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Healthy Gut Microbiome Variation, Disease-Related Declines Described in New Studies

NEW YORK (GenomeWeb) – A pair of studies out today are providing new details on gut microbial community characteristics that coincide with conditions such as Crohn's disease or response to salt-heavy diets.

In one of two new papers in Nature, researchers from Belgium outlined findings from a gut microbiome analysis that used a quantitative microbiome profiling (QMP) approach to assess levels of microbial representation in gut communities. For their analysis, the investigators applied the QMP method, which uses a combination of amplicon sequencing and microbial cell-tallying flow cytometry, to fecal samples from 40 individuals.

"Until now, proportional approaches have been the standard in microbiome research," corresponding author Jeroen Raes, a microbiology and immunology researcher affiliated with the University of Leuven and VIB's Center for Microbiology, said in a statement. "However, without quantitative data, percentages cannot tell you whether a particular bacterium is actually becoming more abundant under specific conditions."

With these QMP data, longitudinal stool samples from dozens more healthy individuals, and microbial enterotype profiles for more than 1,100 participants in the Flemish Gut Flora Project (FGFP), including individuals with or without Crohn's disease, the team characterized microbial abundance and enterotypes. The analyses highlighted gut microbiome variation in the healthy individuals and pointed to gut microbiome deficits associated with Crohn's disease, ranging from an overall decline in bacterial abundance and a drop in bacteria from the Bacteroides genus.

"[W]e identify microbial load as a key driver of observed microbiota alterations in a cohort of patients with Crohn's disease, here associated with low-cell-count Bacteroides enterotype," Raes and his co-authors wrote.

The FGFP began in 2012. In the first five years of this population gut microbiome profiling effort, the team has collected around 3,000 stool samples from healthy participants.

For the second gut microbiome study in Nature today, a German- and US-led team examined ties between salt consumption, the gut microbiome, hypertension, and autoimmunity in a mouse models and in a dozen healthy German men who volunteered to take several salt tablets daily for two weeks.

Along with 16S ribosomal RNA sequencing experiments that revealed a drop Lactobacillus murinus and other bacterial species in fecal pellets from high salt-fed mice, the researchers found that hypertension-related pro-inflammatory CD4+ Th-17 T cell levels were enhanced in mice with high salt intake — an effect that was somewhat mitigated by giving the animals doses of L. murinus with their salty food.

The team saw signs of similar interactions in the guts of humans scarfing down high-salt fare for 14 days. In a preliminary, pilot study of 12 men, Lactobacillus bacterial species levels declined in metagenomic sequence data generated from fecal samples, while blood pressure and blood levels of Th17 cells notched higher.

"I think certainly there's some promise in developing probiotics that could be targeted to possibly fixing some of the effects of a high-salt diet, but people shouldn't think they can eat fast food and then pop a probiotic, and it will be canceled out," that study's co-senior author Eric Alm, director of the Massachusetts Institute of Technology's Center for Microbiome Informatics and Therapeutics, said in a statement.