Maternal diet may modulate human milk microbiota, but the effects of nutritional supplements are unknown. We examined the associations of prenatal diet and supplement use with milk microbiota composition. Mothers reported prenatal diet intake and supplement use using self-administered food frequency and standardised questionnaires, respectively. The milk microbiota was profiled using 16S rRNA gene sequencing. Associations of prenatal diet quality, dietary patterns, and supplement use with milk microbiota diversity and taxonomic structure were examined using Wilcoxon signed-rank tests and multivariable models adjusting for relevant confounders. A subset of 645 mothers participating in the CHILD Cohort Study (originally known as the Canadian Healthy Infant Longitudinal Development Study) provided one milk sample between 2 and 6 months postpartum and used prenatal multivitamin supplements ≥4 times a week. After adjusting for confounders, vitamin C supplement use was positively associated with milk bacterial Shannon diversity (β = 0.18, 95% CI = 0.05, 0.31) and Veillonella and Granulicatella relative abundance (β = 0.54; 95% CI = 0.05, 1.03 and β = 0.44; 95% CI = 0.04, 0.84, respectively), and negatively associated with Finegoldia relative abundance (β = -0.31; 95% CI = -0.63, -0.01). Fish oil supplement use was positively associated with Streptococcus relative abundance (β = 0.26; 95% CI = 0.03, 0.50). Prenatal diet quality and dietary patterns were not associated with milk microbiota composition. Prenatal vitamin C and fish oil supplement use were associated with differences in the milk microbiota composition. Future studies are needed to confirm our findings and elucidate mechanisms linking maternal supplement use to milk microbiota and child health.

Enterotoxigenic Escherichia coli (ETEC) is one of the major bacterial infections, causing substantial economic losses globally in the swine industry. This study aimed to investigate the impact of low Saccharomyces cerevisiae fermentation postbiotics (SCFP), high SCFP, essential oil (EO), or their combination on the growth performance and health of weanling pigs during ETEC infection. Forty-eight male weanling pigs were randomly allocated to five groups: 1) control group (CON-basal diet, n = 16); 2) low SCFP group (LSC-basal diet + 1.25 g/kg SCFP, n = 8); 3) high SCFP group (HSC-basal diet + 2 g/kg SCFP, n = 8); 4) essential oil group (EO-basal diet + 0.4 g/kg EO, n = 8); 5) the SCFP and EO combination group (SE-basal diet + 1.25 g/kg SCFP + 0.4 g/kg EO, n = 8). On day 15 of the trial, pigs in CON were divided into positive control (PC) and negative control (NC), and all pigs, except in NC, were challenged with ETEC. Under the normal condition, dietary LSC, HSC, EO, and EO all increased average daily gain (ADG) (P < 0.05), and decreased F:G ratio (P < 0.05) accompanied by decreased malondialdehyde (MDA) and increases in catalase (CAT), total superoxide dismutase (T-SOD), total antioxidant capacity (T-AOC) indicating enhanced anti-oxidative capacity, as well as decreased IL-2, IL-8, INF-gamma, indicating mitigated systemic inflammation. During ETEC infection, all treatments alleviated ETEC-induced ADG reduction, diarrhea, damages in intestinal permeability and morphology, and down-regulation of tight junctions (Claudin1, ZO-1, and Occludin), while HSC and EO exhibited additional protections. All treatments increased CAT, T-SOD, and T-AOC, and decreased MDA in serum and jejunal mucosa at similar degrees (P < 0.05). Moreover, all treatments alleviated ETEC-induced inflammation as shown by decreased IL-6, TNF-alpha, INF-gamma, and increased IL-4 and IL-10 in serum or jejunal mucosa (P < 0.05), and enhanced the immunity by increased serum IgG and mucosal sIgA (P < 0.05). HSC and SE further reduced mucosal INF-gamma and TNF-alpha than LSC or EO aligning with their additional protection against diarrhea during ETEC infection. Additionally, the key gut bacteria (e.g., Terrisporobacter) related to the benefits of SCFP and EO were identified. In sum, all treatments enhanced growth performance and protected against ETEC-induced intestinal damage through the regulation of redox and immune homeostasis. HSP and SE offered extra protection during disease for their additional control of inflammation. Our study provided new insight into the use of feed additives in the context of animal health states.

Abstract 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 4 treatments from 4 weeks before until 12 weeks 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, USA). Grain-based SARA challenges were conducted during week 5 (SARA1) and week 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 reduced microbiota richness and diversity and caused fluctuations in major bacterial phyla in rumen liquid microbiota in lactating dairy cows. Supplementation of SCFP postbiotics could attenuate adverse effects of SARA on rumen liquid microbiota.

Pruritic dermatitis (PD) is a common presentation of canine allergic skin diseases, with diversity in severity and treatment response due to complex etiopathogenesis. Evidence suggests the gut microbiota (GM) may contribute to the development of canine allergies. A 10-week double-blind randomized controlled trial evaluated a novel probiotic and nutraceutical blend (PNB) on clinical signs of skin allergy, health measures, and the GM of privately owned self-reported pruritic dogs. A total of 105 dogs were enrolled, with 62 included in pruritus and health analysis and 50 in microbiome analysis. The PNB supported greater improvement of owner-assessed clinical signs of PD at week 2 than the placebo (PBO). More dogs that received the PNB shifted to normal pruritus (digital PVAS10-N: <2) by week 4, compared to week 7 for the PBO. While a placebo effect was identified, clinical differences were supported by changes in the GM. The PNB enriched three probiotic bacteria and reduced abundances of species associated with negative effects. The PBO group demonstrated increased abundances of pathogenic species and reduced abundances of several beneficial species. This trial supports the potential of the PNB as a supplemental intervention in the treatment of PD; however, further investigation is warranted, with stricter diagnostic criteria, disease biomarkers and direct veterinary examination.

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.

Rapid degradation of barley grain (BG, Hordeum vulgare) starch in the rumen can seriously impair rumen fermentation efficiency. Some strategies to curb the negative effects of grain feeding and hamper dysfermentation rely on the usage of phytogenic substances or organic acids. In order to process BGs, they were steeped in 5% lactic acid (BGLA), oregano (BGORE) or thyme (BGTHY) extracts for 48 h. Therefore, an in situ study was conducted to assess the effect of either processed BG or unprocessed BG (control; BGCTRL) on ruminal degradation kinetics (a; soluble fraction, b; potential degradable fraction, c; fractional degradation rate) and effective rumen degradability (ERD) of dry matter (DM), crude protein (CP) and starch. In vitro trials with a 2 x 2 x 4 factorial design were also used to assess the effect of diets which contained intact or processed BGs with different CP [160 (P16) vs. 170 (P17)] g/kg DM) and ruminal protein degradability percentages [90 (low degradability; LD) vs. 115 (high degradability; HD) g/kg DM] on rumen gas production characteristics (b; asymptotic gas volume, c; the constant rate of gas production), yield of microbial crude protein (MCP) and effective utilizable crude protein in the duodenum (EuCP). In situ data demonstrated that BG(LA) compared with BG(CTRL) had significantly lower fractions of "a" (0.22 vs. 0.26, P=0.03) and "c" (0.10 vs. 0.17, P<0.01) and ERD of starch (0.53 vs. 0.64, P.01). The treatment of BGs with the plant extracts, however, was not able to change the in situ parameters relatively to BG(CTRL). Results of the in vitro trials indicated that diets containing processed BG had higher MCP when compared with BG(CTRL) (19.74 vs. 15.85 mg/250 mg DM, P<0.01). Lactic acid and ORE-treated barley decreased the gas production constant rate (c; mL/h) and gas volume after 2 h compared with BG(CTRL) (P <= 0.05). Our study revealed that processed BG can alter the rumen starch degradation pattern, and rumen gas production parameters and increase MCP and EuCP.

Subacute ruminal acidosis (SARA) is a metabolic disorder in dairy cows that is associated with dysbiosis of rumen and hindgut microbiomes, translocation of immunogenic compounds from the gut lumen into blood circulation, and systemic inflammatory response. In this study we hypothesized that Saccharomyces cerevisiae fermentation products (SCFP) attenuate the increases in ruminal and peripheral bacterial endotoxin concentrations and the inflammation resulting from repeated induction of SARA. Lactating Holstein dairy cows (parity 2 and 3+, n = 32) were fed diets with or without SCFP (all from Diamond V) and subjected to 2 episodes of SARA challenges. Cows received a basal total mixed ration (TMR) containing 34% neutral detergent fiber and 18.6% starch, dry matter (DM) basis. Treatments were randomly assigned to control (basal TMR and 140 g/d of ground corn with no SCFP) or 1 of 3 SCFP treatments: basal TMR and 14 g/d Original XPC (SCFPa), 19 g/d NutriTek (SCFPb-1×), or 38 g/d NutriTek (SCFPb-2×) mixed with 126, 121, or 102 g/d of ground corn, respectively. Treatments were implemented from 4 wk before until 12 wk after parturition. During wk 5 (SARA1) and wk 8 of lactation (SARA2), grain-based SARA challenges were conducted by gradually replacing 20% of DM of the basal TMR over 3 d with pellets containing 50% wheat and 50% barley. Ruminal fluid, fecal, and blood samples were collected weekly during Pre-SARA1 (wk 4, as baseline), Post-SARA1 (wk 7), and Post-SARA2 (wk 10 for blood and wk 12 for rumen and fecal parameters) stages, and twice a week during the challenges SARA1 and SARA2. Rumen papillae samples were taken only during Pre-SARA1 and Post-SARA2. We measured the concentrations of free lipopolysaccharides (LPS) in the rumen fluid and feces; free LPS and lipoteichoic acid (LTA) endotoxins in peripheral plasma; interleukin (IL)-1β and IL-6 in peripheral serum; acute-phase proteins, serum amyloid A (SAA), and LPS-binding protein in peripheral plasma; haptoglobin (Hp) in peripheral serum; and myeloperoxidase (MPO) in rumen papillae. Induction of SARA episodes increased free LPS concentrations in rumen fluid and tended to increase LTA in peripheral plasma. The SARA episodes increased concentration of circulating SAA and tended to increase that of IL-1β compared with Pre-SARA1. Induction of SARA did not affect the concentrations of circulating IL-6, Hp, and MPO. The SCFP supplementation reduced plasma concentrations of LTA and SAA and serum concentration of IL-1β compared with control. Additionally, SCFPb-2× tended to reduce ruminal LPS in second-parity cows compared with control. Overall, SCFP supplementation appeared to stabilize the rumen environment and reduce proinflammatory status, hence attenuating adverse digestive and inflammatory responses associated with SARA episodes.

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

Thirty-two dairy cows receiving a basal diet containing 34.9% NDF, and 18.6 % starch, were randomly assigned to four treatments: supplementation either with 140 g/d of ground corn (Control), 126 g/d of ground corn and 14 g/d of XPC (SCFPa, Diamond V Original XPC Cedar Rapids, IA), 121 g/d of ground corn and 19 g/d of NutriTek (SCFPb-1x, NutriTek, Diamond V), or 102 g/d of ground corn and 38 g/d of NutriTek (SCFPb-2x) from 4 wk before until 12 wk after calving. SARA was induced during wk 5 and wk 8 after calving by replacing 20% of the basal diet with pellets containing 50% barley and 50% wheat. Ruminal fluid samples were collected at 6 h after feeding on the second day of wk 4 to wk 10 after calving. Weeks 4, 7 and 10 were considered to be non-SARA. Microbial DNA was extracted, llumina sequenced at the V1–V2 regions of the 16S rRNA gene, and operational taxonomic units (OUT) were assigned using QIIME2. Correlation network analysis (CoNet) determined connections between the relative abundances of OTU, including co-occurrences, and to identify hub OTUs with over 15 connections with other OTUs. The degree of connectedness of phyla was normalized as the total number of positive and negative correlations observed for each phylum divided by their relative abundance in the community. In the Control treatment, SARA reduced positive degree of connectedness (19.33 vs 11.95). In all SCFP treatments, SARA increased the positive degree of connectedness (SCFPb-2x: 25.73 vs 23.50, SCFPb-1x: 87.47 vs 116.32, SCFPa: 34.01 vs 51.56). The relative abundances of the hub taxa Bacteroidales RF16 group and Lachnospiraceae, Christensenellaceae R-7 group and Ricenellaceae RC9 gut group were stabilized by SCFPb-2x. Hence, SCFP attenuated the negative effect of SARA on the co-occurrence patterns in the rumen fluid microbiota.

The human milk microbiome plays an important role in child health and is affected by several factors. We aim to examine whether prenatal diet and supplement intake are associated with human milk microbiota composition. Among the CHILD Cohort Study members, 771 mothers provided data on diet and supplement intake during pregnancy and a milk sample between 2–6 months postpartum. Maternal diet was assessed using a food frequency questionnaire adapted from the Fred Hutchinson Cancer Center. Three dietary patterns were derived using principal component analysis: plant-based, Western, and balanced. The milk microbiome was analyzed using 16S rRNA gene sequencing. Associations between maternal intake and microbial diversity (Shannon index) and genera relative abundances were examined in R using the Wilcoxon signed-rank test adjusted for multiple comparisons. Maternal supplement intake, but not dietary patterns, was associated with human milk microbiota composition. Approximately 88% of the mothers took prenatal multivitamins. Mothers who took fish oil (18%) or folate supplements (17%) during pregnancy had lower microbial diversity than those who did not (mean ± SD: 1.61 ± 0.64 v. 1.79 ± 0.66 for fish oil [p = 0.01] and 1.64 ± 0.64 v. 1.78 ± 0.67 for folate [P = 0.02]). Mothers who took vitamin C supplements (4%), compared to those who did not, had higher microbial diversity (1.99 ± 0.59 v. 1.72 ± 0.65 [P = 0.03]) and higher relative abundance of Veillonella but lower abundances of Finegoldia and Stenotrophomonas (pfdr < 0.05). Compared to the respective supplement non-takers, mothers who took vitamin D supplements (23%) had lower abundance of unclassified Comamonadaceae (pfdr < 0.05), while mothers who took Ca-containing antacids (11%) had higher abundances of Streptococcus, unclassified Gemellaceae, and Rothia but lower abundances of unclassified Comamonadaceae and unclassified Enterobacteriaceae (pfdr < 0.05). Human milk microbiota composition differed among mothers who took specific prenatal supplements. Further analysis is needed to explore additional associations while accounting for covariates that impact the human milk microbiome. CIHR and AllerGen NCE funded the CHILD Cohort Study. The Canadian Lung Association and Canadian Respiratory Research Network funded the milk microbiome sequencing.

Effects of Saccharomyces cerevisiae fermentation products (SCFP) and subacute ruminal acidosis (SARA) on rumen and hindgut fermentation, feed intake, and total tract nutrient digestibilities were determined in 32 lactating Holstein cows between weeks 4 and 9 of lactation. Treatments included control, 14 g·d−1 Diamond V Original XPC™ (SCFPa; Diamond V, Cedar Rapids, IA, USA), 19 g·d−1 NutriTek® (SCFPb-1X; Diamond V), and 38 g·d−1 NutriTek® (SCFPb-2X; Diamond V). During weeks 5 and 8, SARA challenges were conducted by switching from a 18.6% to a 27.9% dry matter (DM) starch diet. This reduced the rumen and feces pH. The durations of the rumen pH below 5.6 during these challenges averaged 175.0, 233.8, 246.9, and 79.3 min·d−1 for the control, SCFPa, SCFPb-1X, and SCFPb-2X treatments, respectively. Hence, SARA was not induced under the SCFPb-2X treatment. The feces pH during the SARA challenges was lowest during SCFPb-2X, suggesting this treatment shifted fermentation from the rumen to the hindgut. The SARA challenges reduced the total tract digestibility of DM, neutral detergent fiber digestibility (NDFd), and phosphorus, but tended to increase that of starch. The SCFPb-2X treatment increased the NDFd from 52.7% to 61.8% (P < 0.05). The SCFPb-2X treatment attenuated impacts of SARA.

Six non-lactating Holstein dairy cows received diets with forage to grain mixture ratios of 100:0 (G0), 75:25 (G25), and 50:50 (G50) that contained 0.5%, 10.0%, and 19.5% dry matter (DM) of starch, respectively. Rumen fluid and feces were sampled, and methane emissions were determined during the last week of 5 wk experimental periods. Taxonomic compositions of microbiota were determined using Illumina 16S rRNA sequencing. Increased grain feeding increased the acidity and volatile fatty acid concentrations of rumen fluid and feces, and decreased methane emissions expressed as L·kg−1 DM. Microbial diversities were highest for G25. The numbers of identified genera in rumen fluid were 185, 182, and 171 for G0, G25, and G50, respectively. In feces, these numbers were 197, 182, and 171 for these diets, respectively. In rumen digesta, seven genera were correlated positively to G0 and negatively to G50, and six genera were correlated negatively to G0 and positively to G50. In feces, 16 genera were correlated positively to G0 and negatively to G50, and 13 genera were correlated negatively to G0 and positively to G50. Increasing grain feeding affected a limited number of genera in rumen digesta and feces. This could not explain treatment effects on the functionalities of microbiota.

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.

Background Effects of Saccharomyces cerevisiae fermentation products (SCFP) on rumen microbiota were determined in vitro and in vivo under a high and a depressed pH. The in vitro trial determined the effects of Original XPC and NutriTek (Diamond V, Cedar Rapids, IA) at doses of 1.67 and 2.33 g/L, respectively, on the abundances of rumen bacteria under a high pH (> 6.3) and a depressed pH (5.8–6.0) using quantitative PCR (qPCR). In the in vivo trial eight rumen-cannulated lactating dairy cows were used in a cross-over design. Cows were randomly assigned to SCFP treatments (Original XPC, Diamond V, Cedar Rapids, IA) or control (No SCFP) before two 5-week experimental periods. During the second period, SCFP treatments were reversed. Cows on the SCFP treatment were supplemented with 14 g/d of SCFP and 126 g/d of ground corn. Other cows received 140 g/d ground corn. During the first 4 wk. of each period, cows received a basal diet containing 153 g/kg of starch. During week 5 of both periods, the rumen pH was depressed by a SARA challenge. This included replacing 208 g/kg of the basal diet with pellets of ground wheat and barley, resulting in a diet that contained 222 g/kg DM of starch. Microbial communities in rumen liquid digesta were examined by pyrosequencing, qPCR, and shotgun metagenomics. Results During the in vitro experiment, XPC and NutriTek increased the relative abundances of Ruminococcus flavefaciens , and Fibrobacter succinogenes determined at both the high and the depressed pH, with NutriTek having the largest effect. The relative abundances of Prevotella brevis , R. flavefaciens , ciliate protozoa, and Bifidobacterium spp. were increased by XPC in vivo. Adverse impacts of the in vivo SARA challenge included reductions of the richness and diversity of the rumen microbial community, the abundances of Bacteroidetes and ciliate protozoa in the rumen as determined by pyrosequencing, and the predicted functionality of rumen microbiota as determined by shotgun metagenomics. These reductions were attenuated by XPC supplementation. Conclusions The negative effects of grain-based SARA challenges on the composition and predicted functionality of rumen microbiota are attenuated by supplementation with SCFP.

Background Quality control including assessment of batch variabilities and confirmation of repeatability and reproducibility are integral component of high throughput omics studies including microbiome research. Batch effects can mask true biological results and/or result in irreproducible conclusions and interpretations. Low biomass samples in microbiome research are prone to reagent contamination; yet, quality control procedures for low biomass samples in large-scale microbiome studies are not well established. Results In this study we have proposed a framework for an in-depth step-by-step approach to address this gap. The framework consists of three independent stages: 1) verification of sequencing accuracy by assessing technical repeatability and reproducibility of the results using mock communities and biological controls; 2) contaminant removal and batch variability correction by applying a two-tier strategy using statistical algorithms (e.g. decontam ) followed by comparison of the data structure between batches; and 3) corroborating the repeatability and reproducibility of microbiome composition and downstream statistical analysis. Using this approach on the milk microbiota data from the CHILD Cohort generated in two batches (extracted and sequenced in 2016 and 2019), we were able to identify potential reagent contaminants that were missed with standard algorithms, and substantially reduce contaminant-induced batch variability. Additionally, we confirmed the repeatability and reproducibility of our reslults in each batch before merging them for downstream analysis. Conclusion This study provides important insight to advance quality control efforts in low biomass microbiome research. Within-study quality control that takes advantage of the data structure ( i.e. differential prevalence of contaminants between batches) would enhance the overall reliability and reproducibility of research in this field.

The pro-inflammatory mediator receptor activator of nuclear factor-kappa B ligand (RANKL) plays a significant role in the development of rheumatoid arthritis; however, its role in inflammatory bowel disease is unknown. Genome-wide association meta-analysis for Crohn’s disease (CD) identified a variant near the TNFSF11 gene that encodes RANKL and CD risk allele increased expression of RANKL in specific cell lines. This study aims to elucidate if the RANKL inhibitor denosumab can reduce the severity of experimental colitis and modify the gut microbiota composition using murine dinitrobenzenesulfonic acid (DNBS)-experimental model of colitis mimicking CD. In colitic conditions, denosumab treatment significantly decreased the pro-inflammatory cytokines IL-6, IL-1β, and TNF-α within the colonic mucosa. Moreover, colitis was accompanied by disruption of gut microbiota, and preventative treatment with denosumab modulated this disruption. Denosumab treatment also modified the alpha- and beta diversity of colonic mucosa and fecal microbiota. These results provide a rationale for considering denosumab as a future potential therapy in CD; however, more detailed experimental and clinical studies are warranted.

Effects of the duration of moderate grain feeding on the taxonomic composition of gastrointestinal microbiota were determined in 15 Holstein yearling steers. Treatments included feeding a diet of 92% dry matter (DM) hay (D0), and feeding a 41.5% barley grain diet for 7 (D7) or 21 d (D21) before slaughter. At slaughter, digesta samples were collected from six regions, i.e., the rumen, jejunum, ileum, cecum, colon, and rectum. Extracted DNA from these samples was analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Three distinct PCoA clusters existed, i.e., the rumen, the jejunum/ileum, and the cecum/colon/rectum. Feeding the grain diet for 7 d reduced microbial diversity in all regions, except the ileum. Extending the duration of grain feeding from 7 to 21 d did not affect this diversity further. Across regions, treatment changed the relative abundances of 89 genera. Most of the changes between D0 and D7 and between D7 and D21 were opposite, demonstrating the resilience of gastrointestinal microbiota to a moderate increase in grain feeding. Results show that the duration of a moderate increase in grain feeding affects how gastrointestinal microbiota respond to this increase.

the rumen to the hindgut. The SARA challenges reduced the total tract digestibility of DM, NDF (NDFd), and P, but tended to increase that of starch. The SCFPb-2X treatment increased 35 the NDFd from 52.7 to 61.8 % (P < 0.05). The SCFPb-2X treatment attenuated impacts of 36 SARA.

Background Fungi constitute an important yet frequently neglected component of the human microbiota with a possible role in health and disease. Fungi and bacteria colonise the infant gastrointestinal tract in parallel, yet most infant microbiome studies have ignored fungi. Milk is a source of diverse and viable bacteria, but few studies have assessed the diversity of fungi in human milk. Results Here we profiled mycobiota in milk from 271 mothers in the CHILD birth cohort and detected fungi in 58 (21.4%). Samples containing detectable fungi were dominated by Candida , Alternaria , and Rhodotorula , and had lower concentrations of two human milk oligosaccharides (disialyllacto-N-tetraose and lacto-N-hexaose). The presence of milk fungi was associated with multiple outdoor environmental features (city, population density, and season), maternal atopy, and early-life antibiotic exposure. In addition, despite a strong positive correlation between bacterial and fungal richness, there was a co-exclusion pattern between the most abundant fungus ( Candida ) and most of the core bacterial genera. Conclusion We profiled human milk mycobiota in a well-characterised cohort of mother-infant dyads and provide evidence of possible host-environment interactions in fungal inoculation. Further research is required to establish the role of breastfeeding in delivering fungi to the developing infant, and to assess the health impact of the milk microbiota in its entirety, including both bacterial and fungal components.