title: Host-Associated Genomic Features of the Novel Uncultured Intracellular Pathogen Ca. Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts.
abstract: Advances in single-cell and mini-metagenome sequencing have enabled important investigations into uncultured bacteria. In this study, we applied the mini-metagenome sequencing method to assemble genome drafts of the uncultured causative agents of epitheliocystis, an emerging infectious disease in the Mediterranean aquaculture species gilthead seabream. We sequenced multiple cyst samples and constructed 11 genome drafts from a novel beta-proteobacterial lineage, Candidatus Ichthyocystis. The draft genomes demonstrate features typical of pathogenic bacteria with an obligate intracellular lifestyle: a reduced genome of up to 2.6 Mb, reduced G + C content, and reduced metabolic capacity. Reconstruction of metabolic pathways reveals that Ca Ichthyocystis genomes lack all amino acid synthesis pathways, compelling them to scavenge from the fish host. All genomes encode type II, III, and IV secretion systems, a large repertoire of predicted effectors, and a type IV pilus. These are all considered to be virulence factors, required for adherence, invasion, and host manipulation. However, no evidence of lipopolysaccharide synthesis could be found. Beyond the core functions shared within the genus, alignments showed distinction into different species, characterized by alternative large gene families. These comprise up to a third of each genome, appear to have arisen through duplication and diversification, encode many effector proteins, and are seemingly critical for virulence. Thus, Ca Ichthyocystis represents a novel obligatory intracellular pathogenic beta-proteobacterial lineage. The methods used: mini-metagenome analysis and manual annotation, have generated important insights into the lifestyle and evolution of the novel, uncultured pathogens, elucidating many putative virulence factors including an unprecedented array of novel gene families.
authors.affiliation: Functional Genomics Center Zurich, University of Zurich, Switzerland.
authors.forename: Weihong
authors.initials: W
authors.lastname: Qi
authors.affiliation: Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich, Switzerland.
authors.forename: Lloyd
authors.initials: L
authors.lastname: Vaughan
authors.affiliation: Hellenic Center for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece.
authors.forename: Pantelis
authors.initials: P
authors.lastname: Katharios
authors.affiliation: Functional Genomics Center Zurich, University of Zurich, Switzerland.
authors.forename: Ralph
authors.initials: R
authors.lastname: Schlapbach
authors.affiliation: Functional Genomics Center Zurich, University of Zurich, Switzerland Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich, Switzerland hss@seth-smith.org.uk.
authors.forename: Helena M B
authors.initials: HM
authors.lastname: Seth-Smith
mesh_terms: D000818:Animals; D005399:Fishes / Q000382:microbiology; D016680:Genome, Bacterial / Q000235:genetics*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D054892:Metagenome / Q000235:genetics*; D010802:Phylogeny; D020560:Proteobacteria / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis; D014774:Virulence / Q000235:genetics
keywords: epitheliocystis; gene duplication-diversification; genome reduction; metabolic pathways; mini-metagenome; virulence