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The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome.

Praveen P, Jordan F, Priami C, Morine MJ - Microbiome (2015)

Bottom Line: This study aims at better understanding the effects of microbial community and feeding mode (breast-fed and formula-fed) on the immune system, by comparing intestinal metagenomic and transcriptomic data from breast-fed and formula-fed babies.Our results show that breast-fed samples co-express genes associated with immunological, metabolic, and biosynthetic activities.Our findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed.

View Article: PubMed Central - PubMed

Affiliation: The Microsoft Research-University of Trento Centre for Computational and Systems Biology, 38068, Rovereto, Italy. praveen@cosbi.eu.

ABSTRACT

Background: The human intestinal microbiota changes from being sparsely populated and variable to possessing a mature, adult-like stable microbiome during the first 2 years of life. This assembly process of the microbiota can lead to either negative or positive effects on health, depending on the colonization sequence and diet. An integrative study on the diet, the microbiota, and genomic activity at the transcriptomic level may give an insight into the role of diet in shaping the human/microbiome relationship. This study aims at better understanding the effects of microbial community and feeding mode (breast-fed and formula-fed) on the immune system, by comparing intestinal metagenomic and transcriptomic data from breast-fed and formula-fed babies.

Results: We re-analyzed a published metagenomics and host gene expression dataset from a systems biology perspective. Our results show that breast-fed samples co-express genes associated with immunological, metabolic, and biosynthetic activities. The diversity of the microbiota is higher in formula-fed than breast-fed infants, potentially reflecting the weaker dependence of infants on maternal microbiome. We mapped the microbial composition and the expression patterns for host systems and studied their relationship from a systems biology perspective, focusing on the differences.

Conclusions: Our findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed. Applying network-based systems biology approach via enrichment of microbial species with host genes revealed the novel key relationships of the microbiota with immune and metabolic activity. This was supported statistically by data and literature.

No MeSH data available.


Related in: MedlinePlus

a Plot showing the distribution of shortest path lengths of a host gene-microbe network under FF and BF conditions. The left skewed distribution of BF networks with smaller diameter (14) shows the small-world properties of the network and a higher robustness (against perturbation) compared to the right skewed FF network with a diameter of 20. b The plot represents the number of nodes that can be reached (Y-axis) after traversing through certain path lengths, (here 1, 2, and 3 along X-axis). The node type referred here are the “DE genes” (differentially expressed genes) from gene expression data, “Species” are the microbes, and “Transient” nodes are the genes mined from literature that were found to share relationship with microbial species. The corresponding networks are available as a network file in Additional file 1 and Additional file 3 (can be opened in cytoscape) and as figures in Additional file 1
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Fig6: a Plot showing the distribution of shortest path lengths of a host gene-microbe network under FF and BF conditions. The left skewed distribution of BF networks with smaller diameter (14) shows the small-world properties of the network and a higher robustness (against perturbation) compared to the right skewed FF network with a diameter of 20. b The plot represents the number of nodes that can be reached (Y-axis) after traversing through certain path lengths, (here 1, 2, and 3 along X-axis). The node type referred here are the “DE genes” (differentially expressed genes) from gene expression data, “Species” are the microbes, and “Transient” nodes are the genes mined from literature that were found to share relationship with microbial species. The corresponding networks are available as a network file in Additional file 1 and Additional file 3 (can be opened in cytoscape) and as figures in Additional file 1

Mentions: Combining the outcomes from the abovementioned results, we could layout the dependence of the microbiota and human system on feeding mode together with the relationship between the microbiota and the human system (see Additional file 1: Figures 0.10 and 0.11 and Additional file 3 (network SIF files)). The differences between the two feeding modes could be observed at this level (Fig. 6). Analyzing the topology of the two networks showed a higher diameter of 20 for the FF than for BF network (14). Furthermore, the BF network showed a considerably higher density and shorter average paths lengths than the FF network (Fig. 6a). These features indicate a greater degree of small-world properties in a BF network and hence robustness against perturbations [31]. To extend our analysis further, we measured the reachability of the nodes starting from a random node in the graph traversing a fixed path length (Fig. 6b). This allows us to measure connectivity in the networks. The results showed that within the denser BF network there are more dependencies (interactions) among the genes than the FF network. The two dense clusters of nodes visible in the BF network (see Additional file 1: Figure 0.10) supports the connectivity analysis done via Fig. 6b.Fig. 6


The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome.

Praveen P, Jordan F, Priami C, Morine MJ - Microbiome (2015)

a Plot showing the distribution of shortest path lengths of a host gene-microbe network under FF and BF conditions. The left skewed distribution of BF networks with smaller diameter (14) shows the small-world properties of the network and a higher robustness (against perturbation) compared to the right skewed FF network with a diameter of 20. b The plot represents the number of nodes that can be reached (Y-axis) after traversing through certain path lengths, (here 1, 2, and 3 along X-axis). The node type referred here are the “DE genes” (differentially expressed genes) from gene expression data, “Species” are the microbes, and “Transient” nodes are the genes mined from literature that were found to share relationship with microbial species. The corresponding networks are available as a network file in Additional file 1 and Additional file 3 (can be opened in cytoscape) and as figures in Additional file 1
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4581423&req=5

Fig6: a Plot showing the distribution of shortest path lengths of a host gene-microbe network under FF and BF conditions. The left skewed distribution of BF networks with smaller diameter (14) shows the small-world properties of the network and a higher robustness (against perturbation) compared to the right skewed FF network with a diameter of 20. b The plot represents the number of nodes that can be reached (Y-axis) after traversing through certain path lengths, (here 1, 2, and 3 along X-axis). The node type referred here are the “DE genes” (differentially expressed genes) from gene expression data, “Species” are the microbes, and “Transient” nodes are the genes mined from literature that were found to share relationship with microbial species. The corresponding networks are available as a network file in Additional file 1 and Additional file 3 (can be opened in cytoscape) and as figures in Additional file 1
Mentions: Combining the outcomes from the abovementioned results, we could layout the dependence of the microbiota and human system on feeding mode together with the relationship between the microbiota and the human system (see Additional file 1: Figures 0.10 and 0.11 and Additional file 3 (network SIF files)). The differences between the two feeding modes could be observed at this level (Fig. 6). Analyzing the topology of the two networks showed a higher diameter of 20 for the FF than for BF network (14). Furthermore, the BF network showed a considerably higher density and shorter average paths lengths than the FF network (Fig. 6a). These features indicate a greater degree of small-world properties in a BF network and hence robustness against perturbations [31]. To extend our analysis further, we measured the reachability of the nodes starting from a random node in the graph traversing a fixed path length (Fig. 6b). This allows us to measure connectivity in the networks. The results showed that within the denser BF network there are more dependencies (interactions) among the genes than the FF network. The two dense clusters of nodes visible in the BF network (see Additional file 1: Figure 0.10) supports the connectivity analysis done via Fig. 6b.Fig. 6

Bottom Line: This study aims at better understanding the effects of microbial community and feeding mode (breast-fed and formula-fed) on the immune system, by comparing intestinal metagenomic and transcriptomic data from breast-fed and formula-fed babies.Our results show that breast-fed samples co-express genes associated with immunological, metabolic, and biosynthetic activities.Our findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed.

View Article: PubMed Central - PubMed

Affiliation: The Microsoft Research-University of Trento Centre for Computational and Systems Biology, 38068, Rovereto, Italy. praveen@cosbi.eu.

ABSTRACT

Background: The human intestinal microbiota changes from being sparsely populated and variable to possessing a mature, adult-like stable microbiome during the first 2 years of life. This assembly process of the microbiota can lead to either negative or positive effects on health, depending on the colonization sequence and diet. An integrative study on the diet, the microbiota, and genomic activity at the transcriptomic level may give an insight into the role of diet in shaping the human/microbiome relationship. This study aims at better understanding the effects of microbial community and feeding mode (breast-fed and formula-fed) on the immune system, by comparing intestinal metagenomic and transcriptomic data from breast-fed and formula-fed babies.

Results: We re-analyzed a published metagenomics and host gene expression dataset from a systems biology perspective. Our results show that breast-fed samples co-express genes associated with immunological, metabolic, and biosynthetic activities. The diversity of the microbiota is higher in formula-fed than breast-fed infants, potentially reflecting the weaker dependence of infants on maternal microbiome. We mapped the microbial composition and the expression patterns for host systems and studied their relationship from a systems biology perspective, focusing on the differences.

Conclusions: Our findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed. Applying network-based systems biology approach via enrichment of microbial species with host genes revealed the novel key relationships of the microbiota with immune and metabolic activity. This was supported statistically by data and literature.

No MeSH data available.


Related in: MedlinePlus