Probiotics Impact Gut Microbiota: Not What’s There but What They are Doing

The idea that consuming the right kind of bacteria in your yogurts or fermented milks could be good for you has been around for over 100 years. Fast forward to modern times and you find a global probiotic industry. There are problems, yes. But the ray of hope that shines in this field is the research.

Bolstered by findings and methodologies developed by global researchers investigating the human microbiome, probiotic research has flourished.  One example of this is a 2011 article by McNulty and colleagues. This publication reports both an animal and human study designed to determine the effect of a probiotic yogurt on the gut microbiome.

You may ask – don’t we already know that probiotics function by “improving the balance of the microflora”? Surprisingly, not really.  That probiotics act at the level of the microbiota was always presumed – hypothesis was offered as fact for decades. Early definitions even imposed this mechanism onto probiotics. But there was little proof of such functionality, and even less proof that the minor changes in microbiota that sometimes were observed were the cause of any benefit. The McNulty study applied modern microbiome and metatranscriptomes methodologies to this question and the results provide some insights into how at least some probiotics impact the microbiome.

In the human study in this paper, 7 healthy adult female twins consumed the probiotic yogurt (containing Bifidobacterium animalis subsp. lactis and 4 strains of lactic starter bacteria) for 7 weeks.  Fecal samples were obtained 4 weeks before, during, and 4 weeks after yogurt consumption.  Consumption of the probiotic yogurt did not result in any significant changes in the proportion of bacterial species harbored in, or the bacterial gene content of, the feces.  However, changes in transcriptional responses (primarily in carbohydrate metabolism pathways) and in urinary metabolites were observed. These results highlight that probiotics may not act at the level of changing populations of colonizing bacteria, but may instead impact the expression of bacterial genes and the bacterial metabolic output. In other words, probiotics may not change what’s there, but may change what they are doing.

The mouse model featured germ-free mice colonized with a defined blend of 15 human commensal bacteria (Bacteroides caccae, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgates, Bacteroides WH2, Clostridium scindens, Clostridium spiroforme, Collinsella aerofaciens, Dorea longicatena, Eubacterium rectale, Faecalibacterium prausnitzii, Parabacteroides distasonis, Ruminococcus obeum and Ruminococcus torques). Gavage with the probiotic yogurt gave similar results as those from the human study, suggesting that this defined mouse model may be very useful for characterizing probiotic mechanisms.

The take-home lessons:

  • Probiotics may not change the types or proportions of bacteria we harbor, but instead may impact the expression of bacterial genes and the bacterial metabolic output.
  • The defined mouse model may be provide a proxy for probiotic function in humans