<i>Methanomethylophilus alvi</i> gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order <i>Methanomassiliicoccales</i> Isolated from the Human Gut and Proposal of the Novel Family <i>Methanomethylophilaceae</i> fam. nov.
The methanogenic strain Mx-05<sup>T</sup> was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order <i>Methanomassiliicoccales</i>. It shares 86.9% 16S rRNA...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-11-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/11/11/2794 |
| _version_ | 1797458327940104192 |
|---|---|
| author | Guillaume Borrel Khaled Fadhlaoui Wajdi Ben Hania Nadia Gaci Gérard Pehau-Arnaudet Prem Prashant Chaudhary Pascal Vandekerckove Nathalie Ballet Monique Alric Paul William O’Toole Marie-Laure Fardeau Bernard Ollivier Jean-François Brugère |
| author_facet | Guillaume Borrel Khaled Fadhlaoui Wajdi Ben Hania Nadia Gaci Gérard Pehau-Arnaudet Prem Prashant Chaudhary Pascal Vandekerckove Nathalie Ballet Monique Alric Paul William O’Toole Marie-Laure Fardeau Bernard Ollivier Jean-François Brugère |
| author_sort | Guillaume Borrel |
| collection | DOAJ |
| description | The methanogenic strain Mx-05<sup>T</sup> was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order <i>Methanomassiliicoccales</i>. It shares 86.9% 16S rRNA gene sequence identity with <i>Methanomassiliicoccus luminyensis</i>, the only member of this order previously isolated. The cells of Mx-05<sup>T</sup> were non-motile cocci, with a diameter range of 0.4–0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H<sub>2</sub> as an electron donor. H<sub>2</sub>/CO<sub>2</sub>, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05<sup>T</sup> required an unknown medium factor(s) provided by <i>Eggerthella lenta</i> and present in rumen fluid. Mx-05<sup>T</sup> grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9–8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L<sup>−1</sup> NaCl (optimum 0.12 mol.L<sup>−1</sup> NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H<sub>4</sub>MPT Wood–Ljungdahl pathway, as described for other <i>Methanomassiliicoccales</i> members. Based on an average nucleotide identity analysis, we propose strain Mx-05<sup>T</sup> as being a novel representative of the order <i>Methanomassiliicoccales</i>, within the novel family <i>Methanomethylophilaceae</i>, for which the name <i>Methanomethylophilus alvi</i> gen. nov, sp. nov. is proposed. The type strain is Mx-05<sup>T</sup> (JCM 31474T). |
| first_indexed | 2024-03-09T16:35:31Z |
| format | Article |
| id | doaj.art-ae3ea8acdd164189bdcfefe0d797dc3c |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T16:35:31Z |
| publishDate | 2023-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-ae3ea8acdd164189bdcfefe0d797dc3c2023-11-24T14:57:17ZengMDPI AGMicroorganisms2076-26072023-11-011111279410.3390/microorganisms11112794<i>Methanomethylophilus alvi</i> gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order <i>Methanomassiliicoccales</i> Isolated from the Human Gut and Proposal of the Novel Family <i>Methanomethylophilaceae</i> fam. nov.Guillaume Borrel0Khaled Fadhlaoui1Wajdi Ben Hania2Nadia Gaci3Gérard Pehau-Arnaudet4Prem Prashant Chaudhary5Pascal Vandekerckove6Nathalie Ballet7Monique Alric8Paul William O’Toole9Marie-Laure Fardeau10Bernard Ollivier11Jean-François Brugère12Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell, 75015 Paris, FranceAix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, FranceAix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, FranceUniversité d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, FranceInstitut Pasteur, Université Paris Cité, Ultrastructural Bioimaging, 75015 Paris, FranceUniversité d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, FranceLesaffre International, Lesaffre Group, 59700 Marcq-en-Barœul, FranceLesaffre International, Lesaffre Group, 59700 Marcq-en-Barœul, FranceUniversité d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, FranceAPC Microbiome Ireland, University College Cork, T12 K8AF Cork, IrelandAix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, FranceAix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, FranceUniversité d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, FranceThe methanogenic strain Mx-05<sup>T</sup> was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order <i>Methanomassiliicoccales</i>. It shares 86.9% 16S rRNA gene sequence identity with <i>Methanomassiliicoccus luminyensis</i>, the only member of this order previously isolated. The cells of Mx-05<sup>T</sup> were non-motile cocci, with a diameter range of 0.4–0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H<sub>2</sub> as an electron donor. H<sub>2</sub>/CO<sub>2</sub>, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05<sup>T</sup> required an unknown medium factor(s) provided by <i>Eggerthella lenta</i> and present in rumen fluid. Mx-05<sup>T</sup> grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9–8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L<sup>−1</sup> NaCl (optimum 0.12 mol.L<sup>−1</sup> NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H<sub>4</sub>MPT Wood–Ljungdahl pathway, as described for other <i>Methanomassiliicoccales</i> members. Based on an average nucleotide identity analysis, we propose strain Mx-05<sup>T</sup> as being a novel representative of the order <i>Methanomassiliicoccales</i>, within the novel family <i>Methanomethylophilaceae</i>, for which the name <i>Methanomethylophilus alvi</i> gen. nov, sp. nov. is proposed. The type strain is Mx-05<sup>T</sup> (JCM 31474T).https://www.mdpi.com/2076-2607/11/11/2794archaeamethanogenshuman gut microbiota<i>Methanomassiliicoccales</i> |
| spellingShingle | Guillaume Borrel Khaled Fadhlaoui Wajdi Ben Hania Nadia Gaci Gérard Pehau-Arnaudet Prem Prashant Chaudhary Pascal Vandekerckove Nathalie Ballet Monique Alric Paul William O’Toole Marie-Laure Fardeau Bernard Ollivier Jean-François Brugère <i>Methanomethylophilus alvi</i> gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order <i>Methanomassiliicoccales</i> Isolated from the Human Gut and Proposal of the Novel Family <i>Methanomethylophilaceae</i> fam. nov. Microorganisms archaea methanogens human gut microbiota <i>Methanomassiliicoccales</i> |
| title | <i>Methanomethylophilus alvi</i> gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order <i>Methanomassiliicoccales</i> Isolated from the Human Gut and Proposal of the Novel Family <i>Methanomethylophilaceae</i> fam. nov. |
| title_full | <i>Methanomethylophilus alvi</i> gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order <i>Methanomassiliicoccales</i> Isolated from the Human Gut and Proposal of the Novel Family <i>Methanomethylophilaceae</i> fam. nov. |
| title_fullStr | <i>Methanomethylophilus alvi</i> gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order <i>Methanomassiliicoccales</i> Isolated from the Human Gut and Proposal of the Novel Family <i>Methanomethylophilaceae</i> fam. nov. |
| title_full_unstemmed | <i>Methanomethylophilus alvi</i> gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order <i>Methanomassiliicoccales</i> Isolated from the Human Gut and Proposal of the Novel Family <i>Methanomethylophilaceae</i> fam. nov. |
| title_short | <i>Methanomethylophilus alvi</i> gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order <i>Methanomassiliicoccales</i> Isolated from the Human Gut and Proposal of the Novel Family <i>Methanomethylophilaceae</i> fam. nov. |
| title_sort | i methanomethylophilus alvi i gen nov sp nov a novel hydrogenotrophic methyl reducing methanogenic archaea of the order i methanomassiliicoccales i isolated from the human gut and proposal of the novel family i methanomethylophilaceae i fam nov |
| topic | archaea methanogens human gut microbiota <i>Methanomassiliicoccales</i> |
| url | https://www.mdpi.com/2076-2607/11/11/2794 |
| work_keys_str_mv | AT guillaumeborrel imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT khaledfadhlaoui imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT wajdibenhania imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT nadiagaci imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT gerardpehauarnaudet imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT premprashantchaudhary imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT pascalvandekerckove imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT nathalieballet imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT moniquealric imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT paulwilliamotoole imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT marielaurefardeau imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT bernardollivier imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov AT jeanfrancoisbrugere imethanomethylophilusalviigennovspnovanovelhydrogenotrophicmethylreducingmethanogenicarchaeaoftheorderimethanomassiliicoccalesiisolatedfromthehumangutandproposalofthenovelfamilyimethanomethylophilaceaeifamnov |