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Related Concept Videos

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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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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Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a...
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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Sequence-based methods for detecting and evaluating the human gut mycobiome.

M J Suhr1, N Banjara1, H E Hallen-Adams1

  • 1Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.

Letters in Applied Microbiology
|December 17, 2015
PubMed
Summary

Fungal gut microbiota in vegetarians was surveyed using multiple methods. While diverse fungi were detected, many are transient, suggesting a smaller core group impacts gut health.

Keywords:
PCRenvironmental mycologyfungimicrobiomemouldsyeasts

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Area of Science:

  • Mycology
  • Microbiome research
  • Human gut ecology

Background:

  • The human gut microbiome includes fungi, but research lags behind bacterial studies.
  • Understanding fungal gut microbiota is crucial for human health and ecology.

Purpose of the Study:

  • To survey the fungal microbiota in healthy humans with a vegetarian diet.
  • To compare the effectiveness of different molecular methods for fungal detection.

Main Methods:

  • Analysis of 16 faecal samples from vegetarian individuals.
  • Fungal identification using molecular cloning, 454 pyrosequencing, and Luminex analyte-specific reagent (ASR) assays targeting the rRNA genes' ITS region.

Main Results:

  • Fungi were detected in all samples, with at least 46 distinct fungal operational taxonomic units (OTUs) identified, primarily from Ascomycota and Basidiomycota phyla.
  • Fusarium was the most abundant genus, followed by Malassezia, Penicillium, Aspergillus, and Candida.
  • No single method detected all fungal diversity; pyrosequencing identified more OTUs but missed some detected by other methods.

Conclusions:

  • Fungi play a role in human gut ecology and health, with ongoing discovery of new species in faecal samples.
  • Many identified fungi may be transient, with a smaller core group potentially impacting the gut.
  • Optimized, targeted, probe-based assays may be the most effective for quantifying the abundance of impactful gut fungi.