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Genomics in the Journals Jul 3, 2014

NEW YORK (GenomeWeb) – Diarrheal disease in children from developing countries seems to coincide with broad changes in the composition of microbial communities in the children's guts, according to a study in Genome Biology.

A University of Maryland-led team used 16S ribosomal RNA gene sequencing to identify gut microbial community members in fecal samples from nearly 1,000 children from The Gambia, Mali, Kenya, and Bangladesh. Roughly half of the children had been diagnosed with moderate to severe diarrhea, while half were unaffected controls.

When they compared the gut microbe community members present in children with or without diarrhea, the researchers saw higher-than-usual levels of both pathogenic and non-pathogenic bacterial species in those afflicted with diarrhea.

The gut microbiomes of affected children tended to contain more Campylobacter jejuni and Streptococcus pasteurianus bugs, for example, and microbes from the Escherichia, Shigella, and Granulicatella species. On the other hand, diarrheal disease typically coincided with a dip in representation by Prevotella and Lactobacillus species.

Additional research is needed to verify such associations and determine whether such microbial shifts are a cause or consequence of diarrheal disease. Still, the investigators expressed enthusiasm about the possibility of using information on the newly detected associations to find new strategies for preventing severe diarrheal disease.


In Nature Genetics, an international team led by investigators in Spain described a chromosome 2 locus with apparent ties to delayed or "late" toxicity risk in individuals receiving radiation treatment for prostate cancer.

The researchers used a three-stage genome-wide association study approach to search for genetic factors involved in susceptibility or resistance to radiotherapy toxicity, starting with genotyping data for 741 Spanish prostate cancer patients who'd been treated with external beam radiotherapy.

With the Spanish patient data — and genotyping information on two more cohorts from the UK and North America comprising around 1,000 more prostate cancer patients — the team searched for genetic variants that were over-represented in patients with acute or late radiation toxicity.

A chromosome 2 locus containing the TANC1 gene stood out in independent and combined analyses of the three cohorts. That gene was already believed to be involved in re-growing damaged muscle tissue, pointing to a possible biological explanation for the association. Even so, the study's authors cautioned that additional research is needed to explore the functional effects of the toxicity-associated variant in TANC1.


A PLOS One study suggested that the Cervus elaphus red deer hunted by the Tyrolean Iceman Ötzi more than 5,000 years ago belonged to a mitochondrial lineage that's no longer common in the Italian Alps.

The University of Camerino's Stefania Luciani and colleagues from Italy and Denmark amplified red deer DNA from shafts of hair found on Ötzi's ancient fur clothing and sequenced stretches of the cytochrome b gene in the deer's mitochondrial DNA using Roche 454 sequencing.

Their phylogenetic analysis of the mitochondrial sequences suggested that the Alpine Copper Age red deer belonged to a western European haplogroup resembling Mesola red deer in northern Italy that disappeared from the Alps and Sardinia as a result of deforestation, hunting, and human population growth. In contrast, the re-introduced red deer that are most common to the Italian Alps today tend to fall in the eastern European mitochondrial lineage.

"[W]e can reasonably hypothesize that the Alpine Copper Age red deer and the Mesola deer have had a common origin from a population of … central Europe genetically affiliated to the western mtDNA lineage," Luciani and colleagues wrote. "Afterwards, the fragmentation of this ancestral population led to the genetic diversification of the haplotype of Mesola due to prolonged isolation."


Members of the Environmental Determinants of Diabetes in the Young, or "TEDDY," study group took a prospective approach to assessing the celiac disease risk associated with two different human leukocyte antigen haplotypes.

As they reported in the New England Journal of Medicine, the researchers followed more than 6,400 children from the US, Finland, Germany, and Sweden, looking at the proportion of those with HLA DR3-DQ2 or DR4-DQ8 haplotypes who went on to develop celiac disease-related autoimmunity.

Consistent with past association studies, results of the analysis indicated that children with one or more copies of the HLA DR3-DQ2 haplotype were at somewhat higher risk of developing celiac disease or celiac disease-related autoimmunity by the age of five years old.

Relative to those with the lower risk DR4-DQ8 haplotype, the children with one copy of the DR3-DQ2 haplotype were roughly twice as likely to develop celiac disease autoimmunity, the study authors reported. The risk was higher for homozygotes carrying two copies of the risk haplotype, who appeared almost six times more prone to celiac disease autoimmunity.

The analysis also uncovered a jump in celiac risk for children born in Sweden, pointing to yet undetermined risk environmental factors in addition to associated genetic features in the HLA region and beyond.

"TEDDY's unique structure of having the same protocol in several countries enables us to search for factors that trigger the disease," Lund University's Daniel Agardh, senior author on the study, said in a statement. "By studying similarities and differences between genes and environmental factors in these countries, we hope to pinpoint risk factors for the disease."

The Scan

Driving Malaria-Carrying Mosquitoes Down

Researchers from the UK and Italy have tested a gene drive for mosquitoes to limit the spread of malaria, NPR reports.

Office Space to Lab Space

The New York Times writes that some empty office spaces are transforming into lab spaces.

Prion Pause to Investigate

Science reports that a moratorium on prion research has been imposed at French public research institutions.

Genome Research Papers on Gut Microbe Antibiotic Response, Single-Cell RNA-Seq Clues to Metabolism, More

In Genome Research this week: gut microbial response to antibiotic treatment, approach to gauge metabolic features from single-cell RNA sequencing, and more.