The Prebiotic and Probiotic Properties of Human Milk: Implications for Infant Immune Development and Pediatric Asthma

The incidence of pediatric asthma has increased substantially in recent decades, reaching a worldwide prevalence of 14%. This rapid increase may be attributed to the loss of “Old Friend” microbes from the human microbiota resulting in a less diverse and “dysbiotic” gut microbiota, which fails to optimally stimulate immune development during infancy. This hypothesis is supported by observations that the gut microbiota is different in infants who develop asthma later in life compared to those who remain healthy. Thus, early life exposures that influence gut microbiota play a crucial role in asthma development. Breastfeeding is one such exposure; it is generally considered protective against pediatric asthma, although conflicting results have been reported, potentially due to variations in milk composition between individuals and across populations. Human milk oligosaccharides (HMOs) and milk microbiota are two major milk components that influence the infant gut microbiota and hence, development of the immune system. Among their many immunomodulatory functions, HMOs exert a selective pressure within the infant gut microbial niche, preferentially promoting the proliferation of specific bacteria including Bifidobacteria. Milk is also a source of viable bacteria originating from the maternal gut and infant oral cavity. As such, breastmilk has prebiotic and probiotic properties that can modulate two of the main forces controlling the gut microbial community assembly, i.e., dispersal and selection. Here, we review the latest evidence, mechanisms and hypotheses for the synergistic and/or additive effects of milk microbiota and HMOs in protecting against pediatric asthma

Diet induced changes in the microbiota and cell composition of rabbit gut associated lymphoid tissue (GALT)

[EN] The gut associated lymphoid tissue (GALT) is the largest immune organ of the body. Although the gut transient and mucosa-associated microbiota have been largely studied, the microbiota that colonizes the GALT has received less attention. The gut microbiome plays an important role in competitive exclusion of pathogens and in development and maturation of immunity. Diet is a key factor affecting the microbiota composition in the digestive tract. To investigate the relation between diet, microbiota and GALT, microbial and cell composition of vermiform appendix (VA) and sacculus rotundus (SR) were studied in two groups of New Zealand white rabbits on different diets. Diet shifted the lymphoid tissue microbiota affecting the presence and/or absence of certain taxa and their abundances. Immunohistochemistry revealed that a higher fibre content diet resulted in M cell hyperplasia and an increase of recently recruited macrophages, whereas T-cell levels remained unaltered in animals on both high fibre and standard diets. These findings indicate that diet has an impact on the microbiota and cell composition of the GALT, which could act as an important microbial recognition site where interactions with beneficial bacteria can take place favouring microbiota replacement after digestive dysregulationsSIAuthors thank Félix Blanco, Sergio Ayuso and Fidel Goiri for animal care and handling. The research was funded by grant (AGL2012-39818-C02-02) from the Spanish Ministry of Economy and Competiveness (MINECO), and by the Department of Economy and Infrastructures (DEI) of the Basque Government. RA held a pre-doctoral fellowship (BFI-2012-237) and a visiting fellowship (EP_2015_1_53) from the Department of Education, Universities and Research of the Basque Governmen

Indicators of induced subacute ruminal acidosis (SARA) in Danish Holstein cows

BACKGROUND: The prevalence of subacute ruminal acidosis (SARA) in dairy cows is high with large impact on economy and welfare. Its current field diagnosis is based on point ruminal pH measurements by oral probe or rumenocentesis. These techniques are invasive and inaccurate, and better markers for the diagnosis of SARA are needed. The goal of this study was to evaluate clinical signs of SARA and to investigate the use of blood, faecal and urinary parameters as indicators of SARA. Six lactating, rumen cannulated, Danish Holstein cows were used in a cross-over study with three periods. The first and second periods included two cows on control diet and two cows on nutritional SARA challenge. The third period only included two cows on SARA challenge. Control diet was a conventional total mixed ration [45.5% dry matter (DM), 17.8% crude protein, 43.8% neutral detergent fibre, and 22.5% acid detergent fibre (DM basis)]. SARA challenge was conducted by substituting control diet with grain pellets (50% wheat/barley) over 3 days to reach 40% grain in the diet. Ruminal pH was measured continuously. Blood samples were collected once daily at 7 h after feeding. Samples of faeces and urine were collected at feeding, and at 7 and 12 h after feeding. Blood samples were analysed for pCO2, pO2, pH, electrolytes, lactate, glucose, packed cell volume (PCV), and total plasma protein concentration. Milk composition, ruminal VFA, and pH of faeces and urine were measured. RESULTS: SARA was associated with decreased (P < 0.05) minimum ruminal, faecal and urinary pH. Daily times and areas of ruminal pH below 5.8, and 5.6 were increased to levels representative for SARA. Significant differences were detected in milk composition and ruminal VFAs. Blood calcium concentration was decreased (P < 0.05), and pCO(2) tended to be increased (P = 0.10). Significant differences were not detected in other parameters. CONCLUSIONS: SARA challenge was associated with changes in faecal and urinary pH, blood calcium concentration and pCO(2). These may be helpful as indicators of SARA. However changes were small, and diurnal variations were present. None of these parameters are able to stand alone as indicators of SARA

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\u2019s 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

Composition and co-occurrence patterns of the microbiota of different niches of the bovine mammary gland: potential associations with mastitis susceptibility, udder inflammation, and teat-end hyperkeratosis

Abstract Background Within complex microbial ecosystems, microbe-microbe interrelationships play crucial roles in determining functional properties such as metabolic potential, stability and colonization resistance. In dairy cows, microbes inhabiting different ecological niches of the udder may have the potential to interact with mastitis pathogens and therefore modulate susceptibility to intramammary infection. In the present study, we investigated the co-occurrence patterns of bacterial communities within and between different niches of the bovine mammary gland (teat canal vs. milk) in order to identify key bacterial taxa and evaluate their associations with udder health parameters and mastitis susceptibility. Results Overall, teat canal microbiota was more diverse, phylogenetically less dispersed, and compositionally distinct from milk microbiota. This, coupled with identification of a large number of bacterial taxa that were exclusive to the teat canal microbiota suggested that the intramammary ecosystem, represented by the milk microbiota, acts as a selective medium that disfavors the growth of certain environmental bacterial lineages. We further observed that the diversity of milk microbiota was negatively correlated with udder inflammation. By performing correlation network analysis, we identified two groups of phylogenetically distinct hub species that were either positively (unclassified Bacteroidaceae and Phascolarctobacterium) or negatively (Sphingobacterium) correlated with biodiversity metrics of the mammary gland (MG). The latter group of bacteria also showed positive associations with the future incidence of clinical mastitis. Conclusions Our results provide novel insights into the composition and structure of bacterial communities inhabiting different niches of the bovine MG. In particular, we identified hub species and candidate foundation taxa that were associated with the inflammatory status of the MG and/or future incidences of clinical mastitis. Further in vitro and in vivo interrogations of MG microbiota can shed light on different mechanisms by which commensal microbiota interact with mastitis pathogens and modulate udder homeostasis

Altering undigested neutral detergent fiber through additives applied in corn, whole barley crop, and alfalfa silages, and its effect on performance of lactating Holstein dairy cows

Objective We hypothesized that silage additives may alter the undigested neutral detergent fiber (uNDF) content through ensiling. Therefore, urea and formic acid were applied to corn, whole barley crop (WBC) and alfalfa to change uNDF content of the ensiled forages. Methods Six experimental diets at two groups of high uNDF (untreated corn and alfalfa silages [CSAS] and untreated whole barley and alfalfa silages [BSAS]) and low uNDF (urea-treated corn silage+untreated alfalfa silage [CSUAS], urea-treated whole barley silage+untreated alfalfa silage [BSUAS], untreated corn silage+formic acid-treated alfalfa silage [CSASF], and untreated whole barley silage+formic acid-treated alfalfa silage [BSASF]), were allocated to thirty-six multiparous lactating Holstein dairy cows. Results The untreated silages were higher in uNDF than additive treated silages, but the uNDF concentrations among silages were variable (corn silage0.05). Milk yield tended to increase in the cows fed high uNDF diets than those fed low uNDF (p = 0.10). The cows fed diet based on urea-treated corn silage had higher milk yield than those fed other silages (p = 0.05). The substitution of corn silage with the WBC silage tended to decrease milk production (p = 0.07). Changing the physical source of NDF supply and the uNDF content from the corn silage to the WBC silage caused a significant increase in ruminal NH3-N concentration, milk urea-N and fat yield (p< 0.05). The cows fed diets based on WBC silage experienced greater rumination time than the cows fed corn silage (p<0.05). Conclusion Administering additives to silages to reduce uNDF may improve the performance of Holstein dairy cows

Postbiotics from Saccharomyces cerevisiae fermentation stabilize rumen solids microbiota and promote microbial network interactions and diversity of hub taxa during grain-based subacute ruminal acidosis (SARA) challenges in lactating dairy cows

BackgroundHigh-yielding dairy cows are commonly fed high-grain rations. However, this can cause subacute ruminal acidosis (SARA), a metabolic disorder in dairy cows that is usually accompanied by dysbiosis of the rumen microbiome. Postbiotics that contain functional metabolites provide a competitive niche for influential members of the rumen microbiome, may stabilize and promote their populations, and, therefore, may attenuate the adverse effects of SARA.MethodsThis study used a total of 32 rumen-cannulated lactating dairy cows, which were randomly assigned into four treatments: no SCFP (control), 14 g/d Original XPC (SCFPa), 19 g/d NutriTek (SCFPb-1X), and 38 g/d NutriTek (SCFPb-2X) (Diamond V, Cedar Rapids, IA) from 4 weeks before until 12 weeks after parturition. Grain-based SARA challenges were conducted during week 5 (SARA1) and week 8 (SARA2) after parturition by replacing 20% dry matter of the base total mixed ration (TMR) with pellets containing 50% ground barley and 50% ground wheat. The DNA of rumen solids digesta was extracted and subjected to V3-V4 16S rRNA gene sequencing. The characteristics of rumen solids microbiota were compared between non-SARA (Pre-SARA1, week 4; Post-SARA1, week 7; and Post-SARA2, weeks 10 and 12) and SARA stages (SARA1/1, SARA1/2, SARA2/1, SARA2/2), as well as among treatments.ResultsBoth SARA challenges reduced the richness and diversity of the microbiota and the relative abundances of the phylum Fibrobacteres. Supplementation with SCFP promoted the growth of several fibrolytic bacteria, including Lachnospiraceae UCG-009, Treponema, unclassified Lachnospiraceae, and unclassified Ruminococcaceae during the SARA challenges. These challenges also reduced the positive interactions and the numbers of hub taxa in the microbiota. The SCFPb treatment increased positive interactions among microbial members of the solids digesta and the number of hub taxa during the SARA and non-SARA stages. The SCFPb-2X treatment prevented changes in the network characteristics, including the number of components, clustering coefficient, modularity, positive edge percentage, and edge density of the microbiota during SARA challenges. These challenges reduced predicted carbohydrate and nitrogen metabolism in microbiota, whereas SCFP supplementation attenuated those reductions.ConclusionsSupplementation with SCFP, especially the SCFPb-2X attenuated the adverse effects of grain-based SARA on the diversity and predicted functionality of rumen solids microbiota

Detection of Antibiotic Resistance Genes in Source and Drinking Water Samples from a First Nations Community in Canada

Access to safe drinking water is now recognized as a human right by the United Nations. In developed countries like Canada, access to clean water is generally not a matter of concern. However, one in every five First Nations reserves is under a drinking water advisory, often due to unacceptable microbiological quality. In this study, we analyzed source and potable water from a First Nations community for the presence of coliform bacteria as well as various antibiotic resistance genes. Samples, including those from drinking water sources, were found to be positive for various antibiotic resistance genes, namely, ampC, tet(A), mecA, -lactamase genes (SHV-type, TEM-type, CTX-M-type, OXA-1, and CMY-2-type), and carbapenemase genes (KPC, IMP, VIM, NDM, GES, and OXA-48 genes). Not surprisingly, substantial numbers of total coliforms, including Escherichia coli, were recovered from these samples, and this result was also confirmed using Illumina sequencing of the 16S rRNA gene. These findings deserve further attention, as the presence of coliforms and antibiotic resistance genes potentially puts the health of the community members at risk.This work was supported by Discovery (A.K., W.G.D.F.) and CreateH2O (A.F.) grants funded by the Natural Science and Engineering Research Council of Canada as well as a University of Manitoba Start-up grant (E.K.). D.M.F. was funded by a Canada Research Chair grant to Peter Loewen, Department of Microbiology, University of Manitoba. R.P. is funded by a postdoctoral fellowship from the Government of Madhya Pradesh, India

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