Peptidomic and glycomic profiling of commercial dairy products: identification, quantification and potential bioactivities.

Peptidomics and glycomics are recently established disciplines enabling researchers to characterize functional characteristics of foods at a molecular level. Milk-derived bioactive peptides and oligosaccharides have garnered both scientific and commercial interest because they possess unique functional properties, such as anti-hypertensive, immunomodulatory and prebiotic activities; therefore, the objective of this work was to employ peptidomic and glycomic tools to identify and measure relative and absolute quantities of peptides and oligosaccharides in widely consumed dairy products. Specifically, we identified up to 2117 unique peptides in 10 commercial dairy products, which together represent the most comprehensive peptidomic profiling of dairy milk in the literature to date. The quantity of peptides, measured by ion-exchange chromatography, varied between 60 and 130 mg/L among the same set of dairy products, which the majority originated from caseins, and the remaining from whey proteins. A recently published bioactive peptide database was used to identify 66 unique bioactive peptides in the dataset. In addition, 24 unique oligosaccharide compositions were identified in all the samples by nano LC Chip QTOF. Neutral oligosaccharides were the most abundant class in all samples (66-91.3%), followed by acidic (8.6-33.7%), and fucosylated oligosaccharides (0-4.6%). Variation of total oligosaccharide concentration ranged from a high of 65.78 to a low of 24.82 mg/L. Importantly, characterizing bioactive peptides and oligosaccharides in a wider number of dairy products may lead to innovations that go beyond the traditional vision of dairy components used for nutritional purposes but that will rather focus on improving human health

Profiling of aminoxyTMT-labeled bovine milk oligosaccharides reveals substantial variation in oligosaccharide abundance between dairy cattle breeds.

Free milk oligosaccharides are bioactive molecules that function as prebiotics and prevent infections that commonly afflict developing infants. To date, few publications have examined the factors affecting bovine milk oligosaccharide production among cattle in the dairy industry. Here we have applied a high-throughput isobaric labeling technique to measure oligosaccharide abundances in milk collected from Danish Holstein-Friesian and Jersey dairy cattle by liquid chromatography-mass spectrometry. With a total of 634 milk samples, this collection represents the largest sample set used for milk oligosaccharide profiling in the current literature. This study is also the first to use isobaric labeling for the purpose of measuring free oligosaccharides in a real sample set. We have identified 13 oligosaccharides that vary significantly by breed, with most structures being more abundant in the milk of Jersey cattle. The abundances of several oligosaccharides were increased in second-parity cows, and correlations between the abundances of oligosaccharide pairs were identified, potentially indicating similarities in their synthetic pathways. Fucosylated oligosaccharide structures were widely identified among both breeds. Improving our understanding of oligosaccharide production will aid in developing strategies to recover these compounds from processing streams and may enable their use as a functional ingredient in foods for infants and adults

A genome-wide association study reveals specific transferases as candidate loci for bovine milk oligosaccharides synthesis.

BackgroundHuman milk oligosaccharides (OS) play a key role in brain and gut microbiota development of the neonate, but the underlying biosynthetic steps of OS in the mammary gland are still largely unknown. As bovine milk contains OS with somewhat similar structures and functionalities there is increased interest in further understanding the genetic basis underlying the OS content of milk for eventual extraction and generation of value-added ingredients for infant formulas and nutraceuticals. The present study is the first to report on genetic parameter estimation as well as on a genome wide association study (GWAS) from the largest bovine milk OS dataset analyzed to date.ResultsIn total 15 different bovine milk OS were monitored. Heritabilities ranged from 0 to 0.68 in Danish Holstein and from 0 to 0.92 in Danish Jersey. The GWAS identified in total 1770 SNPs (FDR < 0.10) for five different OS in Danish Holstein and 6913 SNPs (FDR < 0.10) for 11 OS in Danish Jersey. In Danish Holstein, a major overlapping QTL was identified on BTA1 for LNH and LNT explaining 24% of the variation in these OS. The most significant SNPs were associated with B3GNT5, a gene encoding a glycosyltransferase involved in glycan synthesis. In Danish Jersey, a very strong QTL was detected for the OS with composition 2 Hex 1 HexNAc (isomer 1) on BTA11. The most significant SNP had -log10(P-value) of 52.88 (BOVINEHD1100030300) and was assigned to ABO, a gene encoding ABO blood group glycosyltransferases. This SNP has been reported to be a missense mutation and explains 56% of the OS variation. Other candidate genes of interest identified for milk OS were ALG3, B3GALNT2, LOC520336, PIGV, MAN1C1, ST6GALNAC6, GLT6D1, GALNT14, GALNT17, COLGALT2, LFNG and SIGLEC.ConclusionTo our knowledge, this is the first study documenting a solid breeding potential for bovine milk OS and a strong indication of specific candidate genes related to OS synthesis underlying this genetic influence. This new information has the potential to guide breeding strategies to achieve production of milk with higher diversity and concentration of OS and ultimately facilitate large-scale extraction of bovine milk OS

Seed phytochemicals shape the community structures of cultivable actinobacteria-inhabiting plant interiors of Thai pigmented rice

We examined abundance, bioactivity, and endophytism of cultivable actinobacteria isolated from plant interiors of two Thai pigmented rice cultivars: Hom Nin (HN) rice and Luem Pua (LP) glutinous rice. Both rice cultivars housed the same amount of endophytic actinobacteria (33 isolates each). Microbispora (76%) and Streptomyces (73%) were the predominant endophytic actinobacteria of LP glutinous rice and HN rice, respectively. Sphaerisporangium (9%) was found only in LP glutinous rice. Twelve percent of endophytic actinobacteria was the possibility of discovering novel species from both rice cultivars. Most endophytic actinobacteria exhibited plant growth‐promoting potentials, including antimicrobial activity against test bacteria and phytopathogenic fungi, solubilization of phosphate, and production of biostimulants (i.e., ammonia, indole‐3‐acetic acid, and siderophore) and biocatalysts (i.e., amylase, cellulase, chitinase, lipase, and protease). Our findings revealed that seed phytochemicals of pigmented rice (e.g., anthocyanin, γ‐oryzanol, phytate, antioxidants, and content of amylose) were effectors, shaping the community structures and biofunctions of endophytic actinobacteria. We conclude that pigmented rice is yet a challenging source for discovery of bioactive and novel actinobacteria. This study also provides new insights into the plant‐endophyte interactions by which seed phytochemicals act as a primary checkpoint in the natural selection for establishing unique plant endophytomes

Variations in porcine colostrum oligosaccharide composition between breeds and in association with sow maternal performance

Background: Oligosaccharides (OS) are indigestible carbohydrates naturally found in milk. The composition of porcine colostrum OS may influence the growth and the health of the neonate and consuming optimal concentrations of OS may reduce piglet susceptibility to illness. In this manner, targeted supplementation of animal feed with OS is being explored as a health management tool in the livestock industry. The variation in OS composition between different breeds of pig and its association with the litter performance is currently unknown. The aim of this study was to characterize the colostrum OS composition from sows of different breed and parity and correlate this data with sow maternal traits. Methods: Eighty-three colostrum samples from parities 1 to 8 were gathered from 3 different breeds of sow: 44 Large White sows, 27 Landrace sows and 12 Duroc sows. Samples were taken between the birth of the first and the last piglet from sows that were not pharmacologically induced to farrow. OS were purified from the samples and analysed by MALDI-ToF mass spectrometry (21 OS compositions detected). The farrowing season and the maternal data were recorded for each sow, including the number of live piglets and the litter body weight at birth, at day (d) 3 and at weaning. Results: Five OS compositions, including isomers of the bifidogenic Sialyllactose, Lacto-N-Tetraose and Lacto-N-Hexaose series, were detected in all the samples. Twelve other OS were identified in at least 50% of samples, and their abundances were affected by breed (P < 0.05; 6 of 12), marginally affected by season (P < 0.10; 3 of 12) and never by parity number. The abundances of each OS component were standardized by Z-score scaling (\u3bc = 0 and SD = 1), transformed by principal component analysis, and four similarity clusters were generated. Cluster membership was associated with litter weight gain within 3 days (P = 0.063) and at weaning (P < 0.05), but not with piglet mortality within 3 days. Conclusions: OS composition of colostrum may partially explain the variability in maternal performance within and between different breeds of sow. The obtained OS data can provide useful information for the development of novel prebiotic food supplements for suckling and weaning pigs

Lichens as natural sources of biotechnologically relevant bacteria

International audienceThe search for microorganisms from novel sources and in particular microbial symbioses represents a promising approach in biotechnology. In this context, lichens have increasingly become a subject of research in microbial biotechnology, particularly after the recognition that a diverse community of bacteria other than cyanobacteria is an additional partner to the traditionally recognized algae-fungus mutualism. Here, we review recent studies using culture-dependent as well as culture-independent approaches showing that lichens can harbor diverse bacterial families known for the production of compounds of biotechnological interest and that several microorganisms isolated from lichens, in particular Actinobacteria and Cyanobacteria, can produce a number of bioactive compounds, many of them with biotechnological potential

Whey and Buttermilk-Based Formulas Modulate Gut Microbiota in Mice with Antibiotic-Induced Dysbiosis

ScopeDiet is one of the main factors that modifies intestinal microbiota composition. The search for foods that can reverse situations of intestinal dysbiosis such as that induced by antibiotics is of great interest. Buttermilk and whey are the main by‐products produced by the dairy industry containing bioactive compounds. The aim of this study is to investigate the ability of whey and buttermilk‐based formulas supplemented with lactoferrin and milk fat globule membrane (MFGM) to modulate the effects of clindamycin on mouse intestinal microbiota.Methods and resultsMale C57BL/6 mice are treated with saline (control), clindamycin (Clin), a formula containing whey (F1) or buttermilk (F2), Clin+F1 or Clin+F2, and their fecal microbiota profiles are analyzed by sequencing of 16S rRNA gene using the MinION device. Clin induces alterations in both the composition and metabolic functions of the mice intestinal microbiota. The treatment with F1 or F2 reverses the effects of clindamycin, restoring the levels of Rikenellaceae and Lactobacillaceae families and certain pathways related to short‐chain fatty acids production and tetrahydrofolate biosynthesis.ConclusionWhey and buttermilk supplemented with lactoferrin and MFGM may be a bioactive formula for functional foods to prevent or restore microbiota alterations induced by antibiotic administration

Experiments and simulations on short chain fatty acid production in a colonic bacterial community

Understanding how production of specific metabolites by gut microbes is modulated by interactions with surrounding species and by environmental nutrient availability is an important open challenge in microbiome research. As part of this endeavor, we explore interactions between F. prausnitzii, a major butyrate producer, and B. thetaiotaomicron, an acetate producer, under three different in vitro media conditions in monoculture and coculture. In silico Genome-scale dynamic flux balance analysis (dFBA) models of metabolism in the system using COMETS (Computation of Microbial Ecosystems in Time and Space) are also tested for explanatory, predictive and inferential power. Experimental findings indicate enhancement of butyrate production in coculture relative to F. prausnitzii monoculture but defy a simple model of monotonic increases in butyrate production as a function of acetate availability in the medium. Simulations recapitulate biomass production curves for monocultures and accurately predict the growth curve of coculture total biomass, using parameters learned from monocultures, suggesting that the model captures some aspects of how the two bacteria interact. However, a comparison of data and simulations for environmental acetate and butyrate changes suggest that the organisms adopt one of many possible metabolic strategies equivalent in terms of growth efficiency. Furthermore, the model seems not to capture subsequent shifts in metabolic activities observed experimentally under low-nutrient regimes. Some discrepancies can be explained by the multiplicity of possible fermentative states for F. prausnitzii. In general, these results provide valuable guidelines for design of future experiments aimed at better determining the mechanisms leading to enhanced butyrate in this ecosystem.https://www.biorxiv.org/content/10.1101/444760v1https://www.biorxiv.org/content/10.1101/444760v1Othe