Integrated analysis of gut metabolome, microbiome, and exfoliome data in an equine model of intestinal injury.

BACKGROUND: The equine gastrointestinal (GI) microbiome has been described in the context of various diseases. The observed changes, however, have not been linked to host function and therefore it remains unclear how specific changes in the microbiome alter cellular and molecular pathways within the GI tract. Further, non-invasive techniques to examine the host gene expression profile of the GI mucosa have been described in horses but not evaluated in response to interventions. Therefore, the objectives of our study were to (1) profile gene expression and metabolomic changes in an equine model of non-steroidal anti-inflammatory drug (NSAID)-induced intestinal inflammation and (2) apply computational data integration methods to examine host-microbiota interactions. METHODS: Twenty horses were randomly assigned to 1 of 2 groups (n = 10): control (placebo paste) or NSAID (phenylbutazone 4.4 mg/kg orally once daily for 9 days). Fecal samples were collected on days 0 and 10 and analyzed with respect to microbiota (16S rDNA gene sequencing), metabolomic (untargeted metabolites), and host exfoliated cell transcriptomic (exfoliome) changes. Data were analyzed and integrated using a variety of computational techniques, and underlying regulatory mechanisms were inferred from features that were commonly identified by all computational approaches. RESULTS: Phenylbutazone induced alterations in the microbiota, metabolome, and host transcriptome. Data integration identified correlation of specific bacterial genera with expression of several genes and metabolites that were linked to oxidative stress. Concomitant microbiota and metabolite changes resulted in the initiation of endoplasmic reticulum stress and unfolded protein response within the intestinal mucosa. CONCLUSIONS: Results of integrative analysis identified an important role for oxidative stress, and subsequent cell signaling responses, in a large animal model of GI inflammation. The computational approaches for combining non-invasive platforms for unbiased assessment of host GI responses (e.g., exfoliomics) with metabolomic and microbiota changes have broad application for the field of gastroenterology. Video Abstract.

Culture-independent and dependent evaluation of the equine paranasal sinus microbiota in health and disease.

BACKGROUND: Horses with bacterial sinusitis frequently undergo empirical treatment with antimicrobials, however, in some cases bacterial culture of the affected sinus is used to direct therapy. Data regarding which organisms are part of the commensal microbiota of the equine sinus are lacking making it difficult to interpret culture results and guide empiric antimicrobial selection. OBJECTIVES: Our objectives were to describe the bacterial and fungal microbiota of the paranasal sinuses in clinically normal horses using culture-dependent and independent approaches and to compare the bacterial culture and susceptibility patterns of normal horses with those from horses affected with primary and secondary sinusitis. STUDY DESIGN: Experimental study and descriptive retrospective review of case records. METHODS: Sinus washes were collected from 23 healthy horses. Washes were submitted for routine culture and susceptibility testing and DNA was isolated for next generation sequencing of bacterial and fungal marker genes. For clinical cases of sinusitis, medical records from 2010 to 2017 were reviewed and horses diagnosed with primary and/or secondary sinusitis were included. RESULTS: The paranasal sinus cavity hosts multiple bacterial and fungal organisms. The bacterial microbiota of healthy horses consists largely of uncultivable, aerobic bacteria. While few anaerobes were isolated from normal horses, the majority of clinical cases resulted in growth of anaerobic organisms with no difference in the proportion of aerobic and anaerobic bacteria isolated from clinical cases. MAIN LIMITATIONS: Small sample size in both populations of horses and heterogeneity of the population prevent a more in-depth analysis. CONCLUSIONS: The microbiota of the paranasal sinuses of horses consists primarily of aerobic bacteria and fungal organisms, the majority of which are uncultivable via common clinical methods. Anaerobic bacteria are found in the majority of horses with clinical sinusitis. These findings suggest anaerobic bacteria are associated with sinusitis and their presence should be considered when treating horses with sinusitis.

Comparison of primary closure of incisional hernias in horses with and without the use of prosthetic mesh support.

REASONS FOR PERFORMING STUDY: Repair of incisional hernias in horses has been described previously; however, this report describes the outcome of primary closure of incisional hernias in a large number of horses and compares these results with those of mesh implantation. OBJECTIVE: To report the perioperative care, complications and long-term outcome of primary closure of incisional hernias in horses and to compare these results with a second population of horses in which prosthetic mesh was used. METHODS: Medical records of horses undergoing an incisional herniorrhaphy between 1998 and 2009 were reviewed. Information obtained included case details, factors from the initial surgery that contributed to the hernia formation, method of hernia repair and outcome. Comparisons between horses with and without mesh were made using logistic regression. RESULTS: Thirty-eight horses with primary closure and 9 horses with mesh implantation met inclusion criteria. Long-term follow-up for cases in which a mesh was not used was available for 25 cases; of these, 21 horses (84%) had a normal cosmetic appearance and 4 (16%) had a visible defect. There was no significant difference between the 2 repair methods in terms of age, sex, breed, weight, size of the hernia, number of defects, timing of the repair or cosmetic outcome. Horses in which a mesh was used had significantly longer duration of surgery and hospitalisation, and were significantly more likely to develop post operative complications while having a longer duration of convalescence prior to return to use. CONCLUSIONS: Primary apposition of incisional hernias in horses without the use of mesh support appears to result in a good cosmetic outcome while avoiding the complications associated with mesh implantation in this population of horses. POTENTIAL RELEVANCE: Surgical time, duration of hospitalisation, and post operative complications may be reduced by using this technique of primary repair and avoiding mesh implantation.