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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 The heatmap showing the abundance of microbes at species level, in breast-fed and formula-fed infants. Green and red shades indicate lower and higher percent abundances, respectively, with species along the Y-axis and samples along X-axis. The clustering was performed with the “Ward” method based on Pearson scores. b Scatter plot representing the log p values (Y-axis) and fold changes (X-axis) for microbial abundance to detect the differentially abundant bacterial species. The blue-green circles indicate the differentially abundant microbial species under FF and BF conditions
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Fig2: a The heatmap showing the abundance of microbes at species level, in breast-fed and formula-fed infants. Green and red shades indicate lower and higher percent abundances, respectively, with species along the Y-axis and samples along X-axis. The clustering was performed with the “Ward” method based on Pearson scores. b Scatter plot representing the log p values (Y-axis) and fold changes (X-axis) for microbial abundance to detect the differentially abundant bacterial species. The blue-green circles indicate the differentially abundant microbial species under FF and BF conditions

Mentions: The microbial diversity (see Additional file 1) in our analysis partially differ from Schwartz et al. potentially due to the use of a more updated marker sequence-based database [28] for Bowtie 2 [29]. The filtering of the microbiota results to the species level showed 35 taxonomic species (with 4 of the data points showing equal relatedness with more that one species, hence designated as unclassified (see Additional file 1)). The metagenomic features (microbial abundances) provided a clear distinction between the two feeding types (Fig. 2a). We performed a differential abundance analysis (see “Methods”) that revealed four species to be differentially abundant in the samples given the two feeding types (Fig. 2b). The four species included three Bifidobacterium species together with Ruminococcus gnavus. The gap in diversity also widened for the species level enrichment (see Additional file 1).Fig. 2


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 The heatmap showing the abundance of microbes at species level, in breast-fed and formula-fed infants. Green and red shades indicate lower and higher percent abundances, respectively, with species along the Y-axis and samples along X-axis. The clustering was performed with the “Ward” method based on Pearson scores. b Scatter plot representing the log p values (Y-axis) and fold changes (X-axis) for microbial abundance to detect the differentially abundant bacterial species. The blue-green circles indicate the differentially abundant microbial species under FF and BF conditions
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: a The heatmap showing the abundance of microbes at species level, in breast-fed and formula-fed infants. Green and red shades indicate lower and higher percent abundances, respectively, with species along the Y-axis and samples along X-axis. The clustering was performed with the “Ward” method based on Pearson scores. b Scatter plot representing the log p values (Y-axis) and fold changes (X-axis) for microbial abundance to detect the differentially abundant bacterial species. The blue-green circles indicate the differentially abundant microbial species under FF and BF conditions
Mentions: The microbial diversity (see Additional file 1) in our analysis partially differ from Schwartz et al. potentially due to the use of a more updated marker sequence-based database [28] for Bowtie 2 [29]. The filtering of the microbiota results to the species level showed 35 taxonomic species (with 4 of the data points showing equal relatedness with more that one species, hence designated as unclassified (see Additional file 1)). The metagenomic features (microbial abundances) provided a clear distinction between the two feeding types (Fig. 2a). We performed a differential abundance analysis (see “Methods”) that revealed four species to be differentially abundant in the samples given the two feeding types (Fig. 2b). The four species included three Bifidobacterium species together with Ruminococcus gnavus. The gap in diversity also widened for the species level enrichment (see Additional file 1).Fig. 2

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