Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

Adaptation strategies to manage summer forage shortages improve animal performance and better maintain milk and cheese quality in grass- versus corn-based dairy systems

In semi-mountainous grass-based dairy systems, summer droughts frequently reduce grass availability, with implications for animal performance as well as milk and cheese quality. The objective of our study was to investigate the effect of a simulated summer forage shortage in a traditional semi-mountainous grass-based system versus a corn-based system with part-time grazing. During a 19-wk experiment, 26 Prim'Holstein and 14 Montbéliarde cows were blocked in 4 balanced groups of 10 cows. During the first 8 wk, 2 groups were fed a grass-based diet (75% of grazed grass, 25% of hay and concentrates) and the remainder were fed a corn-based diet (75% mixed ration, 25% of grazed grass). During the following 11 wk, one group in each feeding system was subjected to a reduction in grazed grass intake and a corresponding increase in indoor feeding, resulting in 50% of grazed grass for grass-fed cows and removal of grazed grass for corn-fed cows. Milk yield and composition were recorded during the whole trial, in addition to indoor individual intake. Grass intake was modeled to calculate feed efficiency and estimate methane emissions. At the end of the experiment, bulk milk from each group was sampled for physicochemical and microbiological analyses and processed into Cantal-type cheeses. After 9 wk of ripening, cheeses underwent physicochemical, microbiological and descriptive sensory analyses. Results showed that the complete removal of grazed grass in corn-based system had no effect on milk production but impaired feed efficiency; grass reduction in the grass-based diet better maintained milk yield, enhanced feed efficiency, and reduced methane emission intensity. Cheese softness increased with proportion of grass in the diet, and it was positively correlated with primary proteolysis (αS1-casein and β-casein breakdown) but negatively correlated with the C16:0/C18:1 ratio and the calculated fat melting point. Cheese from cows fed with more grazed grass were the yellowest and had the most pronounced flavors, as well as higher counts of heterofermentative lactobacilli and lactic acid bacteria. Removal of grazed grass from the corn-based diet led to cheese that was less yellow and had less flavor, in line with lower levels of secondary proteolysis. In conclusion, our study suggests that maintaining fresh herbage in corn-based diets is crucial for maintaining cheese quality without impairing animal performance. In grass-based systems, complementation with indoor feeding may have limited effects on product quality but promotes the maintenance of animal performance.

Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications

Mammalian milk contains a variety of complex bioactive and nutritional components and microorganisms. These microorganisms have diverse compositions and functional roles that impact host health and disease pathophysiology, especially mastitis. The advent and use of high throughput omics technologies, including metagenomics, metatranscriptomics, metaproteomics, metametabolomics, as well as culturomics in milk microbiome studies suggest strong relationships between host phenotype and milk microbiome signatures in mastitis. While single omics studies have undoubtedly contributed to our current understanding of milk microbiome and mastitis, they often provide limited information, targeting only a single biological viewpoint which is insufficient to provide system-wide information necessary for elucidating the biological footprints and molecular mechanisms driving mastitis and milk microbiome dysbiosis. Therefore, integrating a multi-omics approach in milk microbiome research could generate new knowledge, improve the current understanding of the functional and structural signatures of the milk ecosystem, and provide insights for sustainable mastitis control and microbiome management.

BIOFILM DAIRY FOODS REVIEW: Microbial Community Tracking from Dairy Farm to Factory: Insights on Biofilm Management for Enhanced Food Safety and Quality

This review aimed to assess the scope of the literature on tracking the microbial community of biofilms, focusing on the dairy farm and processing environments. The majority of studies focused on either production, storage, transport or processing of milk, while 5 combined the investigation of both production and processing facilities. Factors influencing short-term changes in dairy microbiota such as the occurrence of mastitis and season were distinguished from factors revealed through long-term studies, such as feed and weather, rather than the milking equipment. Knowledge gaps were identified in relation to the study design, methods, data analysis and interpretation. The application of DNA sequencing technologies is particularly challenging with respect to samples with low microbial load (milk, swabs). There are few studies on the microbial composition of in situ biofilms, which might require new technologies for detection before sampling. Fundamental studies on the structure of biofilms are needed to identify the on-farm practices impacting the cycle of biofilm development in milking systems.

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.

The microbiota of ensiled forages and of bulk tank milk on dairy cattle farms in northern Sweden

Factors contributing to variations in the quality and microbiota of ensiled forages and in bulk tank microbiota in milk from cows fed different forages were investigated. Nutritional quality, fermentation parameters and hygiene quality of forage samples and corresponding bulk tank milk samples collected in 3 periods from 18 commercial farms located in northern Sweden were compared. Principal coordinates analysis revealed that the microbiota in forage and bulk milk, analyzed using 16S rRNA gene-based amplicon sequencing, were significantly different. The genera Lactobacillus, Weissella, and Leuconostoc dominated in forage samples, whereas Pseudomonas, Staphylococcus, and Streptococcus dominated in bulk milk samples. Forage quality and forage-associated microbiota were affected by ensiling method and by use of silage additive. Forages stored in bunker and tower silos (confounded with use of additive) were associated with higher levels of acetic and lactic acid and Lactobacillus. Forage ensiled as bales (confounded with no use of additive) was associated with higher DM content, water-soluble carbohydrate content, pH, yeast count, and the genera Weissella, Leuconostoc, and Enterococcus. For bulk tank milk samples, milking system was identified as the major factor affecting the microbiota and type of forage preservation had little effect. Analysis of common amplicon sequence variants (ASV) suggested that forage was not the major source of Lactobacillus found in bulk tank milk.

Utility of dairy microbiome as a tool for authentication and traceability

Milk microbiome contributes substantially to the formation of specific organoleptic and physicochemical characteristics of dairy products. The assessment of the composition and abundance of milk microbiota is a challenging task strongly influenced by many environmental factors. Specific dairy products may be designated by the Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) labeling, which however, occasionally fail to differentiate them according to specific quality characteristics, which are defined by different microbiota-driven reactions. Combining the above limitations, the scope of the present study, was to summarize the existing information toward three main issues. First, to assess the influence level of the diet type and grazing to rumen-GI tract, mammary gland, and udder microbiome formation in ruminants. Second, to discuss the factors affecting milk microbiota, as well as the effect of the endo-mammary route on milk microbial taxa. Lastly, to evaluate "milk microbiome" as a tool for product differentiation, according to origin, which will contribute to a more robust PDO and PGI labeling. Although the limitations are still a matter of fact (especially considering the sample collection, process, evaluation, and avoidance of its contamination), significant progress has been made, regarding the identification of the factors affecting dairy products' microbiota and its core composition. In conclusion, although so far not totally efficient in dairy products molecular identification, with the progress in soil, water, plant, and animal host's microbiota assembly's characterization, microbiomics could provide a powerful tool for authentication and traceability of dairy products.

Feeding Cows with Olive Cake Enriched in Polyphenols Improves the Sustainability and Enhances the Nutritional and Organoleptic Features of Fresh Caciocavallo Cheese

In this study, Caciocavallo, a typical cheese produced in Sicily Island (Italy), was obtained from the milk of dairy cows fed with and without enriched olive cake (ECO and CTR, respectively) in order to evaluate nutritional, microbiological, volatile, and sensory differences in cheeses. ECO cheese showed greater (p < 0.05) MUFA and PUFA and polyphenols content and lower SFA content than CTR cheese. Microbiological analyses revealed the absence of Salmonella, Listeria monocytogenes, Escherichia coli, and E. coli O157, and no significant differences in the viable counts of the remaining microbial groups analyzed, between samples. Thermophilic lactococci were more prevalent in ECO cheese. The implementation of a culture-independent method, such as PCR-DGGE analyses, revealed the presence of a more diverse microbial population in both cheeses. Regarding the volatile compounds profile, long-chain free fatty acids were more abundant in the ECO cheese, resulting in a healthier free fatty acid profile. This study also showed that, especially for their appearance and taste, consumers mostly appreciated the ECO cheese. The results show that using enriched olive cake could enhance the sustainability and the quality of Ragusano cheese, improving not only the health of its consumers but also positively influencing tastes and acceptability.

Natural Foraging Selection and Gut Microecology of Two Subterranean Rodents from the Eurasian Steppe in China

As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus, which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax, which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors, such as the ability of both species to degrade cellulose, are not yet clear. In this study, we analyzed the gut bacterial communities and diet compositions of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax, and that the two species of zokors possessed different gut bacterial indicator genera. Differences in the feeding habits of the two species of zokors stem from food composition rather than diversity. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root-type-food- and the rhizome-type-food-dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modeling results show that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax. This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions.

Metagenomic analysis of the bacterial microbiome, resistome and virulome distinguishes Portuguese Serra da Estrela PDO cheeses from similar non-PDO cheeses: An exploratory approach

This study aimed to evaluate the microbiome, resistome and virulome of two types of Portuguese cheese using high throughput sequencing (HTS). Culture-dependent chromogenic methods were also used for certain groups/microorganisms. Eight samples of raw ewe's milk cheese were obtained from four producers: two producers with cheeses with a PDO (Protected Designation of Origin) label and the other two producers with cheeses without a PDO label. Agar-based culture methods were used to quantify total mesophiles, Enterobacteriaceae, Escherichia coli, Staphylococcus, Enterococcus and lactic acid bacteria. The presence of Listeria monocytogenes and Salmonella was also investigated. The selected isolates were identified by 16S rRNA gene sequencing and evaluated to determine antibiotic resistance and the presence of virulence genes. The eight cheese samples analyzed broadly complied with EC regulations in terms of the microbiological safety criteria. The HTS results demonstrated that Leuconostoc mesenteroides, Lactococcus lactis, Lactobacillus plantarum, Lacticaseibacillus rhamnosus, Enterococcus durans and Lactobacillus coryniformis were the most prevalent bacterial species in cheeses. The composition of the bacterial community varied, not only between PDO and non-PDO cheeses, but also between producers, particularly between the two non-PDO cheeses. Alpha-diversity analyses showed that PDO cheeses had greater bacterial diversity than non-PDO cheeses, demonstrating that the diversity of spontaneously fermented foods is significantly higher in cheeses produced without the addition of food preservatives and dairy ferments. Despite complying with microbiological regulations, both PDO and non-PDO cheeses harbored potential virulence genes as well as antibiotic resistance genes. However, PDO cheeses exhibited fewer of these virulence and antibiotic resistance genes compared to non-PDO cheeses. Therefore, the combination of conventional microbiological methods and the metagenomic approach could contribute to improving the attribution of the PDO label to this type of cheese.

Microbial communities in feed, bedding material, and bulk milk - experiences from a feeding trial

There is an increasing interest in the microbiota of the dairy value chain, from field to fork. Studies to understand the effects of environmental, feed and management factors on the raw milk microbiota have been performed to elucidate the origin of the bacteria and find ways to control the presence or absence of specific bacteria. In this study, we explored the microbiota in feedstuff, bedding material and milk on a Swedish dairy farm to investigate the effects of feeding different silages on the bacterial compositions throughout the dairy value chain. Three ensiling treatments were evaluated: without additive, with acid treatment, and with inoculation of starter culture. The silage treatments were fed as partial mixed rations to 67 dairy cows for 3 weeks each, with one treatment fed twice to evaluate if a potential change in milk microbiota could be repeated. The highest average total bacteria counts were found in the used bedding material (9.6 log10 cfu/g), while milk showed the lowest (3.5 log10 cfu/g). Principal coordinate analysis of the weighted UniFrac distance matrix showed clear separation between 3 clusters of materials: 1) herbage, 2) silage and partial mixed ration, and 3) used bedding material and milk. Surprisingly, the expected effect of the ensiling treatments on silage microbiota was not clear. Transfer of major bacteria from the silages and resulting partial mixed rations to the used bedding material was observed, but rarely to milk. The milk microbiota showed most resemblance to that of the used bedding material. Lactobacillus was a major genus in both feed and milk, but investigations at amplicon sequence variant level showed that in most cases the sequences differed between materials. However, low total bacteria count in the milk in combination with a high diversity suggests that results may be biased due to environmental contamination of the milk samples. Considering that the study was performed on a research farm, strict hygienic measures during the feeding experiment may have contributed to the low transfer of bacteria from feed to milk.

Analysis of Human Milk Microbiota in Northern Greece by Comparative 16S rRNA Sequencing vs. Local Dairy Animals

Milk is a biological fluid with a dynamic composition of micronutrients and bioactive molecules that serves as a vital nutrient source for infants. Milk composition is affected by multiple factors, including genetics, geographical location, environmental conditions, lactation phase, and maternal nutrition, and plays a key role in dictating its microbiome. This study addresses a less-explored aspect, comparing the microbial communities in human breast milk with those in mature milk from species that are used for milk consumption. Since mature animal milk is used as a supplement for both the infant (formula) and the child/adolescent, our main aim was to identify shared microbial communities in colostrum and mature human milk. Using 16S rRNA metagenomic sequencing, we focused on characterizing the milk microbiota in the Northern Greek population by identifying shared microbial communities across samples and comparing the relative abundance of prevalent genera. We analyzed ten human milk samples (from five mothers), with five collected three days postpartum (colostrum) and five collected thirty to forty days postpartum (mature milk) from corresponding mothers. To perform an interspecies comparison of human milk microbiota, we analyzed five goat and five bovine milk samples from a local dairy industry, collected fifty to seventy days after birth. Alpha diversity analysis indicated moderate diversity and stability in bovine milk, high richness in goat milk, and constrained diversity in breast milk. Beta diversity analysis revealed significant distinctions among mammalian species, emphasizing both presence/absence and abundance-based clustering. Despite noticeable differences, shared microbial components underscore fundamental aspects across all mammalian species, highlighting the presence of a core microbiota predominantly comprising the Proteobacteria, Firmicutes, and Actinobacteriota phyla. At the genus level, Acinetobacter, Gemella, and Sphingobium exhibit significant higher abundance in human milk compared to bovine and goat milk, while Pseudomonas and Atopostipes are more prevalent in animal milk. Our comparative analysis revealed differences and commonalities in the microbial communities of various mammalian milks and unraveled the existence of a common fundamental milk core microbiome. We thus revealed both species-specific and conserved microbial communities in human, bovine, and goat milk. The existence of a common core microbiome with conserved differences between colostrum and mature human milk underscores fundamental similarities in the microbiota of milk across mammalian species, which could offer valuable implications for optimizing the nutritional quality and safety of dairy products as well as supplements for infant health.

The impact of kit, environment, and sampling contamination on the observed microbiome of bovine milk

In low-microbial biomass samples such as bovine milk, contaminants can outnumber endogenous bacteria. Because of this, milk microbiome research suffers from a critical knowledge gap, namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelia and stripped and cisternal milk and used numerous negative controls, including air and sampling controls and extraction and library preparation blanks, to identify the potential sources of contamination. Two algorithms were used to mathematically remove contaminants and track the potential movement of microbes among samples. Results suggest that the majority (i.e., >75%) of sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. Contaminants in milk samples were primarily sourced from DNA extraction kits and the internal and external skin of the teat, while teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse, and compositionally distinct bacterial profile compared with epithelial samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in milk sample sequences, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during sample collection and processing workflows.IMPORTANCEObtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.

Comparative study of the bacterial community of organic and conventional cow's milk

Agricultural practises such as conventional and organic farming can potentially affect the microbial communities in milk. In the present study, the bacterial diversity of milk was investigated using high-throughput sequencing on ten organic and ten conventional farms in the Azores, a region where milk production is largely based on year-round grazing systems. The microbiota of milk from both production systems was dominated by Bacillota, Pseudomonadota, Actinomycetota and Bacteroidota. The organic milk showed greater heterogeneity between farms, as reflected in the dispersion of diversity indices and the large variation in the relative abundances of the dominant genera. In contrast, conventionally produced milk showed a high degree of similarity within each season. In the conventional production system, the season also had a strong influence on the bacterial community, but this effect was not observed in the organic milk. The LEfSe analysis identified the genus Iamia as significantly (p < 0.05) more abundant in organic milk, but depending on the season, several other genera were identified that distinguished organic milk from conventionally produced milk. Of these, Bacillus, Iamia and Nocardioides were associated with the soil microbiota in organic farming.

Bovine milk microbiota: Key players, origins, and potential contributions to early-life gut development

BACKGROUND

Bovine milk is a significant substitute for human breast milk and holds great importance in infant nutrition and health. Apart from essential nutrients, bovine milk also contains bioactive compounds, including a microbiota derived from milk itself rather than external sources of contamination.

AIM OF REVIEW

Recognizing the profound impact of bovine milk microorganisms on future generations, our review focuses on exploring their composition, origins, functions, and applications.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Some of the primary microorganisms found in bovine milk are also present in human milk. These microorganisms are likely transferred to the mammary gland through two pathways: the entero-mammary pathway and the rumen-mammary pathway. We also elucidated potential mechanisms by which milk microbiota contribute to infant intestinal development. The mechanisms include the enhancing of the intestinal microecological niche, promoting the maturation of immune system, strengthening the intestinal epithelial barrier function, and interacting with milk components (e.g., oligosaccharides) via cross-feeding effect. However, given the limited understanding of bovine milk microbiota, further studies are necessary to validate hypotheses regarding their origins and to explore their functions and potential applications in early intestinal development.

Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables

Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk microbiota from several locations across Ireland over 12 months, and by investigating microbiota associations with climatic variables and chemical composition. Shotgun metagenomic sequencing was used to investigate the microbiota of raw milk collected from nine locations (n = 241). Concurrent chemical analysis of the protein, fat, lactose, total solids, nonprotein nitrogen contents, and titratable acidity (TA) of the same raw milk were performed. Although the raw milk microbiota was highly diverse, a core microbiota was found, with Pseudomonas_E, Lactococcus, Acinetobacter, and Leuconostoc present in all samples. Microbiota diversity significantly differed by season and location, with differences in seasonality and geography corresponding to 11.8% and 10.5% of the variation in the microbiota. Functional and antibiotic resistance profiles also varied across season and location. The analysis of other metadata revealed additional interactions, such as an association between mean daily air and grass temperatures with the abundance of spoilage taxa like Pseudomonas species. Correlations were identified between pathogenic, mastitis-related species, fat content, and the number of sun hours, suggesting a seasonal effect. Ultimately, this study expands our understanding of the interconnected nature of the microbiota, environment/climate variables, and chemical composition of raw milk and provides evidence of a season- and location-specific microbiota.

IMPORTANCE

The microbiota of raw milk is influenced by many factors that encourage or prevent the introduction and growth of both beneficial and undesirable microorganisms. The seasonal and geographical impacts on the microbial communities of raw milk have been previously seen, but the relationships with environmental factors and the chemical composition has yet to be investigated. In this year-long study, we found that while raw milk is highly diverse, a core microbiota was detected for Irish raw milk, with strong evidence of seasonal and geographical influence. We also found associations between groups of microorganisms, environmental factors, and milk composition, which expand current knowledge on the relationships between microbial and chemical composition and the climate. These results provide evidence for the development of a tool to allow for the prediction of raw milk quality and safety.

Exploring the link between microbial community structure and flavour compounds of traditional fermented yak milk in Gannan region

Traditional fermented yak milk has immense cultural and nutritional significance for Tibetan herders. In this study, we investigated the microbial community structure and flavour compounds in traditional fermented yak milk from three distinct regions of Gannan to explore the relationship between microbial composition and flavour compounds. The findings revealed significant variations in flavour compounds and the bacterial microbiota among the samples from the three regions. The dominant species identified in fermented yak milk were Streptococcus salivarius subsp. Thermophilus, Lactobacillus helveticus, and Kluyveromyces marxianus. Bidirectional orthogonal partial least-squares (O2PLS) analysis highlighted five bacterial genera and three fungal genera as contributors to the production of flavour-related compounds. Furthermore, regression analysis revealed that the Lactobacillus and Streptococcus genera were associated with the production of 2,3-pentanedione as well as eight predicted KEGG pathways. These findings provide valuable insights into the intricate relationship between flavour compounds and microbiota in traditional fermented yak milk.

Contribution of microorganisms from pit mud to volatile flavor compound synthesis in fermented grains for nongxiangxing baijiu brewing

BACKGROUND

Nongxiangxing baijiu (NB) is known for its distinct flavor profile, which is attributed to key aroma compounds. The exposed fermentation technique, utilizing daqu and solid-state fermentation in pit muds, plays a crucial role in flavor development. Though previous studies have investigated the impact of microorganisms from pit ?ud and fermented grains on flavor compound production, a comprehensive understanding of microbial functions in the entire pit fermentation system is lacking. Herein, we aimed to explore the role of pit-mud-derived microorganisms in shaping the microbial community and flavor compound synthesis in NB.

RESULTS

There are 76 volatile flavor compounds that have been identified in fermented grains during NB fermentation. The main flavor compounds in NB clustered within the same network module, and 27.27% of microorganisms in the core modules of the fermented grain co-occurrence network originated from pit mud. The relationship between pit mud microorganisms and flavor compounds revealed a significant positive correlation (92%). Notably, Prevotella and Sarocladium were identified as the main contributors to this effect on flavor.

CONCLUSION

Microorganisms originating from pit mud influenced the composition and activity of microorganisms in fermented grains and facilitated the production of flavor compounds in NB. © 2023 Society of Chemical Industry.

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.

Associations between the Bacterial Composition of Farm Bulk Milk and the Microbiota in the Resulting Swedish Long-Ripened Cheese

The maturation of a traditional Swedish long-ripened cheese has shown increasing variation in recent years and the ripening time is now generally longer than in the past. While the cheese is reliant on non-starter lactic acid bacteria for the development of its characteristic flavour, we hypothesised that the observed changes could be due to variations in the microbiota composition and number of bacteria in the raw milk used for production of the cheese. To evaluate associations between microbiota in the raw milk and the resulting cheese, three clusters of commercial farms were created to increase variation in the microbiota of dairy silo milk used for cheese production. Cheese production was performed in three periods over one year. Within each period, milk from the three farm clusters was collected separately and transported to the cheese production facility. Following pasteurisation, the milk was processed into the granular-eyed cheese and matured at a dedicated cheese-ripening facility. For each cheese batch, farm bulk and dairy silo milk samples, a starter culture, early process samples and cheese samples from different stages of maturation (7-20 months) were collected and their microbiota characterised using 16S rRNA amplicon sequencing. The microbiota in the farm bulk milk differed significantly between periods and clusters. Differences in microbiota in dairy silo milk were observed between periods, but not between farm clusters, while the cheese microbiota differed between periods and clusters. The top 13 amplicon sequence variants were dominant in early process samples and the resulting cheese, making up at least 93.3% of the relative abundance (RA). Lactococcus was the dominant genus in the early process samples and, together with Leuconostoc, also dominated in the cheese samples. Contradicting expectations, the RA of the aroma-producing genus Lactobacillus was low in cheese during ripening and there was an unexpected dominance of starter lactic acid bacteria even at the later stages of cheese ripening. To identify factors behind the recent variations in ripening time of this cheese, future studies should address the effects of process variables and the dairy environment.

Teat-apex colonizer Bacillus from healthy cows antagonizes mastitis-causing Staphylococcus aureus biofilms

Staphylococcus aureus is the most frequent causal agent of bovine mastitis, which is largely responsible for milk production losses worldwide. The pathogen's ability to form stable biofilms facilitates intramammary colonization and may explain disease persistence. This virulence factor is also highly influential in the development of chronic intramammary infections refractory to antimicrobial therapy, which is why novel therapies that can tackle multiple targets are necessary. Since udder microbiota have important implications in mastitis pathogenesis, they offer opportunities to develop alternative prophylactic and therapeutic strategies. Here, we observed that a Bacillus strain from the teat apex of lactating cows was associated to reduce colonization by S. aureus. The strain, identified as Bacillus sp. H21, was able to antagonize in-formation or mature S. aureus biofilms associated to intramammary infections without affecting cell viability. When exploring the metabolite responsible for this activity, we found that a widespread class of Bacillus exopolysaccharide, levan, eliminated the pathogenic biofilm under evaluated conditions. Moreover, levan had no cytotoxic effects on bovine cellular lines at the biologically active concentration range, which demonstrates its potential for pathogen control. Our results indicate that commensal Bacillus may counteract S. aureus-induced mastitis, and could therefore be used in novel biotechnological strategies to prevent and/or treat this disease.

The impact of environmental conditions and milk type on microbial communities of wooden vats and cheeses produced therein

Wooden vats are used in the production of some traditional cheeses as the biofilms on wooden vat surfaces are known to transfer large quantities of microbes to cheese. Variability in microbial communities on wooden vats could lead to inconsistent cheese production. In the present study, the influences of environmental conditions and milk type (raw or heat-treated) on the microbial composition of vat biofilms and cheeses made in the vats were studied using amplicon sequencing of bacterial 16S rRNA and fungal internal transcribed spacer genes. Results showed that the microbial composition of biofilms was influenced by environmental conditions but not the milk type used in cheese production. The microbial composition of cheeses can be further affected by bacterial contributions from milk and the selective forces of environmental conditions. Results of this study suggest that controlling environmental conditions could maintain a more consistent microbial composition of biofilms on wooden vats and resulting cheeses. The use of wooden vats coupled with heat-treated milk at one or more stages of cheese production might be a viable approach to produce cheese with high microbial diversities and reduce risks of undesirable microbes related to food safety and quality.

Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet

Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.

Microbiota and Resistome Analysis of Colostrum and Milk from Dairy Cows Treated with and without Dry Cow Therapies

This study investigated the longitudinal impact of methods for the drying off of cows with and without dry cow therapy (DCT) on the microbiota and resistome profile in colostrum and milk samples from cows. Three groups of healthy dairy cows (n = 24) with different antibiotic treatments during DCT were studied. Colostrum and milk samples from Month 0 (M0), 2 (M2), 4 (M4) and 6 (M6) were analysed using whole-genome shotgun-sequencing. The microbial diversity from antibiotic-treated groups was different and higher than that of the non-antibiotic group. This difference was more evident in milk compared to colostrum, with increasing diversity seen only in antibiotic-treated groups. The microbiome of antibiotic-treated groups clustered separately from the non-antibiotic group at M2-, M4- and M6 milk samples, showing the effect of antibiotic treatment on between-group (beta) diversity. The non-antibiotic group did not show a high relative abundance of mastitis-causing pathogens during early lactation and was more associated with genera such as Psychrobacter, Serratia, Gordonibacter and Brevibacterium. A high relative abundance of antibiotic resistance genes (ARGs) was observed in the milk of antibiotic-treated groups with the Cephaguard group showing a significantly high abundance of genes conferring resistance to cephalosporin, aminoglycoside and penam classes. The data support the use of non-antibiotic alternatives for drying off in cows.

Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd

BACKGROUND

Host-associated microbes are major determinants of the host phenotypes. In the present study, we used dairy cows with different scores of susceptibility to mastitis with the aim to explore the relationships between microbiota composition and different factors in various body sites throughout lactation as well as the intra- and inter-animal microbial sharing.

RESULTS

Microbiotas from the mouth, nose, vagina and milk of 45 lactating dairy cows were characterized by metataxonomics at four time points during the first lactation, from 1-week pre-partum to 7 months post-partum. Each site harbored a specific community that changed with time, likely reflecting physiological changes in the transition period and changes in diet and housing. Importantly, we found a significant number of microbes shared among different anatomical sites within each animal. This was between nearby anatomic sites, with up to 32% of the total number of Amplicon Sequence Variants (ASVs) of the oral microbiota shared with the nasal microbiota but also between distant ones (e.g. milk with nasal and vaginal microbiotas). In contrast, the share of microbes between animals was limited (< 7% of ASVs shared by more than 50% of the herd for a given site and time point). The latter widely shared ASVs were mainly found in the oral and nasal microbiotas. These results thus indicate that despite a common environment and diet, each animal hosted a specific set of bacteria, supporting a tight interplay between each animal and its microbiota. The score of susceptibility to mastitis was slightly but significantly related to the microbiota associated to milk suggesting a link between host genetics and microbiota.

CONCLUSIONS

This work highlights an important sharing of microbes between relevant microbiotas involved in health and production at the animal level, whereas the presence of common microbes was limited between animals of the herd. This suggests a host regulation of body-associated microbiotas that seems to be differently expressed depending on the body site, as suggested by changes in the milk microbiota that were associated to genotypes of susceptibility to mastitis.

Absence of changes in the milk microbiota during Escherichia coli endotoxin induced experimental bovine mastitis

Changes in the milk microbiota during the course of mastitis are due to the nature of a sporadic occurring disease difficult to study. In this study we experimentally induced mastitis by infusion of Escherichia coli endotoxins in one udder quarter each of nine healthy lactating dairy cows and assessed the bacteriological dynamics and the milk microbiota at four time points before and eight time points after infusion. As control, saline was infused in one udder quarter each of additionally nine healthy cows that followed the same sampling protocol. The milk microbiota was assessed by sequencing of the 16 S rRNA gene and a range of positive and negative controls were included for methodological evaluation. Two different data filtration models were used to identify and cure data from contaminating taxa. Endotoxin infused quarters responded with transient clinical signs of inflammation and increased SCC while no response was observed in the control cows. In the milk microbiota data no response to inflammation was identified. The data analysis of the milk microbiota was largely hampered by laboratory and reagent contamination. Application of the filtration models caused a marked reduction in data but did not reveal any associations with the inflammatory reaction. Our results indicate that the microbiota in milk from healthy cows is unaffected by inflammation.

Seasonal Variation in Raw Milk VOC Profile within Intensive Feeding Systems

The study aimed to assess the seasonal variation in raw milk volatile organic compounds (VOCs) from three indoor feeding systems based on maize silage (n = 31), silages/hay (n = 19) or hay (n = 16). After headspace solid-phase microextraction (HS-SPME), VOC profiles were determined by gas chromatography (GC). Chemical and VOC (log₁₀ transformations of the peak areas) data were submitted to a two-way ANOVA to assess the feeding system (FS) and season (S) effects; an interactive principal component analysis (iPCA) was also performed. The interaction FS × S was never significant. The FS showed the highest (p < 0.05) protein and casein content for hay-milk samples, while it did not affect any VOCs. Winter milk had higher (p < 0.05) proportions of protein, casein, fat and some carboxylic acids, while summer milk was higher (p < 0.05) in urea and 2-pentanol and methyl aldehydes. The iPCA confirmed a seasonal spatial separation. Carboxylic acids might generate from incomplete esterification in the mammary gland and/or milk lipolytic activity, while aldehydes seemed to be correlated with endogenous lipid or amino acid oxidation and/or feed transfer. The outcomes suggested that VOCs could be an operative support to trace raw milk for further mild processing.

Dietary Live Yeast Supplementation Influence on Cow’s Milk, Teat and Bedding Microbiota in a Grass-Diet Dairy System

The supplementation of animal feed with microbial additives remains questioning for the traditional or quality label raw milk cheeses with regard to microbial transfer to milk. We evaluated the effect of dietary administration of live yeast on performance and microbiota of raw milk, teat skin, and bedding material of dairy cows. Two balanced groups of cows (21 primiparous 114 ± 24 DIM, 18 multiparous 115 ± 33 DIM) received either a concentrate supplemented with Saccharomyces cerevisiae CNCM I-1077 (1 × 1010 CFU/d) during four months (LY group) or no live yeast (C group). The microbiota in individual milk samples, teat skins, and bedding material were analysed using culture dependent techniques and high-throughput amplicon sequencing. The live yeast supplementation showed a numerical increase on body weight over the experiment and there was a tendency for higher milk yield for LY group. A sequence with 100% identity to that of the live yeast was sporadically found in fungal amplicon datasets of teat skin and bedding material but never detected in milk samples. The bedding material and teat skin from LY group presented a higher abundance of Pichia kudriavzevii reaching 53% (p < 0.05) and 10% (p < 0.05) respectively. A significant proportion of bacterial and fungal ASVs shared between the teat skin and the milk of the corresponding individual was highlighted.

Maternal rumen and milk microbiota shape the establishment of early-life rumen microbiota in grazing yak calves

Early-life gut microbial colonization and development exert a profound impact on the health and metabolism of the host throughout the life span. The transmission of microbes from the mother to the offspring affects the succession and establishment of the early-life rumen microbiome in newborns, but the contributions of different maternal sites to the rumen microbial establishment remain unclear. In the present study, samples from different dam sites (namely, oral, rumen fluid, milk, and teat skin) and rumen fluid of yak calves were collected at 6 time points between d 7 and 180 postpartum to determine the contributions of the different maternal sites to the establishment of the bacterial and archaeal communities in the rumen during early life. Our analysis demonstrated that the dam's microbial communities clustered according to the sites, and the calves' rumen microbiota resembled that of the dam consistently regardless of fluctuations at d 7 and 14. The dam's rumen microbiota was the major source of the calves' rumen bacteria (7.9%) and archaea (49.7%) compared with the other sites, whereas the potential sources of the calf rumen microbiota from other sites varied according to the age. The contribution of dam's rumen bacteria increased with age from 0.36% at d 7 to 14.8% at d 180, whereas the contribution of the milk microbiota showed the opposite trend, with its contribution reduced from 2.7% at d 7 to 0.2% at d 180. Maternal oral archaea were the main sources of the calves' rumen archaea at d 14 (50.4%), but maternal rumen archaea became the main source gradually and reached 66.2% at d 180. These findings demonstrated the potential microbial transfer from the dam to the offspring that could influence the rumen microbiota colonization and establishment in yak calves raised under grazing regimens, providing the basis for future microbiota manipulation strategies during their early life.

Characterization of rumen, fecal, and milk microbiota in lactating dairy cows

Targeting the gastrointestinal microbiome for improvement of feed efficiency and reduction of production costs is a potential promising strategy. However little progress has been made in manipulation of the gut microbiomes in dairy cattle to improve milk yield and milk quality. Even less understood is the milk microbiome. Understanding the milk microbiome may provide insight into how the microbiota correlate with milk yield and milk quality. The objective of this study was to characterize similarities between rumen, fecal, and milk microbiota simultaneously, and to investigate associations between microbiota, milk somatic cell count (SCC), and milk yield. A total of 51 mid-lactation, multiparous Holstein dairy cattle were chosen for sampling of ruminal, fecal, and milk contents that were processed for microbial DNA extraction and sequencing. Cows were categorized based on low, medium, and high SCC; as well as low, medium, and high milk yield. Beta diversity indicated that ruminal, fecal, and milk populations were distinct (p &lt; 0.001). Additionally, the Shannon index demonstrated that ruminal microbial populations were more diverse (p &lt; 0.05) than were fecal and milk populations, and milk microbiota was the least diverse of all sample types (p &lt; 0.001). While diversity indices were not linked (p &gt; 0.1) with milk yield, milk microbial populations from cows with low SCC demonstrated a more evenly distributed microbiome in comparison to cows with high SCC values (p = 0.053). These data demonstrate the complexity of host microbiomes both in the gut and mammary gland. Further, we conclude that there is a significant relationship between mammary health (i.e., SCC) and the milk microbiome. Whether this microbiome could be utilized in efforts to protect the mammary gland remains unclear, but should be explored in future studies.

Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods

Although bacterial detection by 16S rRNA gene amplicon DNA sequencing is a widely-applied technique, standardized methods for sample preparation and DNA extraction are needed to ensure accuracy, reproducibility, and scalability for automation. To develop these methods for bovine bulk milk, we assembled and tested a bacterial cell mock community (BCMC) containing bacterial species commonly found in milk. The following protocol variations were examined:: BCMC enumeration (colony enumeration or microscopy), sample volume (200 μl to 30 ml), sample storage condition (frozen in PBS or 25% glycerol or exposure to freeze-thaw cycles), cell lysis method (bead-beating, vortex, enzymatic), and DNA extraction procedure (MagMAX Total, MagMAX CORE, and MagMAX Ultra 2.0, with and without either Proteinase K or RNase A). Cell enumeration by microscopy was more accurate for quantification of the BCMC contents. We found that least 10 mL (≥ 10⁴ cells in high quality milk) is needed for reproducible bacterial detection by 16S rRNA gene amplicon DNA sequencing, whereas variations in storage conditions caused minor differences in the BCMC. For DNA extraction and purification, a mild lysis step (bead-beating for 10 s at 4 m/s or vortexing at 1800 rpm for 10 s) paired with the MagMAX Total kit and Proteinase K digestion provided the most accurate representation of the BCMC. Cell lysis procedures conferred the greatest changes to milk microbiota composition and these effects were confirmed to provide similar results for commercial milk samples. Overall, our systematic approach with the BCMC is broadly applicable to other milk, food, and environmental samples therefore recommended for improving accuracy of culture-independent, DNA sequence-based analyses of microbial composition in different habitats.

A 16S rRNA Sequencing Study Describing the Environmental Microbiota of Two Powdered Infant Formula Built Facilities

Microbial safety is critically important for powdered infant formula (PIF) fed to neonates, with under-developed immune systems. The quality and safety of food products are dictated by those microorganisms found in both raw materials and the built production environment. In this study, a 2-year monitoring program of a production environment was carried out in two PIF factories located in the Republic of Ireland, and the environmental microbiome in different care areas of these sites was studied by using a 16S ribosomal RNA (rRNA)-based sequencing technique. Results highlighted a core microbiome associated with the PIF factory environment containing 24 bacterial genera representing five phyla, with Acinetobacter and Pseudomonas as the predominant genera. In different care areas of the PIF factory, as hygiene standards increased, deciphered changes in microbial community compositions became smaller over time and approached stability, and bacteria dominating the care area became less influenced by the external environment and more by human interactions and raw materials. These observations indicated that the microbial composition can be altered in response to environmental interventions. Genera Cronobacter and Salmonella were observed in trace amounts in the PIF factory environment, and bacterial genera known to be persistent in a stressed environment, such as Acinetobacter, Bacillus, Streptococcus, and Clostridium, were likely to have higher abundances in dry environment-based care areas. To our knowledge, this is the first study to characterize the PIF production environment microbiome using 16S rRNA-based sequencing. This study described the composition and changing trends of the environmental microbial communities in different care areas of the PIF manufacturing facility, and it provided valuable information to support the safer production of PIF in the future.

Comparison of Dynamics of Udder Skin Microbiota From Grazing Yak and Cattle During the Perinatal Period on the Qinghai–Tibetan Plateau

The perinatal period has an important impact on the health of ruminants, and the imbalance of udder skin microbiota might be an important inducement of bovine mastitis. However, it is not clear how the perinatal period affects the microbial structure and stability of the udder skin of yak and cattle. Here, we used 16S rRNA gene high-throughput sequencing to analyze the udder skin microbiota of yak and cattle during the perinatal period. We found that the diversity and richness of microbiota of bovine udder skin during 1–2 weeks postpartum were significantly lower than those in the 1–2 weeks prenatal and 1-month postpartum period (Wilcoxon, p < 0.05). Besides, we found sharing of 2,533 OTUs in the udder skin microbiota of yak and cattle during the perinatal period, among which the core microbiota at the genera level was mainly composed of Staphylococcus, Moraxella, and Acinetobacter. However, the genus Acinetobacter was significantly abundant in the udder skin of cattle during 1–2 weeks postpartum. The NMDS and LEfSe results showed that the perinatal period had more effects on the composition and stability of microbial community in the udder skin of cattle compared to yak, particularly during 1–2 weeks postpartum. In addition, the average content of total whey proteins and immunoglobulin G of whey protein were significantly higher in the yak colostrum when compared to those found in the cattle (p < 0.05). In conclusion, the structure of udder skin microbiota of yak during the perinatal period is more stable than that of cattle in the same habitat, and 1–2 weeks postpartum may be a potential window period to prevent cattle mastitis.

Bacterial Composition and Interactions in Raw Milk and Teat Skin of Dairy Cows

The microbiota in raw milk plays an important role in the health of dairy cows and the safety of dairy products, which might be influenced by that in teat skin. However, the microbiota composition in raw milk and teat skin, as well as the bacterial interaction between the two adjacent spatial locations, remains elusive. Here, we investigated the composition, diversity, and co-occurrence network of the bacterial communities in raw milk and on teat skin, as well as the shift of bacterial communities during the teat bath using 469 samples from 156 individual cows. We observed that raw milk and teat skin harbored significantly different bacterial communities according to an assessment of the genera numbers (p < 0.05) and PCoA analysis (ANOSIM p < 0.05). The microbiota in raw milk was dominated by Proteobacteria (58.5% in relative abundance) at the phylum level and by Pseudomonas (51.2%) at the genus level, while that in teat skin was dominated by Firmicutes (46.9%) at the phylum level and by Pseudomonas (11.0%) at the genus level. We observed a massive difference between the bacterial subnetworks in raw milk and teat, and the bacterial abundance in these two adjacent spatial locations was positively correlated (p < 0.05). Using Bayesian algorithms, we identified that 92.1% of bacteria in raw milk were transferred from teat skin, while 63.6% of bacteria on teat skin were transferred from raw milk. Moreover, microbiota composition in teat skin could be affected by the teat bath with iodine disinfectant, which tended to be more similar to that in raw milk after the teat bath (p < 0.05), while the abundance of the dominant genus Pseudomonas significantly increased (p < 0.05). These findings expand our knowledge on the microbiota composition in teat skin and raw milk, as well as the interaction between these two adjacent spatial locations.

Influence of Post-Milking Treatment on Microbial Diversity on the Cow Teat Skin and in Milk

In dairy cattle, teat disinfection at the end of milking is commonly applied to limit colonization of the milk by pathogenic microorganisms via the teat canal. The post-milking products used can irritate the teat skin and unbalance its microbial population. Our study aimed to assess the impact of different milking products on the balance of the microbial communities on the teat skin of cows and in their milk. For 12 weeks at the end of each milking operation, three groups of seven Holstein dairy cows on pasture received either a chlorhexidine gluconate-based product (G) or a hydrocolloidal water-in-oil emulsion (A), or no post-milking product (C). The composition of the bacterial and fungal communities on the teat skin and in the milk were characterized using a culture-dependent method and by high-throughput sequencing of marker genes to obtain amplicon sequence variants (ASVs). The individual microbiota on the cows’ teat skin was compared for the first time to that of a cow pool. In contrast to the milk, the post-milking treatment influenced the microbiota of the teat skin, which revealed a high microbial diversity. The water-in-oil emulsion appeared to slightly favour lactic acid bacteria and yeasts and to limit the development of undesirable bacteria such as Pseudomonas and Staphylococcus.

Longitudinal dynamics of the bovine udder microbiota

BACKGROUND

In recent years, the number of studies concerning microbiota of the intramammary environment has increased rapidly due to the development of high-throughput sequencing technologies that allow mapping of microbiota without culturing. This has revealed that an environment previously thought to be sterile in fact harbours a microbial community. Since this discovery, many studies have investigated the microbiota of different parts of the udder in various conditions. However, few studies have followed the changes that occur in the udder microbiota over time. In this study, the temporal dynamics of the udder microbiota of 10 cows, five with a low somatic cell count (SCC, SCC < 100,000 cells/mL) and five with a high SCC (SCC > 100,000 cells/mL), were followed over 5 months to gather insights into this knowledge gap.

RESULTS

Analysis of the temporal changes in the microbial composition of milk from udders with a low SCC revealed a dynamic and diverse microbiota. When an imbalance due to one dominating genus was recorded, the dominant genus quickly vanished, and the high diversity was restored. The genera dominating in the samples with a high SCC remained the dominant genera throughout the whole sampling period. These cows generally displayed a heightened SCC or an intramammary infection in at least one quarter though-out the sampling period.

CONCLUSION

Our results show that the bovine udder has a diverse microbiota, and that the composition and diversity of this community affects udder health with regards to SCC. Understanding what influences the composition and stability of this community has important implications for the understanding, control, and treatment of mastitis.

The Influence of Bacteria Causing Subclinical Mastitis on the Structure of the Cow’s Milk Microbiome

Mastitis is the most expensive disease of dairy cattle across the world and is the main reason for the use of antibiotics in animal husbandry. The aim of this study was to analyze the microbiome of raw milk obtained from a semi-subsistence farm located in the Kuyavian–Pomeranian Voivodeship in Poland. Milk from healthy cows and from cows with subclinical mastitis was analyzed. The following pathogenic bacteria were found in milk from individuals with subclinical mastitis: Escherichia coli or Streptococcus agalactiae. The composition of drinking milk was assessed on the basis of 16S rRNA gene sequencing using the Ion Torrent platform. Based on the conducted research, significant changes in the composition of the milk microbiome were found depending on the physiological state of the cows. The microbiome of milk from healthy cows differed significantly from the milk from cows with subclinical mastitis. Two phyla dominated in the milk from healthy cows: Firmicutes and Proteobacteria, in equal amounts. On the contrary, in the milk from cows with diagnosed subclinical mastitis, one of the types dominated: either Firmicutes or Proteobacteria, and was largely predominant. Moreover, the milk microflora from the ill animals were characterized by lower values of the determined biodiversity indicators than the milk from healthy cows. The presence of pathogenic bacteria in the milk resulted in a significant reduction in the share of lactic acid bacteria in the structure of the population of microorganisms, which are of great importance in the production technology of regional products.

Effect of Peanut Shell and Rice Husk Bedding for Dairy Cows: An Analysis of Material Properties and Colostrum Microbiota

Simple Summary

The provision of appropriate bedding is important for the welfare of dairy cows. Before bedding can be selected, it is critical to understand the properties of the bedding, including its impact on milk microbiota. The objective of this article was to evaluate the influence of three materials for use as bedding on physicochemical properties, bacterial counts and colostrum microbiota of cows. Our results demonstrate that peanut shells appear to be a suitable bedding material for cows. These experiments provide empirical support for the use of peanut shells and rice husks as bedding material for dairy cows and illustrates the effects of bedding types on the colostrum microbiota of dairy cows.

Abstract

The aim of this study was to evaluate peanut shells and rice husks as bedding for dairy cows. We analyzed material properties including dry matter, water holding capacity, pH level and bacterial counts. Bedding treatments were compared with a one-way ANOVA using twelve cows split into three groups. Colostrum microbiota was analyzed by sequencing of the V3–V4 region of the 16S rRNA gene. Dry matter content was higher in rice husks compared with peanut shells. No treatment effects were found for water holding capacity and pH level. Streptococcus agalactia counts in peanut shell bedding were lower than in rice husk bedding, and Pseudomonas aeruginosa counts were not different between beddings. A significant enrichment for Enhydrobacter and Pantoea were detected in the colostrum of cows that used peanut shells compared with other beddings. Colostrum of cows housed on a peanut–rice combination had a greater relative abundance of Pseudomonas and Corynebacterium than those housed on peanut shells or rice husks. Higher numbers of Bacteroides, Akkermansia, Alistipes, Ruminococcaceae_UCG-014, Coriobacteriaceae_UCG-002 and Intestinimona were found in the colostrum of cows housed on rice husk bedding over other bedding types. These results suggest that bedding types were associated with the growth and diversity of colostrum bacterial loads. In addition, dry matter in peanut shells was lower than found in rice husks, but there was also a lower risk of mastitis for peanut shell bedding than other beddings.

Seasonality and Geography Have a Greater Influence than the Use of Chlorine-Based Cleaning Agents on the Microbiota of Bulk Tank Raw Milk

Cleaning of the production environment is vital to ensure the safety and quality of dairy products. Although cleaning with chlorine-based agents is widely adopted, it has been associated with detrimental effects on milk quality and safety, which has garnered increasing interest in chlorine-free cleaning. However, the influence of these methods on the milk microbiota is not well documented. This study investigated the factors that influence the raw milk microbiota, with a focus on the differences when chlorine-based and chlorine-free cleaning of milking equipment are used. Bulk tank raw milk was sampled during three sampling months (April, August, and November), from farms across Ireland selected to capture the use of different cleaning methods, i.e., exclusively chlorine-based (n = 51) and chlorine-free cleaning (n = 92) and farms that used chlorine-free agents for the bulk tank and chlorine-based cleaning agents for the rest of the equipment (n = 28). Shotgun metagenomic analysis revealed the significant influence of seasonal and geographic factors on the bulk tank milk microbiota, indicated by differences in diversity, taxonomic composition, and functional characteristics. Taxonomic and functional profiles of samples collected in November clustered separately from those of samples collected in other months. In contrast, cleaning methods only accounted for 1% of the variation in the bulk tank milk bacterial community, and samples collected from farms using chlorine-based versus chlorine-free cleaning did not differ significantly, suggesting that the chlorine-free approaches used did not negatively impact microbiological quality. This study shows the value of shotgun metagenomics in advancing our knowledge of the raw milk microbiota. IMPORTANCE The microbiota of raw milk is affected by many factors that can control or promote the introduction of undesirable microorganisms. Chlorine-based cleaning agents have been commonly used due to their effectiveness in controlling undesirable microorganisms, but they have been associated with the formation of chlorine residues that are detrimental to product quality and may impact consumer health. Chlorine-free alternatives have been recommended in some countries, but the influence of cleaning agents on the milk microbiota is unknown. Here, we investigated the influence of cleaning methods and other factors on bulk tank raw milk. Results showed that season and location had a greater influence on the milk microbiota than the cleaning agents used. Indeed, the similar microbiota compositions of raw milk from farms that used chlorine-based and those that used chlorine-free cleaning methods supports the further use of chlorine-free cleaning agents in dairy production.

Composition, Succession, and Source Tracking of Microbial Communities throughout the Traditional Production of a Farmstead Cheese

Prior to the advent of milk pasteurization and the use of defined-strain starter cultures, the production and ripening of cheese relied on the introduction and growth of adventitious microbes from the environment. This study characterized microbial community structures throughout a traditional farmstead cheese production continuum and evaluated the role of the environment in microbial transfer. In total, 118 samples (e.g., raw milk, cheese, and environmental surfaces) were collected from milk harvesting through cheese ripening. Microbial communities were characterized based on amplicon sequencing of bacterial 16S rRNA and fungal internal transcribed spacer genes using the Illumina MiSeq platform. Results indicated that the environment in each processing room harbored unique microbial ecosystems and consistently contributed microbes to milk, curd, and cheese. The diverse microbial composition of milk was initially attributed to milker hands and cow teats and then changed substantially following overnight ripening in a wooden vat to one dominated by lactic acid bacteria, including Lactococcus lactis, Lactobacillus, and Leuconostoc, as well as fungi such as Exophiala, Kluyveromyces, and Candida. Additional microbial contributions were attributed to processing tools, but the composition of the cheese paste remained relatively stable over 60 days of ripening. In contrast, rind communities that were largely influenced by direct contact with bamboo aging mats showed a distinct succession pattern compared to the interior sections. Overall, these findings highlight the critical role of traditional tools and practices in shaping the microbial composition of cheese and broaden our understanding of processing environments as important sources of microbes in food. IMPORTANCE Throughout the 20th century, especially in the United States, sanitation practices, pasteurization of milk, and the use of commercial defined-strain starter cultures have enhanced the safety and consistency of cheese. However, these practices can reduce cheese microbial diversity. The rapid growth of the artisanal cheese industry in the United States has renewed interest in recapturing the diversity of dairy products and the microbes involved in their production. Here, we demonstrate the essential role of the environment, including the use of wooden tools and cheesemaking equipment, as sources of dominant microbes that shape the fermentation and ripening processes of a traditional farmstead cheese produced without the addition of starter cultures or direct inoculation of any other bacteria or fungi. These data enrich our understanding of the microbial interactions between products and the environment and identify taxa that contribute to the microbial diversity of cheese and cheese production.

Analysis of Cow-Calf Microbiome Transfer Routes and Microbiome Diversity in the Newborn Holstein Dairy Calf Hindgut

Hindgut microorganisms in newborn calves play an important role in the development of immunity and metabolism, and optimization of performance. However, knowledge of the extent to which microbiome colonization of the calf intestine is dependent on maternal characteristics is limited. In this study, placenta, umbilical cord, amniotic fluid, colostrum, cow feces, and calf meconium samples were collected from 6 Holstein cow-calf pairs. Microbial composition was analyzed by 16S rRNA gene high-throughput sequencing, and maternal transfer characteristics assessed using SourceTracker based on Gibbs sampling to fit the joint distribution using the mean proportions of each sample with meconium as the "sink" and other sample types as different "sources." Alpha and beta diversity analyses revealed sample type-specific microbiome features: microbial composition of the placenta, umbilical cord, amniotic fluid, colostrum, and calf feces were similar, but differed from cow feces (p < 0.05). Compared with profiles of meconium vs. placenta, meconium vs. umbilical cord, and meconium vs. colostrum, differences between the meconium and amniotic fluid were most obvious. SourceTracker analysis revealed that 23.8 ± 2.21% of the meconium OTUs matched those of umbilical cord samples, followed by the meconium-placenta pair (15.57 ± 2.2%), meconium-colostrum pair (14.4 ± 1.9%), and meconium-amniotic fluid pair (11.2 ± 1.7%). The matching ratio between meconium and cow feces was the smallest (10.5 ± 1%). Overall, our data indicated that the composition of the meconium microflora was similar compared with multiple maternal sites including umbilical cord, placenta, colostrum, and amniotic fluid. The umbilical cord microflora seemed to contribute the most to colonization of the fecal microflora of calves. Bacteria with digestive functions such as cellulose decomposition and rumen fermentation were mainly transmitted during the maternal transfer process.

Next-Generation Food Research: Use of Meta-Omic Approaches for Characterizing Microbial Communities Along the Food Chain

Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread of antimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Microbial transfers from permanent grassland ecosystems to milk in dairy farms in the Comté cheese area

The specificity of dairy Protected Designation of Origin (PDO) products is related to their “terroir” of production. This relationship needs better understanding for efficient and sustainable productions preserving the agroecological equilibrium of agroecosystems, especially grasslands. Specificity of PDO Comté cheese was related to the diversity of natural raw milk bacterial communities, but their sources need to be determined. It is hypothesized that raw milk indigenous microbial communities may originate from permanent grazed grasslands by the intermediate of dairy cows according to the sequence soil–phyllosphere–teat–milk. This hypothesis was evaluated on a 44 dairy farms network across PDO Comté cheese area by characterizing prokaryotic and fungal communities of these compartments by metabarcoding analysis (16S rRNA gene: V3–V4 region, 18S rRNA gene: V7–V8 region). Strong and significant links were highlighted between the four compartments through a network analysis (0.34 < r < 0.58), and were modulated by soil pH, plant diversity and elevation; but also by farming practices: organic fertilization levels, cattle intensity and cow-teat care. This causal relationship suggests that microbial diversity of agroecosystems is a key player in relating a PDO product to its “terroir”; this under the dependency of farming practices. Altogether, this makes the “terroir” even more local and needs to be considered for production sustainability.

Graduate Student Literature Review: Current understanding of the influence of on-farm factors on bovine raw milk and its suitability for cheesemaking

Relationships between dairy farm practices, the composition and properties of raw milk, and the quality of the resulting cheese are complex. In this review, we assess the effect of farm factors on the quality of bovine raw milk intended for cheesemaking. The literature reports several prominent farm-related factors that are closely associated with milk quality characteristics. We describe their effects on the composition and technological properties of raw milk and on the quality of the resulting cheese. Cow breed, composite genotype, and protein polymorphism all have noticeable effects on milk coagulation, cheese yield, and cheese composition. Feed and feeding strategy, dietary supplementation, housing and milking system, and seasonality of milk production also influence the composition and properties of raw milk, and the resulting cheese. The microbiota in raw milk is influenced by on-farm factors and by the production environment, and may influence the technological properties of the milk and the sensory profile of certain cheese types. Advances in research dealing with the technological properties of raw milk have undoubtedly improved understanding of how on-farm factors affect milk quality attributes, and have refuted the concept of one milk for all purposes. The specific conditions for milk production should be considered when the milk is intended for the production of cheese with unique characteristics. The scientific identification of these conditions would improve the current understanding of the complex associations between raw milk quality and farm and management factors. Future research that considers dairy landscapes within broader perspectives and develops multidimensional approaches to control the quality of raw milk intended for long-ripening cheese production is recommended.

Both sampling seasonality and geographic origin contribute significantly to variations in raw milk microbiota, but sampling seasonality is the more determining factor

Accurately profiling and characterizing factors shaping raw milk microbiota would provide practical information for detecting microbial contamination and unusual changes in milk. The current work was an observational study aiming to profile the microbiota of raw milk collected across wide geographic regions in China in different seasons and to investigate the contribution of geographical, seasonal, and environmental factors in shaping the raw milk microbiota. A total of 355 raw cow milk samples from healthy Holsteins and 41 environmental samples (farm soil and surface of milking room floor) were collected from 5 dairy farms in 5 Chinese provinces (namely, Daqing in Heilongjiang province, Jiaozuo in Henan province, Qingyuan in Guangdong province, Suqian in Jiangsu province, and Yinchuan in Ningxia Hui Autonomous Region) in January, May, and September 2018. The microbial communities in raw milk and farm environmental samples were determined using the PacBio small-molecule real-time circular consensus sequencing, which generated high-fidelity microbiota profiles based on full-length 16S rRNA genes; such technology was advantageous in producing accurate species-level information. Our results showed that both seasonality and sampling region were significant factors influencing the milk microbiota; however, the raw milk microbiota was highly diverse according to seasonality, and sampling region was the less determining factor. The wide variation in raw milk microbial communities between samples made it difficult to define a representative species-level core milk microbiota. Nevertheless, 3 most universal milk-associated species were identified: Lactococcus lactis, Enhydrobacter aerosaccus, and Acinetobacter lwoffii, which were consistently detected in 99%, 95%, and 94% of all analyzed milk samples, respectively (n = 355). The top taxa accounting for the overall seasonal microbiota variation were Bacillus (Bacillus cereus, Bacillus flexus, Bacillus safensis), Lactococcus (Lactococcus lactis, Lactococcus piscium, Lactococcus raffinolactis), Lactobacillus (Lactobacillus helveticus, Lactobacillus delbrueckii), Lactiplantibacillus plantarum, Streptococcus agalactiae, Enhydrobacter aerosaccus, Pseudomonas fragi, and Psychrobacter cibarius. Unlike the milk microbiota, the environmental microbiota did not exhibit obvious pattern of seasonal or geographic variation. However, this study was limited by the relatively low number and types of environmental samples, making it statistically not meaningful to perform further correlation analysis between the milk and environmental microbiota. Nevertheless, this study generated novel information on raw milk microbiota across wide geographic regions of China and found that seasonality was more significant in shaping the raw milk microbiota compared with geographic origin.

DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid

Untargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis may reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in the food industry. However, before these approaches can be applied, it is imperative to verify that the most appropriate methods are used at every step of the process: gathering of primary material, laboratory methods, data analysis, and interpretation. The focus of this study is on gathering the primary material, in this case, DNA. We used bovine milk as a model to (i) evaluate commercially available kits for their ability to extract nucleic acids from inoculated bovine milk, (ii) evaluate host DNA depletion methods for use with milk, and (iii) develop and evaluate a selective lysis-propidium monoazide (PMA)-based protocol for host DNA depletion in milk. Our results suggest that magnetically based nucleic acid extraction methods are best for nucleic acid isolation of bovine milk. Removal of host DNA remains a challenge for untargeted sequencing of milk, highlighting the finding that the individual matrix characteristics should always be considered in food testing. Some reported methods introduce bias against specific types of microbes, which may be particularly problematic in food safety, where the detection of Gram-negative pathogens and hygiene indicators is essential. Continuous efforts are needed to develop and validate new approaches for untargeted metagenomics in samples with large amounts of DNA from a single host. IMPORTANCE Tracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of the microbial composition. Because the genetic material of higher organisms present in food (e.g., cow in milk or beef, wheat in flour) is around 1,000 times larger than the bacterial content, challenges exist in gathering the information of interest. Additionally, specific bacterial characteristics can make them easier or harder to detect, adding another layer of complexity to this issue. In this study, we demonstrate the impact of using different methods for the ability to detect specific bacteria and highlight the need to ensure that the most appropriate methods are being used for each particular sample.

Milk Lactose as a Biomarker of Subclinical Mastitis in Dairy Cows

Bovine subclinical mastitis can cause great harm to dairy herds because of its negative impact on milk production and quality and cow health. Improved diagnostic tools are needed to maximise the control of subclinical mastitis distribution and ensure the high quality of milk as an industrial product. Between 2015 and 2020, seventy-two dairy herds were screened for bovine subclinical mastitis causative agents to identify the relationship between seasons, lactose levels and subclinical mastitis infection. The predominant species found in the milk samples were mixed microbiota, coagulase-negative Staphylococcus and Staphylococcus aureus. Yeasts were found exclusively in autumn, while Enterococcus spp. and Escherichia coli were only found in summer and autumn. A negative correlation was detected between milk lactose and number of somatic cells in milk (-0.471; p < 0.001). The lactose levels in milk were closely associated with the prevalence (%) of subclinical mastitis pathogens, such as Streptococcus agalactiae (y = -1.8011x + 10.867, R2 = 0.9298), Staph. aureus (y = -3.5216x + 25.957, R2 = 0.8604) and other Streptococci (y = -0.5956x + 7.6179, R2 = 0.6656). These findings suggest that milk lactose may be used as a biomarker of suspected udder inflammation in modern health prevention programmes for cows to reduce the prevalence of subclinical mastitis pathogens in dairy cattle herds.

Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR

Abstract

The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy^® PowerFood^® Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers.

Key points

• Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota.

• Reduction of eukaryotic DNA by enzymatic digestion.

• Shift of detected microbiome caused by high cycle numbers in library-PCR.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11353-4.