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They include the \u201cbrain-eating amoeba\u201d\n                      <jats:italic toggle=\"yes\">Naegleria fowleri<\/jats:italic>\n                      , an opportunistic pathogen that causes primary amoebic meningoencephalitis, a rare but fatal infection of humans. Beyond their direct pathogenicity, protists can also act as environmental reservoirs for intracellular bacterial pathogens, such as\n                      <jats:italic toggle=\"yes\">Legionella<\/jats:italic>\n                      spp., to persist and multiply in the environment. In this study, we carried out single-cell genome sequencing of two uncultivated\n                      <jats:italic toggle=\"yes\">Naegleria<\/jats:italic>\n                      species isolated from the River Leam in England. From single cells, we generated two highly complete\n                      <jats:italic toggle=\"yes\">Naegleria<\/jats:italic>\n                      genomes. Phylogenetic analyses placed these species as close relatives of\n                      <jats:italic toggle=\"yes\">Naegleria fultoni<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">Naegleria pagei<\/jats:italic>\n                      . Exploring\n                      <jats:italic toggle=\"yes\">Naegleria<\/jats:italic>\n                      evolutionary genomics, we identified gene families encoding antistasin-like domains, which have been characterized as factors that inhibit coagulation in blood-feeding leeches. Antistasin-like domains were identified in all sequenced\n                      <jats:italic toggle=\"yes\">Naegleria<\/jats:italic>\n                      species and their close relative\n                      <jats:italic toggle=\"yes\">Willaertia magna,<\/jats:italic>\n                      yet are otherwise largely restricted to animal genomes. Significantly, we recovered highly complete bacterial genomes from each\n                      <jats:italic toggle=\"yes\">Naegleria<\/jats:italic>\n                      single-cell sample. Phylogenomic analysis revealed that both bacteria belong to the Legionellaceae family. Both bacterial genomes encode comprehensive sets of secretion systems and effector arsenals. We identified putative\n                      <jats:italic toggle=\"yes\">Legionella<\/jats:italic>\n                      effectors that resemble TAL (Transcription activator-like) effectors from plant pathogenic\n                      <jats:italic toggle=\"yes\">Xanthomonas<\/jats:italic>\n                      spp. in terms of protein sequence and predicted structure, representing a potentially novel class of\n                      <jats:italic toggle=\"yes\">Legionella<\/jats:italic>\n                      effectors. Our study highlights the advantages of single-cell environmental genomics approaches, which enable direct association of intracellular pathogens with their hosts to better understand the evolution of host-pathogen interactions.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Beyond their direct pathogenic potential, amoebae and other protists found in the environment can indirectly threaten human health by serving as reservoirs for intracellular bacterial pathogens to persist, evolve, and multiply in the environment. Despite their importance, protist-bacterial interactions remain poorly understood. In this study, we employed single-cell genomics to sequence the genomes of two uncultivated\n                        <jats:italic toggle=\"yes\">Naegleria<\/jats:italic>\n                        amoebae, both harboring novel\n                        <jats:italic toggle=\"yes\">Legionella<\/jats:italic>\n                        bacteria. From individual cells, we recovered highly complete eukaryotic and bacterial cobiont genome assemblies. Our work demonstrates the power of single-cell sequencing approaches in directly linking intracellular pathogens to their hosts to better understand the evolution of protist-bacterial interactions and the role that protists play in facilitating bacterial pathogens to persist long term in the environment.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/msphere.00352-25","type":"journal-article","created":{"date-parts":[[2025,8,27]],"date-time":"2025-08-27T13:00:32Z","timestamp":1756299632000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Comparative single-cell genomics of two uncultivated\n                    <i>Naegleria<\/i>\n                    species harboring\n                    <i>Legionella<\/i>\n                    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