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.

Keywords: Autotrophy; Bacilli; Environmental Tenericutes; Gut microbiome; Pathogen.

Fig. 1

Phylogenetic trees of Tenericutes. The maximum-likelihood phylogenetic trees were constructed by concatenated conserved proteins (a) and 16S rRNA genes (b). The bootstrap values (> 50) are denoted by the dots on the branches. The colors of the inner layer indicate the positions of the different environmental lineages and groups of Tenericutes in the trees. Sources of the environmental lineages are shown as shapes in different colors in the outer layer

Fig. 2

Phylogenetic positions of Tenericutes families in Bacilli. Representative genomes from orders of Bacilli were used to construct the phylogenomics tree using concatenated conserved proteins by IQ-TREE and RAxML. The bootstrap values were shown as triangles (50–90) and dots (> 90) with a red color for the results of RAxML and deep blue for those of IQ-TREE, respectively. The red clades represent the orders of Tenericutes. The Bacilli genomes for Erysipelotrichales and the other orders in purple were selected from GTDB. RFN20, RF39, ML615 were environmental clades named in GTDB and were phylogenetically placed within the NCBI clades consisting of human gut lineages 1, 2 and bioreactor group, respectively

Fig. 3

Distribution of genes and pathways in the Tenericutes lineages. Tenericutes lineages were grouped using an agglomerative hierarchical clustering on the basis of the distribution of COGs within each group. The color and size of each dot represent the percentage of genomes within each lineage that carries the gene. The functions of these genes are shown in Additional file 3: Table S1

Fig. 4

Schematic metabolism of RFN20 and RF39. We depicted the metabolic models based on gene annotation results of four representative genomes of RFN20 and RF39 (see Table 1). Solid squares indicate presence of the genes responsible for a step or a pathway. The products depicted in the MEP/DOXP pathway are 1-deoxy-xylulose 5-P, 2-C-methyl-D-erythritol 4-P, 4-(Cytidine 5′-PP)-2-C-methyl-erythritol, 2-P-4-(cytidine 5′-PP)-2-C-methyl-erythritol, 2-C-methyl-erythritol 2,4-PP, 1-hydroxy-2-methyl-2-butenyl 4-PP, dimethylallyl-PP, isopentenyl-PP, and farnesyl-PP