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

Abstract

Tenericutes 26 2 ABSTRACT 27 The metabolic capacity, stress response and evolution of uncultured environmental 28 Tenericutes have remained elusive, since previous studies have been largely focused on 29 pathogenic species. In this study, we expanded analyses on Tenericutes lineages that 30 inhabit various environments using a collection of 840 genomes. Several novel 31 environmental lineages were discovered inhabiting the human gut, ground water, 32 bioreactors and hypersaline lake and spanning the Haloplasmatales and 33 Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes 34 genomes revealed that some uncultured Tenericutes are affiliated with novel clades in 35 Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut 36 lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. 37We detected habitat-specific functional patterns between the pathogenic, gut and the 38 environmental Tenericutes, where genes involved in carbohydrate storage, carbon 39 fixation, mutation repair, environmental response and amino acid cleavage are 40 overrepresented in the genomes of environmental lineages. We hypothesize that the two 41 major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen 42 producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall 43 peptidoglycan precursors secretion is a potential adaptive strategy employed by these 44 lineages in response to the gut environment. This study uncovers the characteristic 45 functions of environmental Tenericutes and their relationships with Bacilli, which 46 sheds new light onto the pathogenicity and evolutionary processes of 47 Mycoplasmatales. 48 IMPORTANCE 49 Environmental Tenericutes bacteria were recently discovered in numerous 50 environments. However, our current collection of Tenericutes genomes was 51 overrepresented by those for pathogens. Our phylogenomics study displays the 52 relationships between all the available Tenericutes, as well as those between 53Tenericutes and the clades in Bacilli, which casts lights into the uncertain boundary 54 between the environmental lineages of Tenericutes and Bacilli. By comparing the 55 3 genomes of the environmental and pathogenic Tenericutes, we revealed the metabolic 56 pathways and adaptive strategies of the Tenericutes in the different environments and 57 hosts. We also predicted the metabolism of the two major gut lineages RF39 and 58 RFN20 of Tenericutes, indicating their potential importance in stabilization of the gut 59 microbiome and contribution to human health. 60 61 INTRODUCTION 62The phylum Tenericutes is composed of bacteria lacking a peptidoglycan cell wall. 63The most well-studied clade belonging to this phylum is Mollicutes, which contains 64 medically relevant genera, including Mycoplasma, Ureaplasma and Acholeplasma. 65 All reported mollicutes are commensals or obligate parasites of humans, domestic 66 animals, plants and insects (1). Most studies so far have focused on pathogenic stra...