Integrated Analysis of Human Milk Microbiota With Oligosaccharides and Fatty Acids in the CHILD Cohort.

Background: Human milk contains many bioactive components that are typically studied in isolation, including bacteria. We performed an integrated analysis of human milk oligosaccharides and fatty acids to explore their associations with milk microbiota. Methods: We studied a sub-sample of 393 mothers in the CHILD birth cohort. Milk was collected at 3-4 months postpartum. Microbiota was analyzed by 16S rRNA gene V4 sequencing. Oligosaccharides and fatty acids were analyzed by rapid high-throughput high performance and gas liquid chromatography, respectively. Dimension reduction was performed with principal component analysis for oligosaccharides and fatty acids. Center log-ratio transformation was applied to all three components. Associations between components were assessed using Spearman rank correlation, network visualization, multivariable linear regression, redundancy analysis, and structural equation modeling. P-values were adjusted for multiple comparisons. Key covariates were considered, including fucosyltransferase-2 (FUT2) secretor status of mother and infant, method of feeding (direct breastfeeding or pumped breast milk), and maternal fish oil supplement use. Results: Overall, correlations were strongest between milk components of the same type. For example, FUT2-dependent HMOs were positively correlated with each other, and Staphylococcus was negatively correlated with other core taxa. Some associations were also observed between components of different types. Using redundancy analysis and structural equation modeling, the overall milk fatty acid profile was significantly associated with milk microbiota composition. In addition, some individual fatty acids [22:6n3 (docosahexaenoic acid), 22:5n3, 20:5n3, 17:0, 18:0] and oligosaccharides (fucosyl-lacto-N-hexaose, lacto-N-hexaose, lacto-N-fucopentaose I) were associated with microbiota α diversity, while others (C18:0, 3'-sialyllactose, disialyl-lacto-N-tetraose) were associated with overall microbiota composition. Only a few significant associations between individual HMOs and microbiota were observed; notably, among mothers using breast pumps, Bifidobacterium prevalence was associated with lower abundances of disialyl-lacto-N-hexaose. Additionally, among non-secretor mothers, Staphylococcus was positively correlated with sialylated HMOs. Conclusion: Using multiple approaches to integrate and analyse milk microbiota, oligosaccharides, and fatty acids, we observed several associations between different milk components and microbiota, some of which were modified by secretor status and/or breastfeeding practices. Additional research is needed to further validate and mechanistically characterize these associations and determine their relevance to infant gut and respiratory microbiota development and health.

Impact of Saskatoon berry powder on insulin resistance and relationship with intestinal microbiota in high fat-high sucrose diet-induced obese mice.

The present study examined the impact of Saskatoon berry powder (SBp) on insulin resistance, inflammation and intestinal microbiota in diet-induced obese mice. Male C57 BL/6 J mice were fed control diet, high fat-high sucrose (HFHS) diet or HFHS+5% SBp (HFHS+B) diet for 15 weeks. The composition of fecal bacterial community was characterized using the Illumina sequencing of V4 region of 16S rRNA gene. HFHS diet increased body weight, fasting plasma glucose, cholesterol, triglycerides, insulin, homeostatic model assessment-insulin resistance, monocyte adhesion, tumor necrosis factor-α, plasminogen activator inhibitor-1, monocyte chemotactic protein-1, intracellular cell adhesion molecule-1, urokinase plasminogen activator and its receptor in plasma or aortae compared to the control diet. HFHS+B diet postponed the increase in body weight, suppressed HFHS diet-induced disorders in the metabolic and inflammatory variables. The ratio of Firmicutes/Bacteroidetes in the HFHS group was higher than that in the control group (P<.01), and that in the HFHS+B group was lower than that in the HFHS group (P<.05). The abundances of S24-7 family negatively correlated with body weight and tested metabolic or inflammatory variables. The results suggest that SBp attenuated HFHS diet-induced metabolic disorders and vascular inflammation in gut microbiota in mice.

Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation.

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, mechanisms underlying this association are yet poorly understood. In the present study, we sought to explore the association of BoLA gene polymorphism with the dynamics of mammary microbiota during the first week of lactation. RESULTS: Colostrum and milk samples were collected from multiparous Holstein dairy cows at the day of calving and days 1 and 6 after calving. Microbiota profiling was performed using high-throughput sequencing of the V1-V2 regions of the bacterial 16S rRNA genes and ITS2 region of the fungal ribosomal DNA. Polymorphism of BoLA genes was determined using PCR-RFLP of exon 2 of the BoLA-DRB3. In general, transition from colostrum to milk resulted in increased species richness and diversity of both bacterial and fungal communities. The most dominant members of intramammary microbiota included Staphylococcus, Ruminococcaceae, and Clostridiales within the bacterial community and Alternaria, Aspergillus, Candida, and Cryptococcus within the fungal community. Comparing the composition of intramammary microbiota between identified BoLA-DRB3.2 variants (n = 2) revealed distinct clustering pattern on day 0, whereas this effect was not significant on the microbiota of milk samples collected on subsequent days. On day 0, proportions of several non-aureus Staphylococcus (NAS) OTUs, including those aligned to Staphylococcus equorum, Staphylococcus gallinarum, Staphylococcus sciuri, and Staphylococcus haemolyticus, were enriched within the microbiota of one of the BoLA-DRB3.2 variants, whereas lactic acid bacteria (LAB) including Lactobacillus and Enterococcus were enriched within the colostrum microbiota of the other variant. CONCLUSION: Our results suggest a potential role for BoLA-gene polymorphism in modulating the composition of colostrum microbiota in dairy cows. Determining whether BoLA-mediated shifts in the composition of colostrum microbiota are regulated directly by immune system or indirectly by microbiota-derived colonization resistant can have important implications for future development of preventive/therapeutic strategies for controlling mastitis.

Composition of the teat canal and intramammary microbiota of dairy cows subjected to antimicrobial dry cow therapy and internal teat sealant.

Antimicrobial dry cow therapy (DCT) is an important component of mastitis control programs aimed to eliminate existing intramammary infections and prevent the development of new ones during the dry period. However, to what extent the microbiota profiles of different niches of the udder change during the dry period and following administration of DCT remains poorly understood. Therefore, the main objective of the present study was to qualitatively evaluate dynamics of the microbiota of teat canal (TC) and mammary secretions (i.e., milk and colostrum) of healthy udder quarters subjected to DCT using a long-acting antimicrobial product, containing penicillin G and novobiocin, in combination with internal teat sealant. To this end, TC swabs (n = 58) and their corresponding milk (n = 29) and colostrum samples (n = 29) were collected at the time of drying off and immediately after calving from clinically healthy udder quarters of Holstein dairy cows from a commercial dairy farm. All samples were subjected to DNA extraction and high-throughput sequencing of the V1-V2 hypervariable regions of bacterial 16S rRNA genes. Overall, shifts were more pronounced within the microbiota of mammary secretions than the TC. In particular, microbiota of colostrum samples collected immediately after calving were less species-rich compared with the pre-DCT milk samples. Proportions of several bacterial genera belonging to the phylum Proteobacteria, including Pseudomonas, Stenotrophomonas, and unclassified Alcaligenaceae, were enriched within the microbiota of colostrum samples, whereas Firmicutes genera, including Butyrivibrio, unclassified Clostridiaceae, and unclassified Bacillales, were overrepresented in pre-DCT milk microbiota. Apart from shifts in the proportion of main bacterial genera and phyla, qualitative analysis revealed a high degree of commonality between pre-DCT and postpartum microbiota of both niches of the udder. Most importantly, a considerable number of bacterial genera and species commonly regarded as mastitis pathogens or opportunists (or both), including Staphylococcus spp., unclassified Enterobacteriaceae, and Corynebacterium spp., were shared between pre-DCT and postpartum microbiota of mammary secretions. Percentage of shared bacterial genera and species was even higher between pre-DCT and postpartum microbiota of TC samples, suggesting that the DCT approach of the present study had limited success in eliminating a considerable proportion of bacteria during the dry period.

Assessment of complementary feeding of Canadian infants: effects on microbiome & oxidative stress, a randomized controlled trial.

BACKGROUND: The World Health Organization recommends exclusive breastfeeding until 6 months followed by introduction of iron-rich complementary foods (CFs). The aim of this study was to determine the impact of different iron-rich CFs on infant gut inflammation and microbiota. METHODS: Eighty-seven exclusively breastfed infants were randomly assigned to receive one of the following as their first CF: iron-fortified cereal (Cer), iron-fortified cereal with fruit (Cer + Fr), or meat (M). Urine and stool samples were collected to assess reactive oxygen species (ROS) generation, gut microbiota and inflammation. RESULTS: Fecal iron differed across feeding groups (p < 0.001); levels were highest in the Cer group and lowest in M group. A significant increase of fecal ROS formation (p < 0.002) after the introduction of CFs was observed, but did not differ across feeding groups. Fecal calprotectin increased within all groups after the introduction of CFs (p = 0.004). Gut microbiota richness increased after introduction of M or Cer + Fr. Regardless of feeding group, Coriobacteriaceae were positively correlated with ROS and Staphylococcaceae were negatively correlated with calprotectin. CONCLUSIONS: Choice of first CF may influence gut inflammation and microbiota, potentially due to variations in iron absorption from different foods. Further research is warranted to fully characterize these associations and to establish implications for infant health. This study was registered in the ClinicalTrial.gov registry (Identifier No. NCT01790542 ). TRIAL REGISTRATION: This study was registered in the ClinicalTrial.gov registry under the name "Assessment of Complementary Feeding of Canadian Infants" (Identifier No. NCT01790542 ) February 6, 2013.

Metagenomic analysis of rumen microbial population in dairy heifers fed a high grain diet supplemented with dicarboxylic acids or polyphenols.

BACKGROUND: The aim of this study was to investigate the effects of two feed supplements on rumen bacterial communities of heifers fed a high grain diet. Six Holstein-Friesian heifers received one of the following dietary treatments according to a Latin square design: no supplement (control, C), 60 g/day of fumarate-malate (organic acid, O) and 100 g/day of polyphenol-essential oil (P). Rumen fluid was analyzed to assess the microbial population using Illumina sequencing and quantitative real time PCR. RESULTS: The P treatment had the highest number of observed species (P < 0.10), Chao1 index (P < 0.05), abundance based coverage estimated (ACE) (P < 0.05), and Fisher's alpha diversity (P < 0.10). The O treatment had intermediate values between C and P treatments with the exception of the Chao1 index. The PCoA with unweighted Unifrac distance showed a separation among dietary treatments (P = 0.09), above all between the C and P (P = 0.05). The O and P treatments showed a significant increase of the family Christenenellaceae and a decline of Prevotella brevis compared to C. Additionally, the P treatment enhanced the abundance of many taxa belonging to Bacteroidetes, Firmicutes and Tenericutes phyla due to a potential antimicrobial activity of flavonoids that increased competition among bacteria. CONCLUSIONS: Organic acid and polyphenols significantly modified rumen bacterial populations during high-grain feeding in dairy heifers. In particular the polyphenol treatment increased the richness and diversity of rumen microbiota, which are usually high in conditions of physiological rumen pH and rumen function.

Use of dicarboxylic acids and polyphenols to attenuate reticular pH drop and acute phase response in dairy heifers fed a high grain diet.

BACKGROUND: The aim of this study was to determine the ability of two feed additives, a fumarate-malate (FM) and a polyphenol-essential oil mixture (PM), in attenuating the drop of ruminal pH and the metabolic and immune response resulting from an excessively high grain diet. Six heifers were used in a 3 × 3 Latin square experiment and fed a low starch (LS) diet for 14 d, followed by a high starch (HS) diet for 8 d (NDF 33.6%, starch 30.0% DM). In the last 5 days of each period, barley meal was added to decrease rumen pH. During HS feeding all animals were randomly assigned to one of the following three dietary treatments: no supplement/control (CT), a daily dose of 60 g/d of FM, or 100 g/d of PM. Reticular pH was continuously recorded using wireless boluses. On d 21 of each period, rumen fluid was collected by rumenocentesis (1400 h), together with blood (0800 h) and fecal samples (0800, 1400, and 2100 h). RESULTS: The correlation coefficient of pH values obtained using the boluses and rumenocentesis was 0.83. Compared with CT and PM, the FM treatment led to a lower DMI. Nadir pH was lowest during CT (5.40, 5.69, and 5.62 for CT, FM and PM, respectively), confirming the effectiveness of both supplements in reducing the pH drop caused by high grain feeding. This result was confirmed by the highest average time spent daily below 5.6 pH (199, 16 and 18 min/d) and by the highest acetate to propionate ratio of the CT fed heifers. The PM decreased the concentrations of neutrophils (2.9, 3.2, and 2.8 10(9)/L) and acute phase proteins: SAA (37.1, 28.6 and 20.1 µg/mL), LBP (4.1, 3.8, and 2.9 µg/mL), and Hp (675, 695 and 601 µg/mL). Free lipopolysaccharides (LPS) were detected in blood and feces, but their concentrations were not affected by treatments, as the remaining blood variables. CONCLUSIONS: Data suggest that both additives could be useful in attenuating the effects of excessive grain feeding on rumen pH, but the PM supplement was more effective than FM in reducing the inflammatory response compared to CT.