Gregor Reid’s research while affiliated with Lawson Health Research Institute and other places

Background The application of ‘-omics’ technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into the functions which are actively expressed and differential between states of health and disease. Results We conducted a meta-analysis of vaginal metatranscriptomes from three studies, split into exploratory (n = 42) and validation (n = 297) datasets, accounting for the compositional nature of sequencing data and differences in scale between healthy and BV microbiomes. Conducting differential expression analyses on the exploratory dataset, we identified a multitude of strategies employed by microbes associated with states of health and BV to evade host cationic antimicrobial peptides (CAMPs); putative mechanisms used by BV-associated species to resist and counteract the low vaginal pH; and potential approaches to disrupt vaginal epithelial integrity so as to establish sites for adherence and biofilm formation. Moreover, we identified several distinct functional subgroups within the BV population, distinguished by genes involved in motility, chemotaxis, biofilm formation and co-factor biosynthesis. After defining molecular states of health and BV in the validation dataset using KEGG orthology terms rather than community state types, differential expression analysis confirmed earlier observations regarding CAMP resistance and compromising epithelial barrier integrity in healthy and BV microbiomes and also supported the existence of motile vs. non-motile subgroups in the BV population. These findings were independent of the enzyme classification system used (KEGG or EggNOG). Conclusions Our findings highlight a need to focus on functional rather than taxonomic differences when considering the role of microbiomes in disease and identify pathways for further research as potential BV treatment targets. CwG4qJAdVu5eAuU4jPyBusVideo Abstract

The paradigm that the vaginal microbiota is a protective gateway for the urinary and reproductive systems has endured for more than a century and driven decades of probiotic research. Evidence robustly supports the notion that healthy urogenital microbiomes are predominantly colonized by lactobacilli, particularly Lactobacillus crispatus, which can acidify the local environment and protect against urogynecologic pathogen colonization. However, recent studies are beginning to delve deeper into the intricate mechanistic interactions connecting the microbiome, its diverse functional potential, host immunity, pathogens, and the development of urogenital diseases. Leveraging these emerging insights alongside past successes presents promising opportunities for future therapies aimed at enhancing the management of conditions such as bacterial vaginosis, urinary tract infections, bladder pain, urinary incontinence, and beyond.

Probiotics are typically marketed as foods and dietary supplements, categories for products intended to maintain health in generally healthy populations and which, unlike drugs, cannot claim to treat or cure disease. This review addresses the existing evidence that probiotics are beneficial to healthy people. Our approach was to perform a descriptive review of efficacy evidence that probiotics can prevent urinary, vaginal, gastrointestinal, and respiratory infections, and improve risk factors associated with cardiovascular health or reduce antibiotic use. Other endpoints such as mental, dental, or immune health were not specifically addressed. We concluded that there is sufficient evidence of efficacy and safety for clinicians and consumers to consider using specific probiotics for some indications – such as the use of probiotics to support gut function during antibiotic use or to reduce the risk of respiratory tract infections – for certain people. However, we did not find a sufficiently high level of evidence to support unconditional, population-wide recommendations for other preventive endpoints we reviewed for healthy people. Although evidence for some indications is suggestive of the preventive benefits of probiotics, additional research is needed.

Ethanolamine is an abundant compound in the gastrointestinal tract and a valuable source of carbon and nitrogen for pathogenic bacteria harboring ethanolamine utilization (eut) genes. Eut-positive pathogens can consume free ethanolamine to outcompete commensal microbes, which often lack eut genes, and establish infection. Ethanolamine can also act as a host recognition signal for eut-positive pathogens to upregulate virulence genes during colonization. Therefore, reducing free ethanolamine titers may represent a novel approach to preventing infection by eut-positive pathogens. Interestingly, the commensal microorganism Levilactobacillus brevis ATCC 14869 was found to encode over 18 eut genes within its genome. This led us to hypothesize that L. brevis can compete with eut-positive pathogens by clearing free ethanolamine from the environment. Our results demonstrate that despite being unable to metabolize ethanolamine under most conditions, L. brevis ATCC 14869 responds to the compound by increasing the expression of genes encoding proteins involved in microcompartment formation and adhesion to the intestinal epithelial barrier. The improved intestinal adhesion of L. brevis in the presence of ethanolamine also enhanced the exclusion of eut-positive pathogens from adhering to intestinal epithelial cells. These findings support further studies to test whether L. brevis ATCC 14869 can counter enteric pathogens and prevent or reduce the severity of infections. Overall, the metabolic capabilities of L. brevis ATCC 14869 offer a unique opportunity to add to the armamentarium of antimicrobial therapies as well as our understanding of the mechanisms used by beneficial microbes to sense and adapt to host microenvironments.

The application of ‘-omics’ technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into the functions which are actively expressed and differential between states of health and disease. We conducted a meta-analysis of vaginal metatranscriptomes from three studies, split into exploratory ( n = 44) and validation ( n = 297) datasets, accounting for the compositional nature of sequencing data and differences in scale between healthy and BV microbiomes. Conducting differential abundance analyses on the exploratory dataset, we identified a multitude of strategies employed by microbes associated with states of health and BV to evade host cationic antimicrobial peptides (CAMPs); putative mechanisms used by BV-associated species to resist and counteract the low vaginal pH; and potential approaches to disrupt vaginal epithelial integrity so as to establish sites for adherence and biofilm formation. Moreover, we identified several distinct functional subgroups within the BV population, distinguished by genes involved in motility, chemotaxis, biofilm formation and co-factor biosynthesis. After defining molecular states of health and BV in the validation dataset using KEGG orthology terms rather than community state types, differential abundance analysis confirmed earlier observations regarding CAMP resistance and compromising epithelial barrier integrity in healthy and BV microbiomes, and also supported the existence of motile vs. non-motile subgroups in the BV population. Our findings highlight a need to focus on functional rather than taxonomic differences when considering the role of microbiomes in disease and identify pathways for further research as potential BV treatment targets.

A Gram-negative, motile, rod-shaped bacterial strain, CA-0114 T , was isolated from the midgut of a western honey bee, Apis mellifera . The isolate exhibited ≤96.43 % 16S rRNA gene sequence identity (1540 bp) to members of the families Enterobacteriaceae and Erwiniaceae . Phylogenetic trees based on genome blast distance phylogeny and concatenated protein sequences encoded by conserved genes atpD , fusA, gyrB , infB , leuS , pyrG and rpoB separated the isolate from other genera forming a distinct lineage in the Enterobacteriaceae . In both trees, the closest relatives were Tenebrionicola larvae YMB-R21 T and Tenebrionibacter intestinalis BIT-L3 T , which were isolated previously from Tenebrio molitor L., a plastic-eating mealworm. Digital DNA–DNA hybridization, orthologous average nucleotide identity and average amino acid identity values between strain CA-0114 T and the closest related members within the Enterobacteriaceae were ≤23.1, 75.45 and 76.04 %, respectively. The complete genome of strain CA-0114 T was 4 451669 bp with a G+C content of 52.12 mol%. Notably, the apparent inability of strain CA-0114 T to ferment d -glucose, inositol and l -rhamnose in the API 20E system is unique among closely related members of the Enterobacteriaceae . Based on the results obtained through genotypic and phenotypic analysis, we propose that strain CA-0114 T represents a novel species and genus within the family Enterobacteriaceae , for which we propose the name Apirhabdus apintestini gen. nov., sp. nov. (type strain CA-0114 T =ATCC TSD-396 T =DSM 116385 T ).

Microbial management is central to aquaculture’s efficiency. Pediococcus acidilactici MA18/5M has shown promising results promoting growth, modulation of the immune response, and disease resistance in many fishes. However, the mechanisms through which this strain confers health benefits in fish are poorly understood, particularly in Pacific salmonid models. Briefly, the aims of this study were to i) assess the protective effects of P. acidilactici MA18/5M by examining gut barrier function and the expression of tight junction (TJ) and immune genes in vitro and in vivo, and ii) to determine the protective effects of this strain against a common saltwater pathogen, Vibrio anguillarum J382. An in vitro model of the salmonid gut was employed utilizing the cell line RTgutGC. Barrier formation and integrity assessed by TEER measurements in RTgutGC, showed a significant decrease in resistance in cells exposed only to V. anguillarum J382 for 24 h, but pre-treatment with P. acidilactici MA18/5M for 48 h mitigated these effects. While P. acidilactici MA18/5M did not significantly upregulate tight junction and immune molecules, pre-treatment with this strain protected against pathogen-induced insults to the gut barrier. In particular, the expression of ocldn was significantly induced by V. anguillarum J382, suggesting that this molecule might play a role in the host response against this pathogen. To corroborate these observations in live fish, the effects of P. acidilactici MA18/5M was evaluated in Chinook salmon reared in real aquaculture conditions. Supplementation with P. acidilactici MA18/5M had no effect on Chinook salmon growth parameters after 10 weeks. Interestingly, histopathological results did not show alterations associated with P. acidilactici MA18/5M supplementation, indicating that this strain is safe to be used in the industry. Finally, the expression pattern of transcripts encoding TJ and immune genes in all the treatments suggest that variation in expression is more likely to be due to developmental processes rather than P. acidilactici MA18/5M supplementation. Overall, our results showed that P. acidilactici MA18/5M is a safe strain for use in fish production, however, to assess the effects on growth and immune response previously observed in other salmonid species, an assessment in adult fish is needed.

Chinook salmon is a native species of the Canadian Pacific coast with potential economic and environmental benefits for aquaculture. However, its production is jeopardized by low tolerance to high densities and disease susceptibility. Due to this, Chinook salmon represents a great candidate for evaluating the effect of non-polluting alternatives to vaccines and antibiotics, such as probiotics. Preliminary studies have suggested that certain probiotic strains may be able to enhance fish growth, antioxidant activity, food digestibility, modulate the host microbial community in the digestive tract, and prevent bacterial infections. However, there is currently no evidence of its effects in Chinook salmon. Here, we used the commercially available, low-cost multi-strain probiotic used by humans, to determine the impact on Chinook salmon growth, survival, immune response, and gut barrier integrity. Fish were randomly assigned to four netpens and given either regular (control) feed or supplemented with probiotics for 4, 10, or 14 months. After this, fish were transferred to troughs and challenged with Vibrio anguillarum. Probiotic supplementation for 14 months decreased mortality by ∼10% compared to the control treatment. However, no positive effects of this probiotic supplementation on fish growth occurred. Despite the improvement in survival associated to long-term probiotic supplementation, the expression of the immune genes il1b, il8, il10, tnfa, camp, hamp, and transferrin in head kidney, spleen, and hindgut tissues did not fully provide the specific innate immune mechanisms that could be associated with a better protection. Decreased expression of cldn1 and ocln in fish supplemented for 14 months compared to 4- and 10-months suggested that probiotic treatment during the freshwater and saltwater cycle confers a better protection and intestinal integrity, resulting in an improved survival. Although it was not possible to observe differences in IgM and IgT protein levels between probiotic-supplemented fish and the control treatment in plasma, head kidney, spleen, and hindgut, this study represents the first measurement of total IgT protein levels in Chinook salmon. In summary, probiotic supplementation modulated the early inflammatory response against V. anguillarum infection and helped improve the survival of Chinook salmon aquaculture in an environmentally sustainable manner when applied in freshwater and up to the transition to saltwater growth phase.