Source Paper
Brain?Gut?Microbe Communication in Health and Disease
Sue Grenham, Gerard Clarke, John F. Cryan, Timothy G. Dinan
Frontiers in Physiology • 2011
Source Paper
Sue Grenham, Gerard Clarke, John F. Cryan, Timothy G. Dinan
Frontiers in Physiology • 2011
Bidirectional signalling between the gastrointestinal tract and the brain is regulated at neural, hormonal, and immunological levels. This construct is known as the brain-gut axis and is vital for maintaining homeostasis. Bacterial colonization of the intestine plays a major role in the post-natal development and maturation of the immune and endocrine systems. These processes are key factors underpinning central nervous system (CNS) signaling. Recent research advances have seen a tremendous improvement in our understanding of the scale, diversity, and importance of the gut microbiome. This has been reflected in the form of a revised nomenclature to the more inclusive brain-gut-enteric microbiota axis and a sustained research effort to establish how communication along this axis contributes to both normal and pathological conditions. In this review, we will briefly discuss the critical components of this axis and the methodological challenges that have been presented in attempts to define what constitutes a normal microbiota and chart its temporal development. Emphasis is placed on the new research narrative that confirms the critical influence of the microbiota on mood and behavior. Mechanistic insights are provided with examples of both neural and humoral routes through which these effects can be mediated. The evidence supporting a role for the enteric flora in brain-gut axis disorders is explored with the spotlight on the clinical relevance for irritable bowel syndrome, a stress-related functional gastrointestinal disorder. We also critically evaluate the therapeutic opportunities arising from this research and consider in particular whether targeting the microbiome might represent a valid strategy for the management of CNS disorders and ponder the pitfalls inherent in such an approach. Despite the considerable challenges that lie ahead, this is an exciting area of research and one that is destined to remain the center of focus for some time to come.
Objective: To evaluate the impact of the microbiota on morphological and physiological parameters by comparing germ-free animals with conventionally colonized counterparts
This is a Germ-Free Animal Studies protocol using Rodents (mice and rats implied) as the model organism. The procedure involves 9 procedural steps, 2 equipment items. Extracted from a 2011 paper published in Frontiers in Physiology.
Model and subjects
Rodents (mice and rats implied) • Not specified in methods • unknown • Not specified in methods • Not specified in methods
Study window
Estimated timing pending
Core workflow
Establish germ-free animal colony • Establish conventionally colonized control group • Assess morphological parameters
Primary readouts
Key equipment and reagents
Verified items
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Maintain animals in sterile uterine environment during prenatal development using surgical delivery to eliminate post-natal colonization of the gastrointestinal tract
Note: Surgical delivery replaces normal birthing process to prevent microbial colonization
“Their use is based on the sterile uterine environment present during prenatal development with surgical delivery replacing the normal birthing process, thus eliminating the opportunity for post-natal colonization of the GIT”
Rear control animals using standard conventional housing allowing normal post-natal microbial colonization
Note: These animals serve as comparison group to germ-free animals
“Subsequent comparison with their conventionally colonized counterparts allows inferences to be drawn regarding the morphological and physiological parameters”
Evaluate structural differences between germ-free and conventional animals including cecum size, intestinal surface area, enterochromaffin cell area, Peyer's Patches size, and villous thickness
Note: Germ-free animals show greatly enlarged cecum, reduced intestinal surface area, increased enterochromaffin cell area, smaller Peyer's Patches and smaller villous thickness compared to conventional controls
“The morphological consequences of growing up germ-free were evidenced by the greatly enlarged cecum, reduced intestinal surface area, increased enterochromaffin cell area, smaller Peyer's Patches and smaller villous thickness in these animals compared to conventional controls”
Evaluate normal GIT motility and peristalsis function in both germ-free and conventional animals
Note: Microbiota is essential for normal GIT motility with deficits due to perturbations in peristalsis from impaired smooth muscle layer function
“It is known that the microbiota is essential for normal GIT motility, with deficits due in part to perturbations in peristalsis on the back of impaired smooth muscle layer function”
Measure epithelial cell proliferation and turnover rates in germ-free versus conventional animals
Note: Intestinal epithelial cell turnover is much slower in germ-free animals than conventionally reared animals
“Intestinal epithelial cell turnover is much slower in GF animals than conventionally reared animals”
Evaluate intestinal barrier function including tight junction protein expression and epithelial integrity
Note: Commensal flora recognition by toll-like receptors is necessary to induce increased epithelial cell proliferation and maintain barrier function
“Commensal flora recognition by toll-like receptors (TLRs) is necessary to induce increased epithelial cell proliferation thus accelerating repair of the epithelial surface following injury”
Evaluate development and function of GALT including Peyer's patches, mesenteric lymph nodes, plasma cells, and IgA secretion
Note: Germ-free animals have decreased plasma cells and IgA, decreased expression of activation markers on intestinal macrophages, decreased MHCII on epithelial cells, decreased nitric oxide and histamine levels
“GF animals have decreased plasma cells and IgA, decreased expression of activation markers on intestinal macrophages, decreased MHCII on epithelial cells, decreased nitric oxide, and histamine levels in the small intestine”
Measure Peyer's patch follicles and mesenteric lymph node characteristics in germ-free versus conventional animals
Note: Peyer's patch follicles are reduced in number and size and mesenteric lymph nodes are smaller, less cellular, and lack germinal centers in germ-free animals
“Peyer's patch follicles are reduced in number and size and the mesenteric lymph nodes are smaller, less cellular, and do not have germinal centers in GF animals”
Evaluate caloric requirements and vitamin status in germ-free versus conventional animals
Note: Germ-free animals require higher caloric intake to maintain same body weight as conventional animals and are prone to vitamin deficiencies
“GF animals require a higher caloric intake to maintain the same body weight as conventional animals and are prone to vitamin deficiencies”
This section explains what the experiment is doing, which readouts matter, what the data artifacts usually look like, and how the analysis should flow from raw capture to reported result.
To evaluate the impact of the microbiota on morphological and physiological parameters by comparing germ-free animals with conventionally colonized counterparts
Objective
To evaluate the impact of the microbiota on morphological and physiological parameters by comparing germ-free animals with conventionally colonized counterparts
Subjects
From paperRodents (mice and rats implied) • Not specified in methods • unknown • Not specified in methods • Not specified in methods
Cohort notes
From paperRodents follow a similar colonization pattern to humans and form the rationale for use of germ-free animals
Establish germ-free animal colony (Throughout prenatal and early post-natal period)
Establish conventionally colonized control group (Throughout study period)
Assess morphological parameters (Not specified in methods)
Assess gastrointestinal motility (Not specified in methods)
Cecum size
From paperNot specified in methods section
Artifact type
Endpoint measurements summarized by group or timepoint
Comparison focus
Compare endpoint magnitude between groups, timepoints, or both
Intestinal surface area
From paperNot specified in methods section
Artifact type
Endpoint measurements summarized by group or timepoint
Comparison focus
Compare endpoint magnitude between groups, timepoints, or both
Enterochromaffin cell area
From paperNot specified in methods section
Artifact type
Endpoint measurements summarized by group or timepoint
Comparison focus
Compare endpoint magnitude between groups, timepoints, or both
Peyer's Patches size
From paperNot specified in methods section
Artifact type
Endpoint measurements summarized by group or timepoint
Comparison focus
Compare endpoint magnitude between groups, timepoints, or both
Cecum size
From paperRaw artifact
Per-sample or per-animal endpoint measurements collected during the experiment
Processed artifact
Structured table with cleaned measurements ready for comparison
Final reported form
Summary statistics and between-group or across-timepoint comparisons
Intestinal surface area
From paperRaw artifact
Per-sample or per-animal endpoint measurements collected during the experiment
Processed artifact
Structured table with cleaned measurements ready for comparison
Final reported form
Summary statistics and between-group or across-timepoint comparisons
Enterochromaffin cell area
From paperRaw artifact
Per-sample or per-animal endpoint measurements collected during the experiment
Processed artifact
Structured table with cleaned measurements ready for comparison
Final reported form
Summary statistics and between-group or across-timepoint comparisons
Peyer's Patches size
From paperRaw artifact
Per-sample or per-animal endpoint measurements collected during the experiment
Processed artifact
Structured table with cleaned measurements ready for comparison
Final reported form
Summary statistics and between-group or across-timepoint comparisons
Acquisition
Collect raw experimental outputs with enough metadata to preserve sample identity, condition, and timing.
Preprocessing / cleaning
Not specified in methods section
Scoring or quantification
Quantify the primary readouts for this experiment: Cecum size; Intestinal surface area; Enterochromaffin cell area; Peyer's Patches size.
Statistical comparison
Statistical method not yet structured for this page.
Reporting output
Report representative outputs alongside summary comparisons for Cecum size, Intestinal surface area, Enterochromaffin cell area, Peyer's Patches size.
Source links and direct wording from the methods section for validation and deeper review.
Citation
Sue Grenham et al. (2011). Brain?Gut?Microbe Communication in Health and Disease. Frontiers in Physiology
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