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Related Concept Videos

The Oral Microbiota01:27

The Oral Microbiota

The oral microbiome includes a complex ecosystem comprising over 700 microbial species, identified through genomic sequencing and culture-based analyses to date. This community includes a core microbiome, found universally among individuals, and a variable component influenced by environmental factors such as diet, lifestyle, and host genetics. Site-specific conditions, including oxygen gradients, pH levels, and nutrient availability, determine the spatial distribution of these microorganisms...
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 the Oral Microbiota01:28

Development of the Oral Microbiota

The establishment of the oral microbiome begins before birth, challenging the long-held belief that the fetal oral cavity is sterile. The presence of oral microbes such as Streptococcus and Fusobacterium in amniotic fluid suggests that microbial exposure may occur in utero, potentially through translocation from the maternal oral or gastrointestinal tract. This early colonization primes the neonatal immune system and sets the stage for subsequent microbial succession. Maternal health,...
Microbiota of the Respiratory Tract01:29

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...
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...
Human Virome01:26

Human Virome

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 only with...

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Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface
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Published on: July 4, 2018

The human oral microbiome.

Floyd E Dewhirst1, Tuste Chen, Jacques Izard

  • 1Department of Molecular Genetics, The Forsyth Institute, 245 First St., Cambridge, MA 02142, USA. fdewhirst@forsyth.org

Journal of Bacteriology
|July 27, 2010
PubMed
Summary
This summary is machine-generated.

The Human Oral Microbiome Database (HOMD) catalogs over 600 oral bacteria, providing a crucial resource for understanding the oral microbiome's role in health and disease. This database aids in identifying and classifying novel oral taxa.

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Published on: August 30, 2016

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • The human oral cavity harbors a complex microbiome with over 600 bacterial species across distinct habitats.
  • Current characterization relies on methods like 16S rRNA gene sequencing, but many oral taxa lack proper taxonomic identification.
  • Existing databases often reference unclassified phylotypes by clone or accession numbers, hindering comprehensive analysis.

Purpose of the Study:

  • To create a curated, phylogeny-based database of oral 16S rRNA gene sequences, the Human Oral Microbiome Database (HOMD).
  • To analyze a large dataset of oral microbial 16S rRNA gene clones to identify and quantify oral taxa.
  • To provide a web-accessible resource for researchers studying the oral microbiome.

Main Methods:

  • Compilation of 16S rRNA gene sequences into a phylogeny-based database (HOMD).
  • Bioinformatic analysis of 36,043 16S rRNA gene clones from oral microbiota studies.
  • Taxonomic classification and identification of novel candidate taxa within the oral microbiome.

Main Results:

  • The HOMD initially includes 619 taxa across 13 phyla.
  • Analysis of oral microbiota clones identified 1,179 taxa, with a significant proportion (68%) being uncultivated phylotypes.
  • A substantial number of novel taxa (434) are proposed for addition to the HOMD upon validation.

Conclusions:

  • The HOMD represents the first curated description of a human-associated microbiome, offering a valuable taxonomic framework.
  • The database and associated analyses enhance the ability to identify and understand the roles of oral microbial taxa.
  • HOMD provides essential tools for future research into the oral microbiome's impact on human health and disease.