scholarly journals Microbial community structure and composition is associated with host species and sex in Sigmodon cotton rats

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Britton A. Strickland ◽  
Mira C. Patel ◽  
Meghan H. Shilts ◽  
Helen H. Boone ◽  
Arash Kamali ◽  
...  
Keyword(s):  
Animal Model ◽  
Microbial Communities ◽  
Viral Infections ◽  
Therapeutic Potential ◽  
Rrna Gene ◽  
Cotton Rat ◽  
Cotton Rats ◽  
The Impact ◽  
Comprehensive Characterization

Abstract Background The cotton rat (genus Sigmodon) is an essential small animal model for the study of human infectious disease and viral therapeutic development. However, the impact of the host microbiome on infection outcomes has not been explored in this model, partly due to the lack of a comprehensive characterization of microbial communities across different cotton rat species. Understanding the dynamics of their microbiome could significantly help to better understand its role when modeling viral infections in this animal model. Results We examined the bacterial communities of the gut and three external sites (skin, ear, and nose) of two inbred species of cotton rats commonly used in research (S. hispidus and S. fulviventer) by using 16S rRNA gene sequencing, constituting the first comprehensive characterization of the cotton rat microbiome. We showed that S. fulviventer maintained higher alpha diversity and richness than S. hispidus at external sites (skin, ear, nose), but there were no differentially abundant genera. However, S. fulviventer and S. hispidus had distinct fecal microbiomes composed of several significantly differentially abundant genera. Whole metagenomic shotgun sequencing of fecal samples identified species-level differences between S. hispidus and S. fulviventer, as well as different metabolic pathway functions as a result of differential host microbiome contributions. Furthermore, the microbiome composition of the external sites showed significant sex-based differences while fecal communities were not largely different. Conclusions Our study shows that host genetic background potentially exerts homeostatic pressures, resulting in distinct microbiomes for two different inbred cotton rat species. Because of the numerous studies that have uncovered strong relationships between host microbiome, viral infection outcomes, and immune responses, our findings represent a strong contribution for understanding the impact of different microbial communities on viral pathogenesis. Furthermore, we provide novel cotton rat microbiome data as a springboard to uncover the full therapeutic potential of the microbiome against viral infections.

scholarly journals Microbial Community Structure and Composition is Associated With Host Species and Sex in Sigmodon Cotton Rats

2020 ◽  
Author(s):  
Britton Strickland ◽  
Mira Patel ◽  
Meghan H. Shilts ◽  
Helen H. Boone ◽  
Arash Kamali ◽  
...  
Keyword(s):  
Animal Model ◽  
Microbial Communities ◽  
Viral Infections ◽  
Therapeutic Potential ◽  
Small Animal ◽  
Rrna Gene ◽  
Small Animal Model ◽  
Cotton Rat ◽  
Cotton Rats ◽  
The Impact

Abstract Background: The cotton rat (genus Sigmodon) is an essential small animal model for the study of human infectious disease and viral therapeutic development. However, the impact of the host microbiome on infection outcomes has not been explored in this model, partly due to the lack of a comprehensive characterization of microbial communities across different cotton rat species. Understanding the dynamics of their microbiome could significantly help to better understand its role during when modeling viral infections in this small animal model.Results: We examined the bacterial communities of the gut and three external sites (skin, ear, and nose) of two inbred species of cotton rats commonly used in research (S. hispidus and S. fulviventer) by using 16S rRNA gene sequencing, constituting the first comprehensive catalog of the cotton rat microbiome. We showed that S. fulviventer maintained higher alpha diversity and richness than S. hispidus at external sites (skin, ear, nose), but there were no differentially abundant genera. However, S. fulviventer and S. hispidus had distinct fecal microbiomes composed of several significantly differentially abundant genera. Whole metagenomic shotgun sequencing of fecal samples identified species-level differences between S. hispidus and S. fulviventer, as well as different metabolic pathway functions as a result of differential host microbiome contributions. Furthermore, the microbiome composition of the external sites showed significant sex-based differences while fecal communities were not largely different. Conclusions: Our study shows that host genetic background potentially exerts homeostatic pressures, resulting in distinct microbiomes for two different inbred cotton rat species. Because of the numerous studies that have uncovered strong relationships between host microbiome, viral infection outcomes, and immune responses, our findings represent a strong contribution for understanding the impact of different microbial communities on viral pathogenesis. Furthermore, we provide novel cotton rat microbiome data as a springboard to uncover the full therapeutic potential of the microbiome against viral infections.

scholarly journals ­­­Microbial Community Structure and Composition is Associated with Host Species and Sex in Sigmodon Cotton Rats

2020 ◽  
Author(s):  
Britton Strickland ◽  
Mira Patel ◽  
Meghan H. Shilts ◽  
Helen H. Boone ◽  
Arash Kamali ◽  
...  
Keyword(s):  
Animal Model ◽  
Microbial Communities ◽  
Viral Infections ◽  
Therapeutic Potential ◽  
Small Animal ◽  
Rrna Gene ◽  
Small Animal Model ◽  
Cotton Rat ◽  
Cotton Rats ◽  
The Impact

Abstract Background: The cotton rat (genus Sigmodon) is an essential small animal model for the study of human infectious disease and viral therapeutic development. However, the impact of the host microbiome on infection outcomes has not been explored in this model, partly due to the lack of a comprehensive characterization of microbial communities across different cotton rat species. Understanding the dynamics of their microbiome could significantly help to better understand its role during when modeling viral infections in this small animal model.Results: We examined the bacterial communities of the gut and three external sites (skin, ear, and nose) of two inbred species of cotton rats commonly used in research (S. hispidus and S. fulviventer) by using 16S rRNA gene sequencing, constituting the first comprehensive catalog of the cotton rat microbiome. We showed that S. fulviventer maintained higher alpha diversity and richness than S. hispidus at external sites (skin, ear, nose), but there were no differentially abundant genera. However, S. fulviventer and S. hispidus had distinct fecal microbiomes composed of several significantly differentially abundant genera. Whole metagenomic shotgun sequencing of fecal samples identified species-level differences between S. hispidus and S. fulviventer, as well as different metabolic pathway functions as a result of differential host microbiome contributions. Furthermore, the microbiome composition of the external sites showed significant sex-based differences while fecal communities were not largely different. Conclusions: Our study shows that host genetic background potentially exerts homeostatic pressures, resulting in distinct microbiomes for two different inbred cotton rat species. Because of the numerous studies that have uncovered strong relationships between host microbiome, viral infection outcomes, and immune responses, our findings represent a strong contribution for understanding the impact of different microbial communities on viral pathogenesis. Furthermore, we provide novel cotton rat microbiome data as a springboard to uncover the full therapeutic potential of the microbiome against viral infections.

scholarly journals Microbial drivers of methane emissions from unrestored industrial salt ponds

2021 ◽  
Author(s):  
Jinglie Zhou ◽  
Susanna M. Theroux ◽  
Clifton P. Bueno de Mesquita ◽  
Wyatt H. Hartman ◽  
Ye Tian ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Methane Flux ◽  
Methane Emissions ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Salt Ponds ◽  
Salt Pond ◽  
Reference Wetlands ◽  
Reference Wetland ◽  
The Impact

AbstractWetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

scholarly journals Assessing high-throughput environmental DNA extraction methods for meta-barcode characterization of aquatic microbial communities

2018 ◽  
Vol 17 (1) ◽  
pp. 37-49 ◽  
Author(s):  
Abdolrazagh Hashemi Shahraki ◽  
Subba Rao Chaganti ◽  
Daniel Heath
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput ◽  
Environmentally Friendly ◽  
Environmental Dna ◽  
Magnetic Bead ◽  
Extraction Methods ◽  
Environmental Research ◽  
Rrna Gene

Abstract The characterization of microbial community dynamics using genomic methods is rapidly expanding, impacting many fields including medical, ecological, and environmental research and applications. One of the biggest challenges for such studies is the isolation of environmental DNA (eDNA) from a variety of samples, diverse microbes, and widely variable community compositions. The current study developed environmentally friendly, user safe, economical, and high throughput eDNA extraction methods for mixed aquatic microbial communities and tested them using 16 s rRNA gene meta-barcoding. Five different lysis buffers including (1) cetyltrimethylammonium bromide (CTAB), (2) digestion buffer (DB), (3) guanidinium isothiocyanate (GITC), (4) sucrose lysis (SL), and (5) SL-CTAB, coupled with four different purification methods: (1) phenol-chloroform-isoamyl alcohol (PCI), (2) magnetic Bead-Robotic, (3) magnetic Bead-Manual, and (4) membrane-filtration were tested for their efficacy in extracting eDNA from recreational freshwater samples. Results indicated that the CTAB-PCI and SL-Bead-Robotic methods yielded the highest genomic eDNA concentrations and succeeded in detecting the core microbial community including the rare microbes. However, our study recommends the SL-Bead-Robotic eDNA extraction protocol because this method is safe, environmentally friendly, rapid, high-throughput and inexpensive.

scholarly journals Energy and Exergy Analyses of Stirling Engine using CFD Approach

2020 ◽  
Vol 77 (1) ◽  
pp. 100-123
Author(s):  
Sherihan El- Ghafour ◽  
Nady Mikhael ◽  
Mohamed El- Ghandour
Keyword(s):  
Energy Analysis ◽  
Stirling Engine ◽  
Recovery Processes ◽  
Energy And Exergy ◽  
Main Driver ◽  
The Impact ◽  
Exergy Analyses ◽  
Comprehensive Characterization

A comprehensive characterization of the GPU-3 Stirling engine losses with the aid of the CFD approach is presented. Firstly, a detailed description of the losses-related phenomena along with the method of calculating each type of loss are addressed. Secondly, an energy analysis of the engine is carried out in order to specify the impact of each type of losses on the performance. Finally, the design effectivity of each component of the engine is investigated using an exergy analysis. The results reveal that the hysteresis loss occurs mainly within the working spaces due to the flow jetting during the first part of the expansion strokes. Additionally, the pressure difference between the working spaces is the main driver for the flow leakage through the appendix gap. The exposure of the displacer top wall to the jet of hot gas flowing into the expansion space during expansion stroke essentially increases the shuttle heat loss. A new definition for the regenerator effectiveness is presented to assess the quality of the heat storage and recovery processes. The energy analysis shows that regenerator thermal loss and pumping power represent the largest part of the engine losses by about 9.2% and 7.5% of the heat input, respectively. The exergy losses within regenerator and cold space are the highest values among the components, consequently, they need to be redesigned.

scholarly journals Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

2021 ◽  
Vol 12 ◽  
Author(s):  
Charles S. Cockell ◽  
Bettina Schaefer ◽  
Cornelia Wuchter ◽  
Marco J. L. Coolen ◽  
Kliti Grice ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Granitic Rocks ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Deep Subsurface ◽  
Cell Biomass ◽  
Colonization Potential ◽  
The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

Characterization of the depth-related changes in the microbial communities in Lake Hovsgol sediment by 16S rRNA gene-based approaches

2008 ◽  
Vol 46 (2) ◽  
pp. 125-136 ◽  
Author(s):  
Young-Do Nam ◽  
Youlboong Sung ◽  
Ho-Won Chang ◽  
Seong Woon Roh ◽  
Kyoung-Ho Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Rrna Gene ◽  
Lake Hovsgol

scholarly journals Comprehensive characterization of claudin-low breast tumors reflects the impact of the cell-of-origin on cancer evolution

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Roxane M. Pommier ◽  
Amélien Sanlaville ◽  
Laurie Tonon ◽  
Janice Kielbassa ◽  
Emilie Thomas ◽  
...  
Keyword(s):  
Breast Tumors ◽  
Cancer Evolution ◽  
Cell Of Origin ◽  
The Impact ◽  
Comprehensive Characterization

Water management and phenology influence the root-associated rice field microbiota

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Matteo Chialva ◽  
Stefano Ghignone ◽  
Paolo Cozzi ◽  
Barbara Lazzari ◽  
Paola Bonfante ◽  
...  
Keyword(s):  
Water Management ◽  
Microbial Communities ◽  
Rice Field ◽  
Water Status ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Upland Conditions ◽  
The Impact ◽  
Comprehensive Study

ABSTRACT Microbial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.

scholarly journals A comprehensive characterization of the impact of mycophenolic acid on the metabolism of Jurkat T cells

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Ana A. Fernández-Ramos ◽  
Catherine Marchetti-Laurent ◽  
Virginie Poindessous ◽  
Samantha Antonio ◽  
Céline Petitgas ◽  
...  
Keyword(s):  
T Cells ◽  
Mycophenolic Acid ◽  
Jurkat T Cells ◽  
The Impact ◽  
Comprehensive Characterization
Sign in / Sign up

Export Citation Format

Share Document