Fermented dairy products influence on human gut microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB26974 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2598370.fastq.gz | Fastqsanger.gz | |||
| ERR2598380.fastq.gz | Fastqsanger.gz | |||
| ERR2598390.fastq.gz | Fastqsanger.gz | |||
| ERR2598400.fastq.gz | Fastqsanger.gz | |||
| ERR2598410.fastq.gz | Fastqsanger.gz |
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Project description:Shotgun proteomics analysis of 14 different Enterococcus strains from dairy and fermented products.
2022-10-13 | PXD036435 | Pride
Project description:The consumption of fermented food has been linked to positive health outcomes due to a variety of functional properties. Fermented dairy constitutes a major dietary source and contains lactoseas main carbohydrate and living starter cultures. To investigate whether nutritional and microbial modulation impacted intestinal microbiota composition and activity, we employed fecal microbiota fermentations and a dairy model system consisting of lactose and β-galactosidase positive and negative Streptococcus thermophilus. Based on 16S rRNA gene based microbial community analysis, we observed that lactose addition increased the abundance of Bifidobacteriaceae, and of Veillonellaceae and Enterobacteraceae in selected samples. The supplied lactose was hydrolysed within 24 h of fermentation and led to higher expression of community indigenous β-galactosidases. Targeted protein analysis confirmed that bifidobacteria contributed most β-galactosidases together with other taxa including Escherichia coli and Anaerobutyricum hallii. Lactose addition led to 1.1-1.8 fold higher levels of butyrate compared to controls likely due to (i) lactate-crossfeeding and (ii) direct lactose metabolism by butyrate producing Anaerobutyricum and Faecalibacterium spp. Representatives of both genera used lactose to produce butyrate in single cultures. When supplemented at around 5.5 log cells mL-1, S. thermophilus or its beta-galactosidase negative mutant outnumbered the indigenous Streptococcaceae population at the beginning of fermentation but had no impact on lactose utilisation and final SCFA profiles. This study brings forward new fundamental insight into interactions of major constituents of fermented dairy with the intestinal microbiota. We provide evidence that lactose addition increases fecal microbiota production of butyrate through cross-feeding and direct metabolism without contribution of starter cultures.
2025-01-30 | PXD054534 | Pride
Project description:Introduction: Fermented milk products are part of the staple diet for many Mediterranean populations. Most of these traditional foods are enriched with lactobacilli and other lactic acid bacteria and metabolites resulting from lactose fermentation. There is currently very little scientific knowledge on the influence of diet supplementation with fermented milk on the gut microbiota metabolism and composition. Methods: We integrated 16S rRNA gene-based taxonomic profiling with metaproteomic-based functional analysis to investigate the gut microbiota modifications in rats exposed for 8 weeks to diet supplementation with casu axedu, a traditional fermented milk produced within rural communities in Sardinia (Italy). Results and Discussion: Several taxa showed a significantly increased abundance at the end of the dietary treatment, including Phascolarctobacterium, Prevotella, Blautia glucerasea, and Akkermansia muciniphila, while Bifidobacterium, Lachnoclostridium, Odoribacter, Bacteroides dorei and Dubosiella newyorkensis were decreased compared to the control rats. Metaproteomic analysis highlighted a striking reshape of the Prevotella proteome profile in agreement with its blooming in casu axedu-fed animals, suggesting an increase of the glycolytic activity through the Embden Meyerhof Parnas Pathway over the Entner Doudoroff Pathway. Moreover, an increased production of succinate was observed, which in turn significantly boosted the abundance of Phascolartcobacterium and its production of propionate. Fermented milk consumption was also associated with promotion of microbial synthesis of branched chain essential amino acids L-valine and L-leucine. Finally, metaproteomic data indicated a reduction of bacterial virulence factors and host inflammatory markers, suggesting that the consumption of casu axedu can have beneficial effects on the gut mucosa health.
2025-09-29 | PXD054645 | Pride
Project description:Understanding how the human gut microbiota and host are impacted by probiotic bacterial strains requires carefully controlled studies in humans, and in mouse models of the gut ecosystem where potentially confounding variables that are difficult to control in humans can be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of adult female monozygotic twin pairs through repeated sampling 4 weeks prior to, 7 weeks during, and 4 weeks following consumption of a commercially-available fermented milk product (FMP) containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were studied prior to and after gavage with all five sequenced FMP strains. 140 samples total. Evaluation of changes in a model community's structure over time after exposure to a consortium of 5 fermented milk product (FMP) strains.
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Project description:Understanding how the human gut microbiota and host are impacted by probiotic bacterial strains requires carefully controlled studies in humans, and in mouse models of the gut ecosystem where potentially confounding variables that are difficult to control in humans can be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of adult female monozygotic twin pairs through repeated sampling 4 weeks prior to, 7 weeks during, and 4 weeks following consumption of a commercially-available fermented milk product (FMP) containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were studied prior to and after gavage with all five sequenced FMP strains. 73 samples total. Evaluation of changes in a model community's metatranscriptome over time after exposure to a consortium of 5 fermented milk product (FMP) strains (40 samples); evaluation of the gene expression of the FMP strains in other in vitro conditions, including MRS medium (B. animalis subsp. lactis only, 4 samples) and a commercial FMP fermentation (all 5 strains, 6 samples); evaluation of the gene expression of native human microbiomes before and after the consumption of a commercial FMP (23 samples).
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Project description:Bacillus licheniformis-fermented products (BLFP) are probiotics with antibacterial, antiviral, and anti-inflammatory properties that can improve growth performance. This study aimed to, firstly, compare the fecal microbiota of cats with chronic diarrhea (n = 8) with that of healthy cats (n = 4) from the same household using next-generation sequencing and, secondly, evaluate the effectiveness of oral administration of BLFP in relieving clinical signs and altering the intestinal microbiota in diarrheal cats. Six out of eight cats with diarrhea showed clinical improvement after BLFP administration for 7 days, and in two cats the stool condition was normal. A higher Firmicutes/Bacteroidetes ratio was noted in the feces of diarrheal cats without clinical improvement as compared with those in the healthy control group and in the diarrheal cats with clinical improvement after receiving BLFP. The phylum Bacteroidetes and class Bacteroidia decreased significantly in diarrheal cats regardless of BLFP administration. Blautia spp., Ruminococcus torques, and Ruminococcus gnavus, which belong to the Clostridium cluster XIVa and have been reported as beneficial to intestinal health, increased significantly in feces after BLFP treatment. Furthermore, a significant decrease in Clostridium perfringens was noted in diarrheal cats after BLFP administration. Overall, BLFP could be a potential probiotic to relieve gastrointestinal symptoms and improve fecal microbiota in cats with chronic diarrhea.
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Project description:Accumulated data suggests that the gut microbiome can rapidly respond to changes in diet. Consumption of fermented dairy products (FDP) fortified with probiotic microbes may be associated with positive impact on human health. However, the extent and details of the possible impact of FDP consumption on gut community structure tends to vary across individuals. We used microbiome analysis to characterize changes in gut microbiota composition after 30 days of oral intake of a yoghurt fortified with Bifidobacterium animalis subsp. lactis BB-12. 16S rRNA gene sequencing was used to assess the gut microbial composition before and after FDP consumption in healthy adults (n = 150). Paired comparison of gut microbial content demonstrated an increase in presence of potentially beneficial bacteria, particularly, Bifidobacterium genus, as well as Adlercreutzia equolifaciens and Slackia isoflavoniconvertens. At a functional level, an increased capacity to metabolize lactose and synthesize amino acids was observed accompanied by a lowered potential for synthesis of lipopolysaccharides. Cluster analysis revealed that study volunteers segregated into two groups with post-intervention microbiota response that was dependent on the baseline microbial community structure.
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