Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China ( = 76), Denmark ( = 100), and France ( = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs ( < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of , XQ INN 246, and were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.
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http://dx.doi.org/10.3390/ani11072139 | DOI Listing |
Environ Res
January 2025
College of Energy and Environment, Inner Mongolia University of Science and Technology,Baotou 014010, P. R. China; Collaborative Innovation Center of Autonomous Region for Ecological Protection and Comprehensive Utilization in the Inner Mongolia Section of the Yellow River Basin, Baotou 014010, P. R. China. Electronic address:
The coexistence of different microbial communities is fundamental to the sustainability of many ecosystems, yet our understanding of the relationships among microbial communities in plateau cold-region lakes affected by seasonal ice cover remains limited. This research involved investigating three lakes in the Inner Mongolia segment of the Yellow River basin during frozen and unfrozen periods in two habitats: water bodies and sediments. The research examined the composition and function of bacteria, archaea, and fungi across different times and habitats within the basin, their response to environmental variables in water and sediment, and inter-domain interactions between bacteria-archaea and bacteria-fungi were compared using interdomain ecological network (IDEN).
View Article and Find Full Text PDFMicrobiome
January 2025
Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, China.
Background: While Gangba sheep being well known for their unique flavour and nutritional value, harsh environmental factors negatively affect their growth and development, leading to poor productivity. The gastrointestinal tract microbiota plays an important role in host nutrient absorption and metabolism. The identification of dynamic changes in the gastrointestinal microbial communities and their functions is an important step towards improving animal production performance and health.
View Article and Find Full Text PDFiScience
January 2025
Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece.
The genome of () DSM 2661 was the first Archaeal genome to be sequenced in 1996. Subsequent sequence-based annotation cycles led to its first metabolic reconstruction in 2005. Leveraging new experimental results and function assignments, we have now re-annotated creating an updated resource with novel information and testable predictions in a pathway-genome database available at BioCyc.
View Article and Find Full Text PDFWorld J Microbiol Biotechnol
January 2025
Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China.
Nitrification, the oxidation of ammonium to nitrate via nitrite, links nitrogen fixation and nitrogen loss processes, playing key roles in coastal nitrogen cycle. However, few studies have simultaneously examined both ammonia-oxidizing and nitrite-oxidizing microbes. This work investigated the abundance and community structure of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) using archaeal amoA gene, bacterial amoA gene, and NOB nxrB gene, respectively, through q-PCR and Sanger sequencing along the Changjiang Estuary salinity gradient.
View Article and Find Full Text PDFMicrob Ecol
January 2025
College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
Estuarine ecosystems are among the most important natural ecosystems on Earth and contribute substantially to human survival and development. The Yellow River Estuary (YRE) is the second largest estuary in China. Microbial communities play an essential role in the material cycle and energy flow in estuarine ecosystems.
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