Microbiomes Across (Agricultural) Systems

Beginning in early 2019, I participated as one of the guest editors for the Microbiomes Across Biological Systems special call hosted by three PLoS Journals. The journal collection was officially released in early 2020, but due to the global upheaval this year, the overview piece planned by the guest editors was not able to be completed. Here is a partial overview, written by myself and written by Dr. Noelle Noyes, Assistant Professor at the University of Minnesota.

Diet and gut systems

Ecosystem dynamics are important at any scale

As humans, animals, and plants are key members of their environmental ecosystems, so too are microorganisms key members of the host-associated ecosystems in which they reside.  Throughout eons of interactions between microorganisms and macroorganism hosts, specialized and reproducible host-microbial interactions developed, leading to inherent differences in the microbial communities residing within even closely-related microorganism hosts (Bennett et al. 2020; Loo et al. 2020; Sun et al. 2020).  The strength and outcome of each of these host-microbial interactions can sway the trajectory of that host’s life, and decades of research has only barely uncovered the mechanisms behind the exorbitantly complicated relationships between host and microbial community.  In part, this is because the host microbiome does not develop in isolation; it is dependent on the environment (e.g. Bennett et al. 2020), on diet (e.g. Taylor et al. 2020), on the host signalment (e.g. Jacobs et al. 2020), and upon all the minute details of that hosts’s life which informs the “who”, when, why, and how of host-microbial interactions. To better understand biological systems, we must evaluate them at different scales, from the microbial ecosystems to the environmental ones, and how microbial selection and transfer are the mechanisms by which these scalable ecosystems are connected.

Your gut microbiota are what you eat

Diet is the most consistent and striking aspect of a host’s lifestyle which can select for different microbial communities in the gastrointestinal tract (Bloodgood et al. 2020; Loo et al. 2020;  Lü et al. 2020; Ogato et al. 2020; Sun et al. 2020; Taylor et al. 2020), and especially at different locations along the GI tract depending on localized anatomy and organ-specific environmental conditions (Subotic et al. 2020; Lourenco et al. 2020).  The amount of different macronutrients, such as proteins, fats, or carbohydrates, in a diet selectively encourage different biochemical capabilities in the gut microbiome and the microbial members which can thrive under those conditions (Lourenco et al. 2020).  At a finer resolution, the specific types of each nutrient, and their availability for catabolism will also affect the gut microbiome (Taylor et al. 2020).  

Yet, diet may affect the microbiome of different host species in nuanced ways, based on dissimilar anatomy of the gastrointestinal tract, the relative stability of host-microbial interactions and host reliance on their gut microbiota, and the relative stability of the diet of the host. For example, specialized herbivores which possess a four-chambered stomach, known as ruminants, are dependent on the presence of fibrolytic microbiota, yet due to the overwhelming microbial diversity present in their GI tract they have functional redundancy which allows for a great deal of latitude in the specific microbial species present in their communities.  Microbiota in the rumen of cattle are easily swayed by changes in diet composition (Lourenco et al. 2020; Ogato et al. 2020), as were microbiota in sea turtles (Bloodgood et al. 2020) and potato ladybird beetles (Lü et al. 2020), whereas diet composition seems to affect only the less abundant community members in the honeybee gut (Taylor et al. 2020).  

The impact of diet on the gut microbiome and host health is an active and long-standing research field, yet the depth and breadth of dietary effects leaves many questions yet unanswered, particularly in cases where feeding the animal host is prioritized over feeding the gut microbiota specifically.  Animal production and weight gain is a primary goal of feeding strategies in agriculture, often with detrimental effects to the functionality of gut microbiome which can lead to systemic health problems in the animal if the perturbation to the microbiome is extensive or protracted. An understanding of how host-microbial ecosystems can be altered over time to prevent such health problems is important (Ogato et al. 2020). Similarly, wild animal recovery programs opt for diets to support weight gain in malnourished animals, even when the diet composition is contrary to their natural diet. In recovering juvenile sea turtles, feeding an omnivorous diet to promote weight gain over the herbivorous diet these turtles consume at this stage of life causes changes in gut microbiota profiles and it is unknown how this may affect long-term digestive function and health (Bloodgood et al. 2020).

An interesting and understudied aspect of the effects of diet on the gut microbiome is the potential for knock-on effects across microbial ecosystems.  For example, changing the diet may impact the gut bacterial profiles based on “who” is directly catabolizing those nutrients, but may also impact other microorganisms which are supported by the byproducts of that microbial digestion.  Similarly, therapeutics targeting some microbial community members may inadvertently alter other community members.  A deeper understanding of how diet and medication affects the entire microbial community and not just selected members can reveal insight into community dynamics and the relative risk of medications to cause disruptions.  For example, anthelmintic in beagles were shown to not alter fecal microbial communities (Fujishiro et al. 2020).

Environment to host to host: microbial transfer highlights connections between systems

Yet, what constitutes a beneficial microbiome for one animal species may be detrimental to another animal species. A dramatic example of this is vector-borne infectious disease, in which symbiotic or neutral members of an insect microbiome are highly pathogenic in other animals which have not learned to tolerate or control those particular microorganisms. Bacteria carried by arthropods, such as mosquitos, flies, or ticks, may provide nutrition or disease-mitigation benefits to its arthropod host yet cause widespread disease and mortality in humans and animals (Bennett et al. 2020). Interaction with the ecosystem can recruit microbial members to a host-associated microbial community.  Habitat destruction alters the quality of the environment and thus microbial transfer from environment to insect, and this can make arthropod microbial communities more variable (Bennett et al. 2020). It is yet unknown if these knock-on changes to the arthropod microbiota will have positive or negative impacts for vector-borne diseases.  

Studies such as Bennet et al. (2020), which put host-associated gut microbial community assessment into the context of habitat quality and environmental microbial transfer, remind us that microbial communities do not exist in isolation.  Understanding how the environment shapes the microbial communities which shape the host is a critical aspect to understanding the connectedness between biological systems.  Further, it better illuminates the dynamics of microbial transmission and when they are and are not transferred.  Maternal transfer is a well-demonstrated mechanism of vertical transmission of microorganisms, and transfer between social pairs is a method of horizontal transmission of microorganisms, both often demonstrated via microbial community similarity analysis.  However, when pair-bonded tree swallows are sampled asynchronously, there is no significant level of similarity in their gut microbiota (Hernandez et al. 2020).

The need to put host-associated gut microbial community assessment into the context of environment is also highlighted in Loo et al. (2020), in which habitat and geographic location impacted the gut microbiome of island finches independently of foraging diet data. Environmental conditions, localized plant diversity, and localized niche competition can also impact the type, nutritional content, and life stage of plant life, which can in turn impact the gut microbiota recruited in those host animals consuming plants.  As discussed in Jacobs et al. (2020), when animals are removed from their natural environments and held in captivity, where local macro-biodiversity is dramatically reduced, there is often a corresponding decline in host gut microbial diversity which can impact animal health.  In semi-captive situations, such as beehives, animals may still freely encounter diverse environmental microorganisms, but the habitat or housing design may impact host behavior and/or stress response due to interactions with humans.  Chronic stress has been demonstrated to negatively impact the diversity and functionality of host-associated microbial communities in the gut by altering the host immune system and its latitude for microbial tolerance. Thus, even at the very localized scale, environmental conditions and habitat play a role in host-microbial interactions (Subotic et al. 2020).

Featured papers, which can be found here.

  • Bennett et al. Habitat disturbance and the organization of bacterial communities in Neotropical hematophagous arthropods
  • Bloodgood et al. The effect of diet on the gastrointestinal microbiome of juvenile rehabilitating green turtles (Chelonia mydas)
  • Fujishiro et al. Evaluation of the effects of anthelmintic administration on the fecal microbiome of healthy dogs with and without subclinical Giardia spp. and Cryptosporidium canis infections
  • Hernandez et al. Cloacal bacterial communities of tree swallows (Tachycineta bicolor): Similarity within a population, but not between pair-bonded social partners
  • Jacobs et al. California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals
  • Loo et al. An inter-island comparison of Darwin’s finches reveals the impact of habitat, host phylogeny, and island on the gut microbiome
  • Lourenco et al. Comparison of the ruminal and fecal microbiotas in beef calves supplemented or not with concentrate
  • Lü et al. Host plants influence the composition of the gut bacteria in Henosepilachna vigintioctopunctata.
  • Ogato et al. Long-term high-grain diet altered the ruminal pH, fermentation, and composition and functions of the rumen bacterial community, leading to enhanced lactic acid production in Japanese Black beef cattle during fattening
  • Subotic et al. Honey bee microbiome associated with different hive and sample types over a honey production season
  • Taylor et al. The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera)

Water systems

written by Dr. Noelle Noyes, University of Minnesota

Environmental and physiochemical factors structure water-associated microbiomes

Water bodies are highly diverse ecosystems, and this is reflected in the articles of this Special Edition, which investigate the microbiomes of Indian mangroves, Icelandic cold springs, Antarctic lakes, urban lakes in Beijing, and Pacific seawater. A common theme emerging from this diverse collection is that water-associated microbiomes are highly influenced by the nutrient and physiochemical properties of the water body itself; and that these properties, in turn, are influenced by the surrounding atmospheric and environmental inputs. For example, nitrogen levels were correlated with microbial composition in Mangrove-associated and Beijing urban lake water samples (Dhal et al 2020, Wang et al 2020), and nitrogen fixation capacity of the microbiome was found to vary significantly by water depth within Antarctic benthic mats (Dillon et al 2020). pH levels were found to influence the microbiomes of Icelandic cold springs  (Guðmundsdóttir et al 2019) and Mangrove-associated waters (Dhal et al 2020); and the archaeal composition of Beijing urban lake sediment (Wang et al 2020). 

Water-associated microbiomes are dynamic across gradients, geography and time

While water bodies exhibit heterogeneous physiochemical and nutrient properties depending on their environmental and geographical circumstances, the articles in this collection demonstrate that many water-associated microbiomes fluctuate predictably and periodically. For example, the diversity of seawater microbiomes exhibited diel fluctuation, which itself was characterized by rhythmic changes in temperature and concentrations of nitrate, ammonium, phosphate and silicate (Weber et al 2020). Microbiome structure and composition also correlated with gradients established by water depth (Dillon et al 2020, Weber et al 2020), eutrophication (Dhal et al 2020), and distance from coral reefs (Weber et al 2020). These findings emphasize the importance of the physical environment from which water samples are collected, and the fact that water and water-associated samples are inherently connected to — and impacted by — features that may be located far away from the actual sampling site. This highlights the importance of contextualizing sampling sites both temporally and spatially.

Featured papers, which can be found here.

  • Paltu Kumar Dhal et al, Insights on aquatic microbiome of the Indian Sundarbans mangrove areas
  • Megan L. Dillon et al, Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica
  • Ragnhildur Guðmundsdóttir et al, Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus
  • Yuxin Wang et al, Comparative Study on Archaeal Diversity in the Sediments of Two Urban Landscape Water Bodies
  • Amy Apprill et al, Diel, daily, and spatial variation of coral reef seawater microbial communities
  • Robert Hilderbrand et al, Using the microbiome to assess the ecological condition of headwater streams

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

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!

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

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.

Manuscript published on the effect of low/high fat diets on health and intestinal bacteria

Several years ago, during my Ph.D. at the University of Vermont, I provided wet-lab and DNA sequence analysis work for a project investigating the health effects of a low or high fat diet on mice with Dr. Huawei Zeng of the USDA Agricultural Research Service.  It was just recently published in the Journal of Nutritional Biochemistry!

Abstract

Consumption of an obesigenic/high-fat diet (HFD) is associated with a high colon cancer risk and may alter the gut microbiota. To test the hypothesis that long-term high-fat (HF) feeding accelerates inflammatory process and changes gut microbiome composition, C57BL/6 mice were fed HFD (45% energy) or a low-fat (LF) diet (10% energy) for 36 weeks. At the end of the study, body weights in the HF group were 35% greater than those in the LF group. These changes were associated with dramatic increases in body fat composition, inflammatory cell infiltration, inducible nitric oxide synthase protein concentration and cell proliferation marker (Ki67) in ileum and colon. Similarly, β-catenin expression was increased in colon (but not ileum). Consistent with gut inflammation phenotype, we also found that plasma leptin, interleukin 6 and tumor necrosis factor α concentrations were also elevated in mice fed the HFD, indicative of chronic inflammation. Fecal DNA was extracted and the V1–V3 hypervariable region of the microbial 16S rRNA gene was amplified using primers suitable for 454 pyrosequencing. Compared to the LF group, the HF group had high proportions of bacteria from the family Lachnospiraceae/Streptococcaceae, which is known to be involved in the development of metabolic disorders, diabetes and colon cancer. Taken together, our data demonstrate, for the first time, that long-term HF consumption not only increases inflammatory status but also accompanies an increase of colonic β-catenin signaling and Lachnospiraceae/Streptococcaceae bacteria in the hind gut of C57BL/6 mice.