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Series GSE239472 Query DataSets for GSE239472
Status Public on Jan 31, 2024
Title Acute gastrointestinal permeability after traumatic brain injury in mice precedes a bloom in Akkermansia muciniphila supported by intestinal hypoxia
Organism Mus musculus
Experiment type Other
Summary Traumatic brain injury (TBI) initiates not only complex neurovascular and glial changes within the brain but also pathophysiological responses that extend beyond the central nervous system. The peripheral response to TBI has become an intensive area of research, as these systemic perturbations can induce dysfunction in multiple organ systems. As there are no approved therapeutics for TBI, it is imperative that we investigate the peripheral response to TBI to identify targets for future intervention. Of particular interest is the gastrointestinal (GI) system. Even in the absence of polytrauma, brain-injured individuals are at increased risk of suffering from GI-related morbidity and mortality. Symptoms such as intestinal dysmotility, inflammation, ulceration, and fecal incontinence can drastically diminish quality of life. The GI tract is inhabited by trillions of microbes that have been implicated as modulators of many neurological disorders. Clinical and preclinical studies implicate gut dysbiosis, a pathological imbalance in the normally symbiotic microbiota, as both a consequence of TBI as well as a contributing factor to brain damage. However, our understanding of this interplay is still limited. While relatively little is known about the effects of TBI on the structure and function of the GI tract, prior studies report that experimental TBI induces intestinal barrier dysfunction and morphological changes. To confirm these findings in the current model of TBI, male C57BL/6J mice underwent a sham control or a controlled cortical impact (CCI) procedure to induce a contusive brain injury, and intestinal permeability was assessed at 4 h, 8 h, 1 d, and 3 d post-injury. An acute, transient increase in permeability was observed at 4 h after CCI. Histological analyses of the ileum and colon at multiple time points from 4 h to 4 wks revealed no overt morphological changes, suggesting that CCI induced a short-lived physiologic dysfunction without major structural alterations to the GI tract. As the microbiome is a modulator of GI physiology, we performed 16s gene sequencing on fecal samples collected prior to and over the first month after CCI or sham injury. Microbial community diversity was assessed using common metrics of alpha and beta diversity. Alpha diversity was lower in the CCI injury group and beta diversity differed among groups, although these effects were not observed in all metrics. Subsequent differential abundance analysis revealed that the phylum Verrucamicrobiota was increased in CCI mice at 1, 2, and 3 d post-injury when compared to sham mice. Subsequent qPCR identified the Verrucamicrobiota species as Akkermansia Muciniphila, an obligate anaerobe that resides in and helps regulate the intestinal mucus layer and barrier. To determine whether TBI promotes changes to the GI tract favorable for the proliferation of A. muciniphila, mucus-producing goblet cells and the level of GI hypoxia were evaluated. Goblet cell density in the medial colon was significantly increased at 1 d, while colon hypoxia was significantly increased at 3 d. Taken together, these studies show that CCI induces transient intestinal barrier dysfunction followed by increased goblet cell density and hypoxia in the colon with a concomitant increase in A. muciniphila that may suggest a compensatory response to systemic stress after TBI.
 
Overall design To investigate the effect of traumatic brain injury (TBI) on the gut microbiome we utilized a controlled cortical impact (CCI) model of TBI in male C57bl/6j mice with the control group being considered a sham mouse. Sham mice received all parts of the CCI procedure except for the impact to exposed dura (nSHAM = 6, nCCI =7).To establish a timecourse of microbiome changes, fecal samples were collected prior to injury (00d below) and at 1 day (01d), 2 days (02d), 3 days (03d), 1 week (07d), 2 weeks (14d), and 4 weeks (28d) after sham or CCI procedure. Fecal samples were flash frozen and stored at -80C until DNA extraction (QIAamp PowerFecal Pro DNA kit)
Sequencing of the 16s rRNA gene was conducted by the University of Kentucky Genomics Core using the Illumina MiSeq platform. Sequencing libraries were prepared as per Illumina documentation for the V3-V4 region using the suggested primers (Fwd: 5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG; Rev: 5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTA TCTAATCC), quantified, and normalized prior to sequencing
Resultant paired end reads were joined, processed, and analyzed within R using dada2 and phyloseq (based on the workflow published by Callahan, Sankaran, Fukuyama, McMurdie and Holmes; 2017) to obtain an OTU table, Taxonomy table (SILVA 138), and phylogenetic tree within a phyloseq object. Two samples were excluded for low sequencing depth: the 03d and 14d samples from Sham4. Diversity metrics were then generated for various alpha and beta diverisity metrics. Due to large variation in read depth, sequences were rarefied for alpha diversity metrics only.
To assess differential abundance, we chose to compare injury groups at matched timepoints. ANCOM-BC was run to generate differential abundance comparisons between sham and CCI mice at each timepoint for the phylum, class, order, and family level (results are found in supplementary file).
 
Contributor(s) DeSana AJ, Estus S, Barrett T, Saatman KE
Citation(s) 38316862
Submission date Jul 27, 2023
Last update date Feb 15, 2024
Contact name Anthony Joseph DeSana
E-mail(s) desanaaj@ucmail.uc.edu, anthony.desana@uky.edu, a.desana15@gmail.com
Organization name University of Kentucky
Department Physiology/ SCoBIRC
Lab Kathryn E. Saatman
Street address 741 South Limestone, 4th Floor, SCoBIRC
City Lexington
State/province Kentucky
ZIP/Postal code 40506-0509
Country USA
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (89)
GSM7665726 feces, Sham, 00d, biolrep1
GSM7665727 feces, Sham, 01d, biolrep1
GSM7665728 feces, Sham, 02d, biolrep1
Relations
BioProject PRJNA999350

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE239472_ANCOM-BC_All_results_tables.xlsx 160.4 Kb (ftp)(http) XLSX
GSE239472_TBI_timecourse_Animal_metadata.csv.gz 1.6 Kb (ftp)(http) CSV
GSE239472_TBI_timecourse_OTU_TabNoC_ANCOMBC.csv.gz 287.3 Kb (ftp)(http) CSV
GSE239472_TBI_timecourse_Taxonomy_Tab_ANCOMBC.csv.gz 21.7 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record
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