Consumption of traditional Sardinian fermented milk promotes changes in the rat gut microbiota composition and functions
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Abbondio M., Palomba A., Serra M., Fraumene C., Di Meo C., Marongiu F., Sau R., Pagnozzi D., Laconi E., Tanca A., Uzzau S.
Journal
BMC microbiology
Year
2025
BACKGROUND: 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, as well as with metabolites resulting from lactose fermentation. Currently, there is very little scientific knowledge on how dietary supplementation with fermented milk affects the composition of the gut microbiota and its metabolic activities. RESULTS: We integrated 16 S rRNA gene-based taxonomic profiling with metaproteomics-based functional analysis to investigate gut microbiota changes in rats exposed to an 8-week dietary supplementation with casu axedu, a traditional fermented milk produced within rural communities in Sardinia (Italy). Several microbial taxa showed a significantly increased abundance at the end of the dietary treatment, including Phascolarctobacterium, Prevotella, Blautia glucerasea, and Lactococcus lactis, while Bacteroides dorei and Helicobacter rodentium were decreased compared to the control rats. Metaproteomic analysis highlighted a striking reshaping of the Prevotella proteome 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 enzymes involved in succinate biosynthesis was observed, which in turn significantly boosted the abundance of Phascolarctobacterium and its production of propionate. Fermented milk consumption also promoted 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. CONCLUSIONS: Our integrated multi-omics approach reveals that dietary supplementation with the traditional Sardinian fermented milk, casu axedu, induces significant shifts in the rat gut microbiota composition and function, characterized by the enrichment of beneficial taxa and metabolic pathways associated with improved gut health and reduced inflammation.
Experiment 1
Needs review
Subjects
- Location of subjects
- Italy
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Rattus norvegicus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- (R)-lactic acid (-)-lactic acid,(2R)-2-hydroxypropanoic acid,(R)-(-)-lactic acid,C3H6O3,D-2-Hydroxypropanoic acid,D-2-Hydroxypropionic acid,D-Lactic acid,D-lactic acid,D-Milchsaeure,LACTIC ACID,(R)-lactic acid
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ctrl (Control group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FM (Fermented milk group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats fed standard chow-diet supplemented with casu axedu (Traditional Sardinian fermented sheep milk) for 8 weeks.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Figure 3
Description: Comparison of gut microbiota composition between rats fed a standard chow diet (control group) and those fed chow supplemented with fermented milk casu axedu (20% w/w) over eight weeks, analysed using 16S rRNA gene sequencing and metaproteomics.
Abundance in Group 1: increased abundance in FM (Fermented milk group)
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia glucerasea | ||
| Lactococcus lactis | ||
| Phascolarctobacterium | ||
| Prevotella |
Revision editor(s): Fadimatou Inna
Signature 2
Needs review
Source: Figure 3
Description: Comparison of gut microbiota composition between rats fed a standard chow diet (control group) and those fed chow supplemented with fermented milk casu axedu (20% w/w) over eight weeks, analysed using 16S rRNA gene sequencing and metaproteomics.
Abundance in Group 1: decreased abundance in FM (Fermented milk group)
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter rodentium | ||
| Phocaeicola dorei |
Revision editor(s): Fadimatou Inna
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ctrl (control) diet
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FM (fermented milk) diet
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Gut microbiota of rats after 8 weeks of dietary treatment comparing fermented milk-fed (FM) rats to control (Ctrl) rats.
- Sequencing type
- Not specified
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Not specified
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- T-Test
Signature 1
Needs review
Source: Figure 4
Description: Comparison of gut microbiota composition between rats fed a standard chow diet (control group) and those fed chow supplemented with fermented milk casu axedu (20% w/w) over eight weeks.
Abundance in Group 1: increased abundance in FM (fermented milk) diet
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus albus | ||
| Phocaeicola massiliensis | ||
| Phascolarctobacterium succinatutens |
Revision editor(s): Fadimatou Inna
Signature 2
Needs review
Source: Figure 4
Description: Comparison of gut microbiota composition between rats fed a standard chow diet (control group) and those fed chow supplemented with fermented milk casu axedu (20% w/w) over eight weeks.
Abundance in Group 1: decreased abundance in FM (fermented milk) diet
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter rodentium | ||
| Phocaeicola dorei |
Revision editor(s): Fadimatou Inna
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