Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 4

Expanding the cultivable human archaeome: sp. nov. and strain ‘GRAZ-2’ from human faeces Open Access

Abstract

Two mesophilic, hydrogenotrophic methanogens, WWM1085 and GRAZ-2, were isolated from human faecal samples. WWM1085 was isolated from an individual in the United States and represents a novel species within the genus GRAZ-2 (=DSM 116045) was retrieved from a faecal sample of a European, healthy woman and represents a novel strain within this species. Both representatives form non-flagellated, short rods with variable morphologies and the capacity to form filaments. Both isolates showed the typical fluorescence of F and methane production. Compared to GRAZ-2, WWM1085 did not accumulate formate when grown with H and CO. The optimal growth conditions were at 35–39 °C and pH 6.5–7.5. Full genome sequencing revealed a genomic difference of WWM1085 to the type strain of DSM 861 (=PS), with 93.55% average nucleotide identity (ANI) and major differences in the sequence of its gene (3.3% difference in nucleotide sequence). Differences in the 16S rRNA gene sequence were very minor, and thus distinction based on this gene marker might not be possible. GRAZ-2 was identified as a novel strain within the species (ANI 99.04% to DSM 861 [=PS]). Due to the major differences between WWM1085 and type strain DSM 861 (=PS) in phenotypic, genomic and metabolic features, we propose sp. nov. as a novel species with WWM1085 as the type strain (DSM 116060 = CECT 30992).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): faecal methanogens , human archaeome , Methanobrevibacter intestini and Methanobrevibacter smithii
Funding
This study was supported by the:
  • Austrian Research Promotion Agency (Award 870454)
    • Principle Award Recipient: TobiasMadl
  • Austrian Research Promotion Agency (Award 864690)
    • Principle Award Recipient: TobiasMadl
  • Austrian Science Fund (Award W1226)
    • Principle Award Recipient: TobiasMadl
  • Austrian Science Fund (Award DOC130)
    • Principle Award Recipient: TobiasMadl
  • Austrian Science Fund (Award I3792)
    • Principle Award Recipient: TobiasMadl
  • Austrian Science Fund (Award P28854)
    • Principle Award Recipient: TobiasMadl
  • Austrian Science Fund (Award COE 7)
    • Principle Award Recipient: ChristineMoissl-Eichinger
  • Austrian Science Fund (Award P 30796)
    • Principle Award Recipient: ChristineMoissl-Eichinger
  • Austrian Science Fund (Award 32697)
    • Principle Award Recipient: ChristineMoissl-Eichinger
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006751
2025-04-16
2025-05-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/75/4/ijsem006751.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006751&mimeType=html&fmt=ahah

References

  1. Borrel G, Brugère JF, Gribaldo S, Schmitz RA, Moissl-Eichinger C. The host-associated archaeome. Nat Rev Microbiol 2020; 18:622–636 [View Article] [PubMed]
     [Google Scholar]
  2. Youngblut ND, Reischer GH, Dauser S, Maisch S, Walzer C et al. Vertebrate host phylogeny influences gut archaeal diversity. Nat Microbiol 2021; 6:1443–1454 [View Article] [PubMed]
     [Google Scholar]
  3. Thomas CM, Desmond-Le Quéméner E, Gribaldo S, Borrel G. Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom. Nat Commun 2022; 13:3358 [View Article] [PubMed]
     [Google Scholar]
  4. Global Catalogue of Microorganisms https://gcm.wdcm.org/
  5. Kumpitsch C, Fischmeister FPS, Mahnert A, Lackner S, Wilding M et al. Reduced B12 uptake and increased gastrointestinal formate are associated with archaeome-mediated breath methane emission in humans. Microbiome 2021; 9:1–18 [View Article] [PubMed]
     [Google Scholar]
  6. Bryant MP, Tzeng SF, Robinson IM, Joiner AEJ. In Pohland FG. ed Anaerobic Biological Treatment Processes American Chemical Society; pp 23–40 [View Article]
     [Google Scholar]
  7. Miller TL, Wolin MJ. Fermentation by the human large intestine microbial community in an in vitro semicontinuous culture system. Appl Environ Microbiol 1981; 42:400–407 [View Article] [PubMed]
     [Google Scholar]
  8. Rinke C, Chuvochina M, Mussig AJ, Chaumeil P-A, Davín AA et al. A standardized archaeal taxonomy for the genome taxonomy database. Nat Microbiol 2021; 6:946–959 [View Article] [PubMed]
     [Google Scholar]
  9. Chibani CM, Mahnert A, Borrel G, Almeida A, Werner A et al. A catalogue of 1,167 genomes from the human gut archaeome. Nat Microbiol 2022; 7:48–61 [View Article] [PubMed]
     [Google Scholar]
  10. Luton PE, Wayne JM, Sharp RJ, Riley PW. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 2002; 148:3521–3530 [View Article] [PubMed]
     [Google Scholar]
  11. Jennings ME, Chia N, Boardman LA, Metcalf WW. Draft genome sequence of Methanobrevibacter smithii Isolate WWM1085, obtained from a human stool sample. Genome Announc 2017; 5:e01055-17 [View Article] [PubMed]
     [Google Scholar]
  12. Mohammadzadeh R, Mahnert A, Duller S, Moissl-Eichinger C. Archaeal key-residents within the human microbiome: characteristics, interactions and involvement in health and disease. Curr Opin Microbiol 2022; 67:102146 [View Article] [PubMed]
     [Google Scholar]
  13. Duller S, Vrbancic S, Szydłowski Ł, Mahnert A, Blohs M et al. Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome. Nat Commun 2024; 15:7593 [View Article] [PubMed]
     [Google Scholar]
  14. Hungate RE. Chapter IV A roll tube method for cultivation of strict anaerobes. Methods Microbiol 1969; 3:117–132 [View Article]
     [Google Scholar]
  15. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979; 43:260 [View Article] [PubMed]
     [Google Scholar]
  16. Li Y, Crouzet L, Kelly WJ, Reid P, Leahy SC et al. Methanobrevibacter boviskoreani JH1T growth on alcohols allows development of a high throughput bioassay to detect methanogen inhibition. Curr Res Microb Sci 2023; 4:100189 [View Article] [PubMed]
     [Google Scholar]
  17. Paul K, Nonoh JO, Mikulski L, Brune A. “Methanoplasmatales,” thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens. Appl Environ Microbiol 2012; 78:8245–8253 [View Article] [PubMed]
     [Google Scholar]
  18. Walker JJ, Pace NR. Phylogenetic composition of Rocky Mountain endolithic microbial ecosystems. Appl Environ Microbiol 2007; 73:3497–3504 [View Article] [PubMed]
     [Google Scholar]
  19. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 2013; 41:e1 [View Article] [PubMed]
     [Google Scholar]
  20. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  21. Edgar RC. Muscle: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinf 2004; 5:113 [View Article] [PubMed]
     [Google Scholar]
  22. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  23. Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 2016; 44:W232–5 [View Article] [PubMed]
     [Google Scholar]
  24. Vallenet D, Calteau A, Dubois M, Amours P, Bazin A et al. MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. Nucleic Acids Res 2020; 48:D579–D589 [View Article] [PubMed]
     [Google Scholar]
  25. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  26. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  27. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ 2016 [View Article]
     [Google Scholar]
  28. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
     [Google Scholar]
  29. Hofmann M, Norris PR, Malik L, Schippers A, Schmidt G et al. Metallosphaera javensis sp. nov., a novel species of thermoacidophilic archaea, isolated from a volcanic area. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  30. Weber Y, Sinninghe Damsté JS, Hopmans EC, Lehmann MF, Niemann H. Incomplete recovery of intact polar glycerol dialkyl glycerol tetraethers from lacustrine suspended biomass. Limnol Oceanogr Methods 2017; 15:782–793 [View Article]
     [Google Scholar]
  31. Lengger SK, Hopmans EC, Sinninghe Damsté JS, Schouten S. Impact of sedimentary degradation and deep water column production on GDGT abundance and distribution in surface sediments in the Arabian Sea: Implications for the TEX86 paleothermometer. Geochim Cosmochim Acta 2014; 142:386–399 [View Article]
     [Google Scholar]
  32. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
     [Google Scholar]
  33. Besseling MA, Hopmans EC, Boschman RC, Sinninghe Damsté JS, Villanueva L. Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone. Biogeosciences 2018; 15:4047–4064 [View Article]
     [Google Scholar]
  34. Schumann P. 5-peptidoglycan structure. In Methods in Microbiology vol 38 2011 pp 101–129 [View Article]
     [Google Scholar]
  35. Will SE, Henke P, Boedeker C, Huang S, Brinkmann H et al. Day and night: metabolic profiles and evolutionary relationships of six axenic non-marine cyanobacteria. Genome Biol Evol 2019; 11:270–294 [View Article] [PubMed]
     [Google Scholar]
  36. Hiller K, Hangebrauk J, Jäger C, Spura J, Schreiber K et al. MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. Anal Chem 2009; 81:3429–3439 [View Article] [PubMed]
     [Google Scholar]
  37. Neumann-Schaal M, Hofmann JD, Will SE, Schomburg D. Time-resolved amino acid uptake of Clostridium difficile 630Δerm and concomitant fermentation product and toxin formation. BMC Microbiol 2015; 15:281 [View Article] [PubMed]
     [Google Scholar]
  38. Dieterle F, Ross A, Schlotterbeck G, Senn H. Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. application in 1H NMR metabonomics. Anal Chem 2006; 78:4281–4290 [View Article] [PubMed]
     [Google Scholar]
  39. Bohus E, Coen M, Keun HC, Ebbels TMD, Beckonert O et al. Temporal metabonomic modeling of L-arginine-induced exocrine pancreatitis. J Proteome Res 2008; 7:4435–4445 [View Article] [PubMed]
     [Google Scholar]
  40. Hedjazi L, Gauguier D, Zalloua PA, Nicholson JK, Dumas M-E et al. mQTL.NMR: an integrated suite for genetic mapping of quantitative variations of (1)H NMR-based metabolic profiles. Anal Chem 2015; 87:4377–4384 [View Article] [PubMed]
     [Google Scholar]
  41. Ruaud A, Esquivel-Elizondo S, Cuesta-Zuluaga J, Waters JL, Angenent LT et al. Syntrophy via interspecies H2 transfer between christensenella and methanobrevibacter underlies their global cooccurrence in the human gut. mBio 2020; 11: [View Article]
     [Google Scholar]
  42. Miller TL, Wolin MJ, Conway de Macario E, Macario AJ. Isolation of Methanobrevibacter smithii from human feces. Appl Environ Microbiol 1982; 43:227–232 [View Article] [PubMed]
     [Google Scholar]
  43. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979; 43:260–296 [View Article]
     [Google Scholar]
  44. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinf 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  45. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genom 2013; 14:913 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006751
Loading
Expanding the cultivable human archaeome: Methanobrevibacter intestini sp. nov. and strain Methanobrevibacter smithii ‘GRAZ-2’ from human faeces
Int J Syst Evol Microbiol 75, 006751 (2025); https://doi.org/10.1099/ijsem.0.006751
/content/journal/ijsem/10.1099/ijsem.0.006751
/content/journal/ijsem/10.1099/ijsem.0.006751
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error