Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome.

Practical considerations in fecal sample collection for microbiome research include time to sample storage, time of collection, and hindgut position during terminal collections. Here, parallel experiments were performed to investigate the relative effect of these factors on microbiome composition in mice colonized with two different vendor-origin microbiomes. 16S rRNA amplicon sequencing of immediately flash-frozen feces showed no difference in alpha or beta diversity compared to samples incubated up to 9 h at room temperature. Samples collected in the morning showed greater alpha diversity compared to samples collected in the afternoon. While a significant effect of time was detected in all hindgut regions, the effect increased from cecum to distal colon. This study highlights common scenarios in microbiome research that may affect outcome measures of microbial community analysis. However, we demonstrate a relatively low effect size of these technical factors when compared to a primary experimental factor with large intergroup variability.

Field study examining the mucosal microbiome in equine glandular gastric disease.

Equine glandular gastric disease (EGGD) is a common disease among athletic horses that can negatively impact health and performance. The pathophysiology of this EGGD remains poorly understood. Previous studies using controlled populations of horses identified differences in the gastric glandular mucosal microbiome associated with disease. The objective of this study was to compare the gastric microbiome in horses with EGGD and those without across multiple barns and differing management practices. We hypothesized that alterations in the microbiome of the gastric glandular mucosa are associated with EGGD. A secondary objective was to perform a risk factor analysis for EGGD using the diet and management data collected. Microbial populations of biopsies from normal pyloric mucosa of horses without EGGD (control biopsies), normal pyloric mucosa of horses with EGGD (normal biopsies) and areas of glandular mucosal disruption in horses with EGGD (lesion biopsies) were compared. Lesion biopsies had a different microbial community structure than control biopsies. Control biopsies had a higher read count for the phylum Actinomycetota compared to lesion biopsies. Control biopsies also had an enrichment of the genera Staphylococcus and Lawsonella and the species Streptococcus salivarius. Lesion biopsies had an enrichment of the genera Lactobacillus and Actinobacillus and the species Lactobacillus equigenerosi. These results demonstrate differences in the gastric glandular microbiome between sites of disrupted mucosa in horses with EGGD compared to pyloric mucosa of horses without EGGD. Risk factor analysis indicated that exercise duration per week was a risk factor for EGGD.

Effect of Sugar Beet Pulp on the Composition and Predicted Function of Equine Fecal Microbiota.

The purpose of this study is to determine the effect of the partial replacement of dietary hay with sugar beet pulp (SBP) on the composition and predicted function of the fecal microbiota of healthy adult horses. Fecal samples were collected daily for 12 days from six adult horses after removal from pasture, including a five-day acclimation period, and a seven-day period following the introduction of SBP into their diet, and compared to six untreated horses over a comparable period. Fecal DNA was subjected to 16S rRNA amplicon sequencing and a longitudinal analysis was performed comparing the composition and predicted function. While no significant treatment-associated changes in the richness, alpha diversity, or beta diversity were detected, random forest regression identified several high-importance taxonomic features associated with change over time in horses receiving SBP. A similar analysis of the predicted functional pathways identified several high-importance pathways, including those involved in the production of L-methionine and butyrate. These data suggest that feeding SBP to healthy adult horses acutely increases the relative abundance of several Gram-positive taxa, including Cellulosilyticum sp., Moryella sp., and Weissella sp., and mitigates the predicted functional changes associated with removal from pasture. Large-scale studies are needed to assess the protective effect of SBP on the incidence of the gastrointestinal conditions of horses.

The contribution of maternal oral, vaginal, and gut microbiota to the developing offspring gut.

There is limited understanding of how the microbiota colonizing various maternal tissues contribute to the development of the neonatal gut microbiota (GM). To determine the contribution of various maternal microbiotic sites to the offspring microbiota in the upper and lower gastrointestinal tract (GIT) during early life, litters of mice were sacrificed at 7, 9, 10, 11, 12, 14, and 21 days of age, and fecal and ileal samples were collected. Dams were euthanized alongside their pups, and oral, vaginal, ileal, and fecal samples were collected. This was done in parallel using mice with either a low-richness or high-richness microbiota to assess the consistency of findings across multiple microbial compositions. Samples were analyzed using 16S rRNA amplicon sequencing. The compositional similarity between pup and dam samples were used to determine the contribution of each maternal source to the composition of the neonate fecal and ileal samples at each timepoint. As expected, similarity between neonate and maternal feces increased significantly over time. During earlier time-points however, the offspring fecal and ileal microbiotas were closer in composition to the maternal oral microbiota than other maternal sites. Prominent taxa contributed by the maternal oral microbiota to the neonate GM were supplier-dependent and included Lactobacillus spp., Streptococcus spp., and a member of the Pasteurellaceae family. These findings align with the microbial taxa reported in infant microbiotas, highlighting the translatability of mouse models in this regard, as well as the dynamic nature of the GM during early life.

Wild mouse gut microbiota limits initial tuberculosis infection in BALB/c mice.

Mouse models are critical tools in tuberculosis (TB) research. Recent studies have demonstrated that the wild mouse gut microbiota promotes host fitness and improves disease resistance. Here we examine whether the wild mouse gut microbiota alters the immunopathology of TB in BALB/c mice. Conventional BALB/c mice (LabC) and mice born to germ-free BALB/c mothers reconstituted with the wild mouse gut microbiota (WildR) were used in our studies. WildR mice controlled initial TB infection better than LabC mice. The microbial gut communities of LabC mice and WildR mice had similar richness but significantly different composition prior to infection. TB reduced the gut community richness in both cohorts while differences in community composition remained indicating a general TB-induced dysbiosis. The wild mouse gut microbiota did not alter the typical lung histopathology of TB in the BALB/c model that includes unstructured immune cell infiltrates with infected foamy macrophages invading alveolar spaces. Animals of both cohorts mounted robust T cell responses in lungs and spleen with lower absolute counts of CD4 and CD8 T cells in lungs of WildR mice during acute infection, corresponding with observed differences in pathogen load. In summary, LabC mice and WildR mice showed largely overlapping TB immunopathology and pathogen kinetics, with WildR mice controlling early acute infection better than LabC mice.

Restoration of the gut barrier integrity and restructuring of the gut microbiome in aging by angiotensin-(1-7).

Compromised barrier function of colon epithelium with aging is largely due to gut microbial dysbiosis. Recent studies implicate an important role for angiotensin converting enzymes, ACE and ACE2, angiotensins, and the receptors, AT1 receptor (AT1R) and Mas receptor (MasR), in the regulation of colon functions. The present study tested the hypothesis that leaky gut in aging is associated with an imbalance in ACE2/ACE and that the treatment with angiotenisn-(1-7) (Ang-(1-7)) will restore gut barrier integrity and microbiome. Studies were carried out in Young (3-4 months) and old (20-24 months) male mice. Ang-(1-7) was administered by using osmotic pumps. Outcome measures included expressions of ACE, ACE2, AT1R, and MasR, intestinal permeability by using FITC-dextran, and immunohistochemistry of claudin 1 and occludin, and intestinal stem cells (ISCs). ACE2 protein and activity were decreased in Old group while that of ACE were unchanged. Increased intestinal permeability and plasma levels of zonulin-1 in the Old group were normalized by Ang-(1-7). Epithelial disintegrity, reduced number of goblet cells and ISCs in the old group were restored by Ang-(1-7). Expression of claudin 1 and occludin in the aging colon was increased by Ang-(1-7). Infiltration of CD11b+ or F4/80+ inflammatory cells in the old colons were decreased by Ang-(1-7). Gut microbial dysbiosis in aging was evident by decreased richness and altered beta diversity that were reversed by Ang-(1-7) with increased abundance of Lactobacillus or Lachnospiraceae. The present study shows that Ang-(1-7) restores gut barrier integrity and reduces inflammation in the aging colon by restoring the layer of ISCs and by restructuring the gut microbiome.

Standardized Complex Gut Microbiomes Influence Fetal Growth, Food Intake, and Adult Body Weight in Outbred Mice.

Obesity places a tremendous burden on individual health and the healthcare system. The gut microbiome (GM) influences host metabolism and behaviors affecting body weight (BW) such as feeding. The GM of mice varies between suppliers and significantly influences BW. We sought to determine whether GM-associated differences in BW are associated with differences in intake, fecal energy loss, or fetal growth. Pair-housed mice colonized with a low or high microbial richness GM were weighed, and the total and BW-adjusted intake were measured at weaning and adulthood. Pups were weighed at birth to determine the effects of the maternal microbiome on fetal growth. Fecal samples were collected to assess the fecal energy loss and to characterize differences in the microbiome. The results showed that supplier-origin microbiomes were associated with profound differences in fetal growth and excessive BW-adjusted differences in intake during adulthood, with no detected difference in fecal energy loss. Agreement between the features of the maternal microbiome associated with increased birth weight here and in recent human studies supports the value of this model to investigate the mechanisms by which the maternal microbiome regulates offspring growth and food intake.

Ophthalmic viscoelastics commonly used in cataract surgery: A microbiota investigation.

PURPOSE: To survey commonly used, sterile ophthalmic viscoelastic materials used during routine cataract surgery for the presence of bacterial DNA and/or viable bacteria and endotoxin quantification. METHODS: Samples from three different ophthalmic viscoelastic manufacturers and three different production lots per manufacturer were collected for 16 S ribosomal ribonucleic acid (rRNA) sequencing and conventional aerobic and capnophilic bacterial culture. Other samples of viscoelastic material from the same three manufacturers were collected for endotoxin quantification using a commercially available Limulus amebocyte lysate (LAL) assay. Statistical analysis was performed using Sigma Plot 14.0, and R v4.0.2.0. Differences (p ≤ .05) between sample collection sites in total DNA concentration, microbial richness, mean intra-group distances, and endotoxin quantification alongside reagent controls were evaluated. RESULTS: Culture yielded two isolates, identified as Staphylococcus epidermidis and Bacillus megaterium. 16 S rRNA sequencing revealed no differences between brands in richness or overall composition. The most common bacterial DNA detected across all brands was Staphylococcus sp., Cutibacterium sp., Flavobacterium sp., and Lactobacillus sp. A significant difference was found between the median endotoxin concentration between Anvision and Hyvisc® viscoelastic (Anvision: 0.171 EU/mL, Hyvisc®: 0.03 EU/mL; p < .001). CONCLUSIONS: No brand-specific differences in bacterial DNA were detected in the viscoelastic materials. Staphylococcus, Cutibacterium, Flavobacterium, and Lactobacillus were the dominant contributors to the bacterial DNA detected. Although Anvision viscoelastic samples contained significantly more endotoxin than Hyvisc® viscoelastic samples, endotoxin concentrations were below the FDA limit of 0.2 EU/mL for both manufacturers. These data further the understanding of inflammatory outcomes following cataract surgery.

Gut microbiota mediate vascular dysfunction in a murine model of sleep apnoea: effect of probiotics.

BACKGROUND: Obstructive sleep apnoea (OSA) is a chronic prevalent condition characterised by intermittent hypoxia (IH), and is associated with endothelial dysfunction and coronary artery disease (CAD). OSA can induce major changes in gut microbiome diversity and composition, which in turn may induce the emergence of OSA-associated morbidities. However, the causal effects of IH-induced gut microbiome changes on the vasculature remain unexplored. Our objective was to assess if vascular dysfunction induced by IH is mediated through gut microbiome changes. METHODS: Faecal microbiota transplantation (FMT) was conducted on C57BL/6J naïve mice for 6 weeks to receive either IH or room air (RA) faecal slurry with or without probiotics (VSL#3). In addition to 16S rRNA amplicon sequencing of their gut microbiome, FMT recipients underwent arterial blood pressure and coronary artery and aorta function testing, and their trimethylamine N-oxide (TMAO) and plasma acetate levels were determined. Finally, C57BL/6J mice were exposed to IH, IH treated with VSL#3 or RA for 6 weeks, and arterial blood pressure and coronary artery function assessed. RESULTS: Gut microbiome taxonomic profiles correctly segregated IH from RA in FMT mice and the normalising effect of probiotics emerged. Furthermore, IH-FMT mice exhibited increased arterial blood pressure and TMAO levels, and impairments in aortic and coronary artery function (p<0.05) that were abrogated by probiotic administration. Lastly, treatment with VSL#3 under IH conditions did not attenuate elevations in arterial blood pressure or CAD. CONCLUSIONS: Gut microbiome alterations induced by chronic IH underlie, at least partially, the typical cardiovascular disturbances of sleep apnoea and can be mitigated by concurrent administration of probiotics.

Molecular and microbiological evidence of bacterial contamination of intraocular lenses commonly used in canine cataract surgery.

Inflammatory outcomes, including toxic anterior segment syndrome (TASS) and infectious endophthalmitis, are potentially painful, blinding complications following cataract surgery. In an in vitro pilot study, commercially available, sterile foldable intraocular lenses (IOLs) used during routine canine cataract surgery, and their packaging fluid were surveyed for the presence of bacterial DNA and/or viable (cultivable) bacteria. Swabs from IOLs and packaging fluid from three different veterinary manufacturers and three different production lots/manufacturer were collected for 16S ribosomal ribonucleic acid (rRNA) sequencing. Packaging fluid samples were collected for aerobic/capnophilic bacterial culture. Culture yielded one isolate, identified as Staphylococcus epidermidis. 16S rRNA sequencing revealed distinct brand-specific bacterial DNA profiles, conserved between IOLs and packaging fluid of all production lots within each manufacturer. The dominant taxonomy differentiating each manufacturer was annotated as Staphylococcus sp, and was a 100% match to S. epidermidis. Distinct mixtures of bacterial DNA are present and consistent in IOLs and packaging fluid depending on the manufacturer, and Staphylococcus is the dominant contributor to the bacterial DNA detected. Caralens products had a significantly lower amount of Staphylococcus spp. compared to Anvision and Dioptrix products.

Respiratory dysbiosis in cats with spontaneous allergic asthma.

Deviations from a core airway microbiota have been associated with the development and progression of asthma as well as disease severity. Pet cats represent a large animal model for allergic asthma, as they spontaneously develop a disease similar to atopic childhood asthma. This study aimed to describe the lower airway microbiota of asthmatic pet cats and compare it to healthy cats to document respiratory dysbiosis occurring with airway inflammation. We hypothesized that asthmatic cats would have lower airway dysbiosis characterized by a decrease in richness, diversity, and alterations in microbial community composition including identification of possible pathobionts. In the current study, a significant difference in airway microbiota composition was documented between spontaneously asthmatic pet cats and healthy research cats mirroring the finding of dysbiosis in asthmatic humans. Filobacterium and Acinetobacter spp. were identified as predominant taxa in asthmatic cats without documented infection based on standard culture and could represent pathobionts in the lower airways of cats. Mycoplasma felis, a known lower airway pathogen of cats, was identified in 35% of asthmatic but not healthy cats. This article has been published alongside "Temporal changes of the respiratory microbiota as cats transition from health to experimental acute and chronic allergic asthma" (1).

Temporal changes of the respiratory microbiota as cats transition from health to experimental acute and chronic allergic asthma.

In humans, deviation from a core airway microbiota may predispose to development, exacerbation, or progression of asthma. We proposed to describe microbiota changes using 16 rRNA sequencing in samples from the upper and lower airways, and rectal swabs of 8 cats after experimental induction of asthma using Bermuda grass allergen, in acute (6 weeks) and chronic (36 weeks) stages. We hypothesized that asthma induction would decrease richness and diversity and alter microbiota composition and structure in the lower airways, without significantly impacting other sites. After asthma induction, richness decreased in rectal (p = 0.014) and lower airway (p = 0.016) samples. B diversity was significantly different between health and chronic asthma in all sites, and between all time points for lower airways. In healthy lower airways Pseudomonadaceae comprised 80.4 ± 1.3% whereas Sphingobacteriaceae and Xanthobacteraceae predominated (52.4 ± 2.2% and 33.5 ± 2.1%, respectively), and Pseudomonadaceae was absent, in 6/8 cats with chronic asthma. This study provides evidence that experimental induction of asthma leads to dysbiosis in the airways and distant sites in both the acute and chronic stages of disease. This article has been published alongside "Respiratory dysbiosis in cats with spontaneous allergic asthma" (1).

Dietary and management factors influence the equine gastric microbiome.

OBJECTIVE: The purpose of this study was to characterize the relationship of diet and management factors with the glandular gastric mucosal microbiome. We hypothesize that the gastric mucosal microbial community is influenced by diet and management factors. Our specific objective is to characterize the gastric mucosal microbiome in relation to these factors. ANIMALS: 57 client-owned horses in the southern Louisiana region with and without equine glandular gastric disease. PROCEDURES: Diet and management data were collected via a questionnaire. Gastroscopy was used for evaluation of equine gastric ulcer syndrome and collection of glandular mucosal pinch biopsies. 16S rRNA amplicon sequencing was used for microbiome analysis. Similarity and diversity indices and sequence read counts of individual taxa were compared between diet and management factors. RESULTS: Differences were detected in association with offering hay, type of hay, sweet feed, turnout, and stalling. Offering hay and stalling showed differences in similarity indices, whereas hay type, sweet feed, and turnout showed differences in similarity and diversity indices. Offering hay, hay type, and sweet feed were also associated with differences in individual sequence read counts. CLINICAL RELEVANCE: This study provides preliminary characterization of the complex relationship between the glandular gastric microbiome and diet/management factors. The ideal microbiome to promote a healthy glandular gastric environment remains unknown.

The G Protein-Coupled Receptor, VPAC1, Mediates Vasoactive Intestinal Peptide-Dependent Functional Homeostasis of the Gut Microbiota.

BACKGROUND AND AIMS: Vasoactive intestinal peptide (VIP) is a neuropeptide involved in the regulation of feeding behavior and circadian rhythms, metabolism, and immunity. Previous studies revealed the homeostatic effects of VIP signaling on the gut microbiota. VIP-deficient mice demonstrate a gut microbiota dysbiosis characterized by reduced α-diversity and decreased relative abundance (RA) of Gram-positive Firmicutes. However, the mechanism by which VIP signaling affects changes in the microbiota is unknown. METHODS: To investigate the role of the 2 cognate G protein-coupled receptors for VIP (VPAC1 and VPAC2) in VIP-mediated homeostasis of the microbiota, fecal samples from VPAC1- and VPAC2-deficient, heterozygous, and wild-type littermate mice were assessed via targeted amplicon sequencing. Their microbiota profiles were additionally compared with microbiota from VIP-deficient, heterozygous, and wild-type littermates, where genotype-dependent changes in the composition and predicted function of each cohort were compared. RESULTS: While wild-type mice in each line differed in α-diversity and ß-diversity, consistent changes in both metrics were observed in VIP-deficient and VPAC1-deficient mice. This includes a dramatic reduction in α-diversity, increased RA of Proteobacteria and Bacteroidetes, and decreased RA of Lachnospiraceae, Ruminococcaceae, Muribaculaceae, and Rikenellaceae. Specific amplicon sequence variants and predicted functions found to differ significantly based on VIP or VPAC1 genotype were concordant in their directions of change. Multiplatform predicted functional profiling suggested a defective VIP-VPAC1 axis was associated with reduced amino acid degradation along with reduced quinol and quinone biosynthesis. Furthermore, alterations in predicted functions include increased sugar degradation, nitrate reduction, and fatty acid biosynthetic pathways, among other changes. CONCLUSION: We conclude that VIP signaling through VPAC1 is critical for the maintenance of normal function of the gut microbiota.

The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota.

Research investigating the gut microbiome (GM) during a viral infection may necessitate inactivation of the fecal viral load. Here, we assess how common viral inactivation techniques affect 16S rRNA-based analysis of the gut microbiome. Five common viral inactivation methods were applied to cross-matched fecal samples from sixteen female CD-1 mice of the same GM background prior to fecal DNA extraction. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA. Treatment-dependent effects on DNA yield, genus-level taxonomic abundance, and alpha and beta diversity metrics were assessed. A sodium dodecyl sulfate (SDS)-based inactivation method and Holder pasteurization had no effect on measures of microbial richness, while two Buffer AVL-based inactivation methods resulted in a decrease in detected richness. SDS inactivation, Holder pasteurization, and the AVL-based inactivation methods had no effect on measures of alpha diversity within samples or beta diversity between samples. Fecal DNA extracted with TRIzol-treated samples failed to amplify and sequence, making it unsuitable for microbiome analysis. These results provide guidance in the 16S rRNA microbiome analysis of fecal samples requiring viral inactivation.