Five new publications in June! (updated)

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.

I’ve already done the blog post and project page for the ‘particle size’ paper, so I’ll move on.


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. AnimalAccepted.

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. Type of agricultural management system alters plant-soil feedback on Triticum aestivum and Pisum sativum. Basic and Applied Ecology. Accepted.


And as a reminder, I’m a guest editor for the PLoS ” Microbiome Across Biological Systems” special issue call, which is accepting submissions into August!

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.