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Dynamics of bacterial communities of intramammary microbiota during the first week of lactation. a Bar graphs show the proportion of predominant bacterial genera of intramammary secretions during the first week of lactation. Color codes were used to relate the average proportion of genera to BoLA variants, x-axis relates the proportion of bacterial genera to days in milk, and error bars denote 95% confidence intervals. b Associations of bacterial genera with BoLA variants and DIM were analyzed with generalized linear mixed effect model (package glmmTMB). The total count of OTUs assigned to each genus were offset to the library size (total count of OTUs detected in each sample) and then used as the response variable in a negative binomial model where BoLA variants, DIM, and their interaction were included as fixed effects whereas the effect of individual cows were included as the random effect. Estimated group means, confidence intervals (CI), and pairwise comparisons for effects of BstY variants and DIM were derived using the package emmeans. Multiple hypotheses were adjusted by Benjamini and Hochberg false discovery rate (FDR). Genera for which the high and low values of CI do not cross the zero line shows significant log fold change between DIM contrasts. Summary statistics are available in Additional file 2: Table S3
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Background
The interplay between host genotype and commensal microbiota at different body sites can have important implications for health and disease. In dairy cows, polymorphism of bovine major histocompatibility complex (BoLA) gene has been associated with susceptibility to several infectious diseases, most importantly mastitis. However, mechani...
Citations
... A correlation network analysis (CoNet) was used to determine microbial association network and the general organization structure of the microbial community [32]. Positive /negative connections indicates co-occurrence/mutual-exclusion relationships among taxa respectively, and hub taxa were identi ed when they had more than 15 positive/negative connections with other community members [32] as described previously [33,34]. The degree of connectedness, a measure used to determine the in uential capacity of bacterial taxa [35], was explored at the phylum level by dividing the total number of positive and negative edges observed for each phylum by its relative abundance in the community. ...
Background
Subacute ruminal acidosis (SARA) is a common metabolic disorder of high yielding dairy cows, and it is associated with dysbiosis of the rumen and gut microbiome and host inflammation. This study evaluated the impact of two postbiotics from Saccharomyces cerevisiae fermentation products (SCFP) on rumen liquid associated microbiota of lactating dairy cows subjected to repeated grain-based SARA challenges. A total of 32 rumen cannulated cows were randomly assigned to four treatments from 4 wk before until 12 wk after parturition. Treatment groups included a Control diet or diets supplemented with postbiotics (SCFPa, 14 g/d Original XPC; SCFPb-1X, 19 g/d NutriTek; SCFPb-2X, 38 g/d NutriTek, Diamond V, Cedar Rapids, IA). Grain-based SARA challenges were conducted during wk 5 (SARA1) and wk 8 (SARA2) after parturition by replacing 20% DM of the base total mixed ration (TMR) with pellets containing 50% ground barley and 50% ground wheat. Total DNA from rumen liquid samples was subjected to V3-V4 16S rRNA gene amplicon sequencing. Characteristics of rumen microbiota were compared among treatments and SARA stages.
Results
Both SARA challenges reduced the diversity and richness of rumen liquid microbiota, altered the overall composition (β-diversity), and its predicted functionality including carbohydrates and amino acids metabolic pathways. The SARA challenges also reduced the number of significant associations among different taxa, number of hub taxa and their composition in the microbial co-occurrence networks. Supplementation with SCFP postbiotics, in particular SCFPb-2X, enhanced the robustness of the rumen microbiota. The SCFP supplemented cows had less fluctuation in relative abundances of community members when exposed to SARA challenges. The SCFP supplementation promoted the populations of lactate utilizing and fibrolytic bacteria, including members of Ruminococcaceae and Lachnospiraceae, and also increased the numbers of hub taxa during non-SARA and SARA stages. Supplementation with SCFPb-2X prevented the fluctuations in the abundances of hub taxa that were positively correlated with the acetate concentration, and 𝛼- and β-diversity metrics in rumen liquid digesta.
Conclusions
Induction of SARA challenges disrupted rumen liquid microbiota of lactating dairy cows and supplementation with SCFP postbiotics could attenuate adverse effects of SARA on rumen liquid microbiota.
... Moreover, the number of beneficial bacteria was higher in Group B than in Group A. Nevertheless, Group A observed with a slightly higher percentage of Bacilli than Group B. Hence, the different lactation period has a significant influence on the milk microbiota. One of the studies observed the richness of bacterial and fungal microbiota in dairy cows during the colostrum to the milk transformation (Derakhshani et al., 2018). ...
Dromedary camel or Arabian camel (Camelus dromedarius) has great economic importance due to its milk and byproducts. Its milk has high nutrition along with healthy bacteria such as Lactic acid bacteria helpful in the fermentation process. The aim was to compare the probiotic bacteria from one week of lactating camel milk vs one year lactating camel milk to differentiate the potential probiotics. This study analyzed the microbiomes of one year lactating raw camel milk M1, M2 (A) (n = 10) and one week of lactating camel milk M3, M4 (B) (n = 10) through metagenomic analysis of 16S rRNA. In total, 276 species were found in two groups (A and B) and they shared 55 genes. Group B showed a higher number of species (2 2 0) than group A (56). The statistical data on functional annotations such as Card, COG, NOG and Swiss-prot revealed at least one or more contributions from this study sample database. The phylum Proteobacteria contributed largely up to 75 % in group B. In contrast, Ascomycota and Verrucomicrobia existed in higher quantity in group A than in group B and Firmicutes were slightly higher in group A than in group B. Actinobacteria were higher in group B whereas Bacteroidetes dominated in group A than group B. The potential probiotic bacteria found in camel milk including Enterococcus faecalis, Enterococcus faecium, Propionibacterium, Streptococcus thermophilus, Solibacillus silvestris and Akkermansia muciniphila. Despite the probiotic bacteria some pathogenic microbes also resided in the studied samples, hence it is strongly recommended proper sterilization before consumption. This proposed research is to get an efficient microbial consortium of beneficial bacteria and their functional roles.
... Toscano reported differences between Cesarean section and vaginal delivery [33]. Derakhshani observed the role of BoLA-gene polymorphism in modulating the composition of colostrum microbiota in dairy cows [34]. Metzger found the overall bacterial community composition differed among bedding types in dairy farms [35]. ...
Background
Milk microflora is closely associated with the physiology and pathology in the mammary gland, and plays an important role in offspring development. The objective of the study was to illustrate the variation of milk microflora accompanied by the main factors related to milk performance.
Results
Milk samples were collected from 285 cows in Ningxia, China, and then microflora was explored using 16S rRNA pyrosequencing. All samples were grouped with the season (summer and winter), cow status (healthy and subclinical mastitis), farms (6 commercial dairy farms), and parity (primiparity and multiparity). The bacterial diversity, community composition, and abundance were analyzed among different groups. Also, the milk microflora among samples from summer, winter, and colostrum was compared. The results showed that the bacterial diversity of the milk varied significantly between samples from summer and winter. Higher bacterial richness was observed from summer samples than from winter samples. The gut-related genera, Parabacteroides, Staphylococcus, Corynebacterium_1, Sphingomonas, and Lactobacillus, were prevalent in summer milk samples. Although Escherichia_Shigella, Pseudomonas, Streptococcus, Psychrobacter, Rhizobium, Bifidobacterium, and Clostridium_sensu_stricto_1 were common in winter samples. In addition, different farms exhibited differences in bacterial diversity. Subclinical mastitis increased alpha diversity and decreased the enrichment of KEGG pathways in summer. Moreover, significant differences of milk microflora were observed from summer, winter and colostrum samples.
Conclusions
The study revealed that the milk microflora varied companies with seasons, farms, health status, and parities. Also, milk from summer, winter, and colostrum showed their unique microflora characteristics.
... Similarly, parity of the cow [61] and seasonal housing (indoor or outdoor sampling and housing) [62] can impact the milk microbial composition. Stage of lactation, milking hygiene, bedding material and feeding habits affect cow milk microbial composition and diversity [37,48,53,63]. For instance, Doyle et al. (2017) [62] observed that Acinetobacter and Pseudomonas were in lower proportions in milk from indoor-housed animals as compared to outdoor milk samples. ...
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.
... Next, another 2-3 milk streams are discarded, and the teats are wiped with 70% isopropyl alcohol. Once the teats are dry, another 2-3 streams of milk are discarded, and samples are collected [12,[17][18][19][20][21]. This method is extensively used in studies on bovine udder health. ...
... Recent advancements in microbial analysis techniques, including 16S rRNA gene sequencing, metagenomics, transcriptomics, metabolomics, and culturomics have facilitated comprehensive and accurate detection of the milk microbiota. Numerous studies utilizing next-generation sequencing techniques have documented a wide range of microorganisms in bovine milk, specifically from healthy mammary glands, exhibiting site-specific variations [12,14,17,18,[27][28][29]. Moreover, notwithstanding the absence of bacterial growth in certain milk samples during cultural analysis, several investigations have uncovered the presence of bacterial DNA originating from strictly anaerobic microorganisms, including Fusobacterium and Bacteroidetes. ...
... Remarkably, this dominance was observed across colostrum samples regardless of parity. Derakhshani et al. [18,19] also reported the prevalence of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes as the most abundant phyla in bovine colostrum, constituting over 80% of the entire microbiota composition. Of particular note, the relative abundances of Firmicutes and Proteobacteria were almost equal (both approximately 44%-45%). ...
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.
... As an illustration, studies on the digestive microbiota explore its relationship to feed utilization and performance, studies on milk microbiota deal with mammary health and mastitis, or studies on the vaginal microbiota are interested in metritis [1][2][3][4][5][6][7]. Likewise, studies on the effect of host genetics on the microbiota composition mainly focused on specific phenotypes and body-site microbiotas [8][9][10]. ...
... Drastic changes were reported in the vaginal and uterine microbiotas around parturition [2,52]. Milk microbiota composition changes during lactation as well, notably during the first weeks of lactation [8,53]. Beside physiological changes, modifications in housing conditions and diet may contribute to the so-called "time effect" on microbiota. ...
... The influence of breed was also observed on milk microbiota using different breeds farmed under the same conditions [53,72]. Similarly, Derakhshani et al. [8] revealed an association of the bovine leukocyte antigens (BoLA) DRB3.2 gene polymorphism with colostrum microbiota composition of dairy cows. Polymorphism in BoLA has been previously associated with differences in somatic cell counts and mastitis susceptibility [73,74]. ...
Abstract 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 (
... Staphylococcus was not only the dominant genera in the two groups, but also the DIM biomarker with the highest degree of interpretation analysis by the random forest algorithm. Staphylococcus, especially S. aureus and coagulase-negative Staphylococcus, was among the most prevalent genera in studies on both human and cow milk microbiota [1,8,29,35,[61][62][63][64]. S. aureus is traditionally considered a major mastitis-related pathogen [16,65]. ...
The present experiment was carried out to analyze the longitudinal changes in milk microorganisms. For this purpose, milk samples were collected from 12 healthy cows (n = 96; six primiparous cows and six multiparous cows) at eight different time points. The characteristics and variations in microbial composition were analyzed by 16S rRNA gene high-throughput sequencing. In the primiparous group, higher and more stable alpha diversity was observed in transitional and mature milk compared with the colostrum, with no significant difference in alpha diversity at each time point in the multiparous group. Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota were the most dominant phyla, and Pseudomonas, UCG-005, Acinetobacter, Vibrio, Lactobacillus, Bacteroides, Serratia, Staphylococcus, and Glutamicibacter were the most dominant genera in both primiparous and multiparous cow milk. Some typically gut-associated microbes, such as Bacteroides, UCG-005, and Rikenellaceae_RC9_gut_group, etc., were enriched in the two groups. Biomarker taxa with the day in time (DIM) were identified by a random forest algorithm, with Staphylococcus showing the highest degree of interpretation, and the difference in milk microbiota between the two groups was mainly reflected in 0 d–15 d. Additionally, network analysis suggested that there were bacteria associated with the total protein content in milk. Collectively, our results disclosed the longitudinal changes in the milk microbiota of primiparous and multiparous cows, providing further evidence in dairy microbiology.
... It has also been shown that bacterial diversity varies with somatic cell count (SCC), which is the most commonly used marker of inflammation for bovine mammary health [16]. The microbiota in milk has also been studied and associated to history of intra-mammary infection [17], cow genotype [18] and farm environment [19]. However, the idea of a microbiota in bovine milk has been challenged due to its incompatibility with current knowledge about mammary gland immunology and mastitis control plans [20]. ...
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.
Supplementary Information
The online version contains supplementary material available at 10.1186/s13567-023-01179-5.
... However, in the present study, Butyrivibrio accounted for significantly greater abundances in GBV LMU cows and correlated accordingly negatively with MU lac . Considering the major occurrence of this genus together with the findings of Derakhshani et al. (2018), who suggested Butyrivibrio as a major fibrolytic rumen dweller in Holsteins with a major effect on ruminal fermentation, we might speculate whether Butyrivibrio affects dietary N digestibility by its fermentation activity and therefore promotes FecN losses. At this time, the causality between host genetics, Butyrivibrio abundances, and N utilization and N excretion remains unclear but warrants further research. ...
Increasing the nitrogen-utilization efficiency (NUE) of dairy cows by breeding selection would offer advantages from nutritional, environmental, and economic perspectives. Because data collection of NUE phenotypes is not feasible in large cow cohorts, the cow individual milk urea concentration (MU) has been suggested as an indicator trait. Considering the symbiotic interplay between dairy cows and their rumen microbiome, individual MU was thought to be influenced by host genetics and by the rumen microbiome, the latter in turn being partly attributed to host genetics. To enhance our knowledge of MU as an indicator trait for NUE, we aimed to identify differential abundant rumen microbial genera between Holstein cows with divergent genomic breeding values for MU (GBVMU; GBVHMU vs. GBVLMU, where H and L indicate high and low MU phenotypes, respectively). The microbial genera identified were further investigated for their correlations with MU and 7 additional NUE-associated traits in urine, milk, and feces in 358 lactating Holsteins. Statistical analysis of microbial 16S rRNA amplicon sequencing data revealed significantly higher abundances of the ureolytic genus Succinivibrionaceae UCG-002 in GBVLMU cows, whereas GBVHMU animals hosted higher abundances of Clostridia unclassified and Desulfovibrio. The entire discriminating ruminal signature of 24 microbial taxa included a further 3 genera of the Lachnospiraceae family that revealed significant correlations to MU values and were therefore proposed as considerable players in the GBVMU-microbiome-MU axis. The significant correlations of Prevotellaceae UCG-003, Anaerovibrio, Blautia, and Butyrivibrio abundances with MU measurements, milk nitrogen, and N content in feces suggested their contribution to genetically determined N-utilization in Holstein cows. The microbial genera identified might be considered for future breeding programs to enhance NUE in dairy herds.
... Polymorphisms in this region are associated with individual differences in an immune response to a particular infectious disease, such as mastitis [10], tick-borne disease [11,12], foot and mouth disease [13], bovine herpesvirus 1 [14], and bovine papillomavirus-induced bladder cancer [15]. Moreover, Bo-LA-DRB3 polymorphism affects dairy cattle productivity such as milk quality and production rate during a mastitis infection [16], the microbiota in colostrum and milk [17], as well as reproduction rates in neosporosis [18]. Particularly, BoLA-DRB3 is reportedly associated with mastitis and somatic cell count (SCC) [19][20][21][22][23][24]. ...
Enzootic bovine leukosis caused by the bovine leukemia virus (BLV) results in substantial damage to the livestock industry; however, we lack an effective cure or vaccine. BoLA-DRB3 polymorphism in BLV-infected cattle is associated with the proviral load (PVL), infectivity in the blood, development of lymphoma, and in utero infection of calves. Additionally, it is related to the PVL, infectivity, and anti-BLV antibody levels in milk. However, the effects of the BoLA-DRB3 allele and BLV infection on dairy cattle productivity remain poorly understood. Therefore, we investigated the effect of BLV infection and BoLA-DRB3 allele polymorphism on dairy cattle productivity in 147 Holstein dams raised on Japanese dairy farms. Our findings suggested that BLV infection significantly increased milk yield. Furthermore, the BoLA-DRB3 allele alone, and the combined effect of BLV infection and the BoLA-DRB3 allele had no effect. These results indicate that on-farm breeding and selection of resistant cattle, or the preferential elimination of susceptible cattle, does not affect dairy cattle productivity. Additionally, BLV infection is more likely to affect dairy cattle productivity than BoLA-DRB3 polymorphism.
