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Glycan cross-feeding activities between bifidobacteria under in vitro conditions.

Turroni F, Özcan E, Milani C, Mancabelli L, Viappiani A, van Sinderen D, Sela DA, Ventura M - Front Microbiol (2015)

Bottom Line: The glycan-associated metabolic features encoded by bifidobacteria are believed to be strongly influenced by cross-feeding activities due to the co-existence of strains with different glycan-degrading properties.This enhanced growth phenomenon was confirmed by whole genome transcriptome analyses, which revealed co-cultivation-associated transcriptional induction of PRL2010 genes involved in carbohydrate metabolism, such as those encoding for carbohydrate transporters and associated energy production, and genes required for translation, ribosomal structure, and biogenesis, thus supporting the idea that co-cultivation of certain bifidobacterial strains with B. bifidum PRL2010 causes enhanced metabolic activity, and consequently increased lactate and/or acetate production.Overall, these data suggest that PRL2010 cells benefit from the presence of other bifidobacterial strains.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma Italy.

ABSTRACT
Bifidobacteria colonize the gut of various mammals, including humans, where they may metabolize complex, diet-, and host-derived carbohydrates. The glycan-associated metabolic features encoded by bifidobacteria are believed to be strongly influenced by cross-feeding activities due to the co-existence of strains with different glycan-degrading properties. In this study, we observed an enhanced growth yield of Bifidobacterium bifidum PRL2010 when co-cultivated with Bifidobacterium breve 12L, Bifidobacterium adolescentis 22L, or Bifidobacterium thermophilum JCM1207. This enhanced growth phenomenon was confirmed by whole genome transcriptome analyses, which revealed co-cultivation-associated transcriptional induction of PRL2010 genes involved in carbohydrate metabolism, such as those encoding for carbohydrate transporters and associated energy production, and genes required for translation, ribosomal structure, and biogenesis, thus supporting the idea that co-cultivation of certain bifidobacterial strains with B. bifidum PRL2010 causes enhanced metabolic activity, and consequently increased lactate and/or acetate production. Overall, these data suggest that PRL2010 cells benefit from the presence of other bifidobacterial strains.

No MeSH data available.


Related in: MedlinePlus

Transcriptomic profiling of genes predicted to be involved in the metabolism of carbohydrates by bifidobacteria in response to the different bi- associations. (A) The heat-map of transcriptional profiling of genes up-regulated in B. bifidum PRL2010 when this strain was co-cultivated with B. adolescentis 22L on starch-based medium. (B) The heat-map representing the transcriptional profiling of genes up-regulated in B. bifidum PRL2010 and in B. breve 12L when they were grown in bi-association on starch-based medium. (C) The heat-map representing the transcriptional profiling of genes up-regulated in B. bifidum PRL2010 and B. breve 12L when they were co-cultivated on xylan-based medium. (D) The heat-map representing the transcriptional profiling of the up-regulated genes in B. bifidum PRL2010 when was co-cultivated with B. thermophilum JCM1207 on xylan-based medium. Colors (black to green) represent the average signal intensity.
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Figure 3: Transcriptomic profiling of genes predicted to be involved in the metabolism of carbohydrates by bifidobacteria in response to the different bi- associations. (A) The heat-map of transcriptional profiling of genes up-regulated in B. bifidum PRL2010 when this strain was co-cultivated with B. adolescentis 22L on starch-based medium. (B) The heat-map representing the transcriptional profiling of genes up-regulated in B. bifidum PRL2010 and in B. breve 12L when they were grown in bi-association on starch-based medium. (C) The heat-map representing the transcriptional profiling of genes up-regulated in B. bifidum PRL2010 and B. breve 12L when they were co-cultivated on xylan-based medium. (D) The heat-map representing the transcriptional profiling of the up-regulated genes in B. bifidum PRL2010 when was co-cultivated with B. thermophilum JCM1207 on xylan-based medium. Colors (black to green) represent the average signal intensity.

Mentions: In order to evaluate the molecular aspects behind the cross-feeding activity as observed for some of the bi-associations involving the PRL2010–22L strain combination, or the PRL2010–12L strain combination when cultivated on starch, or the PRL2010–JCM1207 combination when grown on xylan, RNAseq experiments of these strain combinations cultivated on either of these substrates were performed. In order to increase the robustness of our RNAseq data, two technical replicates starting from the same library for each RNAseq trial were performed. When compared to the reference condition (mono-association) it was identified that the number of genes whose expression in either PRL2010 or the other strains, was significantly up-regulated (greater than or equal to twofold change, p < 0.005) ranged from 0 to 121. We used cluster orthologous gene (COG) analysis in order to identify differentially transcribed genes that may contribute to specific biological functions within the gut. As illustrated in Figure 1, carbohydrate metabolism, corresponding to COG category [G], is one of the COG functions of PRL2010 most significantly affected by the interaction with another bifidobacterial strain. This is probably due to a response to the presence of specific breakdown capabilities exploited by 22L, 12L, or JCM1207 cells. In this context, we observed an up-regulation of an ABC-type transporter-encoding gene (BBPR_1824), as well as an major facilitator superfamily (MFS) transporter-encoding gene (BBPR_0146), thus possibly involved in the uptake of simple sugars when co-cultivated with 22L or 12L cells on MRS containing starch as a unique carbon source (Figure 3). This finding can be explained by the fact that the extracellular amylases encoded by strains 22L (Duranti et al., 2014) and 12L (Bottacini et al., 2014) generate simple carbohydrates, which may then be imported by PRL2010 cells through its carbohydrate transporter arsenal (Turroni et al., 2012). Other transcriptionally induced genes of B. bifidum PRL2010 cells encompass enolase (BBPR_0711), glucose-6-phosphate isomerase (BBPR_354), phosphoglycerate kinase (BBPR_1038), glyceraldehyde 3-phosphate dehydrogenase (BBPR_0587), and phosphoglycerate mutase (BBPR_1487), whose functions are predicted to be related to (carbohydrate-dependent) energy production and conversion through the glycolytic pathway (Supplementary Figure S1). These observations indicate that PRL2010 cells have enhanced flux through their central fermentative pathway in the presence of 22L or 12L cells. Notably, we also observed the enhanced transcription of genes encoding the various subunits of the ATPase system of PRL2010 strain, which may occur in response to medium acidification as a result of enhanced metabolic activity. Co-cultivation of PRL2010 cells with strain JCM1207 on a xylan-based medium also increased the transcription levels of genes that are predicted to be involved in the carbohydrate metabolism (Figure 3). In particular, 121 genes of PRL2010 exhibited transcriptional up-regulation. The upregulated genes include several ORFs-encoding glycolytic enzymatic repertoire of PRL2010, such as enolase (BBPR_0711), phosphoglycerate mutase (BBPR_1487), and pyruvate kinase (BBPR_0747; Figure 3).


Glycan cross-feeding activities between bifidobacteria under in vitro conditions.

Turroni F, Özcan E, Milani C, Mancabelli L, Viappiani A, van Sinderen D, Sela DA, Ventura M - Front Microbiol (2015)

Transcriptomic profiling of genes predicted to be involved in the metabolism of carbohydrates by bifidobacteria in response to the different bi- associations. (A) The heat-map of transcriptional profiling of genes up-regulated in B. bifidum PRL2010 when this strain was co-cultivated with B. adolescentis 22L on starch-based medium. (B) The heat-map representing the transcriptional profiling of genes up-regulated in B. bifidum PRL2010 and in B. breve 12L when they were grown in bi-association on starch-based medium. (C) The heat-map representing the transcriptional profiling of genes up-regulated in B. bifidum PRL2010 and B. breve 12L when they were co-cultivated on xylan-based medium. (D) The heat-map representing the transcriptional profiling of the up-regulated genes in B. bifidum PRL2010 when was co-cultivated with B. thermophilum JCM1207 on xylan-based medium. Colors (black to green) represent the average signal intensity.
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Related In: Results  -  Collection

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Figure 3: Transcriptomic profiling of genes predicted to be involved in the metabolism of carbohydrates by bifidobacteria in response to the different bi- associations. (A) The heat-map of transcriptional profiling of genes up-regulated in B. bifidum PRL2010 when this strain was co-cultivated with B. adolescentis 22L on starch-based medium. (B) The heat-map representing the transcriptional profiling of genes up-regulated in B. bifidum PRL2010 and in B. breve 12L when they were grown in bi-association on starch-based medium. (C) The heat-map representing the transcriptional profiling of genes up-regulated in B. bifidum PRL2010 and B. breve 12L when they were co-cultivated on xylan-based medium. (D) The heat-map representing the transcriptional profiling of the up-regulated genes in B. bifidum PRL2010 when was co-cultivated with B. thermophilum JCM1207 on xylan-based medium. Colors (black to green) represent the average signal intensity.
Mentions: In order to evaluate the molecular aspects behind the cross-feeding activity as observed for some of the bi-associations involving the PRL2010–22L strain combination, or the PRL2010–12L strain combination when cultivated on starch, or the PRL2010–JCM1207 combination when grown on xylan, RNAseq experiments of these strain combinations cultivated on either of these substrates were performed. In order to increase the robustness of our RNAseq data, two technical replicates starting from the same library for each RNAseq trial were performed. When compared to the reference condition (mono-association) it was identified that the number of genes whose expression in either PRL2010 or the other strains, was significantly up-regulated (greater than or equal to twofold change, p < 0.005) ranged from 0 to 121. We used cluster orthologous gene (COG) analysis in order to identify differentially transcribed genes that may contribute to specific biological functions within the gut. As illustrated in Figure 1, carbohydrate metabolism, corresponding to COG category [G], is one of the COG functions of PRL2010 most significantly affected by the interaction with another bifidobacterial strain. This is probably due to a response to the presence of specific breakdown capabilities exploited by 22L, 12L, or JCM1207 cells. In this context, we observed an up-regulation of an ABC-type transporter-encoding gene (BBPR_1824), as well as an major facilitator superfamily (MFS) transporter-encoding gene (BBPR_0146), thus possibly involved in the uptake of simple sugars when co-cultivated with 22L or 12L cells on MRS containing starch as a unique carbon source (Figure 3). This finding can be explained by the fact that the extracellular amylases encoded by strains 22L (Duranti et al., 2014) and 12L (Bottacini et al., 2014) generate simple carbohydrates, which may then be imported by PRL2010 cells through its carbohydrate transporter arsenal (Turroni et al., 2012). Other transcriptionally induced genes of B. bifidum PRL2010 cells encompass enolase (BBPR_0711), glucose-6-phosphate isomerase (BBPR_354), phosphoglycerate kinase (BBPR_1038), glyceraldehyde 3-phosphate dehydrogenase (BBPR_0587), and phosphoglycerate mutase (BBPR_1487), whose functions are predicted to be related to (carbohydrate-dependent) energy production and conversion through the glycolytic pathway (Supplementary Figure S1). These observations indicate that PRL2010 cells have enhanced flux through their central fermentative pathway in the presence of 22L or 12L cells. Notably, we also observed the enhanced transcription of genes encoding the various subunits of the ATPase system of PRL2010 strain, which may occur in response to medium acidification as a result of enhanced metabolic activity. Co-cultivation of PRL2010 cells with strain JCM1207 on a xylan-based medium also increased the transcription levels of genes that are predicted to be involved in the carbohydrate metabolism (Figure 3). In particular, 121 genes of PRL2010 exhibited transcriptional up-regulation. The upregulated genes include several ORFs-encoding glycolytic enzymatic repertoire of PRL2010, such as enolase (BBPR_0711), phosphoglycerate mutase (BBPR_1487), and pyruvate kinase (BBPR_0747; Figure 3).

Bottom Line: The glycan-associated metabolic features encoded by bifidobacteria are believed to be strongly influenced by cross-feeding activities due to the co-existence of strains with different glycan-degrading properties.This enhanced growth phenomenon was confirmed by whole genome transcriptome analyses, which revealed co-cultivation-associated transcriptional induction of PRL2010 genes involved in carbohydrate metabolism, such as those encoding for carbohydrate transporters and associated energy production, and genes required for translation, ribosomal structure, and biogenesis, thus supporting the idea that co-cultivation of certain bifidobacterial strains with B. bifidum PRL2010 causes enhanced metabolic activity, and consequently increased lactate and/or acetate production.Overall, these data suggest that PRL2010 cells benefit from the presence of other bifidobacterial strains.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma Italy.

ABSTRACT
Bifidobacteria colonize the gut of various mammals, including humans, where they may metabolize complex, diet-, and host-derived carbohydrates. The glycan-associated metabolic features encoded by bifidobacteria are believed to be strongly influenced by cross-feeding activities due to the co-existence of strains with different glycan-degrading properties. In this study, we observed an enhanced growth yield of Bifidobacterium bifidum PRL2010 when co-cultivated with Bifidobacterium breve 12L, Bifidobacterium adolescentis 22L, or Bifidobacterium thermophilum JCM1207. This enhanced growth phenomenon was confirmed by whole genome transcriptome analyses, which revealed co-cultivation-associated transcriptional induction of PRL2010 genes involved in carbohydrate metabolism, such as those encoding for carbohydrate transporters and associated energy production, and genes required for translation, ribosomal structure, and biogenesis, thus supporting the idea that co-cultivation of certain bifidobacterial strains with B. bifidum PRL2010 causes enhanced metabolic activity, and consequently increased lactate and/or acetate production. Overall, these data suggest that PRL2010 cells benefit from the presence of other bifidobacterial strains.

No MeSH data available.


Related in: MedlinePlus