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Related Concept Videos

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,...
209

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Recruiting human microbiome shotgun data to site-specific reference genomes.

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Reference genomes are crucial for analyzing human microbiome shotgun metagenomes. Site-specific genomes significantly aid in mapping reads, highlighting the need for more comprehensive microbial genome sequencing.

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Area of Science:

  • Microbiology
  • Genomics
  • Human Health

Background:

  • The human body hosts diverse microbial communities vital for health and disease.
  • Reference genomes are essential for understanding complex microbial metagenomes.
  • Current efforts focus on sequencing microbial genomes from various human body sites.

Purpose of the Study:

  • To demonstrate the utility of reference genomes in analyzing human microbiome shotgun metagenomes.
  • To assess the mapping efficiency of shotgun reads to existing reference genomes.
  • To investigate the site-specificity and variation within the human microbiome.

Main Methods:

  • Analysis of 55 shotgun metagenomes from 5 major human body sites and 16 sub-sites.
  • Alignment of sequence reads to a comprehensive database of 2780 reference genomes, including 1583 human microbiome references.
  • Comparison of read mapping percentages based on reference genome origin (general vs. body-site specific).

Main Results:

  • An average of 62.3% of shotgun reads mapped to reference genomes.
  • No single reference genome was found across all body sites.
  • Body-site specific reference genomes accounted for an average of 58.8% of mapped reads.
  • Proximal or symmetrical body sites exhibited the most similarity in microbial communities.

Conclusions:

  • Reference genomes are highly valuable for human microbiome research.
  • Further sequencing of site-specific microbial genomes is necessary, even for well-studied areas.
  • Significant variation exists within microbiomes, challenging comparative studies across individuals and time.