ArticleMicrobiome2024
Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities.
Article in Microbiome, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- nf-core/magmap: Map metatranscriptomes to large collections of genomes.Bioinformatics (Oxford, England) · 2026Article
- Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.Briefings in bioinformatics · 2026Review
- Synergistic Regulation of Bile Acid-Driven Nitrogen Metabolism by Swollenin in Ruminants: A Microbiota-Targeted Strategy to Improve Nitrogen Use Efficiency.Animals : an open access journal from MDPI · 2026Article
- Exercise prescription for mood and cognition: targeting the microbiota-gut-brain axis through short-chain fatty acids.Frontiers in microbiology · 2026Review
- The crosstalk between host and rumen microbiome in cattle: insights from multi-omics approaches and genome-wide association studies.World journal of microbiology & biotechnology · 2025Review
- Salinization alters microbial methane cycling in freshwater sediments.Environmental microbiome · 2025Article
- The Future of Anaerobic Digestion: Challenges and Opportunities.Bioengineering (Basel, Switzerland) · 2025Article
- Biodegradation of synthetic organic pollutants: principles, progress, problems, and perspectives.FEMS microbiology reviews · 2025Review
- Integrated genomics, metagenomics and metatranscriptomics to reveal the biocontrol mechanism ofFrontiers in microbiology · 2025Article
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11 authors.
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Abstract
backgroundDespite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry.
resultsIn this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role.
conclusionOverall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.
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