Browsing by Author "Yeoman, Carl J."

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Biogenic Amines Increase the Odds of Bacterial Vaginosis and Affect the Growth of and Lactic Acid Production by Vaginal Lactobacillus spp.
(American Society for Microbiology, 2021-04) Borgogna, Joanna-Lynn C.; Shardell, Michelle D.; Grace, Savannah G.; Santori, Elisa K.; Americus, Benjamin; Li, Zhong; Ulanov, Alexander; Forney, Larry; Nelson, Tiffanie M.; Brotman, Rebecca M.; Ravel, Jacques; Yeoman, Carl J.
Bacterial vaginosis (BV) is the most common vaginal disorder of reproductive-aged women, yet its etiology remains enigmatic. One clinical symptom of BV, malodor, is linked to the microbial production of biogenic amines (BA). Using targeted liquid chromatography mass spectrometry, we analyzed 149 longitudinally collected vaginal samples to determine the in vivo concentrations of the most common BAs and then assessed their relationship to BV and effect upon the growth kinetics of axenically cultured vaginal Lactobacillus species. Increases in cadaverine, putrescine, and tyramine were associated with greater odds of women transitioning from L. crispatus-dominated vaginal microbiota to microbiota that have a paucity of Lactobacillus spp. and from Nugent scores of 0 to 3 to Nugent scores of 7 to 10, consistent with BV. Exposure to putrescine lengthened the lag time and/or slowed the growth of all vaginal Lactobacillus spp. except L. jensenii 62G. L. iners AB107’s lag time was lengthened by cadaverine but reduced in the presence of spermidine and spermine. The growth rate of L. crispatus VPI 3199 was slowed by cadaverine and tyramine, and strain-specific responses to spermine and spermidine were observed. BAs were associated with reduced production of d- and l-lactic acid by vaginal Lactobacillus spp., and this effect was independent of their effect upon Lactobacillus species growth. The exceptions were higher levels of d- and l-lactic acid by two strains of L. crispatus when grown in the presence of spermine. Results of this study provide evidence of a direct impact of common biogenic amines on vaginal Lactobacillus spp.
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.
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.
Determinants of the postprandial triglyceride response to a high-fat meal in healthy overweight and obese adults
(Springer Nature, 2021-09) Wilson, Stephanie M.; Maes, Adam P.; Yeoman, Carl J.; Walk, Seth T.; Miles, Mary P.
Background. Dyslipidemia is a feature of impaired metabolic health in conjunction with impaired glucose metabolism and central obesity. However, the contribution of factors to postprandial lipemia in healthy but metabolically at-risk adults is not well understood. We investigated the collective contribution of several physiologic and lifestyle factors to postprandial triglyceride (TG) response to a high-fat meal in healthy, overweight and obese adults. Methods. Overweight and obese adults (n = 35) underwent a high-fat meal challenge with blood sampled at fasting and hourly in the 4-hour postprandial period after a breakfast containing 50 g fat. Incremental area under the curve (iAUC) and postprandial magnitude for TG were calculated and data analyzed using a linear model with physiologic and lifestyle characteristics as explanatory variables. Model reduction was used to assess which explanatory variables contributed most to the postprandial TG response. Results. TG responses to a high-fat meal were variable between individuals, with approximately 57 % of participants exceeded the nonfasting threshold for hypertriglyceridemia. Visceral adiposity was the strongest predictor of TG iAUC (β = 0.53, p = 0.01), followed by aerobic exercise frequency (β = 0.31, p = 0.05), insulin resistance based on HOMA-IR (β = 0.30, p = 0.04), and relative exercise intensity at which substrate utilization crossover occurred (β = 0.05, p = 0.04). For postprandial TG magnitude, visceral adiposity was a strong predictor (β = 0.43, p < 0.001) followed by aerobic exercise frequency (β = 0.23, p = 0.01), and exercise intensity for substrate utilization crossover (β = 0.53, p = 0.01). Conclusions. Postprandial TG responses to a high-fat meal was partially explained by several physiologic and lifestyle characteristics, including visceral adiposity, insulin resistance, aerobic exercise frequency, and relative substrate utilization crossover during exercise.
Differences in amino acid catabolism by gut microbes with/without prebiotics inclusion in GDDY-based diet affect feed utilization in rainbow trout
(2017-09) Betiku, Omolola C.; Yeoman, Carl J.; Gaylord, T. Gibson; Duff, Glenn C.; Hamerly, Timothy; Bothner, Brian; Block, Stephanie S.; Sealey, Wendy M.
There is the need to enhance feed efficiency and growth of rainbow trout to reduce production costs of cultured fish. This study conducted a 3 × 4 factorial experiment with three graded levels of grain distiller dried yeast (GDDY) protein (0%, 50%, 75%) as replacement for fishmeal and four different prebiotics inclusion levels (0% (control), 0.4%, 1% mannooligosaccharides (MOS), and 1% GroBiotic A). The feeding trial was conducted for 12 weeks during which fish were fed daily to apparent satiation. Growth of rainbow trout was not affected by replacement of fishmeal with GDDY, but feed conversion ratio (P < 0.0001) was greater at the highest level of GDDY inclusion. Increasing GDDY inclusion significantly increased feed intake (P < 0.00015), which resulted in poor feed utilization. Acetic (P = 0.1994), propionic (P = 0.8037), butyric (P = 0.6268), valeric (P = 0.5877), and isovaleric (P = 0.5919) acids profiles did not differ by diet nor with inclusion of MOS or GroBiotic A. Whole shotgun metagenomic analyses of the gastrointestinal tract (GIT) microbiota revealed enrichment in the fungal phyla Ascomycota and Basidiomycota and the bacterial phylum Actinobacteria in the GDDY-fed fish compared to those fed the control fishmeal-based diet, which may be reflective of the species endogenous in GDDY. Microbial genes involved in branched-chain amino acid metabolism (glutamate, glutamine, aspartate) (P = 0.028) and glutamate dehydrogenase clusters (P = 0.0192), were also elevated in the fish fed the 75% GDDY-based diet. The results from this study indicate the potential for microbially-mediated catabolism of the non-essential amino acids, and suggest this activity may significantly influence efficient utilization of dietary nitrogen in the yeast-based protein diet.
Dryland Cropping Systems, Weed Communities, and Disease Status Modulate the Effect of Climate Conditions on Wheat Soil Bacterial Communities
(2020-08) Ishaq, Suzanne L.; Seipel, Tim F.; Yeoman, Carl J.; Menalled, Fabian D.
Little knowledge exists on how soil bacteria in agricultural settings are impacted by management practices and environmental conditions in current and predicted climate scenarios. We assessed the impact of soil moisture, soil temperature, weed communities, and disease status on soil bacterial communities in three cropping systems: (i) conventional no-till (CNT) systems utilizing synthetic pesticides and herbicides, (ii) USDA-certified tilled organic (OT) systems, and (iii) USDA-certified organic systems with sheep grazing (OG). Sampling date within the growing season and associated soil temperature and moisture exerted the greatest effect on bacterial communities, followed by cropping system, Wheat streak mosaic virus (WSMV) infection status, and weed community. Soil temperature was negatively correlated with bacterial richness and evenness, while soil moisture was positively correlated with bacterial richness and evenness. Soil temperature and soil moisture independently altered soil bacterial community similarity between treatments. Inoculation of wheat with WSMV altered the associated soil bacteria, and there were interactions between disease status and cropping system, sampling date, and climate conditions, indicating the effect of multiple stressors on bacterial communities in soil. In May and July, cropping system altered the effect of climate change on the bacterial community composition in hotter conditions and in hotter and drier conditions compared to ambient conditions, in samples not treated with WSMV. Overall, this study indicates that predicted climate modifications as well as biological stressors play a fundamental role in the impact of cropping systems on soil bacterial communities.
Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla)
(2016-11) Vickova, Klara; Gomez, Andres; Whittier, Christopher A.; Todd, Angelique F.; Yeoman, Carl J.; Nelson, Karen E.; Wilson, Brenda A.; Stumpf, Rebecca M.; Modry, David; White, Bryan A.; Leigh, Steven R.
The mammalian gastrointestinal (GI) microbiome, which plays indispensable roles in host nutrition and health, is affected by numerous intrinsic and extrinsic factors. Among them, antibiotic (ATB) treatment is reported to have a significant effect on GI microbiome composition in humans and other animals. However, the impact of ATBs on the GI microbiome of free-ranging or even captive great apes remains poorly characterized. Here, we investigated the effect of cephalosporin treatment (delivered by intramuscular dart injection during a serious respiratory outbreak) on the GI microbiome of a wild habituated group of western lowland gorillas (Gorilla gorilla gorilla) in the Dzanga Sangha Protected Areas, Central African Republic. We examined 36 fecal samples from eight individuals, including samples before and after ATB treatment, and characterized the GI microbiome composition using Illumina-MiSeq sequencing of the bacterial 16S rRNA gene. The GI microbial profiles of samples from the same individuals before and after ATB administration indicate that the ATB treatment impacts GI microbiome stability and the relative abundance of particular bacterial taxa within the colonic ecosystem of wild gorillas. We observed a statistically significant increase in Firmicutes and a decrease in Bacteroidetes levels after ATB treatment. We found disruption of the fibrolytic community linked with a decrease of Ruminoccocus levels as a result of ATB treatment. Nevertheless, the nature of the changes observed after ATB treatment differs among gorillas and thus is dependent on the individual host. This study has important implications for ecology, management, and conservation of wild primates.
Feed efficiency phenotypes in lambs involve changes in ruminal, colonic, and small-intestine-located microbiota
(2017-06) Perea, K.; Perz, Katharine A.; Olivo, Sarah K.; Williams, Andrew F.; Lachman, Medora M.; Ishaq, Suzanne L.; Thomson, Jennifer M.; Yeoman, Carl J.
Several studies have revealed differences in rumen-located microbes between greatly efficient and inefficient animals; however, how the microbiota vary in the hind gastrointestinal tract (GIT) has only been sparsely explored and how they vary in the small intestine remains to be determined. We therefore sampled the microbiota of the duodenum, jejunum, ileum, colon, and colorectally-obtained feces, in addition to the rumen of 12 lambs that, in a residual feed intake trial, were found to be at either extreme of feed efficiency phenotypes. The 16S rRNA gene (V3-V4 region) profiles of all samples were analyzed and revealed unique microbiota in all GIT locations except the jejunum and ileum (ANOSIM R > 0.2, P < 0.001). Measures of beta-diversity revealed greater dissimilarity between more anatomically distant GIT locations (e.g., Rumen-Duodenum, ANOSIM R = 0.365, P < 0.001; Rumen-Colon, ANOSIM R = 1, P < 0.001) with the nearest distal region typically more similar than the nearest proximal location. The relative abundances of 13 operational taxonomic units (OTUs) from the duodenum, jejunum, colon, and feces, as well as the rumen, differed between efficient and inefficient animals (Bonferroni corrected, P < 0.05), while another 2 OTUs trended toward significance. These OTUs were classified as taxa with known roles in fibrolysis (Fibrobacteres, Ruminococcaceae, and Saccharofermentans) and others that are commonly associated with health (Bifidobacteriaceae, and Christensenellaceae) and dysbiosis (Proteobacteria). Our findings show biospatial delineations of microbiota throughout the GIT and suggest that feed efficiency extends beyond the rumen, transcending these regions, and involves increases in both rumen-and colon-located fibrolytic taxa, increases in bifidobacterial species in the small intestine, and reductions in small intestine and distal GIT-located Proteobacteria.
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 Î²-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.
Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns
(2016-03) Gomez, Andres; Petrzelkova, Klara J.; Burns, Michael B.; Yeoman, Carl J.; Amato, Katherine R.; Vlckova, Klara; Modry, David; Todd, Angelique F.; Jost Robinson, Carolyn A.; Remis, Melissa J.; Torralba, Manolito G.; Morton, Elise; Umaña, Juan D.; Carbonero, Franck; Gaskins, H. Rex; Nelson, Karen E.; Wilson, Brenda A.; Stumpf, Rebecca M.; White, Bryan A.; Leigh, Steven R.; Blekhman, Ran
To understand how the gut microbiome is impacted by human adaptation to varying environments, we explored gut bacterial communities in the BaAka rainforest hunter-gatherers and their agriculturalist Bantu neighbors in the Central African Republic. Although the microbiome of both groups is compositionally similar, hunter-gatherers harbor increased abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome is dominated by Firmicutes. Comparisons with US Americans reveal microbiome differences between Africans and westerners but show western-like features in the Bantu, including an increased abundance of predictive carbohydrate and xenobiotic metabolic pathways. In contrast, the hunter-gatherer gut shows increased abundance of predicted virulence, amino acid, and vitamin metabolism functions, as well as dominance of lipid and amino-acid-derived metabolites, as determined through metabolomics. Our results demonstrate gradients of traditional subsistence patterns in two neighboring African groups and highlight the adaptability of the microbiome in response to host ecology.
Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure
(2017-02) Ishaq, Suzanne L.; Johnson, Stephen P.; Miller, Zachariah J.; Lehnhoff, Erik A.; Olivo, Sarah K.; Yeoman, Carl J.; Menalled, Fabian D.
Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P<0.001) and had more discriminant taxa delineating groups (linear discriminant analysis). Living inoculum soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P<0.05), and more discriminant taxa than conventionally farmed inoculum-treated soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition.
In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses
(American Society for Microbiology, 2021-04) Yeoman, Carl J.; Fields, Christopher J.; Lepercq, Pascale; Ruiz, Philippe; Forano, Evelyne; White, Bryan A.; Mosoni, Pascale
Ruminant animals, including cattle and sheep, depend on their rumen microbiota to digest plant biomass and convert it into absorbable energy. Considering that the extent of meat and milk production depends on the efficiency of the microbiota to deconstruct plant cell walls, the functionality of predominant rumen cellulolytic bacteria, Fibrobacter succinogenes , Ruminococcus albus , and Ruminococcus flavefaciens , has been extensively studied in vitro to obtain a better knowledge of how they operate to hydrolyze polysaccharides and ultimately find ways to enhance animal production.
Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications
(2016-07) Stumpf, Rebecca M.; Gomez, Andres; Amato, Katherine R.; Yeoman, Carl J.; Polk, J. D.; Wilson, Brenda A.; Nelson, Karen E.; White, B. A.; Leigh, Steven R.
Conservation strategies require multifaceted approaches to monitor and protect primate populations, many of which are rapidly declining around the world. We propose that microbial ecology and next-generation microbiome analyses offer valuable perspectives and tools for investigating and monitoring primate health and improving conservation efforts. The microbial communities inhabiting primates and other taxa profoundly affect host health, nutrition, physiology, and immune systems, through relationships that range from commensal and mutualistic to pathogenic. Recent advances in DNA sequencing now make it feasible and economically viable to identify microbiomes among and within hosts. Herein, we highlight several examples in which microbial analyses of primates can aid conservation approaches that are broadly applicable across other taxa. First, we highlight evidence for clear spatial variation (e.g. biogeographic niche specificity, both within the anatomical regions of the host body, as well as in the geographic location of the host) and temporal (e.g. seasonal, ontogenetic) patterns in microbial distribution. We emphasize that microbial communities are sensitive to alterations in the external environment and that microbial diversity correlates with habitat quality, imposing direct health consequences. Incorporating microbial host and biogeographic variation holds great potential for forest corridor assessments and for reintroduction efforts. Finally, microbial pathogens transmitted between humans and wild primate populations carry both direct and indirect conservation implications. Principally, we argue that phylogenetic analyses of infectious pathogens (e.g., Ebola, dengue, Borellia, and Treponema) can aid our understanding of modes of disease transmission and aid conservation disease abatement efforts. The application of microbial analyses to conservation is currently in its infancy but holds enormous potential. To date, no conservation policy or legislation includes microbiome assessments. Integrating new understanding of the patterns of microbial diversity and early signs of impending microbial disruption offer valuable tools for informing conservation strategies and monitoring and promoting primate (including human) health.
Null Mutations of Group A Streptococcus Orphan Kinase RocA: Selection in Mouse Infection and Comparison with CovS Mutations in Alteration of in vitro and in vivo Protease SpeB Expression and Virulence
(2017-01) Feng, Wenchao; Minor, Dylan; Liu, Mengyao; Li, Jinquan; Ishaq, Suzanne L.; Yeoman, Carl J.; Lei, Benfang
Group A Streptococcus (GAS) acquires mutations of virulence regulator CovRS in human and mouse infections that upregulate virulence genes and downregulate protease SpeB. To identify in vivo mutants with novel phenotype, GAS isolates from mouse infection were screened by enzymatic assays for SpeB and platelet-activating factor acetylhydrolase Sse, identifying a new type of variants that had enhanced Sse expression and normal SpeB production (Sse(A+)SpeB(A+)). Sse(A+)SpeB(A+) variants have transcripts levels of CovRS-controlled virulence genes comparable to those of a covS mutant but had no covRS mutations. Genome resequencing of an Sse(A+)SpeB(A+) isolate identified a C605A nonsense mutation in orphan kinase gene rocA, and 6 other Sse(A+)SpeB(A+) isolates also had nonsense mutations or small indels of rocA RocA and CovS mutants have similar enhancement in expression of CovRS-controlled virulence genes at the exponential growth phase; however, mutations of RocA, but not CovS, do not downregulate speB transcription at stationary growth phase and in subcutaneous infection of mice. RocA and CovS mutations have greater enhancement in expression of hasA than spyCEP in mouse skin infection in comparison with wild type GAS. RocA mutants rank between wild type GAS and CovS mutants in skin invasion, inhibition of neutrophil recruitment, and virulence in subcutaneous infection of mice. Thus, GAS RocA mutants can be selected in subcutaneous infection of mice and exhibit distinct gene expression pattern and virulence from CovS mutants. The findings provide novel information for the understanding of GAS fitness mutations in vivo, virulence gene regulation, in vivo gene expression, and virulence.
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 â€“ 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.
Perceived Stress and Molecular-BV in the NIH Longitudinal Study of Vaginal Flora
(Oxford University Press, 2021-05) Turpin, Rodman; Slopen, Natalie; Borgogna, Joanna C.; Yeoman, Carl J.; He, Xin; Miller, Ryan S.; Klebanoff, Mark A.; Ravel, Jacques; Brotman, Rebecca M.
Vaginal microbiota provide the first line of defense against urogenital infections primarily through protective actions of Lactobacillus spp. Perceived stress increases susceptibility to infection through several mechanisms, including suppression of immune function. We investigated if stress was associated with deleterious changes to vaginal bacterial composition in a subsample of 572 women in the Longitudinal Study of Vaginal Flora, sampled from 1999 through 2002. Using Cox proportional-hazard models, both unadjusted and adjusted for sociodemographics and sexual behaviors, participants who exhibited a 5 unit-increase in Cohen’s perceived stress scale had greater risk (aHR=1.40, 95% CI 1.13-1.74) of developing molecular bacterial vaginosis (BV), a state with low Lactobacillus abundance and diverse anaerobic bacteria. A 5-unit stress increase was also associated with greater risks for transitioning from the L. iners-dominated community state type (26% higher) to molecular-BV (aHR=1.26, 95% CI 1.01-1.56) or maintaining molecular-BV from baseline (aHR=1.23, 95% CI 1.01-1.47). Inversely, women with baseline molecular-BV reporting a 5-unit stress increase were less likely to transition to microbiota dominated by L. crispatus, L. gasseri, or L. jensenii (aHR=0.81, 95% CI 0.68-0.99). These findings suggest psychosocial stress is associated with vaginal microbiota composition, inviting a more mechanistic exploration of the relationship between psychosocial stress and molecular-BV.
Physical Activity and Inflammation Phenotype Conversion
(Clinical Exercise Physiology Association, 2019) MIles, Mary P.; Wilson, Stephanie; Yeoman, Carl J.
Inflammation is a protective response to infection or injury; however, persistent microtraumas at the tissue level may result in chronic low-grade inflammation that plays both direct and indirect roles in the development of many diseases and aging. The purpose of this review is to describe the underlying physiology of low-grade inflammation and highlight potential inflammation lowering effects of physical activity (PA). Unique contributions of this review are to introduce the concept of inflammation phenotype flexibility in contrast to the low-grade inflammation state and describe how PA influences inflammation phenotype by altering muscle, gut, adipose, and postprandial metabolism. Pro-inflammatory M1 macrophages and cytokines—such as tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6—contribute to low-grade inflammation. Among the mechanisms that commonly contribute to low-grade inflammation are dysfunctional adipose tissue, a leaky gut, gut microbiota that promotes inflammation, and large postprandial glycemic and lipidemic responses. Physical activity may lower inflammation by decreasing M1 macrophages in visceral adipose tissue, decreasing adipose tissue volume, production of anti-inflammatory myokines, promotion of butyrate-producing members of the gut microbiota, improved gut barrier function, and lowering of postprandial glycemic and lipidemic responses. While exercise has many anti-inflammatory mechanisms, phenotype conversion is complex, multifaceted, and difficult to achieve. Our understanding of how PA influences inflammation must include acute exercise-induced anti-inflammatory effects, contribution to the inflammation state from multiple sources in the body, and phenotypic shifts underpinning low-grade inflammation.
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.
Relationships among intramammary health, udder and teat characteristics, and productivity of extensively managed ewes
(Oxford University Press, 2021-02) Knuth, Ryan M.; Stewart, Whit C.; Taylor, Joshua B.; Bisha, Bledar; Yeoman, Carl J.; Van Emon, Megan L.; Murphy, Thomas W.
Mastitis is an economically important disease and its subclinical state is difficult to diagnose, which makes mitigation more challenging. The objectives of this study were to screen clinically healthy ewes in order to 1) identify cultivable microbial species in milk, 2) evaluate somatic cell count (SCC) thresholds associated with intramammary infection, and 3) estimate relationships between udder and teat morphometric traits, SCC, and ewe productivity. Milk was collected from two flocks in early (<5 d) and peak (30 to 45 d) lactation to quantify SCC (n = 530) and numerate cultivable microbial species by culture-based isolation followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS; n = 243) identification. Within flock and lactation stage, 11% to 74% (mean = 36%) of samples were culture positive. More than 50 unique identifications were classified by MALDI-TOF MS analysis, and Bacillus licheniformis (18% to 27%), Micrococcus flavus (25%), Bacillus amyloliquefaciens (7% to 18%), and Staphylococcus epidermidis (26%) were among the most common within flock and across lactation stage. Optimum SCC thresholds to identify culture-positive samples ranged from 175 × 103 to 1,675 × 103 cells/mL. Ewe productivity was assessed as total 120-d adjusted litter weight (LW120) and analyzed within flock with breed, parity, year, and the linear covariate of log10 SCC (LSCC) at early or peak lactation. Although dependent on lactation stage and year, each 1-unit increase in LSCC (e.g., an increase in SCC from 100 × 103 to 1,000 × 103 cells/mL) was predicted to decrease LW120 between 9.5 and 16.1 kg when significant. Udder and teat traits included udder circumference, teat length, teat placement, and degree of separation of the udder halves. Correlations between traits were generally low to moderate within and across lactation stage and most were not consistently predictive of ewe LSCC. Overall, the frequencies of bacteria-positive milk samples indicated that subclinical mastitis (SCM) is common in these flocks and can impact ewe productivity. Therefore, future research is warranted to investigate pathways and timing of microbial invasion, genomic regions associated with susceptibility, and husbandry to mitigate the impact of SCM in extensively managed ewes.
Soil bacterial community response to cover crop introduction in a wheat-based dryland cropping system
(Frontiers Media SA, 2022-11) Eberly, Jed O.; Bourgault, Maryse; Dafo, Julia M.; Yeoman, Carl J.; Wyffels, Samuel A.; Lamb, Peggy F.; Boss, Darrin L.
The incorporation of cover crops into cropping systems is important for enhancing soil health in agricultural systems. Soil microbes contribute to soil health by supplying key nutrients and providing protection against plant pests, diseases, and abiotic stress. While research has demonstrated the connection between cover crops and the soil microbiology, less is known regarding the impact of cover crops on the soil microbial community in semi-arid regions of the Northern Great Plains. Our objectives were to evaluate changes in the soil bacterial community composition and community networks in wheat grown after multi-species cover crops. Cover crops were compared to continuous cropping and crop/fallow systems and the effects of cover crop termination methods were also evaluated. Cover crops consisted of a cool season multispecies mix, mid-season multispecies mix, and a warm season multispecies mix, which were grown in rotation with winter wheat. A continuous cropping (wheat/barley) and wheat/fallow system were also included along with cover crop termination by grazing, herbicide application, and haying. Cover crop treatments and termination methods had no significant impact on microbial community alpha diversity. Cover crop termination methods also had no significant impact on microbial community beta diversity. Families belonging to the phyla Actinobacteria, Bacterioidota, and Proteobacteria were more abundant in the cool season cover crop treatment compared to the warm season cover crop treatment. Co-occurrence network analysis indicated that incorporation of cool season cover crops or mid-season mixes in a wheat-based cropping system led to greater complexity and connectivity within these microbial networks compared to the other treatments which suggests these communities may be more resilient to environmental disturbances.