Treatment of chronic wounds is becoming increasingly difficult due to antibiotic resistance. Complex natural products with antimicrobial activity, such as honey, are now under the spotlight as alternative treatments to antibiotics. Several studies have shown honey to have broad-spectrum antibacterial activity at concentrations present in honey dressings, and resistance to honey has not been attainable in the laboratory. However not all honeys are the same and few studies have used honey that is well defined both in geographic and chemical terms. Here we have used a range of concentrations of clover honey and a suite of manuka and kanuka honeys from known geographical locations, and for which the floral source and concentration of methylglyoxal and hydrogen peroxide potential were defined, to determine their effect on growth and cellular morphology of four bacteria: Bacillus subtilis, Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa. While the general trend in effectiveness of growth inhibition was manuka>manuka-kanuka blend>kanuka>clover, the honeys had varying and diverse effects on the growth and cellular morphology of each bacterium, and each organism had a unique response profile to these honeys. P. aeruginosa showed a markedly different pattern of growth inhibition to the other three organisms when treated with sub-inhibitory concentrations of honey, being equally sensitive to all honeys, including clover, and the least sensitive to honey overall. While hydrogen peroxide potential contributed to the antibacterial activity of the manuka and kanuka honeys, it was never essential for complete growth inhibition. Cell morphology analysis also showed a varied and diverse set of responses to the honeys that included cell length changes, cell lysis, and alterations to DNA appearance. These changes are likely to reflect the different regulatory circuits of the organisms that are activated by the stress of honey treatment.

RNA-based stable isotope probing (RNA-SIP) and metabolic profiling were used to detect actively glucose-consuming bacteria in a complex microbial community obtained from a murine model system. A faeces-derived microbiota was incubated under anaerobic conditions for 0, 2, and 4 h with 40 mM [U13C]glucose. Isopycnic density gradient ultracentrifugation and fractionation of isolated RNA into labeled and unlabeled fractions followed by 16S rRNA sequencing showed a quick adaptation of the bacterial community in response to the added sugar, which was dominated by unclassified Lachnospiraceae species. Inspection of distinct fractions of isotope-labeled RNA revealed Allobaculum spp. as particularly active glucose utilizers in the system, as the corresponding RNA showed significantly higher proportions among the labeled RNA. With time, the labeled sugar was used by a wider spectrum of faecal bacteria. Metabolic profiling indicated rapid fermentation of [U13C]glucose, with lactate, acetate, and propionate being the principal 13C-labeled fermentation products, and suggested that “cross-feeding” occurred in the system. RNA-SIP combined with metabolic profiling of 13C-labeled products allowed insights into the microbial assimilation of a general model substrate, demonstrating the appropriateness of this technology to study assimilation processes of nutritionally more relevant substrates, for example, prebiotic carbohydrates, in the gut microbiota of mice as a model system.

Mucin desulfation is believed to be a rate-limiting step in mucin degradation by colon bacteria. The activities of enzymes hydrolysing nine linkages found in mucin oligosaccharide chains were measured using model substrates, in extracts of two mucin-degrading bacteria, Prevotella strain RS2 and Bacteroides fragilis. Sulfatases desulfating N-acetylglucosamine-6-sulfate, galactose-6-sulfate and galactose-3-sulfate were found. The genomic DNA downstream from the gene encoding the mucin-desulfating sulfatase (N-acetylglucosamine-6-sulfatase) in Prevotella was sequenced, and two putative genes identified which are likely to be coexpressed with this sulfatase, though their activities are unknown. Northern and Western analyses showed that expression of this short operon of three genes is increased during growth on mucin.

Pectin is abundant in modern day diets, as it comprises the middle lamellae and one-third of the dry carbohydrate weight of fruit and vegetable cell walls. Currently there is no specialized model organism for studying pectin fermentation in the human colon, as our collective understanding is informed by versatile glycan-degrading bacteria rather than by specialist pectin degraders. Here we show that the genome of Monoglobus pectinilyticus possesses a highly specialized glycobiome for pectin degradation, unique amongst Firmicutes known to be in the human gut. Its genome encodes a simple set of metabolic pathways relevant to pectin sugar utilization, and its predicted glycobiome comprises an unusual distribution of carbohydrate-active enzymes (CAZymes) with numerous extracellular methyl/acetyl esterases and pectate lyases. We predict the M. pectinilyticus degradative process is facilitated by cell-surface S-layer homology (SLH) domain-containing proteins, which proteomics analysis shows are differentially expressed in response to pectin. Some of these abundant cell surface proteins of M. pectinilyticus share unique modular organizations rarely observed in human gut bacteria, featuring pectin-specific CAZyme domains and the cell wall-anchoring SLH motifs. We observed M. pectinilyticus degrades various pectins, RG-I, and galactan to produce polysaccharide degradation products (PDPs) which are presumably shared with other inhabitants of the human gut microbiome (HGM). This strain occupies a new ecological niche for a primary degrader specialized in foraging a habitually consumed plant glycan, thereby enriching our understanding of the diverse community profile of the HGM.

The immunostimulatory activity of kanuka honey may be particularly dependent on AGPs derived from the nectar of kanuka flowers.

The fate of stable-isotope (13)C labelled and non-labelled inulin catabolism by the gut microbiota was assessed in a healthy rat model. Sprague-Dawley male rats were randomly assigned to diets containing either cellulose or inulin, and were fed these diets for 3 days. On day (d) 4, rats allocated to the inulin diet received (13)C-labelled inulin. The rats were then fed the respective non-labelled diets (cellulose or inulin) until sampling (d4, d5, d6, d7, d10 and d11). Post feeding of (13)C-labelled substrate, breath analysis showed that (13)C-inulin cleared from the host within a period of 36 hours. Faecal (13)C demonstrated the clearance of inulin from gut with a (13)C excess reaching maximum at 24 hours (d5) and then declining gradually. There were greater variations in caecal organic acid concentrations from d4 to d6, with higher concentrations of acetic, butyric and propionic acids observed in the rats fed inulin compared to those fed cellulose. Inulin influenced caecal microbial glycosidase activity, increased colon crypt depth, and decreased the faecal output and polysaccharide content compared to the cellulose diet. In summary, the presence of inulin in the diet positively influenced large bowel microbial fermentation.

Commercial diets high in animal protein and fat are increasingly being developed for pets, however little is understood about the impacts of feeding such diets to domestic cats. The carbohydrate content of these diets is typically low, and dietary fibre is often not included. Dietary fibre is believed to be important in the feline gastrointestinal tract, promoting stool formation and providing a substrate for the hindgut microbiome. Therefore, we aimed to determine the effects of adding plant-based dietary fibre to a high animal protein and fat diet. Twelve domestic short hair cats were fed three complete and balanced diets in a cross-over design for blocks of 21 days: raw meat (Raw), raw meat plus fibre (2%, ‘as is’ inclusion of inulin and cellulose; Raw+Fibre) and a commercially available Kibble diet. A commercially available canned diet was fed for 21 days as a washout phase. Apparent macronutrient digestibility, faecal output, score, pH, organic acid concentrations and bacteriome profiles were determined. Diet significantly affected all faecal parameters measured. The addition of dietary fibre to the raw meat diet was found to reduce apparent macronutrient digestibility, increase faecal output, pH and score. Thirty one bacterial taxa were significantly affected by diet. Prevotella was found to dominate in the Kibble diet, Clostridium and Fusobacterium in the Raw diet, and Prevotella and a group of unclassified Peptostreptococcaceae in the Raw+Fibre diet. Our results show that diets of different macronutrient proportions can strongly influence the faecal microbiome composition and metabolism, as shown by altered organic acid concentrations and faecal pH, in the domestic cat. The addition of 2% of each fibre to the Raw diet shifted faecal parameters closer to those produced by feeding a Kibble diet. These results provide a basis for further research assessing raw red meat diets to domestic cats.

In humans, aging is associated with changes in the gastrointestinal microbiota; these changes may contribute to the age-related increase in incidence of many chronic diseases, including Type 2 diabetes. The life expectancies of cats are increasing, and they are also exhibiting the same types of diseases. While there are some studies investigating the impacts of diets on gastrointestinal microbiota in young cats, the impacts of aging in older cats has not been explored. We followed a cohort of related kittens, maintained on two commercial diets (kibbled and canned) from weaning (8 weeks) to 5 years of age (260 weeks). We hypothesized that the long-term feeding of specific diet formats would (a) lead to microbial composition changes due to aging, (b) impact body composition, and (c) affect insulin sensitivity in the aging cat. We observed that both diet and age affected fecal microbial composition, and while age correlated with changes in body composition, diet had no effect on body composition. Similarly insulin sensitivity was not affected by age nor diet. 16S rRNA sequencing found unclassified Peptostreptococcaceae were prominent across all ages averaging 21.3% of gene sequence reads and were higher in cats fed canned diets (average of 25.7% of gene sequence reads, vs. 17.0% for kibble-fed cats). Age-related effects on body composition and insulin sensitivity may become apparent as the cats grow older; this study will continue to assess these parameters.