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Related Concept Videos

Introduction to the Human Microbiota01:22

Introduction to the Human Microbiota

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, and disease...
Development of Human Microbiota01:30

Development of Human Microbiota

The human microbiota begins developing at birth and undergoes continual change as we age. Infancy marks a critical period of microbial sensitivity, offering a “window of opportunity” during which beneficial microbes help mature the immune system. By age three, children typically develop a more stable and diverse microbial community. Newborns acquire microbes from their immediate environment; vaginal delivery favors maternal vaginal microbes, while cesarean births favor microbes from the skin...
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Microbiota of the Urogenital Tract

The human urogenital system, once thought to be sterile in healthy individuals, is now recognized as a complex microbial habitat. Advancements in molecular sequencing techniques have revealed that even in healthy adults, the kidneys and bladder harbor microbial populations similar to those found in the distal urethra, albeit in much lower abundance. These resident microorganisms, while generally innocuous, can become opportunistic pathogens under conditions that alter the urogenital...
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Microbiota of the Respiratory Tract

The human respiratory tract, comprising the upper and lower segments, serves as a critical interface with the external environment. The upper respiratory tract (URT)—including the nostrils, sinuses, pharynx, and oropharynx—is heavily colonized by microbes, while the lower respiratory tract (LRT), composed of the larynx, trachea, bronchi, and lungs, was long thought to be sterile. However, recent molecular studies have revealed that the lungs are not devoid of microbes but act more like...
Microbial Morphologies01:29

Microbial Morphologies

Bacterial and archaeal cells exhibit remarkable diversity in shape and structure, critical in their adaptability and functionality. Among bacteria, the most commonly observed shapes include cocci and bacilli. Cocci are spherical and may exist singly or in groupings such as pairs (diplococci), chains (streptococci), clusters (staphylococci), or tetrads. Bacilli, in contrast, are rod-shaped and can also occur as single cells, in pairs, or chains, depending on their environmental and genetic...
Bacterial Phylum Firmicutes01:27

Bacterial Phylum Firmicutes

Firmicutes is a diverse phylum of Gram-positive bacteria characterized by a low GC content in their genomes. This phylum includes organisms with monoderm or diderm cell envelopes, highlighting a complex evolutionary history. Firmicutes comprises several major orders, including Lactobacillales, Clostridiales, and Bacillales, which exhibit remarkable diversity in their morphology, metabolism, and ecological roles.The order Lactobacillales includes lactic acid bacteria, which are fermentative...

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Updated: May 21, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

A core human microbiome as viewed through 16S rRNA sequence clusters.

Susan M Huse1, Yuzhen Ye, Yanjiao Zhou

  • 1Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America. shuse@mbl.edu

Plos One
|June 22, 2012
PubMed
Summary
This summary is machine-generated.

The human microbiome varies significantly across 18 body sites, with oral sites showing the most shared microbial OTUs. Deeper analysis reveals distinct sub-genus populations even within dominant genera like Lactobacillus.

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Area of Science:

  • Microbiology
  • Human Microbiome Research
  • Genomics

Background:

  • The Human Microbiome Project aims to characterize microbial communities across various human body sites.
  • Understanding microbial diversity and distribution is crucial for human health and disease research.

Purpose of the Study:

  • To comprehensively map the microbiota across 18 distinct human body sites in over 200 individuals.
  • To investigate the variability and commonality of microbial communities at different taxonomic levels (genus vs. OTU).

Main Methods:

  • Utilized 16S ribosomal RNA (16S rRNA) gene sequencing (V1-V3 and V3-V5 hypervariable regions).
  • Analyzed sequence data from over 200 individuals across 18 body sites.
  • Defined core operational taxonomic units (OTUs) shared by ≥95% of individuals.

Main Results:

  • Oral sites (saliva, tongue, cheek, gums, throat) exhibited the highest number of core OTUs, followed by nose, stool, and skin.
  • Vaginal sites had the fewest shared OTUs but were dominated by the Lactobacillus genus with distinct sub-genus OTU populations.
  • Microbial richness varied tenfold across body sites, with stool samples being the richest.
  • Genus-level analysis suggested enterotype profiles in stool, but OTU-level analysis revealed distinct vaginal biotypes and blurred stool enterotype distinctions.

Conclusions:

  • Microbial community composition is highly site-specific and varies significantly even within the same genus.
  • The human microbiome exhibits substantial inter-individual variability in richness and abundance, even for ubiquitous or dominant taxa.
  • OTU-level analysis provides a finer resolution for understanding microbial community structure than genus-level analysis.