S. Razin and R. Herrmann, Molecular biology and pathogenicity of mycoplasmas, 2002.

A. Antunes, F. A. Rainey, G. Wanner, M. Taborda, J. Pätzold et al., A new lineage of halophilic, wall-less, contractile bacteria from a brine-filled deep of the Red Sea, J Bacteriol, vol.190, issue.10, pp.3580-3587, 2008.

C. T. Skennerton, M. F. Haroon, A. Briegel, J. Shi, G. J. Jensen et al., Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps, ISME J, vol.10, issue.11, pp.2679-92, 2016.

A. Antunes, I. Alam, E. Dorry, H. Siam, R. Robertson et al., Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake, J Bacteriol, vol.193, issue.17, pp.4551-4553, 2011.

M. L. Pierce and J. E. Ward, Gut microbiomes of the eastern oyster (Crassostrea virginica) and the blue mussel (Mytilus edulis): Temporal variation and the influence of marine aggregate-associated microbial communities. mSphere, vol.4, pp.730-749, 2019.

P. A. Rodrigues, R. G. Ferrari, and C. Ca, Application of molecular tools to elucidate the microbiota of seafood, J Appl Microbiol, vol.124, issue.6, pp.1347-65, 2018.

L. Høj, N. Levy, B. K. Baillie, P. L. Clode, R. C. Strohmaier et al., Crown-of-Thorns Sea star Acanthaster cf. solaris has tissue-characteristic microbiomes with potential roles in health and reproduction, Appl Environ Microb, vol.84, issue.13, pp.181-199, 2018.

J. Guillen, F. Natale, N. Carvalho, J. Casey, J. Hofherr et al., Global seafood consumption footprint, Ambio, vol.48, issue.2, pp.111-133, 2019.

M. Iwamoto, T. Ayers, B. E. Mahon, and D. L. Swerdlow, Epidemiology of seafoodassociated infections in the United States, Clin Microbiol Rev, vol.23, issue.2, pp.399-411, 2010.

C. P. White and D. D. Jewer, Seal finger: a case report and review of the literature, Can J Plas Surg, vol.17, issue.4, pp.133-138, 2009.

E. Orellana, C. Davies-sala, L. D. Guerrero, I. Vardé, M. Altina et al., Microbiome network analysis of cooccurrence patterns in anaerobic co-digestion of sewage sludge and food waste, Water Sci Technol, vol.79, issue.10, pp.1956-65, 2019.

Y. J. Wang, U. Stingl, F. Anton-erxleben, S. Geisler, A. Brune et al., Candidatus Hepatoplasma crinochetorum," a new, stalk-forming lineage of Mollicutes colonizing the midgut glands of a terrestrial isopod, Appl Environ Microb, vol.70, issue.10, pp.6166-72, 2004.

Y. Wang, J. M. Huang, S. L. Wang, Z. M. Gao, A. Q. Zhang et al., Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod bathynomus sp, Environ Microbiol, vol.18, issue.8, pp.2646-59, 2016.

L. He, P. Zhang, J. Huang, F. Zhu, A. Danchin et al., The enigmatic genome of an obligate ancient Spiroplasma symbiont in a hadal holothurian, Appl Environ Microbiol, vol.84, issue.1, pp.1965-1982, 2018.

K. E. Sullam, S. D. Essinger, C. A. Lozupone, M. P. O'connor, G. L. Rosen et al., Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis, Mol Ecol, vol.21, issue.13, pp.3363-78, 2012.

J. H. Yun, S. W. Roh, T. W. Whon, M. J. Jung, M. S. Kim et al., Insect gut bacterial diversity determined by environmental habitat, diet, developmental stage, and phylogeny of host, Appl Environ Microbiol, vol.80, issue.17, pp.5254-64, 2014.

A. Almeida, A. L. Mitchell, M. Boland, S. C. Forster, G. B. Gloor et al., A new genomic blueprint of the human gut microbiota, Nature, vol.568, issue.7753, pp.499-504, 2019.

N. A. Moran, Microbial minimalism: genome reduction in bacterial pathogens, Cell, vol.108, issue.5, pp.583-589, 2002.

W. Lo, G. E. Gasparich, and C. Kuo, Convergent evolution among ruminantpathogenic mycoplasma involved extensive gene content changes

, Genome Biol Evol, vol.10, issue.8, pp.2130-2139, 2018.

V. M. Chernov, O. A. Chernova, A. A. Mouzykantov, E. S. Medvedeva, N. B. Baranova et al., Antimicrobial resistance in mollicutes: known and newly emerging mechanisms, FEMS Microbiol Lett, vol.365, issue.18, p.185, 2018.

C. Citti, E. Dordet-frisoni, L. X. Nouvel, C. H. Kuo, and E. Baranowski, Horizontal gene transfers in mycoplasmas (Mollicutes), Curr Issues Mol Biol, vol.29, pp.3-22, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02628137

C. Blotz and J. Stulke, Glycerol metabolism and its implication in virulence in Mycoplasma, FEMS Microbiol Rev, vol.41, issue.5, pp.640-52, 2017.

D. H. Parks, M. Chuvochina, D. W. Waite, C. Rinke, A. Skarshewski et al., A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life, Nat Biotechnol, vol.36, issue.10, pp.996-1004, 2018.

S. Nayfach, Z. J. Shi, R. Seshadri, K. S. Pollard, and N. C. Kyrpides, New insights from uncultivated genomes of the global human gut microbiome, Nature, vol.568, issue.7753, pp.505-515, 2019.

L. T. Zhang, X. F. Huang, B. Xue, Q. H. Peng, Z. S. Wang et al., Immunization against rumen methanogenesis by vaccination with a new recombinant protein, PLoS One, vol.10, issue.10, p.140086, 2015.

X. Cheng, Y. Wang, J. , G. , Y. He et al., Comparative analysis of the gut microbial communities between two dominant amphipods from the Challenger Deep, Mariana Trench, Deep Sea Res I, vol.151, p.103081, 2019.

S. Sunagawa, L. P. Coelho, S. Chaffron, J. R. Kultima, K. Labadie et al., Structure and function of the global ocean microbiome, Science, vol.348, issue.6237, pp.1261359-1261360, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01233742

A. S. Ramírez, O. M. Vega-orellana, T. Viver, J. B. Poveda, R. S. Rosales et al., First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp, Syst Appl Microbiol, vol.42, issue.4, pp.457-67, 2019.

D. W. Pitta, N. Parmar, A. K. Patel, N. Indugu, S. Kumar et al., Bacterial diversity dynamics associated with different diets and different primer pairs in the rumen of kankrej cattle, PLoS One, vol.9, issue.11, p.111710, 2014.

Y. Shimoji, Y. Yokomizo, T. Sekizaki, Y. Mori, and M. Kubo, Presence of a capsule in Erysipelothrix-Rhusiopathiae and its relationship to virulence for mice, Infect Imm, vol.62, issue.7, pp.2806-2816, 1994.

J. Soppa, From genomes to function: haloarchaea as model organisms, Microbiology, vol.152, issue.3, pp.585-90, 2006.

Y. L. Lyubchenko and L. S. Shlyakhtenko, Visualization of supercoiled DNA with atomic force microscopy in situ, Proc Natl Acad Sci U S A, vol.94, issue.2, pp.496-501, 1997.

M. Kanehisa and G. S. Kegg, Kyoto encyclopedia of genes and genomes, Nucleic Acids Res, vol.28, issue.15, pp.27-30, 2000.

G. E. Gasparich and C. Kuo, Genome analysis-based union of the genus Mesoplasma with the genus Entomoplasma, Int J Syst Evol Microbiol, vol.69, issue.9, pp.2735-2743, 2019.

B. Tjaden, A. Plagens, C. Dorr, B. Siebers, and R. Hensel, Phosphoenolpyruvate synthetase and pyruvate, phosphate dikinase of Thermoproteus tenax: key pieces in the puzzle of archaeal carbohydrate metabolism, Mol Microbiol, vol.60, issue.2, pp.287-98, 2006.

J. I. Yeh, U. Chinte, and S. Du, Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism, Proc Natl Acad Sci, vol.105, issue.9, pp.3280-3285, 2008.

D. I. Andersson and D. Hughes, Muller's ratchet decreases fitness of a DNA-based microbe, Proc Natl Acad Sci, vol.93, issue.2, pp.906-913, 1996.

H. Grosjean and E. Westhof, An integrated, structure-and energy-based view of the genetic code, Nucleic Acids Res, vol.44, issue.17, pp.8020-8060, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01412326

Y. Sakai, K. Miyauchi, S. Kimura, and T. Suzuki, Biogenesis and growth phasedependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons, Nucleic Acids Res, vol.44, issue.2, pp.509-532, 2016.

K. Yamanaka, T. Ogura, H. Niki, and S. Hiraga, Characterization of the smtA gene encoding an S-adenosylmethionine-dependent methyltransferase of Escherichia coli, FEMS Microbiol Lett, vol.133, issue.1-2, pp.59-63, 1995.

S. J. Cai and M. Inouye, EnvZ-OmpR interaction and osmoregulation in Escherichia coli, J Biol Chem, vol.277, issue.27, pp.24155-61, 2002.

J. M. Eraso, L. M. Markillie, H. D. Mitchell, R. C. Taylor, G. Orr et al., The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli, J Bacteriol, vol.196, issue.11, pp.2053-66, 2014.

K. Schuchmann and V. Muller, Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria, Nat Rev Microbiol, vol.12, issue.12, pp.809-830, 2014.

K. J. Thorne and E. Kodicek, The structure of bactoprenol, a lipid formed by lactobacilli from mevalonic acid, Biochem J, vol.99, issue.1, pp.123-130, 1966.

G. Manat, S. Roure, R. Auger, A. Bouhss, H. Barreteau et al., Deciphering the metabolism of undecaprenyl-phosphate: the bacterial cell-wall unit carrier at the membrane frontier. Microb Drug Ris, vol.20, pp.199-214, 2014.

A. Z. Mostafavi, D. K. Lujan, K. M. Erickson, C. D. Martinez, and J. M. Troutman, Fluorescent probes for investigation of isoprenoid configuration and size discrimination by bactoprenol-utilizing enzymes, Bioorganic Med Chem, vol.21, issue.17, pp.5428-5463, 2013.

K. G. Wooldridge and P. H. Williams, Iron uptake mechanisms of pathogenic bacteria, FEMS Microbiol Rev, vol.12, issue.4, pp.325-373, 1993.

W. Mulder-david, S. Eric, M. , M. Jonathan, E. Joshi et al., Insights into [FeFe]-hydrogenase structure, mechanism, and maturation, Structure, vol.19, issue.8, pp.1038-52, 2011.

P. G. Wolf, A. Biswas, S. E. Morales, C. Greening, and H. R. Gaskins, H-2 metabolism is widespread and diverse among human colonic microbes, Gut Microbes, vol.7, issue.3, pp.235-280, 2016.

N. R. Ballor and J. R. Leadbetter, Patterns of [FeFe] hydrogenase diversity in the gut microbial communities of lignocellulose-feeding higher termites, Appl Environ Microb, vol.78, issue.15, pp.5368-74, 2012.

D. H. Parks, M. Imelfort, C. T. Skennerton, P. Hugenholtz, and G. W. Tyson, CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes, Genome Res, vol.25, issue.7, pp.1043-55, 2015.

Y. Huang, P. Gilna, and W. Li, Identification of ribosomal RNA genes in metagenomic fragments, Bioinformatics, vol.25, issue.10, pp.1338-1378, 2009.

L. M. Fu, B. F. Niu, Z. W. Zhu, S. T. Wu, and W. Z. Li, CD-HIT: accelerated for clustering the next-generation sequencing data, Bioinformatics, vol.28, issue.23, pp.3150-3152, 2012.

D. Hyatt, P. F. Locascio, L. J. Hauser, and E. C. Uberbacher, Gene and translation initiation site prediction in metagenomic sequences, Bioinformatics, vol.28, issue.17, pp.2223-2253, 2012.

J. Huerta-cepas, K. Forslund, L. P. Coelho, D. Szklarczyk, L. J. Jensen et al., Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper, Mol Biol Evol, vol.34, issue.8, pp.2115-2137, 2016.

. Hutchison-ca-3rd, R. Y. Chuang, V. N. Noskov, N. Assad-garcia, T. J. Deerinck et al., Design and synthesis of a minimal bacterial genome, Science, vol.351, issue.6280, p.6253, 2016.

M. Y. Galperin, K. S. Makarova, Y. I. Wolf, and E. V. Koonin, Expanded microbial genome coverage and improved protein family annotation in the COG database, Nucleic Acids Res, vol.43, pp.261-270, 2015.

W. Li, J. Huang, P. Zhang, G. Cui, Z. Wei et al., Periodic and spatial spreading of alkanes and Alcanivorax bacteria in deep waters of the Mariana trench, Appl Environ Microbiol, vol.85, issue.3, pp.2089-2107, 2019.

R. K. Patel and M. Jain, NGS QC toolkit: a toolkit for quality control of next generation sequencing data, PLoS One, vol.7, issue.2, p.30619, 2012.

J. Zhang, K. Kobert, T. Flouri, and A. Stamatakis, PEAR: a fast and accurate illumina paired-end reAd mergeR, Bioinformatics, vol.30, issue.5, pp.614-634, 2014.

J. G. Caporaso, K. Bittinger, F. D. Bushman, T. Z. Desantis, G. L. Andersen et al., PyNAST: a flexible tool for aligning sequences to a template alignment, Bioinformatics, vol.26, issue.2, pp.266-273, 2010.

Q. Wang, G. M. Garrity, J. M. Tiedje, and J. R. Cole, Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl Environ Microbiol, vol.73, issue.16, pp.5261-5266, 2007.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, issue.5, pp.1792-1799, 2004.

S. Capellagutiérrez, J. M. Sillamartínez, and T. Gabaldón, TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, issue.15, pp.1972-1975, 2009.

N. Lam-tung, H. A. Schmidt, V. H. Arndt, and M. Bui-quang, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol Biol Evol, vol.32, issue.1, pp.268-74, 2015.

S. Kalyaanamoorthy, B. Q. Minh, T. Wong, A. V. Haeseler, and L. S. Jermiin, ModelFinder: fast model selection for accurate phylogenetic estimates, Nat Meth, vol.14, issue.6, pp.587-596, 2017.

M. Wu and A. J. Scott, Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2, Bioinformatics, vol.28, issue.7, pp.1033-1037, 2012.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.215, issue.3, pp.403-413, 1990.

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