An Unclassified Microorganism: Novel Pathogen Candidate Lurking in Human Airways

Abstract

During the assessments of the correlation of the diseases and the microbiota of various clinical specimens, unique 16S ribosomal RNA (rRNA) gene sequences (less than 80% similarity to known bacterial type strains) were predominantly detected in a bronchoalveolar lavage fluid (BALF) specimen from a patient with chronic lower respiratory tract infection. The origin of this unique sequence is suspected to be the causative agent of the infection. We temporarily named the owner organism of this sequence “IOLA” (Infectious Organism Lurking in Airways). In order to evaluate the significance of IOLA in human lung disorders, we performed several experiments. IOLA-16S rRNA genes were detected in 6 of 386 clone libraries constructed from clinical specimens of patients with respiratory diseases (in our study series). The gene sequences (1,427 bp) are identical, and no significantly similar sequence was found in public databases (using NCBI blastn) except for the 8 shorter sequences detected from patients with respiratory diseases in other studies from 2 other countries. Phylogenetic analyses revealed that the 16S rRNA gene of IOLA is more closely related to eukaryotic mitochondria than bacteria. However, the size and shape of IOLA seen by fluorescent in-situ hybridization are similar to small bacteria (approximately 1 µm with a spherical shape). Furthermore, features of both bacteria and mitochondria were observed in the genomic fragment (about 19 kb) of IOLA, and the GC ratio of the sequence was extremely low (20.5%). Two main conclusions were reached: (1) IOLA is a novel bacteria-like microorganism that, interestingly, possesses features of eukaryotic mitochondria. (2) IOLA is a novel pathogen candidate, and it may be the causative agent of human lung or airway disease. IOLA exists in BALF specimens from patients with remarkable symptoms; this information is an important piece for helping solve the elusive etiology of chronic respiratory disorders.

Production and transplantation of bioengineered lung into a large-animal model

“…The distinct bacterial communities we observed were consistent with other reports for the swine lung (21) and were consistently reproduced in BEL. These evaluations also led to the observation of an infectious organism present in airways, suggesting that this organism may be of pathogenic concern in swine; moreover, IOLA had previously been reported only in the human respiratory tract in association with clinical disease (23).…”

“…One bacterial target was based on identification of 16S sequences that did not align with sequences in the SILVA rRNA database. Specifically, IOLA (infectious organism lurking in airways) (22,23) 16S was seen in one of the transplanted and two of the control animals studied. This result was confirmed through cloning and sequencing of additional genomic fragments using published PCR primers (23).…”

Bacterial composition of nasal discharge in children based on highly accurate 16S rRNA gene sequencing analysis

“…NCBI BLAST search ( https://blast.ncbi.nlm.nih.gov ) results revealed that the representative sequence of OTU 30 shared 99.8% similarity with an unclassified bacterium. Recently, the unclassified bacterium was identified in bronchoalveolar lavage fluids (BALFs) in adults with respiratory disease and was temporally named IOLA (Infectious Organism Lurking in Airways) 18 . IOLA was also detected in specimens from patients with respiratory tract disease and in pig lungs 19 – 21 .…”

“…One of the twelve OTUs unclassified at the phylum level using the RDP Classifier showed high similarity with IOLA according to the NCBI BLAST search. We have previously reported that IOLA is a novel microorganism found in BALFs in adults with respiratory disease 18 . This is the first report of IOLA detected in nasal discharge of children.…”

Data on single-step purification method for dye-labeled DNA sequencing

“…Dye-labeled DNA sequencing technique is still an important tool for clinical decision making on cancer [3] , [4] , [5] , drug metabolism genotyping [6] , [7] , [8] , pathogen identification [9] , [10] , [11] , inherited disease [12] , [13] , [14] , [15] , [16] , [17] and so on [18] , [19] . However, the methods remain laborious and time-consuming.…”