Vollmer, W., Blanot, D. & De Pedro, M. A. Peptidoglycan structure and architecture. FEMS Microbiol. Rev. 32, 149–167 (2008).
Albers, S.-V. & Meyer, B. H. The archaeal cell envelope. Nat. Rev. Microbiol. 9, 414–426 (2011).
Kandler, O. Zellwandstrukturen bei Methan-Bakterien. Naturwissenschaften 66, 95–105 (1979).
König, H., Kralik, R. & Kandler, O. Structure and modifications of pseudomurein in Methanobacleriales. Zentralblatt Für Bakteriol. Mikrobiol. Hyg. Abt Orig. C. 3, 179–191 (1982).
König, H., Kandler, O., Jensen, M. & Rietschel, E. T. The primary structure of the glycan moiety of pseudomurein from Methanobacterium thermoautotrophicum. Hoppe. Seylers Z. Physiol. Chem. 364, 627–636 (1983).
König, H. & Kandler, O. The amino acid sequence of the peptide moiety of the pseudomurein from Methanobacterium thermoautotrophicum. Arch. Microbiol. 121, 271–275 (1979).
Kandler, O. & König, H. Chemical composition of the peptidoglycan-free cell walls of methanogenic bacteria. Arch. Microbiol. 118, 141–152 (1978).
König, H. & Kandler, O. N-Acetyltalosaminuronic acid a constituent of the pseudomurein of the genus Methanobacterium. Arch. Microbiol. 123, 295–299 (1979).
Borrel, G., Brugère, J.-F., Gribaldo, S., Schmitz, R. A. & Moissl-Eichinger, C. The host-associated archaeome. Nat. Rev. Microbiol. 18, 622–636 (2020).
Hook, S. E., Wright, A.-D. G. & McBride, B. W. Methanogens: methane producers of the rumen and mitigation strategies. Archaea 2010, 945785 (2010).
Hoegenauer, C., Hammer, H. F., Mahnert, A. & Moissl-Eichinger, C. Methanogenic archaea in the human gastrointestinal tract. Nat. Rev. Gastroenterol. Hepatol. 19, 805–813 (2022).
Claus, H. & König, H. in Prokaryotic Cell Wall Compounds: Structure and Biochemistry (eds. König, H. et al.) 231–251 https://doi.org/10.1007/978-3-642-05062-6_7 (Springer, 2010).
Alvarez, L., Cordier, B., Van Teeffelen, S. & Cava, F. Analysis of Gram-negative bacteria peptidoglycan by ultra-performance liquid chromatography. Bio-Protoc. 10, e3780 (2020).
Patel, A. V. et al. PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans. eLife 10, e70597 (2021).
Luo, Y., Pfister, P., Leisinger, T. & Wasserfallen, A. The genome of archaeal prophage PsiM100 encodes the lytic enzyme responsible for autolysis of Methanothermobacter wolfeii. J. Bacteriol. 183, 5788–5792 (2001).
Pfister, P., Wasserfallen, A., Stettler, R. & Leisinger, T. Molecular analysis of Methanobacterium phage psiM2. Mol. Microbiol. 30, 233–244 (1998).
Leahy, S. C. et al. The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One 5, e8926 (2010).
Luo, Y., Pfister, P., Leisinger, T. & Wasserfallen, A. Pseudomurein endoisopeptidases PeiW and PeiP, two moderately related members of a novel family of proteases produced in Methanothermobacter strains. FEMS Microbiol. Lett. 208, 47–51 (2002).
Weinberger, V. et al. 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).
Turner, R. D. et al. Peptidoglycan architecture can specify division planes in Staphylococcus aureus. Nat. Commun. 1, 26 (2010).
Wheeler, R., Mesnage, S., Boneca, I. G., Hobbs, J. K. & Foster, S. J. Super-resolution microscopy reveals cell wall dynamics and peptidoglycan architecture in ovococcal bacteria. Mol. Microbiol. 82, 1096–1109 (2011).
Blackman, S. A., Smith, T. J. & Foster, S. J. The role of autolysins during vegetative growth of Bacillus subtilis 168. Microbiology 144, 73–82 (1998).
Guo, L. et al. Insights into the catalytic mechanism of archaeal peptidoglycan endoisopeptidases from methanogenic phages. Int. J. Biol. Macromol. 296, 139672 (2025).
Makarova, K. S., Aravind, L. & Koonin, E. V. A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases. Protein Sci. Publ. Protein Soc. 8, 1714–1719 (1999).
Xu, N., Huang, Z. H., de Jonge, B. L. & Gage, D. A. Structural characterization of peptidoglycan muropeptides by matrix-assisted laser desorption ionization mass spectrometry and postsource decay analysis. Anal. Biochem. 248, 7–14 (1997).
Glauner, B., Höltje, J. V. & Schwarz, U. The composition of the murein of Escherichia coli. J. Biol. Chem. 263, 10088–10095 (1988).
Petitjean, C., Deschamps, P., López-García, P., Moreira, D. & Brochier-Armanet, C. Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life. Mol. Biol. Evol. 32, 1242–1254 (2015).
Schleifer, K. H. & Kandler, O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol. Rev. 36, 407–477 (1972).
Baquero, D. P. et al. Stable coexistence between an archaeal virus and the dominant methanogen of the human gut. Nat. Commun. 15, 7702 (2024).
Medvedeva, S., Borrel, G., Krupovic, M. & Gribaldo, S. A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment. Nat. Microbiol. 8, 2170–2182 (2023).
Vollmer, W., Joris, B., Charlier, P. & Foster, S. Bacterial peptidoglycan (murein) hydrolases. FEMS Microbiol. Rev. 32, 259–286 (2008).
Sham, L.-T., Barendt, S. M., Kopecky, K. E. & Winkler, M. E. Essential PcsB putative peptidoglycan hydrolase interacts with the essential FtsXSpn cell division protein in Streptococcus pneumoniae D39. Proc. Natl Acad. Sci. USA 108, E1061–1069 (2011).
Bartual, S. G. et al. Structural basis of PcsB-mediated cell separation in Streptococcus pneumoniae. Nat. Commun. 5, 3842 (2014).
Fink, C. et al. The targeted deletion of genes responsible for expression of the mth60 fimbriae leads to loss of cell-cell connections in Methanothermobacter thermautotrophicus ΔH. Appl. Environ. Microbiol. 89, e00575-23 (2023).
Zeikus, J. G. & Wolfe, R. S. Methanobacterium thermoautotrophicus sp. n., an anaerobic, autotrophic, extreme thermophile. J. Bacteriol. 109, 707–715 (1972).
Wilson, S. A., Tank, R. K. J., Hobbs, J. K., Foster, S. J. & Garner, E. C. An exhaustive multiple knockout approach to understanding cell wall hydrolase function in Bacillus subtilis. mBio. 14, e0176023 (2023).
Rajguru, V., Chatterjee, S., Garde, S. & Reddy, M. Crosslink cleaving enzymes: the smart autolysins that remodel the bacterial cell wall. Trends Microbiol. 32, 494–506 (2024).
Egan, A. J. F., Errington, J. & Vollmer, W. Regulation of peptidoglycan synthesis and remodelling. Nat. Rev. Microbiol. 18, 446–460 (2020).
Pende, N. et al. SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system. Nat. Commun. 12, 3214 (2021).
Ithurbide, S., Gribaldo, S., Albers, S.-V. & Pende, N. Spotlight on FtsZ-based cell division in Archaea. Trends Microbiol. 30, 665–678 (2022).
van Wolferen, M., Pulschen, A. A., Baum, B., Gribaldo, S. & Albers, S.-V. The cell biology of archaea. Nat. Microbiol. 7, 1744–1755 (2022).
Rohs, P. D. A. & Bernhardt, T. G. Growth and division of the peptidoglycan matrix. Annu. Rev. Microbiol. 75, 315–336 (2021).
Garcia, P. S., Gribaldo, S. & Borrel, G. Diversity and evolution of methane-related pathways in archaea. Annu. Rev. Microbiol. 76, 727–755 (2022).
Bonin, A. S. & Boone, D. R. in The Prokaryotes (eds. Dworkin, M. et al.) 231–243 https://doi.org/10.1007/0-387-30743-5_11 (Springer, 2006).
Thomas, C. M., Desmond-Le Quéméner, E., Gribaldo, S. & Borrel, G. Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom. Nat. Commun. 13, 3358 (2022).
Pfeifer, K. et al. Archaea biotechnology. Biotechnol. Adv. 47, 107668 (2021).
Wheeler, R., Veyrier, F., Werts, C. & Boneca, I. G. Peptidoglycan and Nod receptor. In Glycoscience: Biology and Medicine 737–747 https://doi.org/10.1007/978-4-431-54841-6_147 (Springer Japan, Tokyo, 2015).
Mistry, J. et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 49, D412–D419 (2021).
Yu, N. Y. et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26, 1608–1615 (2010).
Vranken, W. F. et al. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59, 687–696 (2005).
Johnson, L. S., Eddy, S. R. & Portugaly, E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinf. 11, 431 (2010).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Criscuolo, A. & Gribaldo, S. BMGE (block mapping and gathering with entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10, 210 (2010).
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).