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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

The microbiome co-abundance networks based on Bray-Curtis similarity under FF and BF conditions. Node color indicates the genera of the organisms as shown in the legend. The “unclassified” in the species name refers to the sequences that could be attributed to more than one species with equal likelihoods. The isolated nodes represent the absence of co-occurrence among the species
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Fig3: The microbiome co-abundance networks based on Bray-Curtis similarity under FF and BF conditions. Node color indicates the genera of the organisms as shown in the legend. The “unclassified” in the species name refers to the sequences that could be attributed to more than one species with equal likelihoods. The isolated nodes represent the absence of co-occurrence among the species

Mentions: We used the abundance data to understand the relationship among the microbial species detected in the samples. We computed the Bray-Curtis similarity among the samples (see “Methods”) to create two microbial community networks, one for each feeding type (Fig. 3). We conducted a permutation test to check whether our computed microbial community network could have been generated just by chance. We ran a permutation test against 1000 randomly permuted networks with the same set of nodes (preserving the network degree). The p value of 0.0465 for FF networks, and 0.0008 for BF network was obtained (showing that the networks were not just by chance).Fig. 3


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)

The microbiome co-abundance networks based on Bray-Curtis similarity under FF and BF conditions. Node color indicates the genera of the organisms as shown in the legend. The “unclassified” in the species name refers to the sequences that could be attributed to more than one species with equal likelihoods. The isolated nodes represent the absence of co-occurrence among the species
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: The microbiome co-abundance networks based on Bray-Curtis similarity under FF and BF conditions. Node color indicates the genera of the organisms as shown in the legend. The “unclassified” in the species name refers to the sequences that could be attributed to more than one species with equal likelihoods. The isolated nodes represent the absence of co-occurrence among the species
Mentions: We used the abundance data to understand the relationship among the microbial species detected in the samples. We computed the Bray-Curtis similarity among the samples (see “Methods”) to create two microbial community networks, one for each feeding type (Fig. 3). We conducted a permutation test to check whether our computed microbial community network could have been generated just by chance. We ran a permutation test against 1000 randomly permuted networks with the same set of nodes (preserving the network degree). The p value of 0.0465 for FF networks, and 0.0008 for BF network was obtained (showing that the networks were not just by chance).Fig. 3

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