Comprehensive comparative genomics reveals over 50 phyla of free-living and pathogenic bacteria are associated with diverse members of the amoebozoa

Abstract

The Amoebozoa, a group containing predominantly amoeboid unicellular protists has been shown to play an important ecological role in controlling environmental bacteria. Amoebozoans not only graze bacteria but also serve as a safe niche for bacterial replication and harbor endosymbiotic bacteria including dangerous human pathogens. Despite their importance, only a few lineages of Amoebozoa have been studied in this regard. In this research, we conducted a comprehensive genomic and transcriptomic study with expansive taxon sampling by including representatives from the three known clades of the Amoebozoa. We used culture independent whole culture and single cell genomics/transcriptomics to investigate the association of bacteria with diverse amoebozoans. Relative to current published evidence, we recovered the largest number of bacterial phyla (64) and human pathogen genera (51) associated with the Amoebozoa. Using single cell genomics/transcriptomics we were able to determine up to 24 potential endosymbiotic bacterial phyla, some potentially endosymbionts. This includes the majority of multi-drug resistant pathogens designated as major public health threats. Our study demonstrates amoebozoans are associated with many more phylogenetically diverse bacterial phyla than previously recognized. It also shows that all amoebozoans are capable of harboring far more dangerous human pathogens than presently documented, making them of primal public health concern.

The draft genome of Cochliopodium minus reveals a complete meiosis toolkit and provides insight into the evolution of sexual mechanisms in Amoebozoa

“…Permanent, obligatory and transient associations are known between bacteria and amoebae. Previous and our recent studies showed that large bacterial phyla including amoeba resisting bacteria and dangerous human pathogens are associated with amoebae 3 , 4 , 39 . These frequent and intimate encounters and associations might explain the observed large proportion of LGT events from bacteria in amoebae genomes.…”

Draft Genome of Cochliopodium minus (Amoebozoa): Insights into Its Complex Sexual Behavior, Across Domain Gene Acquisitions and Metazoan Type Signaling

“…Permanent, obligatory and transient associations are known between bacteria and amoebae. Previous and our recent studies showed that large bacterial phyla including amoeba resisting bacteria and dangerous human pathogens are associated with amoebae 3,4,38 . These frequent and intimate encounters and associations might explain the observed large proportion of LGT events from bacteria in amoebae genomes.…”

A Small Genome Amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba

“…Comparative genomics of Amoebozoans, encompassing understudied groups, is yielding valuable insights into the evolution and genetic diversity within this group (Chelkha, et al 2020; Tekle, et al 2021a; Tekle, et al 2022a; Tekle, et al 2021b; Tekle, et al 2022b; Zahonova, et al 2022). Our comprehension of Amoebozoa supergroup genomes has hitherto been constrained by well-studied model organisms and other traditional (qualitative) genome data resources, often lacking in-depth details (Eichinger, et al 2005; Glockner and Noegel 2013; Loftus, et al 2005).…”