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Related Concept Videos

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...
Anatomy of the Intestines01:23

Anatomy of the Intestines

Although digestion of proteins, carbohydrates, and lipids may begin in the stomach, it is completed in the intestine. The absorption of nutrients, water, and electrolytes from food and drink also occurs in the intestine. The intestines can be divided into two structurally distinct organs—the small and large intestines.
Small Intestines
The small intestine is an ~7 meter-long tube with an inner diameter of just 2.5 cm. Since most nutrients are absorbed here, the inner lining of the small...
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...
Methods of Classification and Identification01:28

Methods of Classification and Identification

Bacterial identification relies on a diverse array of techniques to classify and understand microorganisms, each tailored to uncover specific characteristics. Traditional morphological approaches, while still valuable, are limited for closely related or structurally simple organisms. Modern methods integrate biochemical, serological, genetic, and advanced molecular tools to achieve greater accuracy.Morphological and Biochemical TechniquesMorphological characteristics, such as cell shape and...
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,...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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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Related Experiment Video

Updated: May 15, 2026

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings
04:16

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings

Published on: February 7, 2025

Machine learning identifies differences between breast milk and formula in the gut microbiome.

Ting Chia Liu1, David Rojas-Velazquez1,2, Sarah Kidwai1

  • 1Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht, The Netherlands.

Gut Microbiome (Cambridge, England)
|May 14, 2026
PubMed
Summary

Machine learning identified key infant gut bacteria differences between breastfed and formula-fed infants. These findings, using 16S rRNA sequencing, were validated across multiple datasets, offering insights into infant microbiome development.

Keywords:
biomarker discoverydeep learningfeature selectionmachine learning

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Area of Science:

  • Microbiome research
  • Pediatric health
  • Bioinformatics

Background:

  • Breast milk composition influences infant gut microbiota and immune system development.
  • Infant formulas aim to mimic breast milk's nutritional and bioactive properties.
  • Understanding infant gut microbiome variations is crucial for health outcomes.

Purpose of the Study:

  • To analyze differences in infant gut microbiome composition between breastfed and formula-fed infants.
  • To identify specific bacterial taxa that differentiate these feeding groups using machine learning.
  • To validate findings across independent infant gut microbiome datasets.

Main Methods:

  • Utilized DADA2 pipeline for 16S rRNA gene sequencing data processing.
  • Applied Recursive Ensemble Feature Selection (REFS) algorithm for biomarker discovery.
  • Analyzed three public 16S rRNA datasets and performed literature review and disease association analysis via MicrobiomeAnalyst.

Main Results:

  • Identified 16 significant bacterial taxa differentiating breastfed from formula-fed infants in the discovery dataset.
  • Validated these taxa across two independent infant gut microbiome datasets.
  • Confirmed significant differences in bacterial composition based on feeding method.

Conclusions:

  • Machine learning techniques effectively identified key taxa distinguishing infant gut microbiomes based on feeding type.
  • Validated findings underscore the impact of breastfeeding versus formula feeding on infant gut microbiota composition.
  • Further research into functional roles and variability is warranted for a comprehensive understanding of infant health.