It's still unclear how gut diversity relates to health, researchers say

An individual human microbiome can be made up of hundreds of different species. According to a review paper published last year by Harvard biostatisticians in the journal Genome Medicine​, the average gut has about 160 different species, give or take.  But as many as 1,150 species have been identified in the guts of different people from all over the world, meaning that the guts of two healthy individuals from different places (or even from the same place) might have very little in common.

Hundreds of bacterial species, and other microbes, too

“​Healthy gut microbiomes as assessed by sequencing are consistently dominated by bacteria of two phyla​—​Bacteroidetes and Firmicutes​—​though even when considering this broad level of classification, individuals vary by more than an order of magnitude in their Firmicutes/Bacteroidetes ratios. Prevalent bacteria in feces that have been identified through molecular techniques have broadened the lists above to include bacteria from at least eight families,​”​ the researchers wrote.

They also noted that while the emphasis has been placed on bacterial species, microbes from other domains such as  archaea, viruses, fungi, and other eukaryotes are also present.  Are they just passengers, or can they play vital roles in keeping a healthy gut microbiome functioning? Still, within that variegated picture, the authors said one thing has emerged clearly: “​If microbial communities assemble on the basis of their coverage of a core set of functions while selecting from a large meta-population of potential colonizers, they are likely to be ecologically diverse, both in terms of richness (number of taxa present) and evenness (abundance of many microbial constituents). High diversity has been generally associated with health and temporal stability.​”​

So what’s the ideal here?  The old saw about a football coach’s job is that it boils down to two things: run the ball; stop the run. But football coaches have an advantage over gut health researchers and product formulators in that they know where the goal line is. What’s the game plan for gut health?  A multispecies probiotic, as advocated by some manufacturers, seems a promising approach.  It could, in a crude way, attack this problem of greater diversity.  On the other hand, administering a probiotic that might colonize well, and create favorable relationships within the microbial community for other species to thrive, might achieve the same thing or better.  Or should we just give people more fiber, and give those good bacteria more stuff to chew on? And, if we can agree that more diverse is better, what kind of diversity should we shoot for?  Are there clues in the host’s genome about what the ideal composition for that person should be?

Glimpsing a far off continent

For researchers, these questions are both exhilarating and frustrating. Frustrating, in that not having definitive answers to some basic issues makes study design a challenge. Exhilarating in that, figuratively speaking, there are whole continents yet to explore.

“​I think nobody can answer these questions at the moment. We assume that more diversity in the gut is good as diseases are often associated with a loss in diversity, and based on ecological consideration that more diverse communities do normally function better,​”​ Dr Jens Walter, PhD, of the University of Alberta in Edmonton told NutraIngredients-USA.

“​However, there is no proof for that, and in other host-associated microbial communities, such as the vagina, less diversity is actually better,​”​ he said.

“​The consensus within the research community is that more diverse is better,​”​ agreed Dr Andrew Benson, PhD.  Benson is a professor of food science and technology at the University of Nebraska and is the director of the Nebraska Food for Health Center.

“​But there is not as much data supporting that assertion as a lot of us would like to have,​”​ he said.

“​The jury is still out on diversity. We still have a lot to learn, but we are moving up the tree now. The first major studies were where you were comparing the microbiomes of a healthy population with subjects suffering from diseases.  Then you have studies that look at the microbiomes that result from different diets.  You find more diversity in these healthy populations, and more diversity in people who are eating what might be construed as healthy diets,​”​ he said.

“​So more diverse means healthier​—​that​’​s clearly the hypothesis.  But I would still say that​’​s what it is​—​a hypothesis,​”​ Benson said.

Benson said that unknown factors could influence the differences from one person to the next and one population to the next.  It makes designing a study a real challenge.

“​People have been thinking about this for some time.  The problem is that it is not easy to tease these factors out of a study.  For instance, the demonstrated differences in the microbiomes of kids who grew up on a farm as opposed to kids from the city​—​there are a lot of factors that could account for those differences,​”​ he said.

At the beginning of a new age

Benson said it’s good to keep in mind that the primary tool of the field—rapid and inexpensive gene sequencing to identify bacterial species in real time—is only about 10 years old.  The exponential growth in data arising from this tool as it is used by thousands of researchers around the globe will bring the diversity issue ever more rapidly into focus, he said.

“​I think we will start to get a handle on this diversity thing. There just isn​’​t enough data at this point.  But if enough people are thinking about this they will come up with some really clever ways to get at the question, and design experiments that will start to account for many of these ecological factors,​”​ Benson said.