Phylogenomic placement of Methanomethylovorans thermophila L2FAW in the Genome Taxonomy Database

2025 · doi:10.1099/acmi.0.001123.v1
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The study sequenced and hybrid-assembled the genome of the methanogenic archaeon Methanomethylovorans thermophila L2FAW using Illumina shotgun and Oxford Nanopore reads, producing a 2.25 Mbp assembly with contigs ≥500 bp and reporting good assembly quality (low L50/L90). The authors placed the genome phylogenomically in the archaeal Genome Taxonomy Database and found it highly similar to a previously reported Methanomethylovorans metagenome-assembled genome (ANI 99.9%). KEGG-based annotation indicated that the organism encodes enzymes required for acetoclastic and hydrogenotrophic methanogenesis, and metabolic modeling predicted formate as a potential substrate, but laboratory assays did not show metabolic activity on acetate, H2-CO2, or formate-containing mixes. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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Abstract

The genome of the methanogenic archaeon Methanomethylovorans thermophila L2FAW was sequenced via Illumina shot-gun and Oxford Nanopore sequencing and subsequently hybrid assembled for the phylogenomic placement in the archaeal Genome Taxonomy Database (GTDB). The assembled genome consists of 2.25 Mbp (contigs ≥ 500 bp) with a G+C content of 37.97%. The quality of the genome is good, which is already apparent from the low L50 (= 1) and L90 (= 2) metrics. Our assembled genome was highly similar to the metagenome assembled genome Methanomethylovorans sp014361205 (GCA_014361205.1_ASM1436120v1_genomic) with an average nucleotide identity (ANI) of 99.9%. Visualization of the amino acid annotation with KEGG Mapper Reconstruction Result revealed that M. thermophila L2FAW harbors all the enzymes necessary for acetoclastic and hydrogenotrophic methanogenesis. Additionally, the predicted metabolic model showed that formate is a potential substrate for M. thermophila L2FAW. Nonetheless, no metabolic activity could be observed in lab tests on acetate, H2-CO2 (80:20 vol/vol, 2000 mbar), and a mixture of H2-CO2 (80:20 vol/vol, 2000 mbar) and formate.
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Full text loading... Abstract The genome of the methanogenic archaeon Methanomethylovorans thermophila L2FAW was sequenced via Illumina shot-gun and Oxford Nanopore sequencing and subsequently hybrid assembled for the phylogenomic placement in the archaeal Genome Taxonomy Database (GTDB). The assembled genome consists of 2.25 Mbp (contigs ≥ 500 bp) with a G+C content of 37.97%. The quality of the genome is good, which is already apparent from the low L50 (= 1) and L90 (= 2) metrics. Our assembled genome was highly similar to the metagenome assembled genome Methanomethylovorans sp014361205 (GCA_014361205.1_ASM1436120v1_genomic) with an average nucleotide identity (ANI) of 99.9%. Visualization of the amino acid annotation with KEGG Mapper Reconstruction Result revealed that M. thermophila L2FAW harbors all the enzymes necessary for acetoclastic and hydrogenotrophic methanogenesis. Additionally, the predicted metabolic model showed that formate is a potential substrate for M. thermophila L2FAW. Nonetheless, no metabolic activity could be observed in lab tests on acetate, H2-CO2 (80:20 vol/vol, 2000 mbar), and a mixture of H2-CO2 (80:20 vol/vol, 2000 mbar) and formate. - Received: - Version Posted: Funding - Austrian Science Fund (Award P 33838) - Principal Award Recipient: Andreas O. Wagner - Austrian Science Fund (Award ESP 7170024) - Principal Award Recipient: Eva Maria Prem

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