Scientists have identified the genes in the probiotic Bifidobacteria longum responsible for improving gut motility.
A research team reporting in the journal Cell Host & Microbe found that B. longum strains possessing the abfA cluster of genes can ameliorate constipation through enhanced utilization of an indigestible fiber called arabinan in the gut.
“We established the causal link between a genetic variant - the abfA cluster - to the key functional difference of probiotic B. longum in multiple model organisms, including mice and humans, and provided mechanistic and ecological insights into how a single gene cluster can affect the gut motility of hosts through arabinan metabolism,” says Qixiao Zhai of Jiangnan University, one of the paper’s co-senior authors.
Globally prevalent bowel disorder
Constipation is a globally prevalent bowel disorder with a worldwide prevalence of 10% to 15%. Impaired gastrointestinal motility has been implicated in gut microbial dysbiosis, which is characterized by a significant decrease in the abundance of beneficial microorganisms, some of which are conventionally known as probiotics. Orally administrated probiotics have therefore been widely used to alleviate symptoms.
Yet the therapeutic effect of probiotics for constipation often varies substantially across strains within the same species. Due to elusive mechanisms, the rational choice of probiotic remains challenging for medical care professionals and patients. In addition, most evidence on the beneficial effects of probiotics on gut motility mainly emerged from studies using a mouse model.
“Probiotic strains were often effective in animal models yet failed in human clinical trials or were poorly validated in humans,” says Jiachao Zhang of Hainan University, the study’s second co-senior author. “Proof-of-concept studies based on a human cohort in combination with evidence from animal studies are urgently needed for translational research.”
Key genetic factors
Zhai, Zhang, and Shi Huang of the University of Hong Kong, the paper’s third co-senior author, set out to identify and systematically validate the key genetic factors of exogenous probiotics or resident gut microbiota affecting gastrointestinal motility. They isolated 185 B. longum strains from 354 Chinese subjects who ranged in age from 0 to 108 years.
From a comprehensive library of wild B. longum strains, they discovered that the effective alleviation of constipation in mice is regulated by the abfA cluster. This key genetic factor preferentially enhances the utilization of arabinan - a common constituent of plant polysaccharides, an indigestible fiber for humans, and a poorly accessible source of nutrients for normal gut microbes.
The researchers further validated the abfA cluster’s functional roles using gene-knockout experiments. In mice with constipation, B. longum, but not an abfA mutant, improved gastrointestinal transit time - an effect that was dependent upon dietary arabinan.
To establish its functional roles for ameliorating constipation in humans, the researchers used a clinical trial and a human-to-mouse fecal microbiota transplantation experiment in combination with metagenomics and metabolomics. In the double-blind, randomized, placebo-controlled clinical trial, supplementation with abfA-cluster-carrying B. longum, but not an abfA-deficient strain, enriched arabinan-utilization residents, increased beneficial metabolites, and improved constipation symptoms.
Across human cohorts, abfA-cluster abundance in the fecal microbiomes predicted constipation, and transplantation of abfA cluster-enriched human microbiota to mice with constipation improved gut motility. Notably, other than B. longum, the abfA gene/cluster is prevalent in gut residents, regulating symptoms in both mice and humans.
The authors say that the abfA cluster is a gut-microbiome therapeutic target for constipation in humans. More broadly, the results suggest that genetic factors governing the unique metabolic capability of probiotics should be primarily considered for screening probiotics or inferring their treatment efficacy for gastrointestinal diseases.
“Collectively, this study identified and systematically characterized a key genetic factor responsible for arabinan utilization that addressed one critical challenge in the probiotic field, namely widespread yet unknown strain specificity in probiotic treatment efficacy,” Huang says.
“Our proof-of-concept study also established generalizable principles for the rational development of colonizable, functional probiotics with persistent treatment efficacy in multiple model organisms. Moreover, the abfA cluster is so prevalent in the gut microbiota that it can be developed as a simple yet powerful biomarker for gastrointestinal diseases.”