Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli

Abstract

Background: The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. Results: Several environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. Conclusions: This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.

Phylogenomic insights into distribution and adaptation of Bdellovibrionota in marine waters

“…4). The by-production of glycerol oxidation is H 2 O 2 , which is cytotoxic (37) and can be used to destroy cell wall structure of prey bacteria after free diffusion of H 2 O 2 into the prey periplasmic space. The coding gene of sn-glycerol-3-phosphate acyltransferase (PlsB), the first enzyme for membrane phospholipid biosynthesis (38), was predicted only in Oligoflexia genomes (Table S6).…”

Characterization of the first cultured free-living representative of Candidatus Izimaplasma uncovers its unique biology

“…Two distinctive features set Tenericutes apart from the Firmicutes: the inability to synthetize precursors of peptidoglycan and thereby forming a cell wall 4–7 , and extreme reduction of the size of genome (between 530 to 2220 kbp) 8,9 . Tenericutes includes the class Mollicutes 2 , three taxa in provisional class Candidatus Izimaplasma 4 , and several taxa of unclassified status. Tenericutes bacteria have evolved a broad range of lifestyles, including free-living, commensalism and parasitism 2 .…”

“…Tenericutes includes the class Mollicutes 2 , three taxa in provisional class Candidatus Izimaplasma 4 , and several taxa of unclassified status. Tenericutes bacteria have evolved a broad range of lifestyles, including free-living, commensalism and parasitism 2 . Up to date, almost all reported Mollicutes (including five orders Mycoplasmatales, Entomoplasmatales, Haloplasmatales, Acholeplasmatales, and Anaeroplasmatales) 10 are commensals or obligate parasites of humans, domestic animals, plants and insects 2 .…”

“…Tenericutes bacteria have evolved a broad range of lifestyles, including free-living, commensalism and parasitism 2 . Up to date, almost all reported Mollicutes (including five orders Mycoplasmatales, Entomoplasmatales, Haloplasmatales, Acholeplasmatales, and Anaeroplasmatales) 10 are commensals or obligate parasites of humans, domestic animals, plants and insects 2 . In comparison, some free-living species are found to be associated with inert substrates (e.g.…”

“…Tenericutes bacteria ubiquitously exist in numerous environments 13 . Environmental 16S rRNA surveys have identified a large number of unknown Tenericutes clades in diverse environments including the deep oceans, introducing the possibility that these Tenericutes may represent free-living microorganisms which conducting a non-host-associated life style 2 . Indeed, free-living Candidatus Izimaplasma 4 and Haloplasma 14 were reported in a deep-sea cold seep and brine pool, respectively.…”