Spirochete Biology Spirochetes That Break with the Prevalent Dogma in : Nonspiral Sphaerochaeta The Chimeric Genome of 2012

Spirochaetes is one of a few bacterial phyla that are characterized by a unifying diagnostic feature, namely, the helical morphology and motility conferred by axial periplasmic flagella. Their unique morphology and mode of propulsion also represent major pathogenicity factors of clinical spirochetes. Here we describe the genome sequences of two coccoid isolates of the recently described genus Sphaerochaeta which are members of the phylum Spirochaetes based on 16S rRNA gene and wholegenome phylogenies. Interestingly, the Sphaerochaeta genomes completely lack the motility and associated signal transduction genes present in all sequenced spirochete genomes. Additional analyses revealed that the lack of flagella is associated with a unique, nonrigid cell wall structure hallmarked by a lack of transpeptidase and transglycosylase genes, which is also unprecedented in spirochetes. The Sphaerochaeta genomes are highly enriched in fermentation and carbohydrate metabolism genes relative to other spirochetes, indicating a fermentative lifestyle. Remarkably, most of the enriched genes appear to have been acquired from nonspirochetes, particularly clostridia, in several massive horizontal gene transfer events (>40% of the total number of genes in each genome). Such a high level of direct interphylum genetic exchange is extremely rare among mesophilic organisms and has important implications for the assembly of the prokaryotic tree of life. IMPORTANCE Spiral shape and motility historically have been the unifying hallmarks of the phylum Spirochaetes. These features also represent important virulence factors of highly invasive pathogenic spirochetes such as the causative agents of syphilis and Lyme disease. Through the integration of genome sequencing, microscopy, and physiological studies, we conclusively show that the spiral morphology and motility of spirochetes are not universal morphological properties. In particular, we found that the genomes of the members of the recently described genus Sphaerochaeta lack the genes encoding the characteristic flagellar apparatus and, in contrast to most other spirochetes, have acquired many metabolic and fermentation genes from clostridia. These findings have major implications for the isolation and study of spirochetes, the diagnosis of spirochete-caused diseases, and the reconstruction of the evolutionary history of this important bacterial phylum. The Sphaerochaeta sp. genomes offer new avenues to link ecophysiology with the functionality and evolution of the spirochete flagellar apparatus. Received 25 January 2012 Accepted 18 April 2012 Published 15 May 2012 Citation Caro-Quintero A, Ritalahti KM, Cusick KD, Löffler FE, Konstantinidis KT. 2012. The chimeric genome of Sphaerochaeta: nonspiral spirochetes that break with the prevalent dogma in spirochete biology. mBio 3(3):e00025-12. doi:10.1128/mBio.00025-12. Editor David Relman, VA Palo Alto Health Care System Copyright © 2012 Caro-Quintero et al. This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Address correspondence to Konstantinos (Kostas) Konstantinidis, kostas@ce.gatech. edu. Spirochaetes is a diverse, deeply branching phylum of Gramnegative bacteria. Members of this phylum share distinctive morphological features, i.e., a spiral shape and axial, periplasmic flagella (1, 2). These traits enable propulsion through highly viscous media and thus are directly associated with the ecological niches spirochetes occupy. For instance, motility mediated by axial flagella represents a major pathogenicity factor that allows strains of the Treponema, Borrelia, and Leptospira genera to invade and colonize host tissues, resulting in important diseases such as Lyme disease and syphilis. Several studies have shown that disruption of the flagellar genes or the chemotaxis genes that control the periplasmic flagella attenuates the pathogenic potential of spirochetes (3–5). The focus on clinical isolates has biased our understanding of the ecology, physiology, and diversity of the phylum Spirochaetes. Indeed, free-living, nonpathogenic spirochetes are greatly underrepresented in culture collections, while culture-independent studies have revealed that spirochetes are ubiquitous in anoxic environments, implying that they are key players in anaerobic food webs (6–9). Consistent with the latter findings, studies of members of the genus Spirochaeta have demonstrated that environmental isolates possess physiological properties distinct from those of their pathogenic relatives; e.g., they encode a diverse set of saccharolytic enzymes (7), while other members of the genus are alkaliphiles (10) and thermophiles (11). More recently, screening of environmental samples revealed a novel genus of free-living spirochetes, Sphaerochaeta (12). Phylogenetic analysis of 16S rRNA genes identified this group as a member of the phylum Spirochaetes, most closely related to the genus Spirochaeta. Interestingly, Sphaerochaeta pleomorpha strain Grapes and Sphaerochaeta globosa strain Buddy are nonmotile and show the same spherical morphology during laboratory cultivation (12). HowRESEARCH ARTICLE May/June 2012 Volume 3 Issue 3 e00025-12 ® mbio.asm. org 1 m b.asm . rg on N ovem er 1, 2014 P ubished by m b.asm . rg D ow nladed fom