The haybiome: Characterising the viable bacterial community profile of four different hays for horses following different pre-feeding regimens

Shotgun metagenomic sequencing reveals the influence of artisanal dairy environments on the microbiomes, quality, and safety of Idiazabal, a raw ewe milk PDO cheese

BACKGROUND

Numerous studies have highlighted the impact of bacterial communities on the quality and safety of raw ewe milk-derived cheeses. Despite reported differences in the microbiota among cheese types and even producers, to the best of our knowledge, no study has comprehensively assessed all potential microbial sources and their contributions to any raw ewe milk-derived cheese, which could suppose great potential for benefits from research in this area. Here, using the Protected Designation of Origin Idiazabal cheese as an example, the impact of the environment and practices of artisanal dairies (including herd feed, teat skin, dairy surfaces, and ingredients) on the microbiomes of the associated raw milk, whey, and derived cheeses was examined through shotgun metagenomic sequencing.

RESULTS

The results revealed diverse microbial ecosystems across sample types, comprising more than 1300 bacterial genera and 3400 species. SourceTracker analysis revealed commercial feed and teat skin as major contributors to the raw milk microbiota (45.6% and 33.5%, respectively), being a source of, for example, Lactococcus and Pantoea, along with rennet contributing to the composition of whey and cheese (17.4% and 41.0%, respectively), including taxa such as Streptococcus, Pseudomonas_E or Lactobacillus_H. Functional analysis linked microbial niches to cheese quality- and safety-related metabolic pathways, with brine and food contact surfaces being most relevant, related to genera like Brevibacterium, Methylobacterium, or Halomonas. With respect to the virulome (virulence-associated gene profile), in addition to whey and cheese, commercial feed and grass were the main reservoirs (related to, e.g., Brevibacillus_B or CAG-196). Similarly, grass, teat skin, or rennet were the main contributors of antimicrobial resistance genes (e.g., Bact-11 or Bacteriodes_B). In terms of cheese aroma and texture, apart from the microbiome of the cheese itself, brine, grass, and food contact surfaces were key reservoirs for hydrolase-encoding genes, originating from, for example, Lactococcus, Lactobacillus, Listeria or Chromohalobacter. Furthermore, over 300 metagenomic assembled genomes (MAGs) were generated, including 60 high-quality MAGs, yielding 28 novel putative species from several genera, e.g., Citricoccus, Corynebacterium, or Dietzia.

CONCLUSION

This study emphasizes the role of the artisanal dairy environments in determining cheese microbiota and, consequently, quality and safety. Video Abstract.

Straight from the horse's mouth: The effect of different feedstuffs on oral pH in horses and ponies

Feedstuffs, especially ensiled forage, may be detrimental to equid oral health by exposing the oral cavity to low pH. This study aimed to identify if salivary pH was altered by 1) a range of different feedstuffs and (2) specifically by feeding haylages with differing nutrient profiles. Two studies were conducted. The first measured oral pH following five feedstuffs, (hay, haylage, unmolassed sugarbeet pulp, unmolassed alfalfa chaff and rolled oats), tested individually over five days. Saliva (≥1 ml) was collected in triplicate, prior to feeding, directly after ingesting 500 g of each feedstuff, then 15 min and 30 min post-prandially. Oral pH was determined (pH meter) within 10 min of collection. In study two, eight ponies, were fed as their total diet, four different haylages over four 15-day periods. Saliva was collected, prior to feeding and immediately after ingesting 500 g of forage on day 1, day 6, and day 12 of each period. Samples were collected and analysed as per study one. All data were analysed by repeated measures ANOVA, and in study two linear regression was used to attempt to predict nutrients that influenced oral pH. All statistics were conducted in Genstat 20 th Ed. Only feeding unmolassed sugarbeet caused a reduction (p<0.001) in oral pH. There were differences in oral pH depending on the type of haylage fed in study two but at all times oral pH post-feeding was the same or greater than basal pH. These studies suggest any feed associated modulation of oral pH in horses may only be short-lived and quickly buffered by saliva. However, these studies only reflect oral pH within the oral cavity around the feeding occasion and may not reflect gingival pH or the effects of different feeds over longer time periods.

Phylogenetic variation in raw cow milk microbiota and the impact of forage combinations and use of silage inoculants

Introduction

The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this ecosystem and previous studies have shown variations in their microbial ecology. However, little is known of the microbiota of forage ration combinations and the transfer rates of associated species to milk.

Methods

We identified raw milk bacteria that may originate from forage rations encompassing either hay (H) or grass/legume silage uninoculated (GL) as the only forage type, or a combination of GL and corn silage uninoculated (GLC), or grass/legume and corn silage both inoculated (GLICI). Forage and milk samples collected in the fall and spring from 24 dairy farms were analyzed using 16S rRNA gene high-throughput sequencing following a treatment with propidium monoazide to account for viable cells.

Results and discussion

Three community types separating H, GL, and GLICI forage were identified. While the H community was co-dominated by Enterobacteriaceae, Microbacteriaceae, Beijerinckiaceae, and Sphingomonadaceae, the GL and GLICI communities showed high proportions of Leuconostocaceae and Acetobacteraceae, respectively. Most of the GLC and GLICI rations were similar, suggesting that in the mixed forage rations involving grass/legume and corn silage, the addition of inoculant in one or both types of feed does not considerably change the microbiota. Raw milk samples were not grouped in the same way, as the GLC milk was phylogenetically different from that of GLICI across sampling periods. Raw milk communities, including the GLICI group for which cows were fed inoculated forage, were differentiated by Enterobacteriaceae and other Proteobacteria, instead of by lactic acid bacteria. Of the 113 amplicon sequence variants (ASVs) shared between forage rations and corresponding raw milk, bacterial transfer rates were estimated at 18 to 31%. Silage-based forage rations, particularly those including corn, share more ASVs with raw milk produced on corresponding farms compared to that observed in the milk from cows fed hay. These results show the relevance of cow forage rations as sources of bacteria that contaminate milk and serve to advance our knowledge of on-farm raw milk contamination.