Seasonal variability of the rumen microbiome in indigenous African cattle: a bioinformatics approach : from pasture to pathways
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| Title: | Seasonal variability of the rumen microbiome in indigenous African cattle: a bioinformatics approach : from pasture to pathways |
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| Authors: | Van Damme, Renaud |
| Contributors: | Sveriges lantbruksuniversitet, Originator |
| Source: | Acta Universitatis Agriculturae Sueciae. |
| Subject Terms: | Microbiology, Mikrobiologi, Bioinformatics (Computational Biology), Bioinformatik (beräkningsbiologi), Bioinformatics and Computational Biology (Methods development to be 10203), Bioinformatik och beräkningsbiologi (Metodutveckling under 10203) |
| Description: | The Ethiopian climate causes cattle to frequently experience cycles of abundant feed availability during the rainy season and severe feed scarcity during the dry season. Using a bioinformatics-driven metagenomics approach, this study reveals how the rainy season favours fibre-degrading taxa and expanded methanogenic and biosynthetic potential. In contrast, the dry season is characterised by reduced metabolic diversity and an increase in opportunistic taxa. To achieve this, novel computational tools were developed and refined, including MUFFIN and PANKEGG. The results collected from extreme drought conditions provide valuable information to ensure that ongoing work to reduce methane emissions through breeding or feed additives does not negatively impact the ability of ruminants to adapt to drought or low-quality feed, which may threaten food security and animal welfare during heatwaves. The study revealed seasonal variations in microbial community structure and metabolic functions. During the rainy season, the microbiome exhibited an increase in acetoclastic methanogens and fibre-degraders. The dry season saw a rise in hydrogenotrophic methanogens. The latter increase reflects a decrease in acetate production, suggesting a decline in access to feed, as well as less efficient fibre breakdown. These findings bring critical insights into the metabolic adaptability and resilience of indigenous cattle microbiomes. The findings also suggest new potential targets for enhancing feed efficiency and promoting environmental sustainability. The microbiome harboured multiple antibiotic resistance genes (ARGs) throughout both seasons. The presence of ARGs exposes the risk of potential resistance spread to pathogens as well as broader ecological implications. In addition to the metagenomic study, a genomic study of Ethiopian cattle breeds highlighted significant genetic diversity and potential adaptive mechanisms to local environmental stressors. Those genetic markers open the possibility for future integration of host-genomic and microbiome analyses. |
| Access URL: | https://res.slu.se/id/publ/142461 https://pub.epsilon.slu.se/id/eprint/38162/contents |
| Database: | SwePub |
Nájsť tento článok vo Web of Science | Abstract: | The Ethiopian climate causes cattle to frequently experience cycles of abundant feed availability during the rainy season and severe feed scarcity during the dry season. Using a bioinformatics-driven metagenomics approach, this study reveals how the rainy season favours fibre-degrading taxa and expanded methanogenic and biosynthetic potential. In contrast, the dry season is characterised by reduced metabolic diversity and an increase in opportunistic taxa. To achieve this, novel computational tools were developed and refined, including MUFFIN and PANKEGG. The results collected from extreme drought conditions provide valuable information to ensure that ongoing work to reduce methane emissions through breeding or feed additives does not negatively impact the ability of ruminants to adapt to drought or low-quality feed, which may threaten food security and animal welfare during heatwaves. The study revealed seasonal variations in microbial community structure and metabolic functions. During the rainy season, the microbiome exhibited an increase in acetoclastic methanogens and fibre-degraders. The dry season saw a rise in hydrogenotrophic methanogens. The latter increase reflects a decrease in acetate production, suggesting a decline in access to feed, as well as less efficient fibre breakdown. These findings bring critical insights into the metabolic adaptability and resilience of indigenous cattle microbiomes. The findings also suggest new potential targets for enhancing feed efficiency and promoting environmental sustainability. The microbiome harboured multiple antibiotic resistance genes (ARGs) throughout both seasons. The presence of ARGs exposes the risk of potential resistance spread to pathogens as well as broader ecological implications. In addition to the metagenomic study, a genomic study of Ethiopian cattle breeds highlighted significant genetic diversity and potential adaptive mechanisms to local environmental stressors. Those genetic markers open the possibility for future integration of host-genomic and microbiome analyses. |
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| ISSN: | 16526880 |
| DOI: | 10.54612/a.77nq392jvl |