Gut feeling: Study finds ingested bacteria can stick for months

Bacteria visiting the digestive system in a spoonful of yogurt or a probiotic capsule can extend their vacation while eating leftovers ignored by the gut’s longtime residents, says new research from the University of Nebraska-Lincoln.

Dozens of prior studies have offered little evidence that bacteria dropping in on the human gut – a vast ecosystem already colonized by roughly 100 trillion microorganisms – stick around for more than a few weeks.

But a recent study from Bob Hutkins, Jens Walter and their colleagues found that a strain of Bifidobacterium longum made itself at home for at least six months in eight of the 23 subjects who consumed it.

“This was really surprising,” said Hutkins, the Khem Shahani Professor of Food Science and Technology. “It was a remarkable finding, because it’s one of the few examples of a probiotic organism successfully colonizing humans.”

The intestinal tracts of those eight subjects generally housed fewer native B. longum than did the other 15, the study reported. This suggests that the visiting B. longum managed to find a niche because they faced less competition for the carbohydrates on which they tend to feed, Hutkins said. When native bifidobacteria were abundant in the gut, however, the visiting B. longum instead passed through after just a short stay.

In that way, Hutkins said, the complex ecosystem of the human gut adheres to the same ecological principles proposed by Charles Darwin more than 150 years ago.

“They both want to make a living in the same place,” said Hutkins, a member of the Nebraska Food for Health Center. “There’s only one job available, if you will, and they’re both competing for that. The guy that’s living there already is well-adapted to that environment (and) knows how to make a living there. So the newcomer has less of a chance.

“There are already bifidobacteria that are well-established (in many people). They probably got there when you were a year old. They may have come from your mom. So they’re there for the long haul.”

Hutkins said this fact partly explains why many touted probiotics – live microorganisms introduced to the gut with the aim of improving health – fail to have much impact. He compared the scenario to his own lawn, which he conceded “probably has many more weeds than grass.”

“If I just throw some grass seed on it in the fall (without pulling the weeds), should I expect that the seed will make my lawn full of green grass in the spring? It would be unrealistic to expect that the foreign organism is going to take over,” he said. “It just won’t, because it doesn’t have the competitive wherewithal to get a foothold and establish itself.”

Yet the new study’s findings also suggest that probiotics could become a form of personalized medicine taken by those whose intestinal tracts lack certain bacterial species, Hutkins said. Previous research has indicated that anomalies in the gut ecosystem may contribute not only to problems with the gut itself – among them, irritable bowel syndrome and Crohn’s disease – but also systemic issues such as Type 2 diabetes, cardiovascular disease and others.

Recent advances have made it possible to characterize the microbial composition of a person’s intestinal tract by analyzing the DNA in their stool, Hutkins said. Those analyses now allow researchers to identify the signature bits of DNA that essentially serve as bacterial barcodes. Sequencing all of the DNA in a sample can even pinpoint which functions – such as the carbohydrate-munching properties exhibited by B. longum – are present in the microbial ecosystem.

“It’s a really remarkable ability that we now have,” Hutkins said. “For $100 or less, you can get a pretty good bird’s-eye view of what your microbiota looks like. So it could be possible that, soon, you could characterize your microbiota and see that this probiotic will work for you but a different probiotic will work for somebody else.”

Fulfilling that potential, Hutkins said, could require a substantial shift in the way the food and probiotic industries operate.

“One of the reasons that probiotics have had mixed results is because the strains – whether they’re in yogurt or in some other food or in supplements – have often been selected on a practical basis,” he said. “They’re easier to grow. They’re easier to freeze-dry. They can sit at room temperature for six months. They’ve been selected on (that) basis, not on their ecological performance.

“We’ve tried to emphasize that strains need to be selected based on the functions they express and how well their genetic composition matches to the individuals who are going to be consuming them. That’s the larger challenge that we’re trying to address.”

The research team published its findings in the journal Cell Host and Microbe. Hutkins and Walter, associate professor at the University of Alberta, authored the study with María Maldonado-Gómez and Inés Martínez, doctoral graduates of Nebraska now at the University of California, Davis and University of Alberta, respectively. The team also included researchers from the University College Cork (Ireland), the University of Parma (Italy) and the University of Minnesota.