PMID- 38022823
OWN - NLM
STAT- MEDLINE
DCOM- 20231201
LR  - 20231217
IS  - 1178-2005 (Electronic)
IS  - 1176-9106 (Print)
IS  - 1176-9106 (Linking)
VI  - 18
DP  - 2023
TI  - Profiling of Microbial Landscape in Lung of Chronic Obstructive Pulmonary Disease 
      Patients Using RNA Sequencing.
PG  - 2531-2542
LID - 10.2147/COPD.S426260 [doi]
AB  - PURPOSE: The aim of the study was to use RNA sequencing (RNA-seq) data of lung 
      from chronic obstructive pulmonary disease (COPD) patients to identify the 
      bacteria that are most commonly detected. Additionally, the study sought to 
      investigate the differences in these infections between normal lung tissues and 
      those affected by COPD. PATIENTS AND METHODS: We re-analyzed RNA-seq data of lung 
      from 99 COPD patients and 93 non-COPD smokers to determine the extent to which 
      the metagenomes differed between the two groups and to assess the reliability of 
      the metagenomes. We used unmapped reads in the RNA-seq data that were not aligned 
      to the human reference genome to identify more common infections in COPD 
      patients. RESULTS: We identified 18 bacteria that exhibited significant 
      differences between the COPD and non-COPD smoker groups. Among these, Yersinia 
      enterocolitica was found to be more than 30% more abundant in COPD. Additionally, 
      we observed difference in detection rate based on smoking history. To ensure the 
      accuracy of our findings and distinguish them from false positives, we 
      double-check the metagenomic profile using Basic Local Alignment Search Tool 
      (BLAST). We were able to identify and remove specific species that might have 
      been misclassified as other species in Kraken2 but were actually Staphylococcus 
      aureus, as identified by BLAST analysis. CONCLUSION: This study highlighted the 
      method of using unmapped reads, which were not typically used in sequencing data, 
      to identify microorganisms present in patients with lung diseases such as COPD. 
      This method expanded our understanding of the microbial landscape in COPD and 
      provided insights into the potential role of microorganisms in disease 
      development and progression.
CI  - (c) 2023 Shin et al.
FAU - Shin, Dongjin
AU  - Shin D
AUID- ORCID: 0009-0005-4578-6531
AD  - Department of Biomedical Sciences, Seoul National University College of Medicine, 
      Seoul, Republic of Korea.
FAU - Kim, Juhyun
AU  - Kim J
AUID- ORCID: 0000-0002-0321-9388
AD  - Department of Biomedical Sciences, Seoul National University College of Medicine, 
      Seoul, Republic of Korea.
FAU - Lee, Jang Ho
AU  - Lee JH
AUID- ORCID: 0000-0002-8226-9585
AD  - Department of Pulmonary and Critical Care Medicine, Asan Medical Center, 
      University of Ulsan College of Medicine, Seoul, Republic of Korea.
FAU - Kim, Jong-Il
AU  - Kim JI
AUID- ORCID: 0000-0002-7240-3744
AD  - Department of Biomedical Sciences, Seoul National University College of Medicine, 
      Seoul, Republic of Korea.
AD  - Department of Biochemistry and Molecular Biology, Seoul National University 
      College of Medicine, Seoul, Republic of Korea.
AD  - Genomic Medicine Institute, Seoul National University, Seoul, Republic of Korea.
AD  - Seoul National University Cancer Research Institute, Seoul, Republic of Korea.
FAU - Oh, Yeon-Mok
AU  - Oh YM
AUID- ORCID: 0000-0003-0116-4683
AD  - Department of Pulmonary and Critical Care Medicine, Asan Medical Center, 
      University of Ulsan College of Medicine, Seoul, Republic of Korea.
LA  - eng
PT  - Journal Article
DEP - 20231110
PL  - New Zealand
TA  - Int J Chron Obstruct Pulmon Dis
JT  - International journal of chronic obstructive pulmonary disease
JID - 101273481
RN  - 63231-63-0 (RNA)
SB  - IM
MH  - Humans
MH  - *Pulmonary Disease, Chronic Obstructive/diagnosis/genetics/microbiology
MH  - Reproducibility of Results
MH  - Lung/microbiology
MH  - Bacteria/genetics
MH  - RNA
MH  - Sequence Analysis, RNA
PMC - PMC10644840
OTO - NOTNLM
OT  - chronic obstructive pulmonary disease
OT  - metagenomics
OT  - microbiome
OT  - next-generation sequencing
COIS- The authors report no conflicts of interest in this work.
EDAT- 2023/11/29 18:42
MHDA- 2023/12/01 06:44
PMCR- 2023/11/10
CRDT- 2023/11/29 15:33
PHST- 2023/08/08 00:00 [received]
PHST- 2023/10/30 00:00 [accepted]
PHST- 2023/12/01 06:44 [medline]
PHST- 2023/11/29 18:42 [pubmed]
PHST- 2023/11/29 15:33 [entrez]
PHST- 2023/11/10 00:00 [pmc-release]
AID - 426260 [pii]
AID - 10.2147/COPD.S426260 [doi]
PST - epublish
SO  - Int J Chron Obstruct Pulmon Dis. 2023 Nov 10;18:2531-2542. doi: 
      10.2147/COPD.S426260. eCollection 2023.