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Genomics in the Journals: Apr 17, 2014

NEW YORK (GenomeWeb News) – In Nature Communications, researchers from Germany, the US, Italy, Tanzania, and the UK described distinct features they found when profiling the gut microbiomes of individuals from an African hunter-gatherer population.

The team used 16S ribosomal RNA gene sequencing, mass spectrometry, and other methods to test fecal samples from 27 Hadza individuals representing two different Rift Valley region groups that have maintained a traditional hunter-gatherer lifestyle. The samples were subsequently compared to those collected from 16 Italian individuals living in cities and consuming a largely Mediterranean diet.

In general, researchers saw far higher levels of diversity and species richness in the Hadza gut microbial communities than in gut microbiomes from the urban Italian individuals, with more than one-third of genera in Hadza gut microbiomes being newly reported.

There were also subtle gut microbial differences between male and female members of the hunter-gatherer population, as well as differences between the Hadza gut microbiomes and those in farming populations from Africa.

When they tested fecal samples from children and adults from farming groups in Malawi and Burkina Faso and compared gut microbial community patterns to those found in Hadza and Italian individuals, the researchers found lower-than usual representation by Bifidobacterium in the hunter-gatherers. On the other hand, Hadza gut microbiomes had higher levels of microbes suspected of assisting in plant digestion, including members of Prevotella and Treponema genera and unclassified members of the Bacteroidetes phylum.

"[T]he characterization of the Hadza [gut microbiome] presents a suite of unique features that suggest specific adaptation to a foraging lifestyle, which includes a large proportion of highly refractory plant foods," corresponding author Amanda Henry, with the Max Planck Institute for Evolutionary Anthropology, and colleagues wrote.

"We expect that detailed study of the function of this [gut microbiome] community will expose a greater number of genetic specializations for degrading polysaccharides than what is currently found in other human populations."

For another Nature Communications study, a team from the US, Canada, and Belgium looked at interactions between various splicing isoforms of genes implicated in autism spectrum disorder.

The researchers focused on 191 genes believed to contribute to ASD, mapping interactions between the genes themselves as well as the brain-expressed RNA splice variants they encode. Those splicing isoforms were cloned from adult and fetal brain samples with the help of high-throughput sequencing and an isoform detection pipeline.

The resulting interactome map, which the group dubbed the Autism Spliceform Interaction Network, pointed to some previously unknown interactions between splice variants of different ASD contributors. It also highlighted interactions between the protein products of ASD risk genes and those linked to other neurodevelopmental conditions.

"What we see from this network is that different variants of the same protein could alter the wiring of the entire system," senior author Lilia Iakoucheva, a psychiatry researcher at the University of California at San Diego, said in a statement.

"With this assembled autism network, we can begin to investigate how newly discovered mutations from patients may disrupt this network," she added. "This is an important task because the mechanism by which mutant proteins contribute to autism in 99.9 percent of cases remains unknown."

A study by investigators from the National Cancer Institute and elsewhere in the journal Cancer Research highlighted metabolites that appear to be found at unusual levels in the urine of individuals with lung cancer.

The team used liquid chromatography-mass spectrometry to gauge the levels of molecules smaller than around 1,500 Daltons in urine samples from 469 individuals with lung cancer and 536 unaffected control individuals.

Following validation testing at additional time points and in other cases and controls, the researchers were left with two compounds found at significantly higher levels in urine samples from individuals with lung cancer: a newly described molecule called creatine riboside and another compound known as N-acetylneuramic acid, or NANA.

That pair of compounds showed particularly enhanced levels in the urine of lung cancer patients with poor outcomes, the study authors noted. Based on their findings so far, they argued that "[c]reatine riboside and NANA may be robust urinary clinical metabolomic markers that are elevated in tumor tissue and associated with early lung cancer diagnosis and worse prognosis."

A brief report in the New England Journal of Medicine from researchers from France, Germany, Guinea, Switzerland, and the Republic of Congo outlined efforts to characterize a form of Zaire ebolavirus (EBOV) that caused a Guinean outbreak reported to the World Health Organization this past March.

After determining that EBOV was behind the often-deadly infections in Guinea, investigators did genome sequencing on the strain, which was then included in a phylogenetic analysis involving four-dozen sequenced viruses from the same filovirus family.

For instance, they found that the version of EBOV behind the Guinea epidemic belongs to a phylogenetic clade distinct from clusters of strains involved in Ebola infections in the Democratic Republic of Congo or Gabon. Together with epidemiological evidence, the genetic data suggests that a new strain of EBOV emerged and began causing infections in Guinea by around December of last year.

"It is possible that EBOV has circulated undetected in this region for some time," senior author Stephan Günther, with Germany's Bernhard Nocht Institute for Tropical Medicine, and his colleagues concluded. "The emergence of the virus in Guinea highlights the risk of EBOV outbreaks in the whole West African sub-region."