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Perspective on the clone library method for infectious diseases.

Kazuhiro Yatera1, Shingo Noguchi1, Hiroshi Mukae2

  • 1Department of Respiratory Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishiku, Kitakyushu City, Fukuoka, 807-8555, Japan.

Respiratory Investigation
|August 17, 2021
PubMed
Summary

Culture-independent molecular methods reveal diverse human microbiomes. Sanger sequencing of the 16S-ribosomal RNA gene aids in identifying bacteria in respiratory infections, highlighting the role of anaerobes.

Keywords:
16S ribosomal RNAClone library methodMicrobiomeRespiratory infection

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Genomics

Background:

  • Culture-independent molecular methods, including DNA sequencing (Sanger, NGS) and metagenomics, are advancing the study of human microbiomes.
  • Accurate bacterial species identification is vital for diagnosing respiratory tract infections, but current NGS methods may lack species-level precision.

Purpose of the Study:

  • To review previous observations of human microbiomes in various infections using Sanger sequencing of the 16S-ribosomal RNA gene.
  • To highlight findings related to bacterial species identification in respiratory infections and other conditions.

Main Methods:

  • Review of studies utilizing clone library methods with Sanger sequencing of the 16S-ribosomal RNA gene.
  • Analysis of microbiome data from bronchoalveolar lavage fluid, pleural effusion, and other sample types.

Main Results:

  • Anaerobes are frequently detected in non-elderly pneumonia patients and play a significant role in pleurisy.
  • Staphylococcus aureus detection rates in hospital-acquired pneumonia may be lower than previously reported.
  • The review covers diverse sites including respiratory tract, urine, feces, and specific conditions like nontuberculous mycobacteriosis and bacterial vaginosis.

Conclusions:

  • Sanger sequencing of the 16S-rRNA gene provides valuable insights into microbial communities associated with various human infections.
  • Further research is needed to refine species-level identification and understand the complex roles of different microorganisms in health and disease.