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EFFECTS OF FEEDING SOLUBLE FIBER (DEXTRIN) TO PIGS PRE- AND POST-WEANING ON GROWTH PERFORMANCE, INTESTINAL MICROBIOME, VOLATILE FATTY ACID (VFA) PRODUCTION, INTESTINAL MORPHOLOGY, AND GENE EXPRESSIONClayton Chastain (7022099) 16 October 2019 (has links)
<p>Forty barrows were used in a 35d experiment to evaluate the effects of supplemental soluble fiber (dextrin) pre- and post-weaning on growth performance, intestinal microbiome, volatile fatty acid (VFA) production, intestinal morphology, and gene expression. Pigs were blocked by litter and BW, and randomly allotted to treatments in a 2x2 factorial design with or without fiber pre-weaning and with or without fiber post-weaning. Dextrin was administered orally through a syringe, after being suspended in chocolate milk from 14d prior to weaning through 3d post-weaning, after which it was included in the diet at 1%. At weaning, pigs were group housed by treatment and allowed ad libitum access to a common starter diet. On d4 post-weaning, pigs were moved to individual pens and fed diets with or without 1% fiber. Weights and feed intake were recorded 14 and 3d prior to weaning, and on d0, 4, 11, and 21 post-weaning. On d0 and d21 post-weaning, pigs were euthanized for collection of tissues and intestinal contents. Ileal, cecal, and colon contents were taken for microbiome analysis, distal large intestine contents were collected for VFA analysis, ileal cross sections were collected for histology, and ileal and cecal mucosal scrapings were collected for intestinal gene expression. Data were analyzed using the GLM procedure of SAS with pig as the experimental unit for growth performance, VFA production, intestinal morphology, and gene expression. Microbiome data were analyzed using Metastats, to find statistical significance between treatments, and then run through R, using the false discovery rate method, to find a multiple test corrections q-value. Growth performance in general was not affected (<i>P</i>> 0.10) by treatment with the exception of d11-21 feed efficiency was improved (<i>P</i>= 0.018) for pigs receiving supplemental fiber prior to weaning. Pigs that received fiber at any point had increased short chain fatty acid (SCFA) producing bacteria (<i>q </i>< 0.05) compared to pigs never receiving fiber. Pigs never receiving fiber had increased bacteria associated with intestinal inflammation (<i>q </i>< 0.05) compared to all other treatment groups. A trend for an interaction (<i>P </i>= 0.054) of pre- and post-weaning fiber supplementation<b></b>was observed for total volatile fatty acid concentration in large intestine contents. An interaction (<i>P </i>= 0.007) of pre- and post-weaning treatments was observed on butyrate, with pigs fed fiber only during pre-weaning having the greatest butyrate concentrations. Pigs fed fiber pre-weaning had decreased isobutyrate concentrations (<i>P </i>= 0.050) and percentages (<i>P</i>=0.040) and a trend for decreased isovalerate as a concentration (<i>P</i>= 0.058) and percent of total VFAs (<i>P </i>= 0.051). Pigs fed fiber post-weaning had increased acetate (<i>P </i>= 0.047). An interaction for butyrate percentages was observed with pigs receiving supplemental fiber only prior to weaning having the highest percent of butyrate (<i>P</i>= 0.029). An interaction for valerate concentrations (<i>P </i>= 0.045) occurred with pigs receiving fiber only prior to weaning having the highest amount of valerate. Valerate as a proportion of total VFAs (<i>P </i>= 0.038) was decreased in pigs receiving supplemental fiber post-weaning. Pigs fed fiber prior to weaning tended to have decreased crypt depths (<i>P </i>= 0.097) compared to pigs that did not receive fiber prior to weaning. In the ileum there was an interaction (<i>P </i>= 0.002) for GLP-2 expression, with pigs receiving supplemental fiber solely before or after weaning having the greatest expression. Occludin expression in the ileum tended to increase with fiber supplementation prior to weaning (<i>P</i>= 0.086) but then tended to decrease with fiber supplementation post-weaning (<i>P</i>= 0.053) In the cecum, there was an interaction (<i>P </i>= 0.049) of pre- and post-weaning fiber supplementation<b></b>on GLP-2 expression. Pigs fed supplemental fiber at any point had increased GLP-2 expression, but pigs that had fiber only after weaning had the greatest GLP-2 expression. Cecal HSP-70 expression also increased with fiber supplementation in pigs fed fiber post-weaning (<i>P </i>= 0.012). Soluble fiber supplementation caused alterations in the intestinal microbiome, VFA concentrations, the intestinal morphology, and in the expression of different intestinal genes.</p> Read more
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Gastrointestinal Microbiota Modulate Antinociceptive Tolerance Development in Mice with Chronic Morphine ExposureMischel, Ryan A 01 January 2018 (has links)
In October 2017, the United States government declared a state of public health emergency in response to the burgeoning prescription opioid epidemic. Opioid analgesics are the gold standard of therapy for moderate to severe pain, but their clinical utility is greatly limited by analgesic tolerance – a primary driver of diminished pain control and opioid dose escalations. Integral in this process are primary afferent sensory neurons in dorsal root ganglia (DRG), the first-order components of nociceptive sensation. With surmounting evidence that morphine and other narcotics can alter gut microbial composition and promote bacterial translocation to other tissues, a question arises of whether the secondary release of bacterial products and pro-inflammatory cytokines can modulate antinociceptive tolerance development. This dissertation examines how gut bacteria depletion with antibiotics modulates the pharmacodynamic properties of chronic morphine in mice. Utilizing a “top-down” experimental approach, this is characterized at the whole-animal, single-cell, and molecular level via behavioral assays of antinociception, whole-cell patch-clamp recordings in DRG neurons, and analysis of tetrodotoxin-resistant (TTX-R) Na+ channel kinetics, respectively. Our findings collectively indicate that the gastrointestinal microbiome is an important modulator of antinociceptive tolerance development with chronic morphine administration. Read more
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Evolution and Niche Specialization of Microbial Taxa in Vaginal Infection and PregnancyGlascock, Abigail L 01 January 2018 (has links)
The vaginal microbiome plays an important role in reproductive health and pregnancy. It has coevolved with humans and has direct effects on reproductive success, rendering selective pressure more pronounced at this site. Herein, we probe coevolution of the vaginal microbiome using a systems-level approach. In Chapter 2, we examine the evolutionary trajectory of two vaginal Veillonellaceae phylotypes evolved from an ancestral gastrointestinal lineage to inhabit the vaginal niche. We present evidence of their divergence and subniche specification and describe their differential associations with vaginal infection and pregnancy. In Chapter 3, we identify ten bacterial taxa, predicted to contribute to the underlying pathology of the sexually transmitted infection trichomoniasis. This ‘pathogroup’, which has undergone conditional differentiation to thrive in the presence of T. vaginalis, includes previously undescribed organisms and putative symbionts. Lastly in Chapter 4, we present the first characterization of BspA proteins, multi-modal virulence factors, in the vaginal microbiome and provide evidence of their extensive horizontal transfer across diverse microbial lineages. We use homology modeling to demonstrate conservation of structural and functional characteristics of these proteins between diverse bacterial taxa and identify structural variants, potentially indicative of subtypes. These findings further our understanding of the contributions of individual bacterial species, bacterial communities and virulence determinants in the health and disease. Furthermore, they lay the groundwork for future work characterizing coevolution of the human vaginal microbiome. These systems-level approaches will facilitate synergy between broad and reductive approaches and inform strategies for modulation of the microbiome and development of more effective therapeutics. Read more
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Evolution, metabolism, and virulence of the oral microbiomeJorth, Peter Allan 02 March 2015 (has links)
The human microbiome has important roles in maintaining health, but dysbiosis of the microbiota can lead to disease. Polymicrobial interactions can result in synergy, producing disease that is worse than the sum of the respective single species infections. Despite this significant impact, synergy is understudied due to the complexity of polymicrobial interactions. Periodontitis is a microbiome-associated disease, and is one of the most common infectious diseases worldwide. Therefore, we have used periodontal disease as a model to study polymicrobial synergy. I have used two complementary approaches to study polymicrobial infections. The opportunistic periodontal pathogen Aggregatibacter actinomycetemcomitans exhibits synergy with streptococci in model murine infections. Because polymicrobial interactions are dependent on organisms’ abilities to sense their environments, I have examined the genetic regulatory mechanisms used by A. actinomycetemcomitans to interact with its environment. Through Northern blot analyses and biochemical approaches, I show that A. actinomycetemcomitans uses non-coding RNAs to regulate amino acid transport. Taking a comparative genomics approach, I demonstrate that A. actinomycetemcomitans DNA uptake systems are evolutionarily linked to genome defense. To describe host-influenced changes in gene expression, I develop a new technique to transcriptionally profile A. actinomycetemcomitans in a murine abscess infection, thereby revealing the importance of specific fermentative and anaerobic respiratory genes for in vivo survival. The long-term goal is to use these studies as a basis to characterize genetic regulatory mechanisms mediating synergy in polymicrobial A. actinomycetemcomitans infections with streptococci and other oral microbes. As a second approach to study polymicrobial infections, I analyze gene expression of healthy and diseased human plaque communities from aggressive periodontitis patients. Profiling ribosome content of healthy and diseased communities, I show that disease communities adopt similar less diverse population structures distinct from healthy populations. In addition to changes in population composition, using community transcriptional profiling I show that a keystone species within diseased communities up-regulates expression of genes involved in making the oral inflammatory molecule butyrate. These studies demonstrate for the first time that microbiome based diseases are marked by gene expression changes in addition to compositional changes. / text Read more
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Deep Sequencing and Functional Analyses Identify a Role of Fusobacterium Species in Colorectal TumorigenesisKostic, Aleksandar David 08 June 2015 (has links)
The tumor microenvironment is a complex community consisting of neoplastic cells, surrounding stromal cells, a broad array of immune cells, and a microbiota. By sheer numbers, the microbiota has its greatest manifestation in colorectal cancer (CRC) because the colon contains up to 100 trillion bacteria, outnumbering human cells by a factor of 10 and encoding a gene-content that is 100-fold larger than that of the human genome. Indeed, previous studies using germ-free mice in a variety of genetic backgrounds have demonstrated that the microbiota can impact colorectal tumorigenesis. In addition, specific strains of enterotoxigenic bacteria have been shown to promote colitis-associated cancer in mice. Here, we explore the composition of the tissue-associated microbiota in human CRC and evaluate the role of tumor-enriched microbes in potentiating colorectal tumorigenesis in mice. Advances in DNA sequencing technology have fueled a renaissance in the microbiome field. Deep sequencing metagenomics enables rapid, culture-independent characterization of a microbial community. We present PathSeq, a highly scalable software tool that performs computational subtraction on high-throughput sequencing data to identify nonhuman nucleic acids. PathSeq makes it possible to analyze sequence datasets as large as human whole-genomes for the purpose of metagenomics and also to discover previously unsequenced microorganisms. We used PathSeq to characterize the composition of the microbiota in human CRCusing whole-genome sequencing on nine tumor/normal pairs and 16S rDNA sequencing on an additional 95 pairs. The genus Fusobacterium was highly enriched in tumors, while the Bacteroidetes and Firmicutes phyla were depleted.We show that in the \(Apc^{Min/+}\) mouse model of intestinal tumorigenesis, Fusobacterium nucleatum increases tumor multiplicity, selectively recruits tumor-infiltrating myeloid cells, and is associated with a pro-inflammatory expression signature that is shared with human fusobacteria-positive colorectal carcinomas. We find that Fusobacterium spp. are enriched in human colonic adenomas relative to surrounding tissues and fusobacterial abundance is increased in stool samples from patients with colorectal adenomas and carcinomas, compared to healthy subjects. Collectively, these data support that fusobacteria may be involved in early stages of intestinal tumorigenesis and, through recruitment of tumor-infiltrating immune cells, may generate a pro-inflammatory tissue microenvironment conducive to colorectal neoplasia progression. Read more
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An exploration of ecological concepts in the context of antimicrobial resistance and the use of phytochemical compounds within the ruminant gut microbiomeKnox, Natalie 12 1900 (has links)
Secondary plant metabolites have recently been gaining interest in livestock production systems following the ban of in-feed antibiotics within the European Union. The rise in antimicrobial resistance found in pathogenic and non-pathogenic bacteria has lead to increased interest in the research community regarding the use of phythochemicals as an alternative to antibiotics. The purpose of this research was to evaluate the impact of including phytochemicals in a livestock production system. Specifically, a high tannin-containing forage, sainfoin (Onobrychis viciifolia), was evaluated in vitro for its antimicrobial effect on Escherichia coli. We determined that phytochemicals alone are not as inhibitory as synthetic antibiotics. Thus, the use of combination therapy to deter the development of antimicrobial resistance was evaluated. A myriad of plant compounds were screened for their synergistic interactions with ciprofloxacin. Geraniol, an essential oil, was identified to possess good antimicrobial activity and synergistic interactions with ciprofloxacin. Therefore the effect of long term exposure to both ciprofloxacin and geraniol were examined. Results demonstrated that once an antimicrobial concentration threshold was reached, resistance to ciprofloxacin increased markedly in the presence of both geraniol and ciprofloxacin. Finally, an in vivo trial was conducted in which forty steers were fed sainfoin or alfalfa over a 9-week period to evaluate its ability to reduce E. coli shedding and its impact on gut microbiota in the context of popular theoretical ecology concepts. Results from the in vivo study indicate that sainfoin was able to promote a slight decrease in generic E. coli shedding which could be maintained throughout the trial. Using high-throughput sequencing, the effect of sainfoin on the microbial ecosystem of the ruminant gut was evaluated. Sainfoin induced a significant shift in the microbial community structure of the rumen and to a lesser extent in the hindgut. Using ecology theories, a hypothesis was formulated regarding the mechanisms that mediate the development of tolerance and the fundamental ecological processes controlling microbial population shifts. Understanding how the gut ecosystem functions and predicting its behaviour in the presence of various fluctuating environmental conditions will enable more efficient manipulation of the rumen and promote best management practices in livestock production. Read more
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Characterizing Immune-modulatory Components of Human Milk: The Fate and Function of Soluble CD14 and the Human Milk MetagenomeWard, Tonya L. 13 May 2014 (has links)
Background
During the first stages of development human infants are either fed human milk or human milk substitutes (infant formulas). The composition of infant formulas and human milk differ drastically, including a difference in protein constituents and bacterial load. Due to the high global frequency of infant formula use, the humanization of infant formulas to better reflect the complex nature of human milk is warranted. To better understand the role of human milk components, the fate and function of a key bacterial sensor in human milk, soluble CD14, was determined. Additionally, the microbiome of human milk was analyzed from a metagenomic standpoint in an attempt to determine which types of bacteria are present in human milk and what their potential biological function might be.
Results
In rodent models, ingested sCD14 persisted in the gastrointestinal tract and was transferred intact into the blood stream. Once transferred to the blood, ingested sCD14 retained its ability to recognize lipopolysaccharide and initiate an immune response in pups. This transfer of sCD14 across the epithelial barrier was also observed in human cells in vitro, where it appears to be dependent on Toll-like receptor 4. Using Illumina sequencing and the MG-RAST pipeline, the human milk metagenome of ten mothers was sequenced. DNA from human milk aligned to over 360 prokaryotic genera, and contained 30,128 open reading frames assigned to various functional categories. The DNA from human milk was also found to harbor immune-modulatory DNA motifs that may play a significant role in immune development of the infant.
Conclusions
Given the complex nature of human milk in comparison to its bovine or plant based substitutes, the results presented in this thesis warrant future modification of infant formulas to include non-nutritive bioactive components. Current human milk components not yet present in infant formulas include the diverse microbiome of human milk, the immune-modulatory DNAs which those microbes harbor, and bioactive human proteins such as sCD14. Read more
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An exploration of ecological concepts in the context of antimicrobial resistance and the use of phytochemical compounds within the ruminant gut microbiomeKnox, Natalie 12 1900 (has links)
Secondary plant metabolites have recently been gaining interest in livestock production systems following the ban of in-feed antibiotics within the European Union. The rise in antimicrobial resistance found in pathogenic and non-pathogenic bacteria has lead to increased interest in the research community regarding the use of phythochemicals as an alternative to antibiotics. The purpose of this research was to evaluate the impact of including phytochemicals in a livestock production system. Specifically, a high tannin-containing forage, sainfoin (Onobrychis viciifolia), was evaluated in vitro for its antimicrobial effect on Escherichia coli. We determined that phytochemicals alone are not as inhibitory as synthetic antibiotics. Thus, the use of combination therapy to deter the development of antimicrobial resistance was evaluated. A myriad of plant compounds were screened for their synergistic interactions with ciprofloxacin. Geraniol, an essential oil, was identified to possess good antimicrobial activity and synergistic interactions with ciprofloxacin. Therefore the effect of long term exposure to both ciprofloxacin and geraniol were examined. Results demonstrated that once an antimicrobial concentration threshold was reached, resistance to ciprofloxacin increased markedly in the presence of both geraniol and ciprofloxacin. Finally, an in vivo trial was conducted in which forty steers were fed sainfoin or alfalfa over a 9-week period to evaluate its ability to reduce E. coli shedding and its impact on gut microbiota in the context of popular theoretical ecology concepts. Results from the in vivo study indicate that sainfoin was able to promote a slight decrease in generic E. coli shedding which could be maintained throughout the trial. Using high-throughput sequencing, the effect of sainfoin on the microbial ecosystem of the ruminant gut was evaluated. Sainfoin induced a significant shift in the microbial community structure of the rumen and to a lesser extent in the hindgut. Using ecology theories, a hypothesis was formulated regarding the mechanisms that mediate the development of tolerance and the fundamental ecological processes controlling microbial population shifts. Understanding how the gut ecosystem functions and predicting its behaviour in the presence of various fluctuating environmental conditions will enable more efficient manipulation of the rumen and promote best management practices in livestock production. Read more
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Effects of in-feed additives on performance, gut microbe ecology, and antimicrobial susceptibility of enterobacteria on nursery pigsWilliams, Hayden Ervin January 1900 (has links)
Master of Science / Department of Animal Sciences and Industry / Joel M. DeRouchey / Jason C. Woodworth / Two experiments using a total of 720 nursery pigs were used to determine the effects of Elarom SES, in-feed antibiotics, zinc, or copper on nursery pig growth performance and fecal consistency. Two experiments using a total of 1,534 nursery pigs were used to determine the effects of formaldehyde inclusion, lysine level, and synthetic amino acid inclusion on nursery pig performance, amino acid utilization, and gut microbial community. One experiment using a total of 300 nursery pigs were used to determine the effects of chlortetracycline (CTC) or a probiotic inclusion on nursery pig growth performance and antimicrobial susceptibility. Experiment 1 determined the effect of Elarom SES, in-feed antibiotics, or zinc on nursery pig performance and fecal consistency. The addition of Elarom SES or ZnO alone reduced ADG, but G:F was poorest when all three additives were fed in combination. Addition of in-feed antibiotics increased ADG and G:F throughout the study. Experiment 2 determined the effects of Elarom SES or copper inclusion on nursery pig performance and fecal consistency. The addition of Elarom SES or increasing copper did not provide consistent benefits in performance. In both experiments, there were no individual or overall treatment effects or treatment × day interactions observed for fecal consistency. Experiment 3 compared the effects of formaldehyde source and lysine level on nursery pig growth performance. Regardless of source or lys level, the inclusion of formaldehyde in nursery pig diets marginally reduced ADG and resulted in poorer G:F. Experiment 4 compared the effects of formaldehyde and synthetic amino acid inclusion level on nursery pig growth performance, amino acid utilization, and gut microbial community. The inclusion of Sal CURB in diets reduced ADG and ending BW while inclusion decreased ADFI. ADFI response was dependent on synthetic amino acid level in the diet. Sal CURB inclusion in diets reduced total and available lysine, but reduced bacterial microflora in treatment feed. Experiment 5 determined the effects of CTC or a probiotic on nursery pig performance and antimicrobial susceptibility. The addition of CTC to diets improved ADG, ADFI, and ending BW. The addition of Poultry Star improved ADFI and d 14 BW, but benefits did not carry throughout the study. Read more
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Are Weight and Diet Related to the Gut Microbiome in Healthy College Students Living in the Dorms? : A Cross-Sectional Observational AnalysisJanuary 2016 (has links)
abstract: College weight gain and obesity are significant problems impacting our society, leading to a considerable number of comorbidities during and after college. Gut microbiota are increasingly recognized for their role in obesity and weight gain. Currently, research exploring the gut microbiome and its associations with dietary intake and body mass index (BMI) is limited among this population. Therefore, the purpose of this study was to assess associations between the gut microbiome, BMI, and dietary intake in a population of healthy college students living in two dorms at Arizona State University (n=90). Cross-sectional analyses were undertaken including 24-hour dietary recalls and anthropometrics (height, weight and BMI). High throughput Bacterial 16S rRNA gene sequencing of fecal samples was performed to quantify the gut microbiome and analyses were performed at phyla and family levels. Within this population, the mean BMI was 24.4 ± 5.3 kg/m2 and mean caloric intake was 1684 ± 947 kcals/day. Bacterial community analysis revealed that there were four predominant phyla and 12 predominant families accounting for 99.3% and 97.1% of overall microbial communities, respectively. Results of this study suggested that a significant association occurred between one principal component (impacted most by 22 microbial genera primarily within Firmicutes) and BMI (R2=0.053, p=0.0301). No significant correlations or group differences were observed when assessing the Firmicutes/Bacteroidetes ratio in relation to BMI or habitual dietary intake. These results provide a basis for gut microbiome research in college populations. Although, findings suggest that groups of microbial genera may be most influential in obesity, further longitudinal research is necessary to more accurately describe these associations over me. Findings from future research may be used to develop interventions to shift the gut microbiome to help moderate or prevent excess weight gain during this important life stage. / Dissertation/Thesis / Masters Thesis Nutrition 2016 Read more
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