Inclusion of whole grains in the diet of humans has been shown to improve the postprandial metabolic response and is considered to promote health and prevent certain diseases. Less is known about effects of different whole grains on the metabolic response in dogs. The objective of the present study was to investigate and compare the metabolic and hormonal response in dogs fed extruded diets containing whole grains from rye, oat or wheat, three commonly grown cereals in the Nordic countries. The study was performed in a cross-over design using 18 healthy adult privately-owned dogs. Three extruded experimental diets were produced containing whole grain flour of either rye (RYE), wheat (WHE) or ground rolled oats (OAT) at 25% inclusion level. The diets were nutritionally complete and comparable in terms of protein and metabolizable energy content. Each diet was fed for 4 wk, with blood sampling on the last day of each period (fasting sample followed by post-prandial samples at 20, 40, 60, 120, 180, and 240 min). The resulting number of repetitions per diet was: WHE: n = 16, OAT: n = 17, RYE: n = 17. The blood samples were analyzed to determine glucose, insulin, glucagon-like peptide-1 (GLP-1), glucagon, triacylglycerol (TAG) and cholesterol concentrations. There were no main effects of diet on postprandial blood response curves and no effect of interaction of diet and time for any of the variables analyzed. Evaluation of area under the curve (AUC) showed higher total concentration following the OAT than WHE diet for glucose (P = 0.035), GLP-1 (P = 0.006) as well as TAG (P = 0.025). Fasting insulin concentration was higher following RYE compared with both other diets (P = 0.005), but there were no differences in insulin AUC between the diets. In the early postprandial phase (0–120 min), there was an overall effect of diet on the ratio of insulin to GLP-1 (P = 0.042). Post hoc test was not significant, but the WHE diet resulted in a numerically higher value than the other two diets. In conclusion, the postprandial response curves were in general similar between the diets and imply that, in dogs, whole rye or oats may not be more beneficial than whole wheat.

Abstract We conducted a longitudinal profiling of environmental resistomes and microbiomes from ten Swedish pig farms in a low–antimicrobial usage context. Samples were collected from pig pen environments and analysed using shotgun metagenomic sequencing. Resistome and microbiome profiles showed stronger temporal than farm-specific variation, with several age-associated trends. Age-related trajectories diverged between microbiome and resistome, indicating that resistance dynamics are shaped by factors beyond microbial succession. The highest relative abundance of resistance determinants was observed for tetracyclines, followed by aminoglycosides, macrolide–lincosamide–streptogramin antibiotics, beta-lactams, and folic acid synthesis inhibitors—drug classes commonly used in Swedish pig production. Resistome patterns were partially associated with phenotypic resistance profiles from previous studies, while analysis of antimicrobial usage alone could not fully explain the observed resistome. Overall, these findings suggest that additional factors beyond antimicrobial usage contribute to the persistence and dissemination of antibiotic resistance genes in pig farm environments.

Wholegrain rye, considered one of the cereals with the highest content of dietary fiber and bioactive compounds, has been linked with reduced risk of cardiometabolic diseases. Thus, biomarkers reflecting its intake and/or the metabolic effect after consumption are essential to better elucidate its health effects. Our aim was to identify plasma metabolite biomarkers associated with a high-fiber rye intervention and to assess the associations between these metabolites, gut microbiota composition, and cardiometabolic risk factors in a 12-week randomized controlled trial comparing a hypocaloric diet with high-fiber rye (n = 108) or refined wheat (n = 99) in participants with obesity. Rye intervention increased plasma concentrations of benzoxazinoids (DIBOA-S) and phenylacetamides (2-HPA-S and 2-HHPA-S), gut microbial metabolites (indolepropionic acid, 2-aminophenol, enterolactone sulfate, and enterolactone glucuronide), betainized compounds (pipecolic-betaine), phenolic acids (2,6-DHBA and gallic acid-4-sulfate), and diverse endogenous metabolites. Microbiota composition changes were increased Eubacterium xylanophilum and Agathobacter and decreased Ruminococcus torques and Romboutsia. Moreover, the intervention effect was mostly captured by changes in metabolites and gut microbiota compared to clinical variables. Gallic acid-4-sulfate and phenylacetamides were associated with reductions in weight, fat mass, BMI, or fasting insulin levels even after adjusting for plasma alkylresorcinols, used as markers for rye intake compliance. Altogether, these metabolites may constitute biomarkers of wholegrain rye cardiometabolic effects.

Aquaculture is recognized as a key future food source, and to sustain increasing production and reduce the ecological footprint, new protein sources are needed. However, replacing the conventional fish and soybean meals may affect fillet quality. This study examined a phylogenetically broad set of protein sources and their effects on sensory attributes and metabolism of rainbow trout (Oncorhynchus mykiss). Five feeds derived from microfungi, black soldier fly, mealworm, blue mussel, and tunicate were evaluated against a soy-based control. Sensory attributes were assessed using Rate-All-That-Apply, and 1H NMR metabolomics to analyze feed and muscle metabolomes. Phylogenetically closer protein sources showed more similar feed and muscle metabolite profiles, and only minor differences in color, root vegetable taste, and aroma were found. Metabolic effects involved osmoregulation, energy, and amino acid metabolism. Overall, insect-based feeds appeared most favorable based on sensory results and product quality biomarkers; however, all tested feeds remained viable.

This study evaluated the prebiotic potential of cello-oligosaccharides (COS) produced from birch (Betula pendula), an under-utilised lignocellulosic source from the forestry industry, on growth performance, mucosal immunity, gut microbiota composition, and antioxidant capacity of juvenile rainbow trout (Oncorhynchus mykiss). In a 45-day trial, the fish were fed with diets containing 0%, 0.1%, 0.5% and 1.5% COS, while a diet containing fructo-oligosaccharides (0.5% FOS) was used as a positive control. Fish fed with the 0.5% and 1.5% COS diets showed significantly (P < 0.05) higher abundance of Ruminococcaceae, Bacillaceae and Lactobacillaceae, in the faecal microbiota. The COS diets also induced higher antioxidant capacity in the gut and serum, but there were no treatment effects (P > 0.05) on growth of rainbow trout. Gene expression analysis of the intestine showed significant elevation (P < 0.05) in expression of complement (c3 and c-type lectin) and receptor (tlr2) genes of the innate immune system in COS-fed fish. However, for cytokine and adaptive immune genes, no significant differences (P > 0.05) in gene transcripts were observed between the COS/FOS diets with the control diet. These results suggest that dietary cello-oligosaccharides can be a useful feed supplement for rainbow trout, which can modulate intestinal microbial communities, innate immune response and antioxidant capacity of the host.

BACKGROUND:Knowledge about the variability of gut microbiota within an individual over time is important to allow meaningful investigations of the gut microbiota in relation to diet and health outcomes in observational studies. Plant-based dietary patterns have been associated with a lower risk of morbidity and mortality and may alter gut microbiota in a favorable direction. OBJECTIVES:To assess the gut microbiota variability during one year and investigate the association between adherence to diet indexes and the gut microbiota in a Danish population. METHODS:Four hundred forty-four participants were included in the Diet, Cancer, and Health - Next Generations MAX study (DCH-NG MAX). Stool samples collected up to three times during a year were analyzed by 16S ribosomal ribonucleic acid gene sequencing. Diet was obtained by 24-hour dietary recalls. Intraclass correlation coefficient (ICC) was calculated to assess temporal microbial variability based on 214 individuals. Diet indexes (Nordic, Mediterranean, and plant-based diets) and food groups thereof were associated with gut microbiota using linear regression analyses. RESULTS:We found that 91 out of 234 genera had an ICC >0.5. We identified three subgroups dominated by Bacteroides, Prevotella 9, and Ruminococcaceae and adherence to diet indexes differed between subgroups. Higher adherence to diet indexes was associated with the relative abundance of 22 genera. Across diet indexes, higher intakes of fruit, vegetables, whole grains/cereals, and nuts were most frequently associated with these genera. CONCLUSIONS:In the DCH-NG MAX study, 39% of the genera had an ICC >0.5 over one year, suggesting that these genera could be studied with health outcomes in prospective analyses with acceptable precision. Adherence to the Nordic, Mediterranean, and plant-based diets differed between bacterial subgroups and was associated with a higher abundance of genera with fiber-degrading properties. Fruits, vegetables, whole grains/cereals, and nuts were frequently associated with these genera.

Salmonids, specifically Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), are commonly farmed and their gut microbiota plays important roles for optimal growth, health, and physiology. However, differences in experimental design, technical factors and bioinformatics make it challenging to compare the results from different studies and draw general conclusions about their influence on the fish gut microbiota. For a more comprehensive understanding of the gut microbiota, we collected all the publicly accessible 16S rRNA gene sequencing data with clearly stated sample metadata from freshwater Atlantic salmon and rainbow trout intestinal contents and mucosa sequenced on the Illumina MiSeq platform. A total of 783 samples from 19 published studies were included in this meta-analysis to test the impact of the technical, environmental, and host-accociated factors. This meta-analysis revealed that all the tested factors significantly influenced the alpha and beta diversities of the gut microbiota of salmon and trout. Technical factors, especially target region and DNA extraction kit, affected the beta diversity to a larger extent, while host-associated and environmental factors, especially diet and initial fish weight, had a higher impact on the alpha diversity. Salmon had a higher alpha diversity and higher abundance of Enterococcus and Staphylococcus than trout, which had higher abundance of Weissella and Mycoplasma. The results of this meta-analysis fill in a critical knowledge gap that demonstrate technical methodologies must be standardized and factors associated with host and environment need to be accounted for in the future design of salmonid gut microbiota experiments. A systematic meta-analysis of 19 studies found that technical factors (target region and DNA extraction kit) had the most significant effects on the fish gut microbiota followed by environmental factors (diet and rearing system) and host factors (initial weight, intestinal region and fish species). Images from Biorender.com. image

Factors contributing to variations in the quality and microbiota of ensiled forages and in bulk tank microbiota in milk from cows fed different forages were investigated. Nutritional quality, fermentation parameters and hygiene quality of forage samples and corresponding bulk tank milk samples collected in 3 periods from 18 commercial farms located in northern Sweden were compared. Principal coordinates analysis revealed that the microbiota in forage and bulk milk, analyzed using 16S rRNA gene-based amplicon sequencing, were significantly different. The genera Lactobacillus, Weissella and Leuconostoc dominated in forage samples, whereas Pseudomonas, Staphylococcus and Streptococcus dominated in bulk milk samples. Forage quality and forage-associated microbiota were affected by ensiling method and by use of silage additive. Forages stored in bunker and tower silos (confounded with use of additive) were associated with higher levels of acetic and lactic acid and Lactobacillus. Forage ensiled as bales (confounded with no use of additive) was associated with higher dry matter content, water-soluble carbohydrate content, pH, yeast count and the genera Weissella, Leuconostoc and Enterococcus. For bulk tank milk samples, milking system was identified as the major factor affecting the microbiota and type of forage preservation had little impact. Analysis of common amplicon sequence variants (ASVs) suggested that forage was not the major source of Lactobacillus found in bulk tank milk.

Background: Cattle colonised by the zoonotic pathogen verotoxin-producing Escherichia coli of serotype O157 (VTEC O157) can shed high levels of the pathogen in their faeces. A suggested key for controlling VTEC O157 is preventing colonisation of individuals.Aim: In this study the role of individual super-shedders and factors related to susceptibility and environmental exposure in the transmission of VTEC O157 among dairy calves are explored.Methods: The association between sex, age, pen hygiene, pen type and stocking density and colonisation of individual calves, established by recto-anal mucosal swabs, on farms where pathogenic VTEC O157 had been confirmed was investigated. In a follow-up sampling, the consistency of previously identified risk factors and the role of shedding pen mates was assessed by studying the risk of new/re-colonisation.Results: The results suggest an important role of stocking density that decreases with age, possibly due to increased resistance to colonisation following exposure. However, previous colonisation did not influence the risk of being colonised in the second sampling. Super-shedders (shedding >103 colony forming units/g faeces) significantly increased the risk of colonisation in peers (OR = 10, CI 4.2–52). In addition, environmental factors associated with survival of the bacteria, affected risk.Conclusion: The results confirm the suggested importance of super-shedders but also emphasises the importance of considering the combined exposure from peers and the environment.

This study evaluated the effect of whole and autolysed Yarrowia lipolytica CBS 7504 strain on growth performance, gut immunity and gut microbiota composition in juvenile rainbow trout (Oncorhynchus mykiss). Fish were fed diets containing 2% and 5% whole or autolysed Y. lipolytica (WY and AY) in a 45-day trial, with a no-yeast diet as control. Log2 fold change analysis of Y. lipolytica diets showed relative change in abundance and association of certain microbial taxa with respect to control such as a correlation between the relative abundance of Desulfovibrionaceae in diets with WY. Moreover, diets at 5% and 2% levels demonstrated a synergistic association with relative levels of Sphingobacteriaceae and Rhodobacteraceae, respectively. However, the overall analyses showed little/no impact of Y. lipolytica supplementation on overall intestinal microbial composition, growth parameters and body indices. Gene expression analysis of the intestine revealed significant elevation in expression of immune-related genes of the complement pathway (c3 and c-type lectin), membrane receptor pathway (tlr2 and tlr5), mucosal innate immune pathway (muc-2), cytokines (tnf-α) and adaptive immune pathway (igt and cd4) in 5% WY. In conclusion, it can be inferred that dietary Y. lipolytica can be a useful functional feed supplement for rainbow trout when used as whole yeast at a 5% inclusion level since it can modulate gut microbial communities and act as a potential immunostimulant for the host.

This study investigated seasonal variations in the composition of the kelp species Saccharina latissima cultivated on the Swedish west coast and, using an in vitro fermentation system, evaluated the effect of fermented whole S. latissima biomass or biomass components on the gut microbiota of broiler chickens. Caecal contents of six Ross 308 broilers fed a standard wheat and soy -based diet were retrieved on two different occasions, with three birds sampled per occasion. Two in vitro fermentation batches (A, B) were established using caecal contents as inoculum, and whole S. latissima, ethanol -washed S. latissima, laminarin extract or inulin (control) as substrate. Total short -chain fatty acid (SCFA) content, gas production, pH and changes in microbiota composition were studied after 6, 12 and 24 h of fermentation. Analysis of seasonal variations revealed that S. latissima harvested in June had the highest laminarin content and lowest ash and crude protein content. Broiler microbiota, SCFA profile, gas production and pH mainly varied depending on fermentation inoculum, but there were also some variations depending on substrate. For instance, uncultured bacterium from Clostridiales_vadinBB60_group showed higher relative abundance (RA) in batch A, while Faecalibacterium showed higher RA in batch B. Whole and ethanol -washed S. latissima resulted in highest RA of unclassified Ruminococcaceae and Tyzzerella for both batches, while ethanol -washed S. latissima and laminarin gave highest RA of Erysipelatoclostridium. Inulin resulted in highest RA for the genus Subdoligranulum. Acetic, nbutyric and propionic acid were the main fermentation products and total SCFA level was higher in batch B. Within batch B, inulin and laminarin generated higher levels of acetic and butyric acid. When using inulin and laminarin, gas production was lower in batch B compared with batch A. In summary, this study showed that S. latissima is a good source of laminarin, especially when harvested in summer. Within the in vitro system, the microbiota was affected by different substrates, but inoculum source was identified as an important contributor to microbial community development during fermentation.

Dietary fiber in dog food is reported to promote healthy gut microbiota, but few studies have investigated the effects of whole-grain cereals, which contain a variety of fiber types and other bioactive compounds. The aim of the present study was to compare the effects of diets containing whole-grain rye (RYE), oats (OAT) and wheat (WHE) on fecal microbiota and short-chain fatty acid production. Eighteen dogs were fed three experimental diets, each for four weeks, in a cross-over design. Fecal samples were collected at the end of each diet period. Analysis of 16S rRNA gene amplicons showed that family Lachnospiraceae and genus Bacteroides were the gut microbial groups most affected by diet, with lowest relative abundance following consumption of RYE and a trend for a corresponding increase in genus Prevotella_9. Fecal acetate and propionate concentrations were higher after consumption of RYE compared with OAT. In conclusion, rye had the strongest effect on gut microbiota and short-chain fatty acids, although the implications for dog gut health are not yet elucidated.

The global prevalence of type 2 diabetes mellitus (T2DM) has surged in recent decades, and the identification of differential glycemic responders can aid tailored treatment for the prevention of prediabetes and T2DM. A mixed meal tolerance test (MMTT) based on regular foods offers the potential to uncover differential responders in dynamical postprandial events. We aimed to fit a simple mathematical model on dynamic postprandial glucose data from repeated MMTTs among participants with elevated T2DM risk to identify response clusters and investigate their association with T2DM risk factors and gut microbiota. Data were used from a 12-week multi-center dietary intervention trial involving high-risk T2DM adults, comparing high- versus low-glycemic index foods within a Mediterranean diet context (MEDGICarb). Model-based analysis of MMTTs from 155 participants (81 females and 74 males) revealed two distinct plasma glucose response clusters that were associated with baseline gut microbiota. Cluster A, inversely associated with HbA1c and waist circumference and directly with insulin sensitivity, exhibited a contrasting profile to cluster B. Findings imply that a standardized breakfast MMTT using regular foods could effectively distinguish non-diabetic individuals at varying risk levels for T2DM using a simple mechanistic model.

Abstract Receiving the same results from repeated analysis of the same sample is a basic principle in science. The inability to reproduce previously published results has led to discussions of a reproducibility crisis within science. For studies of microbial communities, the problem of reproducibility is more pronounced and has, in some fields, led to a discussion on the very existence of a constantly present microbiota. In this study, DNA from 44 bovine milk samples were extracted twice and the V3–V4 region of the 16S rRNA gene was sequenced in two separate runs. The FASTQ files from the two data sets were run through the same bioinformatics pipeline using the same settings and results from the two data sets were compared. Milk samples collected maximally 2 h apart were used as replicates and permitted comparisons to be made within the same run. Results show a significant difference in species richness between the two sequencing runs although Shannon and Simpson's diversity was the same. Multivariate analyses of all samples demonstrate that the sequencing run was a driver for variation. Direct comparison of similarity between samples and sequencing run showed an average similarity of 42%–45% depending on whether binary or abundance‐based similarity indices were used. Within‐run comparisons of milk samples collected maximally 2 h apart showed an average similarity of 39%–47% depending on the similarity index used and that similarity differed significantly between runs. We conclude that repeated DNA extraction and sequencing significantly can affect the results of a low microbial biomass microbiota study.

Fermentation has long been utilized to preserve and enhance the flavor and nutritional value of foods. Recently, fermented foods have gained popularity, reaching new consumer groups due to perceived health benefits. However, the microbial composition of many fermented foods re-mains unknown. Here, we characterized the bacterial composition, diversity, and richness of 47 fermented foods available in Sweden, including kombucha, water kefir, milk kefir, yogurt, plant-based yogurt alternatives, kimchi, sauerkraut, and fermented vegetables. Via 16S rRNA gene sequencing, we identified 2497 bacteria (amplicon sequence variants). The bacterial composition was strongly associated with the type of fermented food, and lactic acid bacteria and/or acetic acid bacteria dominated most samples. However, each fermented food had a unique composition, with kombucha and water kefir having the highest diversity across and within samples. Few bacteria were abundant in multiple foods and food groups. These were Streptococcus thermophilus in yogurts and plant-based yoghurts; Lactococcus lactis in milk kefirs and one water kefir; and Lactiplantibacillus plantarum in kimchi, sauerkraut, and fermented cucumber. The broad range of fermented foods included in this study and their diverse bacterial communities warrant further investigation into the implications of microbial compositions for product traits and potential impact on human health.

BACKGROUND:A mechanistic understanding of the effects of dietary treatment in irritable bowel syndrome (IBS) is lacking. Our aim was therefore to investigate how fermentable oligo- di-, monosaccharides, and polyols (FODMAPs) and gluten affected gut microbiota and circulating metabolite profiles, as well as to investigate potential links between gut microbiota, metabolites, and IBS symptoms.METHODS:We used data from a double-blind, randomized, crossover study with week-long provocations of FODMAPs, gluten, and placebo in participants with IBS. To study the effects of the provocations on fecal microbiota, fecal and plasma short-chain fatty acids, the untargeted plasma metabolome, and IBS symptoms, we used Random Forest, linear mixed model and Spearman correlation analysis.RESULTS:FODMAPs increased fecal saccharolytic bacteria, plasma phenolic-derived metabolites, 3-indolepropionate, and decreased isobutyrate and bile acids. Gluten decreased fecal isovalerate and altered carnitine derivatives, CoA, and fatty acids in plasma. For FODMAPs, modest correlations were observed between microbiota and phenolic-derived metabolites and 3-indolepropionate, previously associated with improved metabolic health, and reduced inflammation. Correlations between molecular data and IBS symptoms were weak.CONCLUSIONS:FODMAPs, but not gluten, altered microbiota composition and correlated with phenolic-derived metabolites and 3-indolepropionate, with only weak associations with IBS symptoms. Thus, the minor effect of FODMAPs on IBS symptoms must be weighed against the effect on microbiota and metabolites related to positive health factors.

Background Rye intake has been associated with beneficial effects on health in human interventions, possibly due to dietary fiber in rye. In dogs, few studies have explored the effects on health of dietary fiber in general, and rye fiber in particular. The aim of this study was to investigate how inclusion of rye, compared with wheat, influenced fecal microbiota composition, short chain fatty acids (SCFA) and apparent total tract digestibility (ATTD) in dogs. Six male Beagle dogs (mean age 4.6 years, SEM 0.95 years; mean body weight 14.6 kg, SEM 0.32 kg) were fed three experimental diets, each for 21 days, including an adaptation period of six days and with 2–2.5 months between diet periods. The diets were similar regarding energy and protein, but had different carbohydrate sources (refined wheat (W), whole grain rye (R), or an equal mixture of both (RW)) comprising 50% of total weight on a dry matter (DM) basis. The diets were baked and titanium dioxide was added for ATTD determination. Fecal samples were collected before and in the end of each experimental period. Fecal microbiota was analyzed by sequencing 16S rRNA gene amplicons and fecal SCFA by high-performance liquid chromatography. Crude protein, crude fat, neutral detergent fiber, and gross energy (GE) in food and feces were analyzed and ATTD of each was determined. Univariate and multivariate statistical methods were applied in data evaluation. Results Faecal microbiota composition, differed depending on diet ( P = 0.002), with samples collected after consumption of the R diet differing from baseline. This was primarily because of a shift in proportion of Prevotella , which increased significantly after consumption of the R diet ( P < 0.001). No significant differences were found for SCFA, but there was a tendency ( P < 0.06) for higher molar proportions of acetic acid following consumption of the R diet. The ATTD of crude protein, crude fat, neutral detergent fiber, and GE was lower after consumption of the R diet compared with the other diets ( P < 0.05). Conclusions Consumption of the R diet, but not RW or W diets, was associated with specific shifts in microbial community composition and function, but also with lower ATTD.

Fermentation of dietary fiber by gut microbes produces short-chain fatty acids (SCFA), but fermentation outcomes are affected by dietary fiber source and microbiota composition. The aim of this study was to investigate the effect of two different fecal microbial compositions on in vitro fermentation of a standardized amount of oat, rye, and wheat breads. Two human fecal donors with different microbial community composition were recruited. Bread samples were digested enzymatically. An in vitro fermentation model was used to study SCFA production, dietary fiber degradation, pH, and changes in microbiota. Feces from donor I had high relative abundance of Bacteroides and Escherichia/Shigella , whereas feces from donor II were high in Prevotella and Subdoligranulum. Shifts in microbiota composition were observed during fermentation. SCFA levels were low in the samples with fecal microbiota from donor I after 8 h of fermentation, but after 24 h acetate and propionate levels were similar in the samples from the different donors. Butyrate levels were higher in the fermentation samples from donor II, especially with rye substrate, where high abundance of Subdoligranulum was observed. Dietary fiber degradation was also higher in the fermentation samples from donor II. In conclusion, fermentation capacity and substrate utilization differed between the two different microbiota compositions.

The effects of early supplementation with oat β-glucan during the suckling period on piglet gut microbiota composition, concentrations of short-chain fatty acids, and gut physiological markers were assessed. Fifty piglets from five litters, balanced for sex and birth weight, were divided within litters into two treatment groups: β-glucan and control. Piglets in the β-glucan group received the supplement three times/week from day 7 of age until weaning. Rectal swab samples were collected from 10 piglets per treatment group (balanced across litters) from week 1 to week 4, and plasma samples were collected at 1, 3, and 4 weeks of age. Additional samples of intestinal tissues and jugular and portal vein plasma were collected from 10 animals at weaning (one per treatment group and litter). The concentrations of short-chain fatty acids in plasma and the microbiota composition in rectal swabs were mainly influenced by piglet age, rather than the supplement. There were significant differences in microbiota composition between litters and several correlations between concentrations of short-chain fatty acids in plasma and specific microbial taxa in rectal swabs. Overall, β-glucan supplementation did not have any clear impact on the gut environment in suckling piglets, whereas a clear age-related pattern emerged.

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.