Characterization of the Bacterial Composition of 47 Fermented Foods in Sweden

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

Differential Responders to a Mixed Meal Tolerance Test Associated with Type 2 Diabetes Risk Factors and Gut Microbiota-Data from the MEDGI-Carb Randomized Controlled Trial

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

Similarity in milk microbiota in replicates

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

Supplementation of Lactobacillus early in life alters attention bias to threat in piglets

Gut microbes play an important role in regulating brain processes and influence behaviour, cognition and emotional states in humans and rodents. Nevertheless, it is not known how ingestion of beneficial microbes modulates emotional states in piglets and whether it can improve welfare. Here we use an attention bias task to assess the effects of Lactobacillus reuteri ATCC-PTA-6475 and Lactobacillus plantarum L1-6 supplementation early in life on emotional states in 33 piglets compared to 31 placebo supplemented piglets. We hypothesized that Lactobacillus supplementation would reduce vigilance behaviour (head at shoulder height or higher) and attention (head oriented towards the threat) in response to an auditory threat. The results showed that the control group increased vigilance behaviour in response to the threat, but there was no increase in the probiotics group. Despite the increased vigilance, the control group paid less attention to the threat. One explanation may be that control piglets avoided looking in the direction of the threat just because they perceived it as more threatening, but further research is necessary to confirm this. In conclusion, Lactobacillus supplementation may be a suitable tool to reduce anxiety, promote a more appropriate response to a challenge and so improve welfare

Chemical composition and physical characteristics of faeces in horses with and without free faecal liquid - two case-control studies

Background Free faecal liquid (FFL) is a condition in horses characterised by two-phase (one solid and one liquid) separation of faeces. Causes of the condition are unknown, but disturbed hindgut fermentation has been suggested as it may alter biochemical composition and appearance of faeces in equines. However, information on faecal composition in horses with FFL is scarce. Faecal chemical composition (dry matter, osmolality, ash, macro minerals, short-chain fatty acids (SCFA) and pH) and physical characteristics (free liquid, sand, water holding capacity and particle size distribution) were compared in horses with (case) and without (control) FFL in two sub-studies. In sub-study I, faeces from 50 case-control horse pairs in Sweden and Norway were sampled in three sampling periods (SP1-SP3). In sub-study II, faeces from 32 case-control horse pairs in Germany were sampled on one occasion. Results In sub-study I, faecal concentration and proportion of lactic acid (of total short-chain fatty acids, SCFA) and water holding capacity was lower in case compared to control horses. Other variables (content of dry matter, ash, sodium, calcium, phosphorous, magnesium, sulphur, and concentrations of i-butyric, n-valeric and total SCFA, ammonia-N as proportion of total N, and pH) were similar in faeces from case and control horses. In sub-study II, all analysed variables were similar in faecal samples from case and control horses. Faecal particle size distribution was similar in case and control horses, but the proportion of larger particles (2 and 1 mm) were lower and proportion of smaller particles (< 1 mm) was higher in sub-study I compared to in sub-study II. Conclusions To the authors' knowledge, this is the first study to investigate faecal chemical composition and physical characteristics in horses with FFL. Case and control horses had similar total SCFA, pH and osmolality, indicating that hindgut fermentation was similar. However, small differences in concentration and proportion (of total SCFA) of lactic acid and water holding capacity of faeces were shown and are of interest for further studies of horses with FFL

In vitro fermentation of substrates from Saccharina latissima by broiler chicken's caecal microbiota

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

Fecal microbiota composition affects in vitro fermentation of rye, oat, and wheat bread

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

Yarrowia lipolytica yeast as a dietary supplement for rainbow trout (Oncorhynchus mykiss): Effects on gut microbiota, health and immunity

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-alpha) 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

Effects of rye inclusion in dog food on fecal microbiota and short-chain fatty acids

BackgroundRye 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.ResultsFaecal 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).ConclusionsConsumption 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

Composition and short-term stability of gut microbiota in lean and spontaneously overweight healthy Labrador retriever dogs

Background The gut microbiota and its metabolic end-products act in close collaboration with the nutrient metabolism of the animal. A relationship between excess adiposity and alterations in gut microbiota composition has been identified in humans and rodents, but data are scarce for overweight dogs. This study compared composition and temporal variations of gut microbiota in healthy lean and spontaneously overweight dogs. The analysis was based on three individual fresh faeces samples from each dog during a 10-day period. Twenty-seven healthy and intact male Labrador retriever dogs were included, 12 of which were classified as lean (body condition score (BCS) 4-5 on a 9-point scale) and 15 as overweight (BCS 6-8). Gut microbiota was analysed by Illumina sequencing of the V3-V4 region of the 16S rRNA gene. Results Lean and overweight groups of dogs were not separated by principal coordinate analysis (PCoA), analysis of similarity (one-way ANOSIM, P = 0.99) or species indicator analysis (IndVal) using operational taxonomic units (OTU) data. Gut microbial taxa at phylum, family or genus level did not differ between lean and overweight dogs in mixed-model repeated measures analyses. Short-term stability, evaluated by similarity index, did not differ between lean and overweight dogs over the 10-day period. Pooled Firmicutes/Bacteroidetes (F/B) ratio was 3.1 +/- 3.7 in overweight dogs and 2.1 +/- 1.2 in lean dogs (P = 0.83). Individual dogs, irrespective of body condition (lean or overweight), displayed variation in mean alpha diversity (Chao-1 index range 122-245, Shannon index range 2.6-3.6) and mean similarity index (range 44-85%). Conclusions Healthy lean and spontaneously overweight Labrador retriever dogs had comparable gut microbiota composition and short-term stability over a 10-day sampling period. There were no alterations in microbial diversity or in relative abundance of specific taxa at phylum, family or genus level in overweight compared to lean dogs. Our findings suggest that there are few detectable differences in gut microbiota composition between healthy spontaneously overweight and lean dogs by the current method. Future application of metagenomic or metabolomic techniques could be used to investigate microbial genes or microbial end-products that may differ even when microbiota compositional analyses fail to detect a significant difference between lean and overweight dogs