Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease

Abstract

Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as "ultramicrobacteria" with a cell volume under 0.1 μm³ and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.

Keywords: candidate phyla radiation; dysbiosis; genome analysis; human microbiome; imaging; taxonomy.

FIG 1

Historical timeline of the discovery of Candidate Phyla Radiation (CPR). The orange boxes represent studies on environmental samples, the blue boxes represent studies on human samples, and the white boxes represent work using genomic sequences from different origins. The references cited are as follows: Torrella and Morita (1), Rheims et al. (3), Hugenholtz et al. (4), Hugenholtz et al. (5), Harris et al. (6), Marcy et al. (7), Podar et al. (174), Abrams et al. (12), Wrighton et al. (199), Rinke et al. (9), Albertsen et al. (10), He et al. (15), Brown et al. (14), Luef et al. (16), Castelle and Banfield (70), and Cross et al. (17).

FIG 2

Rhizomes of genomes illustrating the mosaicism of each Candidate Phyla Radiation (CPR) phylum. Each gene is represented by a curve colored according to the origin: bacterial origin in dark red, CPR origin in pink, Eukarya origin in yellow, virus origin in orange, archaeal origin in dark blue and ORFans in gray. The figures were constructed using the Circos tool. The following genomes were included: Candidatus Berkelbacteria GCA_016432625.1, Candidatus Dojkabacteria HGW GCA_002840365.1, candidate division WWE3 bacterium RIFOXYA1 GCA_001773015.1, Candidatus Peregrinibacteria GCA_016699145.1, Candidatus Nanosynbacter lyticus GCA_000803625.1, candidate division Kazan bacterium GCA_001029795.1, Candidatus Doudnabacteria RIFCSPLOWO2 GCA_001780055.1, Candidatus Wirthbacteria CG2_30_54_11 GCA_001873755.1, Candidatus Gracilibacteria GN02-873 GCA_003260345.1, Candidatus Parcubacteria Gr01-1014_8 GCA_007376385.1, Candidatus Chazhemtobacterium aquaticus GCA_009936135.1 and candidate division SR1 bacterium GCA_015259585.1.

FIG 3

Microscopic observations of images consistent with the structure of CPR in human saliva (A, B), dental plaque (C), and human digestive tract (D). Two saliva and one dental plaque samples, as well as two stool samples, were fixed in a 2.5% glutaraldehyde solution overnight at 4°C. Stool samples were then diluted to 1:10 in 2.5% glutaraldehyde. Fixed oral samples and diluted stool samples were stained using 1% phosphotungstic acid for 3 min and were cyto-centrifuged onto glass slides and sputtered with a 5-μm-thick platinum layer (ion sputter MC1000, Hitachi, Japan). Micrographs were then acquired on an SU5000 SEM (Hitachi, Japan) using a backscatter electron detector at 7 kV in high vacuum mode. Micrographs were recorded at magnifications ranging from ×3,000 to ×35,000.

FIG 4

Heatmap representative of the cultivated CPR strains and their respective bacterial hosts. Red: failed coculture attempts, green: successful coculture.

FIG 5

Successful culture attempts for isolating CPR from the oral microbiota. (A) Purification of CPR using active filtration at 0.2 μm and ultracentrifugation prior to host infection (18). (B) Coculture based on selection through aminoglycoside resistance (15). (C) Reverse genomics (17).

FIG 6

A network representation highlighting the presence of CPR in the different human microbiota and the known bacterial hosts associated with some phyla. This representation was generated using the Cytoscape tool version 3.8.