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Introduction to the Human Microbiota01:22

Introduction to the Human Microbiota

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Microorganisms colonize various regions of the human body, including the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. The total number of microbial cells is estimated to range from 10¹³ to 10¹⁴—comparable to, or exceeding, the number of human somatic cells. This host–microbiome relationship has led to the conceptualization of humans as supraorganisms, wherein microbial communities perform vital roles in development, immunity,...
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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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The human body harbors a vast and diverse viral community known as the human virome. The virome includes bacteriophages that infect bacteria, and eukaryotic viruses that infect human cells. Transient dietary and environmental viruses also contribute to this dynamic ecosystem. Estimates suggest the human body may contain on the order of 10¹³ viral particles, though abundance varies widely by body site and detection method.Comprehensive characterization of the virome has become possible...
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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Deciphering the human microbiome using next-generation sequencing data and bioinformatics approaches.

Yihwan Kim1, InSong Koh2, Mina Rho3

  • 1Department of Biomedical Informatics, Hanyang University, Seoul, Republic of Korea.

Methods (San Diego, Calif.)
|December 3, 2014
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Summary
This summary is machine-generated.

The human microbiome significantly impacts host immunity and metabolism. Computational methods are crucial for analyzing its composition and function, revealing links between gut microbiome dysbiosis and disease.

Keywords:
BioinformaticsHuman microbiomeMetagenomicsNext generation sequencing

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Area of Science:

  • Microbiology
  • Computational Biology
  • Genomics

Background:

  • The human microbiome plays a critical role in host immune and metabolic functions beyond the human genome.
  • Metagenomics enables culture-independent analysis of microbial community composition and function.
  • Gut microbiome dysbiosis is increasingly linked to immune and metabolic disorders.

Purpose of the Study:

  • To review computational methods for human microbiome analysis.
  • To highlight findings from large-scale human microbiome studies.
  • To underscore the association between microbiome alterations and host health.

Main Methods:

  • Utilizing metagenomics for comprehensive microbiome analysis.
  • Employing computational approaches for taxonomy and functional profiling.
  • Analyzing marker genes or whole microbial genomes (shotgun sequencing).

Main Results:

  • Computational methods are essential for dissecting microbiome complexity.
  • Taxonomy profiling uses reference sequences or de novo clustering.
  • Functional profiling faces challenges due to unknown protein families in metagenomic data.

Conclusions:

  • Advanced computational tools are vital for understanding the human microbiome.
  • Dysbiosis in the gut microbiome is a significant factor in immune and metabolic diseases.
  • Further research into microbiome-host interactions is warranted.