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Breast-feeding associated with a healthy infant gut, new study shows


Escherichia coli (a bacterium implicated in some common neonatal infections)
Miami University computational biologist Iddo Friedberg is part of a new study that shows that breast-feeding may contribute to the development of beneficial bacteria in babies. Early colonization of the gut by microbes in infants is critical for development of their intestinal tract and in immune development, according to the study authors. The results showed that the breast-fed babies had a wider range of microbes in their gut than the formula-fed infants but that their immune systems had developed to cope.

The study is published in the April 30, 2012 issue of BioMed Central’s open access journal Genome Biology,
and is an Editor’s Pick.

Study leader Robert Chapkin, of Texas A&M University, explained, “While we found that the microbiome of breast-fed infants is significantly enriched in genes associated with ‘virulence,’ including resistance to antibiotics and toxic compounds, we also found a correlation between bacterial pathogenicity and the expression of host genes associated with immune and defense mechanisms.”

A Research Highlight review of the study states that it is an “important first step towards better understanding the biological mechanisms underlying the parallel development of host and microbiome during early life. They demonstrate the power of new experimental and analytical approaches that enable the simultaneous analysis of the microbiome and the host response.”

Study Design, Bioinformatics

The human intestine is lined by epithelial cells that process nutrients and provide the first line of defense against food antigens and pathogens, observed the study authors. Approximately one-sixth of intestinal epithelial cells are shed every day into feces, providing a non-invasive picture of what is going on inside the gut.

In this study, the researchers used transcriptome analysis to compare the intestines of three- month-old exclusively breast-fed or formula-fed infants, and relate this to their gut microbes. Transcriptome analysis looks at the small percentage of the genetic code that is transcribed into RNA molecules and is a measure of what genes are actively making proteins. Concurrently the microbes (microbiome) were identified by genetic analysis.

Friedberg, part of the bioinformatic analysis team, said, “my role in the study was to design and run the computational genomic analyses needed to figure out which type of bacteria were living in which baby, and what these bacteria were capable of doing.

I also designed and ran a concurrent analysis to look at which genes were expressed in the baby gut in response to the different bacteria and/or diet.”

Breast milk, immune system, microbe population

The study shows that babies that had been fed only breast milk had a wider range of bacterial colonization than formula-fed babies; they also found a link between the bacteria present and changes in the infant’s expression of genes involved in the immune system.

“Our findings suggest that human milk promotes the beneficial crosstalk between the immune system and microbe population in the gut, and maintains intestinal stability,” Chapkin said.

Study authors

The study, “A Metagenomic Study of Diet-Dependent Interaction Between Gut Microflora and Host in Infants Reveals Differences in Developmental and immune Responses” was authored by Scott Schwartz, Texas A&M University; Iddo Friedberg, assistant professor microbiology and computer science (affiliate), Miami University; Ivan Ivanov, Laurie Davidson, Jennifer Goldsby and David Dahl of Texas A&M University; Damir Herman, University of Arkansas; Mei Wang and Sharon Donovan, University of Illinois; and Robert Chapkin, Texas A&M University.

Material also contributed by BioMed Central

Iddo Friedberg: Bioinformatics

"One aspect of bioinformatics is collaboration: bioinformatics labs often have the skills and the know-how to help push experimental research to new frontiers, and generate verifiable hypotheses. My lab has several such collaborations in which we apply computational tools to experimental research problems presented to us," explained Friedberg.

"With the deluge of molecular sequence and structure data, computational molecular biology or bioinformatics is taking center stage in any research that has to do with molecular biology. My laboratory is developing and applying computational models to the basic questions of life: How do genes and genomes evolve? How is life connected in the most basic molecular level?"

Friedberg recently was awarded a $253,700 Advances in Bioinformatics (ABI) Innovation grant from the National Science Foundation.


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