8 research outputs found
Developing Non-invasive Microbial Biomarkers to Inform Elk (C. canadensis) Health in Wild Montana Populations
No full textBackground: The composition of the fecal microbiome of mammals is associated with changes in diet, stress, disease and physical condition of an animal. When managing wildlife, Federal and State agencies currently must rely on invasive sampling and coarse observational demographic data to make their decisions. By developing microbiome-based biomarkers that vary as a function of animal body condition and disease, we hope to provide managers with the ability to monitor direct impacts from environmental stressors on individual animals and the herd. This approach represents a low cost, non-invasive sampling method based simply on fecal pellet collection in the field and intestinal microbiome analysis in the lab. Methods: We analyzed 111 individual wild elk (Cervus canadensis) using Illumina MiSeq sequencing of partial 16S-rRNA gene amplicons from the fecal microbiome. Montana Fish, Wildlife and Parks collected the scat and linked body condition metrics from three GPS collared populations in Montana in winter using helicopter teams and invasive sampling methods. Using the QIIME program and a floating search feature selection with leave-one-out cross validation (CV) we were able to elucidate informative bacterial taxa and general bacterial composition profiles and compare them to known body conditions. Results: This experiment succeeded in initial development and confirmation of microbial biomarkers in elk with individuals from the Sapphire population clustering significantly using CV by pregnancy (CV 92.31%), sex (CV 96.15%) and body fat percentage (CV 96.15%) in females using linear discriminate analysis (LDA). Conclusion: As our microbial biomarker approach matures, we hope to apply it broadly toward the management of wildlife species non-invasively. Non-invasive biomarkers can support endangered species research and conservation when animal populations are fragile and cannot sustain traditional invasive sampling or when more cost effective information is desired
PREDICTING GENE FLOW CORRIDORS AND WILDLIFE HEALTH USING LANDSCAPE GENOMICS AND NON-INVASIVE METAGENOMIC MONITORING: INVESTIGATION OF ELK (CERVUS CANADENSIS) IN THE GREATER YELLOWSTONE ECOSYSTEM
No full textThis work develops and applies novel methods for metagenomic and landscape genomic (LSG) investigation of wildlife populations, specifically in Rocky Mountain elk (Cervus canadensis) in the Greater Yellowstone Ecosystem (GYE). Host fecal microbiomes facilitate and reflect interactions between the host and its environment. We conducted metagenomic surveys and developed a machinelearning classifier for microbiomes that provided new insights into elk-microbiome biogeography, and the impact of fecal microbiomes on host health and the ecology of elk-wolf (Canis lupus) predation. In the microbiome study, we found strong evidence for multiple management-relevant factors structuring elk microbiomes including body fat percentage, sex, age, and elk location. The use of non-invasive fecal sampling for wildlife monitoring requires microbiome stability across time in ambient conditions after defecation. Using a longitudinal experiment and linear mixed models, we confirmed the elk microbiome is stable under varying field conditions and fecal sample age up to 14 days. These findings support the value of the non-invasive fecal microbiomes in augmenting wildlife monitoring techniques. Applying these methods to living and wolf-killed elk microbiomes from the GYE, we found strongly associating bacteria involved in short-chain fatty-acid (SCFA) metabolism. This suggests a link between elk condition and predation vulnerability facilitated by microbial mediators. Landscape connectivity corridors and barriers to gene flow are crucial to planning and management of wildlife populations. Using LSG methods, we identified gene flow corridors, partial barriers, and population structure to guide sexspecific disease interventions in the GYE. Different corridors of gene flow for mitochondrial DNA (mtDNA) and biparentally inherited nuclear DNA (nDNA) were identified. For nDNA, a combined resistance surface of elevation and landcover performed better than geographic (Euclidean) distance in describing genetic patterns and models approximate previously published GPS-based long-distance elk migration routes. Our results suggest interventions limiting female elk dispersal along low-elevation corridors may slow spread of maternally transmitted diseases like brucellosis. This research demonstrates usefulness of host-associated microbiomes and LSG assessments for understanding and monitoring animal health, links to predator-prey interactions, and landscape connectivity. These findings help address difficult problems in applied conservation while the novel microbiome and LSG approaches should be useful in species and systems beyond elk and the GYE
Developing Microbial Biomarkers to Non-invasively Assess Health in Wild Elk (Cervus canadensis) Populations
No full textThe composition of the intestinal bacterial community (intestinal microbiome) of mammals is associated with changes in diet, stress, disease and physical condition of the animal. The relationship between health and the microbiome has been extensively demonstrated in studies of humans and mice; this provides strong support for its potential utility in wildlife. When managing elk (Cervus canadensis), federal and state agencies currently must rely on invasive sampling and coarse demographic data on which to base their decisions. By developing microbiome-based biomarkers that vary as a function of elk body condition and disease (i.e. microbial biomarkers), we hope to provide managers with the ability to monitor direct impacts from environmental stressors on individual animals and the herd. This approach, once established, represents a low cost, non-invasive sampling method based simply on fecal pellet collection in the field and intestinal microbiome analysis in the lab. Montana Fish, Wildlife and Parks collected the scat and linked body condition metrics from four GPS collared populations in Montana in winter 2014, using helicopter teams and invasive sampling methods. We analyzed 111 individual wild elk fecal microbiomes using Illumina MiSeq sequencing of partial 16S-rRNA gene amplicons. Using the QIIME pipeline and a floating search feature selection algorithm (SFFS) with linear discriminate analysis (LDA) and leave-one-out cross validation (CV) we were able to elucidate informative patterns in bacterial taxa presence and abundance by comparing them to various measured body conditions and geographic locations of elk sampled. Microbial biomarkers provide potential for managers to routinely obtain fine scale non-invasive health metrics from scat samples obtained in the field for species of concern
Non-invasive monitoring of multiple wildlife health factors by fecal microbiome analysis
No full text<p>Fecal microbial biomarkers represent a less invasive alternative for acquiring information on wildlife populations than many traditional sampling methodologies. Our goal was to evaluate linkages between fecal microbiome communities in Rocky Mountain elk (<i>Cervus canadensis</i>) and four host factors including sex, age, population, and physical condition (body-fat). We paired a feature-selection algorithm with an LDA-classifier trained on elk differential bacterial abundance (16S-rRNA amplicon survey) to predict host health factors from 104 elk microbiomes across four elk populations. We validated the accuracy of the various classifier predictions with leave-one-out cross-validation using known measurements. We demonstrate that the elk fecal microbiome can predict the four host factors tested. Our results show that elk microbiomes respond to both the strong extrinsic factor of biogeography and simultaneously occurring, but more subtle, intrinsic forces of individual body-fat, sex, and age class. Thus, we have developed and described herein a generalizable approach to disentangle microbiome responses attributed to multiple host factors of varying strength from the same bacterial sequence data set. Wildlife conservation and management presents many challenges, but we demonstrate that non-invasive microbiome surveys from scat samples can provide alternative options for wildlife population monitoring. We believe that, with further validation, this method could be broadly applicable in other species and potentially predict other measurements. Our study can help guide the future development of microbiome-based monitoring of wildlife populations and supports hypothetical expectations found in host-microbiome theory.</p>
Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment
No full textWildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems
DataSheet_2_Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment.xlsx
No full textWildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.</p
DataSheet_1_Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment.docx
No full textWildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.</p
Revisión bibliográfica sobre el uso de medicamentos vencidos como inhibidores de corrosión en acero al carbono en condiciones estáticas
No full textEste trabajo de grado tuvo como objetivo desarrollar un estado del arte a partir de una revisión bibliográfica sobre el uso de inhibidores de corrosión a partir de medicamentos vencidos, se valoraron algunos de los fármacos caducados, estudiados por sus propiedades inhibidoras de la corrosión durante los últimos años. Se revisaron más de cien artículos científicos, cuya información descriptiva (como autor, año de publicación, medio corrosivo, entre otros) fue tabulada para encontrar aquellas similitudes que están siguiendo los autores a la hora de escoger los medicamentos vencidos. Para poder desarrollar esta investigación se consultaron diferentes fuentes bibliográficas tales como las bases de datos de la Universidad San Buenaventura sede Cartagena, y tesis químicas, farmacéuticas, tecnológicas y de la misma línea de investigación. Se revisaron datos como la eficiencia del inhibidor y se indagó acerca de las técnicas utilizadas para el cálculo de las velocidades de corrosión, se realizó un rastreo bibliométrico con el objetivo de analizar la producción de artículos de investigación con base en las categorías preestablecidas. Finalmente, se estudió la metodología implementada en cada estudio, llegando a la conclusión de que los métodos más utilizados por los autores son los de pérdida de peso y técnicas electroquímicas como espectroscopía de impedancia electroquímica, polarización potenciodinámica; además los medios corrosivos más evaluados son los ácidos. Los resultados de esta revisión permiten apreciar que los fármacos caducados tienen un alto potencial como inhibidores de la corrosión para ser aplicados en la industria petroquímica, metalúrgica y eléctrica de la ciudad de Cartagena.This degree project had the objective to develop a state of the art from a bibliographic review on the use of corrosion inhibitors from expired drugs, some of the expired drugs were evaluated, studied for their corrosion inhibiting properties during the last years. More than one hundred scientific articles were reviewed, whose descriptive information (such as author, year of publication, corrosive medium, among others) was tabulated to find those similarities the authors are following when choosing expired medications. In order to develop this research, different bibliographic sources were consulted, such as databases of the San Buenaventura University (Cartagena campus), and chemical, pharmaceutical, technological thesis and the same line of research. Data such as the efficiency of the inhibitor were reviewed and the techniques used to calculate the corrosion rates were investigated, a bibliometric tracing was carried out in order to analyze the production of research articles based on the pre-established categories Finally, the methodology implemented in each study was studied, reaching the conclusion the methods most used by the authors are lossing weight methods and electrochemical techniques such as electrochemical impedance spectroscopy, potentiodynamic polarization; furthermore, the most evaluated corrosive media are acids. The results of this review allow us to appreciate expired drugs have a high potential as corrosion inhibitors to be applied in the petrochemical, metallurgical and electrical industries of the city of CartagenaPregradoIngeniero QuímicoSedes::Cartagena::Línea de investigación ingeniería de procesos (Cartagena
