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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,...
162
Development of Human Microbiota01:30

Development of Human Microbiota

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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...
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Microbiota of the Stomach and Small Intestine01:27

Microbiota of the Stomach and Small Intestine

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The human gastrointestinal (GI) tract is characterized by distinct physicochemical conditions that shape its microbial communities. Among these, the stomach presents a particularly challenging environment for microbial colonization due to its highly acidic pH, ranging from 1 to 3. This extreme acidity effectively limits microbial density. However, certain acid-tolerant microorganisms are capable of surviving in this niche. Notably, Helicobacter pylori can colonize the gastric mucosa,...
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Microbiota of the Large Intestine01:27

Microbiota of the Large Intestine

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The large intestine hosts the most densely populated microbial ecosystem in the human body. This complex community primarily consists of anaerobic bacteria, with Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes) as the predominant groups. The distribution of these microbes varies along different sections of the large intestine, influenced by local environmental factors such as oxygen availability and nutrient composition.The cecum, located at the beginning of the large...
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The Oral Microbiota01:27

The Oral Microbiota

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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...
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Microbiota of the Urogenital Tract01:28

Microbiota of the Urogenital Tract

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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 Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Conducting a microbiome study.

Julia K Goodrich1, Sara C Di Rienzi1, Angela C Poole1

  • 1Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.

Cell
|July 19, 2014
PubMed
Summary
This summary is machine-generated.

This primer guides researchers in designing, executing, and analyzing human microbiome studies. It ensures reproducible research for advancing our understanding of microbial communities and their impact on health and disease.

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Human microbiome research is rapidly advancing, impacting health, disease, and lifestyle.
  • Progress relies on rigorous, reproducible study designs and data analysis.
  • Interdisciplinary collaboration is crucial for comprehensive microbiome investigations.

Purpose of the Study:

  • To provide a foundational guide for researchers entering the field of human microbiome studies.
  • To outline key considerations for the design, execution, and analysis of microbiome research.
  • To facilitate reproducible and impactful contributions to microbiome science.

Main Methods:

  • The primer synthesizes best practices for microbiome study design.
  • It details critical factors for experimental execution and data handling.
  • Recommendations cover statistical analysis and interpretation of microbiome data.

Main Results:

  • Provides a framework for planning and conducting robust microbiome research.
  • Highlights potential pitfalls and offers solutions for common challenges.
  • Empowers researchers to generate reliable and meaningful data.

Conclusions:

  • Adherence to these recommendations will enhance the quality and reproducibility of human microbiome studies.
  • This guide aims to foster new discoveries in the microbiome field.
  • It supports the integration of diverse research approaches for a holistic understanding.