Probiotics are a promising means to manipulate the microbiome, but there is little evidence that they can do this by changing the microbiota composition. (See previous post on this website: Probiotics impact gut microbiota: not what’s there but what they are doing, April 9, 2013.)
Changes in diet are associated with changes in the composition of gut microbial populations. For example, an energy-restricted high-protein diet improved low microbial gene richness in obese or overweight subjects (Cotillard, et al. 2013). (Interestingly, among these obese or overweight individuals, those with low microbial gene richness also had higher insulin resistance and fasting serum triglyceride levels, as well as a tendency towards higher LDL cholesterol and inflammation than those with high microbial gene richness – but I digress.)
Studies looking at changes in microbiota due to probiotic consumption typically document increases (albeit transient) in the genus or species of the probiotic, but there is little evidence that probiotics can reshape a microbial community. Viega et al. (2014) suggest that the lack of such evidence may be due to poor resolution of the phylogenetic tools used to date. These authors looked at changes at the species-level, rather than the less discriminating changes at the genus or phylum level. They fed female IBS subjects yogurt containing Bifidobacterium animalis subsp. lactis, Lactococcus lactis and the yogurt starter bacteria, or a control product with no live microbes. Four unknown species (MGS126, MGS203, MGS106, MGS109) and Bifidobacterium dentium increased and Parabacteroides distasonis, Bilophila wadsworthia (an opportunistic pathogen) and Clostridium sp. HGF-2 decreased. In subjects consuming the control product, Haemophilus parainfluenzae and a 5th unknown species (MGS204) were reduced. In addition, yogurt increased short chain fatty acids. Applying functional genomic tools, the metabolic pathways of the unknown species can be elucidated, providing insight into the metabolic functions of these microbes as part of the overall gut microbial community.
Documenting that probiotics can impact the microbiome is important to understanding mechanisms of how probiotics might be able to improve health. However, ultimately, the need to document health effects in robust, well-conducted human studies is paramount.
Cotillard, et al. Dietary intervention impact on gut microbial gene richness. August 2013.
Veiga, et al. 2014. Changes of the human gut microbiome induced by a fermented milk product. Scientific Reports 4, Article number: 6328, doi:10.1038/srep06328.