotypes in lambs involve changes in ruminal, colonic, and small intestine-located microbiota”, Katheryn Perea; Katharine Perz; Sarah Olivo; Andrew Williams; Medora Lachman; Suzanne Ishaq; Jennifer Thomson; Carl Yeoman (article here).

Katheryn is an undergraduate at New Mexico Institute of Mining and Technology who received an INBRE grant to support her as a visiting researcher at Montana State University in Bozeman, MT over summer 2016.  Here, she worked with Drs. Carl Yeoman and Jennifer Thomson to perform the diversity analysis on the bacteria in the gastrointestinal tract of sheep from a previous study.  These sheep had been designated as efficient or inefficient, based on how much feed was needed for them to grow.  Efficient sheep were able to grow more with less feed, and it was thought this might be due to hosting different symbiotic bacteria which were better at fermenting fibrous plant material into usable byproducts for the sheep.

Samples from the sheep were collected as part of a larger study on feed efficiency performed by MSU graduate students Kate Perz and Medora Lachman, as well as technicians Sarah Olivo and Andrew Williams, and Katheryn performed the data and statistical analysis using some of my guidelines.  This is Katheryn’s first published article, and one I just presented a poster on at the Congress on Gastrointestinal Function in Chicago, IL!

Screen Shot 2017-04-04 at 4.40.45 PM

2017 Congress on Gastrointestinal Function

I just got back from my very first Congress on Gastrointestinal Function, poster tube.jpga small meeting for  researchers with a specific focus on the gastrointestinal tract, which is held every two years in Chicago, Illinois.  The special session this year was on “Early Acquisition and Development of the Gut Microbiota: A Comparative Analysis”.  The rest of the sessions opened up the broader topics of gut ecosystem surveillance and modulation, as well as new techniques and products with which to study the effect of microorganisms on hosts and vice versa.  The research had a strong livestock animal focus, as well as a human health focus, but we also heard about a few studies using wild animals.

As I’ve previously discussed, conferences are a great way to interact with other scientists.  Not only can you learn from similar work, but you can often gain insights into new ways to solve research problems inherent to your system by looking at what people in different fields are trying, something that you might otherwise miss just by combing relevant literature online.  A meeting or workshop is also a great place to meet other similarly focused scientists to set up collaborators that span academia, government, non-profit, and industry sectors.

C9K9XmpXsAA1Xlq.jpg large.jpg
It was great to catch up with Dr. Ben Wenner, now at Purdue Agribusiness, and meet Yairy Roman-Garcia, grad student at the Ohio State University.

This year, I was excited for one of my abstracts to be accepted as a poster presentation, and honored to have the other upgraded from poster to talk!  Stay tuned for details about both of those projects in the coming weeks, and be sure to check this meeting out in April, 2019.