Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Physiology of Enteric Nervous System and Gut Health01:05

Physiology of Enteric Nervous System and Gut Health

383
The gastrointestinal tract, responsible for the digestion and absorption of nutrients, is safeguarded by the intestinal barrier, which consists of secretory, physical, and immune components. At the forefront is the secretory barrier, composed of essential elements such as mucus, gut microbiota, and defense proteins. They collaborate to break down food particles, facilitate nutrient absorption, and maintain optimal gut health. These secretory components ensure the smooth functioning of the...
383
Microorganisms in Medicine and Therapeutics01:29

Microorganisms in Medicine and Therapeutics

184
Microorganisms play a fundamental role in vaccine development, gene therapy, and therapeutic production. Their biological properties are harnessed to advance medicine and public health. Beyond immunization, microorganisms contribute to gut health, antibiotic synthesis, and genetic disease treatment.Live Attenuated and Inactivated VaccinesLive attenuated vaccines, such as the measles, mumps, and rubella (MMR) vaccine, utilize weakened forms of pathogens to closely resemble natural infections.
184
Bacterial Flora of the Large Intestine01:29

Bacterial Flora of the Large Intestine

570
The gut microbiome is formed by a vast and diverse community of bacteria that colonizes our large intestine. These bacteria start residing in the gut from birth and continue diversifying throughout life, influenced by factors such as diet, lifestyle, and stress. The gut bacterial community also includes bacteria from food and those that enter the colon through the anus.
The normal gut flora of the colon plays a critical role in generating essential vitamins such as vitamins K, B5, and B7.
570
What is Monogastric Digestion?01:50

What is Monogastric Digestion?

72.0K
The human body contains a monogastric digestive system. In a monogastric digestive system, the stomach only contains one chamber in which it digests food. Several other animal species also have monogastric digestive systems, including pigs, horses, dogs, and birds. This chapter, however, focuses on the human digestive system.
72.0K
The Roles of Bacteria and Fungi in Plant Nutrition02:11

The Roles of Bacteria and Fungi in Plant Nutrition

38.5K
Plants have the impressive ability to create their own food through photosynthesis. However, plants often require assistance from organisms in the soil to acquire the nutrients they need to function correctly. Both bacteria and fungi have evolved symbiotic relationships with plants that help the species to thrive in a wide variety of environments.
38.5K
Chronic Bowel Disorders: Introduction01:17

Chronic Bowel Disorders: Introduction

523
Chronic bowel diseases are a group of long-term conditions affecting the digestive tract, characterized by inflammation and damage to the gut lining. These conditions primarily include irritable bowel syndrome and inflammatory bowel disease.
Irritable Bowel Syndrome (IBS) is a common disorder affecting the gastrointestinal tract. The distinctive feature is recurrent abdominal pain associated with altered bowel movements, manifesting as constipation, diarrhea, or fluctuating between both. The...
523

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Towards cognition-emotion-behaviour models of nonsuicidal self-injury: a knowledge graph approach.

Health information science and systems·2025
Same author

PIPENN-EMB ensemble net and protein embeddings generalise protein interface prediction beyond homology.

Scientific reports·2025
Same author

Impact of pathogenic mutations of the GLUT1 glucose transporter on solute carrier dynamics using ComDYN enhanced sampling.

F1000Research·2025
Same author

Tree hole rescue: an AI approach for suicide risk detection and online suicide intervention.

Health information science and systems·2024
Same author

CIBRA identifies genomic alterations with a system-wide impact on tumor biology.

Bioinformatics (Oxford, England)·2024
Same author

Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph.

Bioinformatics (Oxford, England)·2023

Related Experiment Video

Updated: Aug 22, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

29.1K

Towards a knowledge graph for pre-/probiotics and microbiota-gut-brain axis diseases.

Ting Liu1,2, Gongjin Lan3, K Anton Feenstra1

  • 1Department of Computer Science, Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands.

Scientific Reports
|November 8, 2022
PubMed
Summary

This study introduces a novel knowledge graph to integrate biological data from scientific literature and databases. This approach enhances the discovery of relationships between pre-/probiotics and microbiota-gut-brain axis diseases.

More Related Videos

A Gut-on-a-Chip Model to Study the Gut Microbiome-Nervous System Axis
09:18

A Gut-on-a-Chip Model to Study the Gut Microbiome-Nervous System Axis

Published on: July 28, 2023

2.8K
An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota
07:15

An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota

Published on: July 31, 2019

9.7K

Related Experiment Videos

Last Updated: Aug 22, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

29.1K
A Gut-on-a-Chip Model to Study the Gut Microbiome-Nervous System Axis
09:18

A Gut-on-a-Chip Model to Study the Gut Microbiome-Nervous System Axis

Published on: July 28, 2023

2.8K
An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota
07:15

An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota

Published on: July 31, 2019

9.7K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Microbiome Research

Background:

  • Scientific literature contains rich biological relationship data but lacks machine-readable structure.
  • Existing biological databases are structured for analysis but lack comprehensive knowledge.
  • Integrating these resources is crucial for advanced biological querying and discovery.

Purpose of the Study:

  • To develop a method for constructing comprehensive knowledge graphs from scientific publications and databases.
  • To investigate the relationships between pre-/probiotics and microbiota-gut-brain axis diseases using the constructed knowledge graph.
  • To demonstrate the enhanced querying capabilities and biological insights gained from integrated knowledge bases.

Main Methods:

  • Creation of two knowledge bases: ppstatement (manual annotations) and ppconcept (automatic annotations).
  • Integration of these knowledge bases with public databases: MeSH, UMLS, and SNOMED CT to form the Pre-/Probiotics Knowledge Graph (PPKG).
  • Validation using four biological query cases to assess performance and the added value of integration.

Main Results:

  • The PPKG successfully integrates manually curated and automatically annotated data with public ontologies.
  • Query cases demonstrated the retrieval of co-occurring concepts relevant to pre-/probiotics and microbiota-gut-brain axis diseases.
  • Combining knowledge bases within PPKG yielded more comprehensive results than using them individually.

Conclusions:

  • The developed approach enables the construction of comprehensive knowledge graphs from diverse biological data sources.
  • The Pre-/Probiotics Knowledge Graph (PPKG) facilitates novel research queries, such as identifying beneficial pre-/probiotic combinations for specific diseases.
  • This integrated knowledge graph has the potential to uncover new biological insights and guide therapeutic strategies.