Abstract
BackgroundThe 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.ResultsSeveral 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.ConclusionsThis 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.
Highlights
The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species
Free-living Izemoplasma (the new name proposed by the Genome Taxonomy Database (GTDB)) and Haloplasma were reported in a deepsea cold seep and brine pool, respectively [2, 3]
70% of the non-redundant sequences were derived from the order Mycoplasmatales, which was largely composed of commensals and pathogens isolated from plants, humans and animals
Summary
The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. Free-living Izemoplasma (the new name proposed by the Genome Taxonomy Database (GTDB)) and Haloplasma were reported in a deepsea cold seep and brine pool, respectively [2, 3] Based on their genomic features, the cell wall-lacking Izemoplasma were predicted to be hydrogen producers and DNA degraders. The Haloplasma contractile genome encodes actin and tubulin homologues, which might be required for its specific motility in deep-sea hypersaline lake [4] These marine environmental Tenericutes exhibit metabolic versatility and adaptive flexibility. Aside from Salmonella and Vibrio pathogens transmitted from aquaculture products [9], there are other unknown pathogenic Mycoplasma isolates from marine animals, such as those causing ‘seal finger’ [10] These pathogens from the ocean may be natural or human pollutants. The spread and diversity of the Tenericutes species in oceans remain unclear
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