Tag: collaboration

Of mice and many samples

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The first mouse study of the Ishaq Lab (in conjunction with the Zhang and Li labs at Husson University) has concluded phase 1, which means that over a few short days, an incredible number of samples needed to be collected, preserved, and processed for further laboratory work (phase 2) which will take through the summer to complete.

Sample collection was made more challenging by the pandemic, because we needed to distance as much as possible, disinfect objects and surfaces, wear masks, and increase the amount of ventilation in a space. Luckily, this type of work lends itself to these types of precautions – not only did we already need to wear a significant amount of protective gear to work with mice or handle their feces, but biosafety work like this requires higher than usual ventilation and frequent sanitation of objects and spaces. Since some of this work could be performed simultaneously in different rooms, we were able to use both Ishaq lab spaces and the ‘mouse house’ to keep people distanced.

During the 40-day mouse study, ‘Team Broccoli’ collected:

  • 640 mouse body weight data measurements
  • 433 fecal samples, which were archived for possible culturing and/or sequencing
  • 400 additional samples collected over two days:
    • 40 blood samples for immune factor identification
    • 360 gut samples
      • Of which, 200 were PMA treated within 12 hours of collection for use in DNA sequencing
      • 160 of which will be cultured to isolate bacteria. This will create 1 ~ 8 isolates per sample that will need to be grown on its own plate, transferred to broth media, and then frozen with glycerol at -80C until they can be revived and studied later this year.
Stacks of petri dishes filled with culture media. The stacks are inside of a vinyl anaerobic chamber, for use with bacterial culturing.
A messy laboratory bench showing dozens of jars, bottles, and graduated cylinders, all of various sizes.
Three small, white, cardboard boxes on a black laboratory bench. The lids are off, revealing about 200 small tubes with sample names written on the lids.
Joe Balkan, performing culturing of bacteria at the anaerobic chamber. Joe is wearing a face mask, and is holding up a culture plate. There are stacks of petri dishes inside the chamber.
A person holding a mouse in a research facility. The person is wearing a hairnet, nitrile gloves, a surgical mask, and a surgical gown. The mouse with dark brown fur is sitting on the top of the person's hand. In the background, there are metal shelves with bins and containers of research supplies.
Person in a research facility holding up their arm with a mouse on it. Person is wearing a hairnet, nitrile gloves, surgical mask, and a surgical gown. They are holding their left arm up to the camera to show off a mouse with dark brown fur sitting on their arm. In the background is a metal shelf with containers of research materials.

2019 review one of Indoor Air’s top downloaded articles for 2018 – 2019!

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A collaborative review article that I was last author on was listed in the top 10% most downloaded papers of 208/2019 in the journal Indoor Air! Even more impressive, this review was published August 20, 2019, and it was still in the top 10% spanning from January 2019 – December 2019!!

This paper stems from my work on the microbiology of the built environment at BioBE, and reviews the interaction between chemistry, microbiology, and health in the built environment. It was co-authored and led by undergraduate students I was mentoring at the time, as well as research associates and PIs from the BioBE lab, and a variety of fabulous collaborators!

From one species to another: A review on the interaction between chemistry and microbiology in relation to cleaning in the built environment

Image of plastic wrapped over soil to inhibit weed growth.

NE IPM funded collaborative proposal!

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I’m pleased to announce that a small grant proposal I am part of was just funded by the Northeastern Integrated Pest Management (IPM) Center! The proposal, “A Working Group on Tarping and Soil Solarization”, brings together researchers and food production professionals from across New England to identify the current use of tarping and soil solarization to prevent weed growth without the use of chemcials, as well as identify barriers to adoption of this practice, and develop research proposals to fill any knowledge gaps related to the use of these methods and their effect on crop production, weed suppression, soil microbiota, and the local ecosystem.

Led by Dr. Sonja Birthisel (UM), the working group team is comprised of Dr. Alicyn Smart (UM), myself, Master Nathalie Lounsbury (UNH), and Eva Kinnebrew (UVM). We will be joined by over a dozen other researchers across New England who perform agricultural research, along with dozens of ‘stakeholders’: producers and other food production professionals who have an interest in the group findings and would make use of any knowledge we generate.

Featured Image Credit: Soil Solarization, Wikimedia

Wild blueberries on a bush.

My first funded proposal at UMaine!

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Now that I’m an assistant professor, a significant amount of my time is spent writing grant proposals to fund projects I’d like to do in the future.

Many large federal or foundational grants take up to a year from submission to funds distribution, and the success rate, especially for newly-established researches, can be quite low. It’s prudent to start writing well in advance of the due date, and to start small, with “pilot projects”.

To that end, I’m pleased to announce that Dr. Lily Calderwood and I just received word that the Wild Blueberry Commission of Maine is funding a pilot project of ours; “Exploration of Soil Microbiota in Wild Blueberry Soils“. We’ll be recruiting 1 – 2 UMaine students for summer/fall 2020 to participate in the research for their Capstone senior research projects.

Dr. Calderwood is an Extension Wild Blueberry Specialist, and Assistant Professor of Horticulture in the School of Food and Agriculture at UMaine. She and I developed this project when meeting for the first time, over coffee. We realized we’d both been at the University of Vermont doing our PhD’s concurrently, and in neighboring buildings! We got to chatting about my work in wheat soil microbial communities, and her work on blueberry production, and the untapped research potential between the two.

This pilot will generate some preliminary data to help us get a first look at the soil microbiota associated with blueberries, and in response to management practices and environmental conditions. From this seed funding, Lily and I hope to cultivate fruitful research projects for years to come!

Featured Image: Wild Maine Blueberries, Wikimedia

Pilot study published on chemicals and bacteria in house dust.

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In October 2017, Dr. Rich Corsi came to visit Oregon for two weeks during a sabbatical from the University of Texas, Austin. During his stay, Rich and I, and other BioBE/ESBL researchers chatted about doing a pilot study that would bring UT’s indoor chemistry work together with BioBE’s indoor microbial work.

Since we began our collaboration in the fall of 2017, only one of the research team is still in their original position (Jeff Kline at ESBL)! Rich Corsi, Ying Xu, and myself have all gone on to faculty positions elsewhere, graduate student Chenyang Bi defended and started a post-doc position, and the two undergrads working with me, Susie Nunez and Samantha Velazquez, graduated and went on to other things! Science collaborations work best when they can stand the test of time and geography. The benefit to everyone moving around is that you are able to hold collaboration meetings in new and exciting places each time.

In addition to the literature review we collaborated on, we eventually did get a research pilot running, and it has now been published in PeerJ!

Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community.

Samantha Velazquez1, Chenyang Bi 2,3, Jeff Kline 1,4, Susie Nunez1, Richard Corsi 3,5, Ying Xu 3,6, Suzanne L. Ishaq1,7*

Affiliations:

1 Biology and the Built Environment Center,  University of Oregon, Eugene, OR, 97403

2 Department of Civil Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 (current)

3 Department of Civil, Architectural and Environmental Engineering, University of Texas, Austin, TX 78712

4 Energy Studies and Buildings Laboratory, University of Oregon, Eugene, OR, 97403

5 Fariborz Maseeh College of Engineering and Computer Science, Portland State University, Portland, OR 97207 (current)

6 Department of Building Science, Tsinghua University, 100084, Beijing, P. R. China (current)

7 School of Food and Agriculture, University of Maine, Orono, ME 04469 (current)

Abstract

Di-2-ethylhexyl phthalate (DEHP) is a plasticizer used in consumer products and building materials, including polyvinyl chloride flooring material. DEHP adsorbs from material and leaches into soil, water, or dust, and presents an exposure risk to building occupants by inhalation, ingestion, or absorption.  A number of bacterial isolates are demonstrated to degrade DEHP in culture, but bacteria may be susceptible to it as well, thus this study examined the relation of DEHP to bacterial communities in dust.  Polyvinyl chloride flooring was seeded with homogenized house dust and incubated for up to 14 days, and bacterial communities in dust were identified at days 1, 7, and 14 using the V3-V4 regions of the bacterial 16S rRNA gene.  DEHP concentration in dust increased over time, as expected, and bacterial richness and Shannon diversity were negatively correlated with DEHP concentration.  Some sequence variants of Bacillus, Corynebacterium jeddahense, Streptococcus, and Peptoniphilus were relatively more abundant at low concentrations of DEHP, while some Sphingomonas, Chryseobacterium, and a member of the Enterobacteriaceae family were relatively more abundant at higher concentrations.  The built environment is known to host lower microbial diversity and biomass than natural environments, and DEHP or other chemicals indoors may contribute to this paucity.

Ciencia y aventura en mexico

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For the past four days, I have been in Monterrey, Mexico, where I have been fostering international scientific relations in meetings and in the mountains.  It was my very first trip to Mexico, and it was an amazing experience.

Monterrey, Mexico around the Hotel Novotel Monterrey Ville

After arriving in Monterrey, I was greeted by a research friend of mine, Dr. Jose Garcia-Mazcorro.  We met a few years ago when Jose emailed me to ask questions about a recently published paper on Saccharomyces probiotic treatment in cattle, and our conversations on the ecological theory behind probiotics led to a review paper on the subject, led by Jose and I. It wasn’t until last August when Jose and I actually met in person, at the ISME conference in Leipzig, Germany.

At dinner, I had the opportunity to meet Jose’s wife, Alecia, who is also a researcher, and their son, and discuss everything from aflatoxin to Stephen King’s “It” (we discovered that their son and I were both reading It when I discussed living in Maine, not far from Derry).

The next day, I woke up at 3:45 am to travel to the mountains for an incredible experience: a small-group tour in Matacanes canyon led by Daniel, a mountaineer with 20 years of experience and owner of Todo Avetura. He and Omar, another guide, led us for 12 hours and taught us about Matacanes canyon while we trekked 13 kilometers (8.7 miles) down waterfalls, through caves, over boulders, and over cliffs. Even the drive into and out of the canyon was an adventure; the steep road into the mountains fords rivers and winds along cliff faces.  In the canyon, I got to do many things for the first time, including rappel down the side of two waterfalls; 27 m (88.6 ft) and 15 m (49.2 ft) into a cave, swim through the absolute dark of a river cave system, and jump off of several cliffs into the water below, including a 9.5 meter (31 ft) jump!  It was supposed to be 10 meters, but that looked just a little too terrifying to try so I chose a spot that looked friendlier.  Turns out that jumping 9.5 meters is a lot like getting up to present in front of a large audience, you just have to get up there and do it before you have time to think about and psych yourself out.

The guides were really passionate about the mountains, and they were particular about safety and not rushing or pushing us to the point where we would get hurt.  If you have the chance, and the cohones, to go to Matacanes, I highly recommend Todo Aventura.

On Monday, sore but no worse for wear, I gingerly toured some of the facilities where Jose is currently working, MNA, an animal nutrition company.  I met with company president and nutritionist Dr. Jorge Kawas, and Jose, Jorge, and I discussed the role of microbes in animal nutrition and health. 

Dr. Jose Garcia-Mazcorro and I at MNA in Monterrey.

Monday night, I got to chat one-on-one with Professor T.J. Nagaraja, an author on the Saccharomyces review and a prominent researcher in rumen acidosis, cattle health, and infectious disease. 

The main reason for my trip to Monterrey was to attend and speak at the XXII UANL-Engorda de Bovinos en Corral Symposium.  I presented the opening seminar titled “Raising feedlot cattle with good microbes in mind” (“Cria y engorda de ganado con buenos microbios en mente”).  The video can be found here, and slides with presentation notes here:

uanl_2019_ishaq_feedlot_cattleDownload

Organized by MNA and UANL, the university in Monterrey, the symposium brings together researchers, producers, animal industry professionals, and students to discuss animal health in feedlot cattle.  I was honored to give the opening talk, which will be available online soon, and pleased to hear that the audience did in fact like microbes more than before my seminar!  Usually when I start talking about the gut microbiome people have the urge to run off and wash their hands…

Unfortunately, I had to jump back on a plane shortly after my talk, as I am heading to give a different presentation at the Wildlife Society meeting in Reno, Nevada tomorrow! But, I have plenty of memories and new project ideas to remember my trip by, and hopefully I will come back to Monterrey soon!

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

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

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

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

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

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

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

Abstract

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.

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

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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 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.

Featured Image Source: Wikimedia Commons

USDA AFRI NIFA Agricultural Production Systems grant awarded to Menalled et al.

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In 2016, I was a post-doc in the Menalled Lab, which studies plant and weed ecology in the context of agricultural production and sustainability.  There, I assessed soil bacterial communities under different farming management practices and climate scenarios.  I also helped to develop a grant proposal, which was just accepted by the USDA AFRI NIFA Agricultural Production Systems!  Leading this project is Dr. Fabian Menalled (as Principal Investigator, or PI), along with a number of other PIs; Dr. Amy Trowbridge, Dr. David Weaver, Dr. Tim Seipel, Dr. Maryse Bourgault, and Dr. Carl Yeoman, and collaborators Dr. Darrin Boss, Dr. Kate Fuller, Dr. Ylva Lekberg, and myself as a subaward PI.  I will again be providing microbial community analysis for this project, and collectively the project investigators will bring expertise in plant ecology, agronomy, economics, soil and plant chemistry, microbial ecology, agroecosystems, and more.

This research and extension project focuses on the needs of dryland agricultural stakeholders and it was designed in close collaboration with the NARC Advisory Board. While I was only able to attend one meeting, other team members regularly meet with Montana producers to discuss current issues and identify locally-sourced needs for agricultural research.  During this project, we will continue to meet with the NARC Advisory Board to share our results, evaluate implications, and better serve the producer community.

Diversifying cropping systems through cover crops and targeted grazing: impacts on plant-microbe-insect interactions, yield and economic returns.

Project summary

The semi-arid section of the Northern Great Plains is one of the
largest expanses of small grain agriculture and low-intensity livestock
production. However, extreme landscape simplification, excessive reliance on
off-farms inputs, and warmer and drier conditions hinder its agricultural
sustainability. This project evaluates the potential of diversifying this region
through the integration of cover crops and targeted grazing. We will complement
field and greenhouse studies to appraise the impact of system diversity,
temperature, and precipitation on key multi-trophic interactions, yields, and
economic outputs. Specifically, we will 1) Assess ecological drivers as well as
agronomic and economic consequences of integrating cover crops and livestock
grazing in semi-arid systems, 2) Evaluate how climate variability modify the
impacts of cover crops and livestock grazing on agricultural outputs. Specifically,
we will 2.1) Compare the effect of increased temperature and reduced moisture
on agronomic and economic performance of simplified and diversified systems,
2.2.) Assess the impact of climate and system diversity on associated biodiversity
(weeds, insect, and soil microbial communities) and above- and belowground
volatile organic (VOC) compound emissions, and 2.3) Evaluate how changes in
microbially induced VOCs influence multitrophic plant-insect interactions.

Objectives

  1. Assess key ecological drivers as well as agronomic and economic consequences of integrating cover crops and livestock grazing in semi-arid production systems
    • Compare the agronomic and economic performance of simplified and diversified systems
    • Assess the impact of cover crops and livestock grazing on the associated biodiversity (weeds, insects, and the soil microbiota)
  2. Evaluate how climate conditions modify the impacts of cover crops and livestock grazing on semi-arid production systems
    • Compare the effect of temperature and soil moisture on agronomic and economic performance of simplified and diversified systems
    • Assess the impact of climate and system diversity on associated biodiversity and above- and belowground volatile organic compound (VOC) emissions
    • Evaluate how changes in VOCs emissions influence important multitrophic interactions such as resistance to wheat stem sawfly and natural enemy host location cues
  3. Integrate the knowledge generated into an outreach program aimed at improving producers’ adoption of sustainable diversified crop-livestock systems

The Hungate 1000 Project is now published!

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The Hungate 1000 Project was a massive undertaking: namely, sequencing the genome of 1000 microorganisms cultured from ruminant animals all over the world, and was both  coordinated and led by the Rumen Microbial Genomics Network.  After years of hard work by some incredible researchers, the Hungate 1000 has just been published in the Nature Biotechnology Journal! The […]