Navigating the archaeal frontier: insights and projections from bioinformatic pipelines DOI Creative Commons

Val Karavaeva,

Filipa L. Sousa

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: Sept. 23, 2024

Archaea continues to be one of the least investigated domains life, and in recent years, advent metagenomics has led discovery many new lineages at phylum level. For majority, only automatic genomic annotations can provide information regarding their metabolic potential role environment. Here, data from 2,978 archaeal genomes was used perform using bioinformatics tools, alongside synteny analysis. These classifications were done assess how good these different tools relation data. Our study revealed that even with lowered cutoffs, several functional models do not capture recently discovered diversity. Moreover, our investigation a significant portion genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial diverse range unclassified proteins is obtained, well-studied organisms like Escherichia coli having substantially lower proportion uncharacterized regions, ranging <5 25%, less studied being comparable archaea 35-40% regions. Leveraging this analysis, we able identify protein markers, thereby providing insights into metabolism dataset. findings underscore substantial gap between classification comprehensive mapping metabolism. Despite advances computational approaches, remains unexplored, highlighting need for extensive experimental validation domain, as well more refined annotation methods. This contributes better understanding underscores importance further research elucidating genomes.

Language: Английский

Microbial oxidation of short-chain gaseous alkanes DOI
Mengxiong Wu, Xiawei Liu, Florin Musat

et al.

Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: April 15, 2025

Language: Английский

Citations

0
Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis DOI Creative Commons
Song‐Can Chen, Sheng Chen, Niculina Musat

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 7, 2024

Microbial formation and oxidation of volatile alkanes in anoxic environments significantly impacts biogeochemical cycles on Earth. The discovery archaea oxidizing via deeply branching methyl-coenzyme M reductase variants, dubbed alkyl-CoM reductases (ACR), prompted the hypothesis archaea-catalysed alkane nature (alkanogenesis). A combination metabolic modelling, anaerobic physiology assays, isotope labeling Candidatus Syntrophoarchaeum catalyzing butane (AOB) show a back flux CO

Language: Английский

Citations

1
Beyond methane, new frontiers in anaerobic microbial hydrocarbon utilizing pathways DOI Creative Commons
Natalie Sarno, Emily Hyde, Valerie De Anda

et al.

Microbial Biotechnology, Journal Year: 2024, Volume and Issue: 17(6)

Published: June 1, 2024

Alkanes, single carbon methane to long-chain hydrocarbons (e.g. hexadecane and tetradecane), are important sources anaerobic microbial communities. In anoxic environments, archaea known utilize produce via the methyl-coenzyme M reductase enzyme (MCR). Recent explorations of new like deep sea sediments, that have coupled metagenomics cultivation experiments revealed divergent MCRs, also referred as alkyl-coenzyme reductases (ACRs) in archaea, with similar mechanisms C

Language: Английский

Citations

0
Navigating the archaeal frontier: insights and projections from bioinformatic pipelines DOI Creative Commons

Val Karavaeva,

Filipa L. Sousa

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: Sept. 23, 2024

Archaea continues to be one of the least investigated domains life, and in recent years, advent metagenomics has led discovery many new lineages at phylum level. For majority, only automatic genomic annotations can provide information regarding their metabolic potential role environment. Here, data from 2,978 archaeal genomes was used perform using bioinformatics tools, alongside synteny analysis. These classifications were done assess how good these different tools relation data. Our study revealed that even with lowered cutoffs, several functional models do not capture recently discovered diversity. Moreover, our investigation a significant portion genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial diverse range unclassified proteins is obtained, well-studied organisms like Escherichia coli having substantially lower proportion uncharacterized regions, ranging <5 25%, less studied being comparable archaea 35-40% regions. Leveraging this analysis, we able identify protein markers, thereby providing insights into metabolism dataset. findings underscore substantial gap between classification comprehensive mapping metabolism. Despite advances computational approaches, remains unexplored, highlighting need for extensive experimental validation domain, as well more refined annotation methods. This contributes better understanding underscores importance further research elucidating genomes.

Language: Английский

Citations

0