Tropical Microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA764563 | ENA |
REPOSITORIES: ENA
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Project description:Patterns in functional diversity of organisms at large spatial scales can provide insight into possible responses to future climate change, but it remains a challenge to link large-scale patterns at the organismal level to their underlying physiological mechanisms. The climate variability hypothesis predicts that temperate ectotherms will be less vulnerable to climate warming than tropical ectotherms, due to their superior acclimatization capacity.We investigate thermal acclimation of three species of Takydromus lizards distributed along a broad latitudinal gradient in China, by studying metabolic modifications at the level of the whole organism,organ, mitochondria, metabolome, and proteome.
2021-12-12 | PXD029083 | Pride
Project description:The airborne microbiome: consistent seasonal trends in the aeroplankton assemblage
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Project description:Seasonal influenza outbreaks represent a large burden for the healthcare system as well as the economy. While the role of the microbiome in the context of various diseases has been elucidated, the effects on the respiratory and gastrointestinal microbiome during influenza illness is largely unknown. Therefore, this study aimed to characterize the temporal development of the respiratory and gastrointestinal microbiome of swine using a multi-omics approach prior and during influenza infection. Swine is a suitable animal model for influenza research, as it is closely related to humans and a natural host for influenza viruses. Our results showed that IAV infection resulted in significant changes in the abundance of Moraxellaceae and Pasteurellaceae families in the upper respiratory tract. To our surprise, temporal development of the respiratory microbiome was not affected. Furthermore, we observed significantly altered microbial richness and diversity in the gastrointestinal microbiome after IAV infection. In particular, we found increased abundances of Prevotellaceae, while Clostridiaceae and Lachnospiraceae decreased. Furthermore, metaproteomics showed that the functional composition of the microbiome, known to be robust and stable under healthy conditions, was heavily affected by the influenza infection. Metabolome analysis proved increased amounts of short-chain fatty acids in the gastrointestinal tract, which might be involved in faster recovery. Furthermore, metaproteome data suggest a possible immune response towards flagellated Clostridia induced during the infection. Therefore, it can be assumed that the respiratory infection with IAV caused a systemic effect in the porcine host and microbiome.
2022-02-16 | PXD024077 | Pride
Project description:<p>Patterns in functional diversity of organisms at large spatial scales can provide insight into possible responses to future climate change, but it remains a challenge to link large-scale patterns at the organismal level to their underlying physiological mechanisms. The climate variability hypothesis predicts that temperate ectotherms will be less vulnerable to climate warming than tropical ectotherms, due to their superior acclimatization capacity. However, metabolic acclimatization occurs over multiple levels of the biological hierarchy, from the enzyme and cellular level, through organ systems, to whole-organism metabolic rate. Previous studies have focused on one or a few biological hierarchy levels, leaving us without a general understanding of how metabolic acclimatization might differ between tropical and temperate species. Here, we investigate thermal acclimatization of 3 species of <em>Takydromus</em> lizards distributed along a broad latitudinal gradient in China, by studying metabolic modifications at the level of the whole organism, organ, mitochondria, metabolome and proteome. As predicted by the climate variability hypothesis, the 2 temperate species <em>T. septentrionalis</em> and <em>T. wolteri</em> had an enhanced acclimation response at the whole organism level compared to the tropical species <em>T. sexlineatus</em>, as measured by respiratory gas exchange rates. However, the mechanisms by which whole organism performance was modified was strikingly different in the 2 temperate species: widespread <em>T. septentrionalis</em> modified organ sizes, while the narrowly distributed <em>T. wolteri</em> relied on mitochondrial, proteomic and metabolomic regulation. We suggest that these 2 mechanisms of thermal acclimatization may represent general strategies used by ectotherms, with distinct ecological costs and benefits. Lacking either of these mechanisms of thermal acclimatization capacity, the tropical species is likely to have increased vulnerability to climate change.</p>
2022-01-20 | MTBLS3627 | MetaboLights
Project description:This study aimed to use pan-viral detection microarrays to identify viruses in serum from cases of acute pediatric febrile illness in a tropical setting. Patient clinical data and serum samples were collected between 2005 and 2009 as part of an ongoing pediatric dengue virus study at the Hospital Infantil Manuel de Jesús Rivera in Managua, Nicaragua. This study focused on patients who presented with dengue-like illness but who tested negative for dengue-virus infection. We hypothesized that non-dengue viruses or previously uncharacterized viruses might be causing these illnesses. The Virochip microarray is capable of detecting known viruses and discovering novel viruses. This series includes 153 arrays corresponding to 148 cases and 5 HeLa controls. Keywords: viral detection, tropical febrile illness, dengue virus, Nicaragua, Virochip
2011-12-31 | GSE28142 | GEO
Project description:Different populations of the same species survive different environments through local adaptation. Temperature is one of the most important driving forces that could result in local adaptation. Here, we studied the influence of extreme low temperature on the survival of two genetically and geographically distinct populations of the free-living Caenorhabditis briggsae. We found that Caenorhabditis briggsae strains of temperate origin had a cold resistant phenotype, while those originating from a tropical climate had reduced survival after cold treatment. Using this phenotypic difference between geographically diverse populations as a model for how species adapt to their local environment, we then analyzed the transcriptional profiles of two Caenorhabditis briggsae strains of tropical and temperate origin to find genes that are involved in survival after extreme cold. In summary, the response to the extreme low temperature that clearly distinguishes the temperate and tropical Caenorhabditis briggsae strains could serve as an excellent example for studying local adaption of species that show genetic separation associated with their geographical distribution.
2021-09-09 | GSE171725 | GEO
Project description:Tropical peatland shotgun metagenomics
| PRJNA937402 | ENA
Project description:This study aimed to use pan-viral detection microarrays to identify viruses in serum from cases of acute pediatric febrile illness in a tropical setting. Patient clinical data and serum samples were collected between 2005 and 2009 as part of an ongoing pediatric dengue virus study at the Hospital Infantil Manuel de Jesús Rivera in Managua, Nicaragua. This study focused on patients who presented with dengue-like illness but who tested negative for dengue-virus infection. We hypothesized that non-dengue viruses or previously uncharacterized viruses might be causing these illnesses. The Virochip microarray is capable of detecting known viruses and discovering novel viruses. This series includes 153 arrays corresponding to 148 cases and 5 HeLa controls. Keywords: viral detection, tropical febrile illness, dengue virus, Nicaragua, Virochip From each serum sample, total nucleic acid was extracted and used to prepare a randomly-primed dsDNA library. These libraries were fluorescently labeled and hybrized to Virochip arrays.
2011-12-31 | E-GEOD-28142 | biostudies-arrayexpress
Project description:Genetic diversity, resistance genes, and negative density dependence in tropical tree seedling dynamics Transcriptome
| PRJNA330734 | ENA