Affiliation:
1. School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
Abstract
Many peptidoglycan-deficient bacteria such as the
Mycoplasmatales
are known host-associated lineages, lacking the environmental resistance mechanisms and metabolic capabilities necessary for a free-living lifestyle. Several peptidoglycan-deficient and non-sporulating orders of interest are thought to be descended from Gram-positive sporulating
Bacilli
through reductive evolution. Here we annotate 2650 genomes belonging to the class
Bacilli
, according to the Genome Taxonomy Database, to predict the peptidoglycan and sporulation phenotypes of three novel orders, RFN20, RF39 and ML615J-28, known only through environmental sequence surveys. These lineages are interspersed between peptidoglycan-deficient non-sporulating orders including the
Mycoplasmatales
and
Acholeplasmatales
, and more typical Gram-positive orders such as the
Erysipelotrichales
and Staphylococcales. We use the extant genotypes to perform ancestral state reconstructions. The novel orders are predicted to have small genomes with minimal metabolic capabilities and to comprise a mix of peptidoglycan-deficient and/or non-sporulating species. In contrast to expectations based on cultured representatives, the order
Erysipelotrichales
lacks many of the genes involved in peptidoglycan and endospore formation. The reconstructed evolutionary history of these traits suggests multiple independent whole-genome reductions and loss of phenotype via intermediate transition states that continue into the present. We suggest that the evolutionary history of the reduced-genome lineages within the class
Bacilli
is one driven by multiple independent transitions to host-associated lifestyles, with the degree of reduction in environmental resistance and metabolic capabilities correlated with degree of host association.
Funder
Australian Research Council