Scholarly Work - Animal & Range Sciences
Permanent URI for this collectionhttps://scholarworks.montana.edu/handle/1/8931
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Item Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints(2019-07-19) Gomez, Andres; Sharma, Ashok Kumar; Mallott, Elizabeth K.; Petrzelkova, Klara J.; Jost Robinson, Carolyn A.; Yeoman, Carl J.; Carbonero, Franck; Pafco, Barbora; Rothman, Jessica M.; Ulanov, Alexander; Vlckova, Klara; Amato, Katherine R.; Schnorr, Stephanie L.; Dominy, Nathaniel J.; Modry, David; Todd, Angelique F.; Torralba, Manolito; Nelson, Karen E.; Burns, Michael B.; Blekhman, Ran; Remis, Melissa; Stumpf, Rebecca M.; Wilson, Brenda A.; Gaskins, H. Rex; Garber, Paul A.; White, Bryan A.; Leigh, Steven R.The gut microbiome of primates, including humans, is reported to closely follow host evolutionary history, with gut microbiome composition being specific to the genetic background of its primate host. However, the comparative models used to date have mainly included a limited set of closely related primates. To further understand the forces that shape the primate gut microbiome, with reference to human populations, we expanded the comparative analysis of variation among gut microbiome compositions and their primate hosts, including 9 different primate species and 4 human groups characterized by a diverse set of subsistence patterns (n = 448 samples). The results show that the taxonomic composition of the human gut microbiome, at the genus level, exhibits increased compositional plasticity. Specifically, we show unexpected similarities between African Old World monkeys that rely on eclectic foraging and human populations engaging in nonindustrial subsistence patterns; these similarities transcend host phylogenetic constraints. Thus, instead of following evolutionary trends that would make their microbiomes more similar to that of conspecifics or more phylogenetically similar apes, gut microbiome composition in humans from nonindustrial populations resembles that of generalist cercopithecine monkeys. We also document that wild cercopithecine monkeys with eclectic diets and humans following nonindustrial subsistence patterns harbor high gut microbiome diversity that is not only higher than that seen in humans engaging in industrialized lifestyles but also higher compared to wild primates that typically consume fiber-rich diets.Item Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed(2019-06) Ishaq, Suzanne L.; Lachman, Medora M.; Wenner, Benjamin A.; Baeza, Amy; Butler, Molly; Gates, Emily; Olivo, Sarah; Geddes, Julie Buono; Hatfield, Patrick G.; Yeoman, Carl J.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. 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. 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 GI transit time, microbial fermentative and hydrolytic activity, and host growth or health is still largely unexplored.Item Ground-Dwelling Arthropod Community Response to Livestock Grazing: Implications for Avian Conservation(2019-08) Goosey, Hayes B.; Smith, Joseph T.; O'Neill, Kevin M.; Naugle, David E.Terrestrial arthropods are a critical component of rangeland ecosystems that convert primary production into resources for higher trophic levels. During spring and summer, select arthropod taxa are the primary food of breeding prairie birds, of which many are imperiled in North America. Livestock grazing is globally the most widespread rangeland use and can affect arthropod communities directly or indirectly through herbivory. To examine effects of management on arthropod community structure and avian food availability, we studied ground-dwelling arthropods on grazed and ungrazed sagebrush rangelands of central Montana. From 2012 to 2015, samples were taken from lands managed as part of a rest-rotation grazing program and from idle lands where livestock grazing has been absent for over a decade. Bird-food arthropods were twice as prevalent in managed pastures despite the doubling of overall activity-density of arthropods in idle pastures. Activity-density on idled lands was largely driven by a tripling of detritivores and a doubling in predators. Predator community structure was simplified on idled lands, where Lycosid spiders increased by fivefold. In contrast, managed lands supported a more diverse assemblage of ground-dwelling arthropods, which may be particularly beneficial for birds in these landscapes if, for example, diversity promotes temporal stability in this critical food resource. Our results suggest that periodic disturbance may enhance arthropod diversity, and that birds may benefit from livestock grazing with periodic rest or deferment.Item Maladaptive nest-site selection by a sagebrush dependent species in a grazing-modified landscape(2019-04) Cutting, Kyle A.; Rotella, Jay J.; Schroff, Sean R.; Frisina, Michael R.; Waxe, James A.; Nunlist, Erika; Sowell, Bok F.Animals are expected to select habitats that maximize their fitness over evolutionary time scales. Yet in human-modified landscapes, habitat selection might not always lead to increased fitness because animals undervalue high-quality resources that appear less attractive than those of lower quality. In the American West, agriculture has modified landscapes, yet little is known about whether agricultural changes alter the reliability of the cues animals use to identify habitat quality; ultimately forming maladaptive breeding strategies where behavioral cues are mismatched with survival outcomes. Using the greater sage-grouse, a species highly dependent upon sagebrush landscapes, we (1) evaluated how females select nesting habitats based on sagebrush type, along with livestock grazing related linear and point features, and other biotic, abiotic characteristics, given hypothesized influences on hiding cover, microclimate and predator travel routes and perches, (2) compared habitat selection information with results for nest survival estimates to evaluate if selection appears to be adaptive or not, and (3) used our results to evaluate the most appropriate strategies for this species in a grazing-modified landscape. Nest-site selection for sagebrush type appears to be maladaptive: in the most-preferred sagebrush type, nest survival rate was one-fourth the rate realized by females nesting in the sagebrush type avoided. Nest survival was four times higher for nests placed away from (>100 m), rather than next to (1 m), the nearest fence, and survival was lower within sites with higher cow pie density (a proxy for previous grazing intensity). Live and dead grasses influenced selection and survival in opposing ways such that dead grass was selected for but resulted in reduced survival while live grass was avoided but resulted in increased survival. Results collectively provide the first empirical evidence that a specific type of sagebrush acts as an ecological trap while another sagebrush type is undervalued. These results also suggest that adding more fences to control livestock grazing systems will likely reduce sage-grouse nest survival.Item Genetic Markers Are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers(2018-03) Golder, Helen M.; Thomson, Jennifer M.; Denman, Stuart E.; McSweeney, Chris S.; Lean, Ian J.Dairy heifers were subjected to a non-life-threatening challenge designed to induce ruminal acidosis by feeding grain and sugar. Large among animal variation in clinical signs of acidosis, rumen metabolite concentrations, and the rumen microbiome occurred. This exploratory study investigates sources of the variation by examining associations between the genome, metabolome, and microbiome, albeit with a limited population. The broader objective is to provide a rationale for a larger field study to identify markers for susceptibility to ruminal acidosis. Initially, heifers (n = 40) allocated to five feed additive groups were fed 20-days pre-challenge with a total mixed ration and additives. Fructose (0.1% of bodyweight/day) was added for the last 10 days pre-challenge. On day 21 heifers were challenged with 1.0% of bodyweight dry matter wheat + 0.2% of bodyweight fructose + additives. Rumen samples were collected via stomach tube weekly (day 0, 7, and 14) and at five times over 3.6 h after challenge and analyzed for pH and volatile fatty acid, ammonia, D-, and L-lactate concentrations. Relative abundance of bacteria and archaea were determined using Illumina MiSeq. Genotyping was undertaken using a 150K Illumina SNPchip. Genome-wide association was performed for metabolite and microbiome measures (n = 33). Few genome associations occurred with rumen pH, concentration of acetate, propionate, total volatile fatty acids, or ammonia, or the relative abundance of the Firmicutes, Bacteroidetes, and Spirochaetes phyla. Metabolites and microbial phyla that had markers associated and quantitative trait loci (QTL) were: acetate to propionate ratio (A:P), D-, L-, and total lactate, butyrate, acidosis eigenvalue, Actinobacteria, Chloroflexi, Euryarchaeota, Fibrobacteres, Planctomycetes, Proteobacteria, and Tenericutes. A putative genomic region overlapped for Actinobacteria, Euryarchaeota, and Fibrobacteres and covered the region that codes for matrix extracellular phosphoglycoprotein (MEPE). Other overlapping regions were: (1) Chloroflexi, Tenericutes, and A:P, (2) L- and total lactate and Actinobacteria, and (3) Actinobacteria, Euryarchaeota, Fibrobacteres, and A:P. Genome-wide associations with the metabolome and microbiome occurred despite the small population, suggesting that markers for ruminal acidosis susceptibility exist. The findings may explain some of the variation in metabolomic and microbial data and provide a rationale for a larger study with a population that has variation in acidosis.Item Ground Juniperus pinchotii and urea in supplements fed to Rambouillet ewe lambs Part 2: Ewe lamb rumen microbial communities(2018-12) Ishaq, Suzanne L.; Yeoman, Carl J.; Whitney, T. R.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 x 2 factorial design with 4 concentrations of ground juniper (15%, 30%, 45%, or 60% of DM) and 2 levels of urea (1% or 3% of DM). Increasing juniper resulted in minor changes in microbial β-diversity (PERMANOVA, pseudo F = 1.33, P = 0.04); however, concentrations of urea did not show detectable broad-scale differences at phylum, family, or genus levels according to ANOSIM (P > 0.05), AMOVA (P > 0.10), and PERMANOVA (P > 0.05). Linear discriminant analysis indicated some genera were specific to certain dietary treatments (P < 0.05), though none of these genera were present in high abundance; high concentrations of juniper were associated with Moraxella and Streptococcus, low concentrations of urea were associated with Fretibacterium, and high concentrations of urea were associated with Oribacterium and Pyramidobacter. Prevotella were decreased by juniper and urea. Ruminococcus, Butyrivibrio, and Succiniclasticum increased with juniper and were positively correlated (Spearman\'s, P < 0.05) with each other but not to rumen factors, suggesting a symbiotic interaction. Overall, there was not a juniper x 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 lowerend BW was likely due to reduced DMI rather than a reduction in microbial fermentative ability.Item Colonic aberrant crypt formation accompanies an increase of opportunistic pathogenic bacteria in C57BL/6 mice fed a high-fat diet(2018-04) Zeng, Huawei; Ishaq, Suzanne L.; Liu, Zhenhua; Bukowsky, Michael R.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.Item Beaver Habitat Selection for 24 Yr Since Reintroduction North of Yellowstone National Park(2018-01) Scrafford, Matthew A.; Tyers, Daniel B.; Patten, Duncan T.; Sowell, Bok F.Beavers (Castor canadensis) disappeared from drainages north of Yellowstone National Park in the mid-1900s because of trapping, a potential tularemia outbreak, and willow (Salix spp.) stand degradation by ungulates. Beavers were reintroduced in 1986 after a 40-yr absence with inventories of active-beaver structures completed each fall after reintroduction for 24 consecutive yr. We used this inventory to evaluate the expansion of beaver populations in a riparian environment recovering from past overuse by ungulates. Specifically, we investigated the density of active-beaver colonies and dams, the change in willow cover, and habitats associated with beaver expansion since reintroduction. Successful establishment and expansion of beavers indicate that sufficient resources were available to the population despite the suboptimal condition of riparian vegetation. Carrying capacity on third-order streams was reached approximately 14 yr after reintroduction (2000) with an average annual density of 1.33 (95th percentile = 1.23 - 1.44 active colonies/stream km) between 2000 and 2010. The average annual density of beaver dams during this time was 2.37 (2.04 - 2.71 active dams/stream km). Despite the beaver population being at carrying capacity in meadows since 2000, willow cover increased by 16% between 1981 and 2011. We speculate that beaver activities, together with reduced ungulate browsing from predation and habitat loss, combined to increase willow cover. Willow cover and height were positively associated with colony longevity, but numerous other influencing variables included secondary channels, sinuosity, stream depth, and sandbar width. Our results provide evidence that beaver reintroduction can be successful in riparian areas where willow stand condition is less than optimal and that beavers might ultimately improve willow condition. We suggest that reducing ungulate use of overgrazed riparian environments will facilitate the reestablishment of beaver populations. We also provide managers with habitats that should be identified in an environment targeted for reintroduction.Item Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract(2018-02) Yeoman, Carl J.; Ishaq, Suzanne L.; Bichi, Elena; Olivo, Sarah K.; Lowe, James; Aldridge, Brian M.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.Item Cigarette smoking is associated with an altered vaginal tract metabolomic profile(2018-01) Nelson, Tiffanie M.; Borgogna, Joanna-Lynn C.; Michalek, R. D.; Roberts, David W.; Rath, J. M.; Glover, E. D.; Ravel, Jacques; Shardell, M. D.; Yeoman, Carl J.; Brotman, Rebecca M.Cigarette smoking has been associated with both the diagnosis of bacterial vaginosis (BV) and a vaginal microbiota lacking protective Lactobacillus spp. As the mechanism linking smoking with vaginal microbiota and BV is unclear, we sought to compare the vaginal metabolomes of smokers and non-smokers (17 smokers/19 non-smokers). Metabolomic profiles were determined by gas and liquid chromatography mass spectrometry in a cross-sectional study. Analysis of the 16S rRNA gene populations revealed samples clustered into three community state types (CSTs) ---- CST-I (L. crispatus-dominated), CST-III (L. iners-dominated) or CST-IV (low-Lactobacillus). We identified 607 metabolites, including 12 that differed significantly (q-value < 0.05) between smokers and non-smokers. Nicotine, and the breakdown metabolites cotinine and hydroxycotinine were substantially higher in smokers, as expected. Among women categorized to CST-IV, biogenic amines, including agmatine, cadaverine, putrescine, tryptamine and tyramine were substantially higher in smokers, while dipeptides were lower in smokers. These biogenic amines are known to affect the virulence of infective pathogens and contribute to vaginal malodor. Our data suggest that cigarette smoking is associated with differences in important vaginal metabolites, and women who smoke, and particularly women who are also depauperate for Lactobacillus spp., may have increased susceptibilities to urogenital infections and increased malodor.
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