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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,...
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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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Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

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Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
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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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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
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Challenges for case-control studies with microbiome data.

J Paul Brooks1

  • 1Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, Richmond; Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond; Department of Supply Chain Management and Analytics, Virginia Commonwealth University, Richmond.

Annals of Epidemiology
|June 4, 2016
PubMed
Summary
This summary is machine-generated.

Reproducible human microbiome research requires addressing challenges in microbial community composition, detecting rare taxa, and choosing appropriate analysis methods. Implementing control experiments can improve data accuracy and enhance the interpretation of disease determinants.

Keywords:
BiasControl experimentsMicrobiomeNormalizationRare taxa

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Area of Science:

  • Microbiome research
  • Human microbiome studies
  • Microbial ecology

Background:

  • Case-control studies are crucial for understanding human microbiome composition in relation to disease.
  • Advancements in sequencing and spectroscopy provide novel microbiome measurements.
  • The impact of methodological choices on case-control analyses remains underappreciated.

Purpose of the Study:

  • To evaluate differences in microbiome composition between cases and controls.
  • To identify specific taxa responsible for observed microbiome variations.
  • To address challenges in conducting reproducible human microbiome research.

Main Methods:

  • Discusses challenges in compensating for microbial community composition differences.
  • Addresses the detection of rare taxa in microbial communities.
  • Evaluates the selection of properly powered analysis methods for microbiome data.

Main Results:

  • Commonly held views in microbiome research are evaluated.
  • Unanswered questions in the field are analyzed.
  • Strategies for overcoming research challenges are suggested.

Conclusions:

  • Recommends incorporating positive and negative control experiments in human microbiome research.
  • Highlights the importance of control experiments for identifying bias, contamination, and technical variation.
  • Suggests that improved protocols can lead to better data adjustments, reduced false positives, and enhanced cross-study interpretation.