Seviour, B. & Nielsen, P. Microbial Ecology of Activated Sludge Preface (IWA Publishing, 2010).
Nielsen, P. H., Saunders, A. M., Hansen, A. A., Larsen, P. & Nielsen, J. L. Microbial communities involved in enhanced biological phosphorus removal from wastewater-a model system in environmental biotechnology. Curr. Opin. Biotechnol. 23, 452–459 (2012).
Google Scholar
Hu, H. et al. Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants. Microbiome 12, 55 (2024).
Google Scholar
Fujii, N. et al. Metabolic potential of the superphylum Patescibacteria reconstructed from activated sludge samples from a municipal wastewater treatment plant. Microbes Environ. 37, ME22012 (2022).
Google Scholar
Albertsen, M. et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 31, 533–538 (2013).
Google Scholar
Marcy, Y. et al. Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl Acad. Sci. USA 104, 11889–11894 (2007).
Google Scholar
He, X. et al. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proc. Natl Acad. Sci. 112, 244–249 (2015).
Google Scholar
Xie, B. et al. Type IV pili trigger episymbiotic association of Saccharibacteria with its bacterial host. Proc. Natl Acad. Sci. USA 119, e2215990119 (2022).
Google Scholar
Wang, Y. et al. Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle. Cell 186, 4803–4817.e4813 (2023).
Google Scholar
Batinovic, S., Rose, J. J., Ratcliffe, J., Seviour, R. J. & Petrovski, S. Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams. Nat. Microbiol. 6, 703–711 (2021).
Google Scholar
Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004 (2018).
Google Scholar
Rheims, H., Rainey, F. & Stackebrandt, E. A molecular approach to search for diversity among bacteria in the environment. J. Ind. Microbiol. 17, 159–169 (1996).
Vigneron, A., Cruaud, P., Guyoneaud, R. & Goñi-Urriza, M. Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations. Front. Microbiol. 13, 1073483 (2023).
Google Scholar
Kuroda, K. et al. Metabolic implications for predatory and parasitic bacterial lineages in activated sludge wastewater treatment systems. Water Res. X 20, 100196 (2023).
Google Scholar
Sartori-Rupp, A. et al. Correlative cryo-electron microscopy reveals the structure of TNTs in neuronal cells. Nat. Commun. 10, 342 (2019).
Google Scholar
Gaisin, V. A., van Wolferen, M., Albers, S.-V. & Pilhofer, M. Distinct life cycle stages of an ectosymbiotic DPANN archaeon. ISME J. 18, wrae076 (2024).
Google Scholar
Johnson, M. D. et al. Large attachment organelle mediates interaction between Nanobdellota archaeon YN1 and its host. ISME J. 18, wrae154 (2024).
Craig, L. et al. Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Mol. Cell 23, 651–662 (2006).
Google Scholar
Portevin, D. et al. A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms. Proc. Natl Acad. Sci. USA 101, 314–319 (2004).
Google Scholar
Marrakchi, H., Lanéelle, M.-A. & Daffé, M. Mycolic acids: structures, biosynthesis, and beyond. Chem. Biol. 21, 67–85 (2014).
Google Scholar
Seidel, M. et al. Identification of a novel arabinofuranosyltransferase AftB involved in a terminal step of cell wall arabinan biosynthesis in Corynebacterianeae, such as Corynebacterium glutamicum and Mycobacterium tuberculosis. J. Biol. Chem. 282, 14729–14740 (2007).
Google Scholar
Besra, G. S. et al. A new interpretation of the structure of the mycolyl-arabinogalactan complex of Mycobacterium tuberculosis as revealed through characterization of oligoglycosylalditol fragments by fast-atom bombardment mass spectrometry and 1H nuclear magnetic resonance spectroscopy. Biochemistry 34, 4257–4266 (1995).
Google Scholar
McNeil, M., Daffe, M. & Brennan, P. Location of the mycolyl ester substituents in the cell walls of mycobacteria. J. Biol. Chem. 266, 13217–13223 (1991).
Google Scholar
McNeil, M., Daffe, M. & Brennan, P. J. Evidence for the nature of the link between the arabinogalactan and peptidoglycan of mycobacterial cell walls. J. Biol. Chem. 265, 18200–18206 (1990).
Google Scholar
Chalut, C., Botella, L., de Sousa-D’Auria, C., Houssin, C. & Guilhot, C. The nonredundant roles of two 4′-phosphopantetheinyl transferases in vital processes of Mycobacteria. Proc. Natl Acad. Sci. USA 103, 8511–8516 (2006).
Google Scholar
Mdluli, K. et al. Inhibition of a Mycobacterium tuberculosis β-ketoacyl ACP synthase by isoniazid. Science 280, 1607–1610 (1998).
Google Scholar
Yoshida, K.-i et al. myo-Inositol catabolism in Bacillus subtilis. J. Biol. Chem. 283, 10415–10424 (2008).
Google Scholar
Yoshida, K.-I., Yamamoto, Y., Omae, K., Yamamoto, M. & Fujita, Y. Identification of two myo-inositol transporter genes of Bacillus subtilis. J. Bacteriol. 184, 983–991 (2002).
Google Scholar
Ghosal, D. et al. Molecular architecture, polar targeting and biogenesis of the Legionella Dot/Icm T4SS. Nat. Microbiol. 4, 1173–1182 (2019).
Google Scholar
Nicastro, D. et al. The molecular architecture of axonemes revealed by cryoelectron tomography. Science 313, 944–948 (2006).
Google Scholar
Petrovski, S. et al. An examination of the mechanisms for stable foam formation in activated sludge systems. Water Res. 45, 2146–2154 (2011).
Google Scholar
Petrovski, S., Batinovic, S., Rose, J. J. & Seviour, R. J. Biological control of problematic bacterial populations causing foaming in activated sludge wastewater treatment plants—phage therapy and beyond. Lett. Appl. Microbiol. 75, 776–784 (2022).
Google Scholar
Rosenberg, M., Gutnick, D. & Rosenberg, E. Adherence of bacteria to hydrocarbons: a simple method for measuring cell-surface hydrophobicity. FEMS Microbiol. Lett. 9, 29–33 (1980).
Google Scholar
Bor, B. et al. Phenotypic and physiological characterization of the epibiotic interaction between TM7x and its basibiont Actinomyces. Microb. Ecol. 71, 243–255 (2016).
Google Scholar
Bedree, J. K. et al. Quorum sensing modulates the epibiotic-parasitic relationship between Actinomyces odontolyticus and its Saccharibacteria epibiont, a Nanosynbacter lyticus strain, TM7x. Front. Microbiol. 9, 2049 (2018).
Google Scholar
Fujii, N. et al. Unique episymbiotic relationship between Candidatus Patescibacteria and Zoogloea in activated sludge flocs at a municipal wastewater treatment plant. Environ. Microbiol. Rep. 16, e70007 (2024).
Google Scholar
Dong, P.-T. et al. Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria. ISME J. 18, wrad034 (2024).
Google Scholar
Zhong, Q. et al. Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence. Proc. Natl Acad. Sci. USA 121, e2319790121 (2024).
Google Scholar
Johnson, M. D. et al. Cell-to-cell interactions revealed by cryo-tomography of a DPANN co-culture system. Nat. Commun. 15, 7066 (2024).
Al-Jourani, O. et al. Identification of D-arabinan-degrading enzymes in mycobacteria. Nat. Commun. 14, 2233 (2023).
Google Scholar
Moreira, D., Zivanovic, Y., López-Archilla, A. I., Iniesto, M. & López-García, P. Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii. Nat. Commun. 12, 2454 (2021).
Google Scholar
Sockett, R. E. Predatory lifestyle of Bdellovibrio bacteriovorus. Annu. Rev. Microbiol. 63, 523–539 (2009).
Google Scholar
Hoffmann, C., Leis, A., Niederweis, M., Plitzko, J. M. & Engelhardt, H. Disclosure of the mycobacterial outer membrane: cryo-electron tomography and vitreous sections reveal the lipid bilayer structure. Proc. Natl Acad. Sci. USA 105, 3963–3967 (2008).
Google Scholar
Sancho-Vaello, E., Albesa-Jové, D., Rodrigo-Unzueta, A. & Guerin, M. E. Structural basis of phosphatidyl-myo-inositol mannosides biosynthesis in mycobacteria. Biochim. et Biophys. Acta (BBA)-Mol. Cell Biol. Lipids 1862, 1355–1367 (2017).
Gilleron, M., Nigou, J., Nicolle, D., Quesniaux, V. & Puzo, G. The acylation state of mycobacterial lipomannans modulates innate immunity response through toll-like receptor 2. Chem. Biol. 13, 39–47 (2006).
Google Scholar
Salman, M., Lonsdale, J. T., Besra, G. S. & Brennan, P. J. Phosphatidylinositol synthesis in mycobacteria. Biochim. et Biophys. Acta (BBA)-Mole. Cell Biol. Lipids 1436, 437–450 (1999).
Chevez-Guardado, R. & Peña-Castillo, L. Promotech: a general tool for bacterial promoter recognition. Genome Biol. 22, 1–16 (2021).
Google Scholar
Ramsey, J. et al. Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. PLOS Comput. Biol. 16, e1008214 (2020).
Google Scholar
Gavalda, S. et al. The Pks13/FadD32 crosstalk for the biosynthesis of mycolic acids in Mycobacterium tuberculosis. J. Biol. Chem. 284, 19255–19264 (2009).
Google Scholar
Pawełczyk, J. & Kremer, L. The molecular genetics of mycolic acid biosynthesis. Microbiol. Spectrum 2, MGM2-0003-2013 (2014).