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The Influencers of Microbial Diversity

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Research published in 2012 entitled "Diversity, Stability and Resilience of the Human Gut Microbiota" takes an expansive look at the multitude of influences on gastrointestinal microbial diversity. Exploring the significance of factors such as age, genes, environment, diet and medication on population, resilience and diversity. Lead author Catherine Lozupone and her team comprehensively break down the various aspects of both a healthy and a dysbiotic gastrointestinal (GI) tract, and the subsequent consequences to the development of future health or disease. 

Most interestingly what this paper explores, is the enormity of both the size or volume of the human microflora and how its variability affects more than just the typically considered gut function.  A diagram entitled "Maintaining the microbial lawn" (Figure 1) emphasises the devastating effects of (especially repeated) antibiotic use, and advocates the potential of  the individualised use of a diverse array of plant-based dietary approaches, bacteriotherapy (i.e. faecal transplants), pre- and probiotics. 

Figure 1

A further diagram (Figure 6) details how the infant's species-poor microbiota matures with repeated reinforcing stimuli into a healthy, species-diverse microbiota. However, when adverse stimuli such as antibiotics, or repeated or persistent stressors (eg. poor diet) pass a certain threshold, the microbiota becomes set in a degraded, but stable state (dysbiosis) which may be populated by distinct species of bacteria from the healthy stable state. The authors point out that combinations of species may be the key to return the ecosystem back to a healthy stable state.  

Figure 6

Dysbiosis has been associated with an ever-expanding array of deleterious health effects such as both functional and inflammatory GI disease, neurological disorders, weight gain, malnutrition and cancer. The authors use the analogy of maintaining a healthy "lawn" and explain how the all-too-often overuse of antibiotics can decimate healthy bacterial populations. Furthermore, compositional changes which may set dysbiotic disease states are diagrammatically explained along with how microbial rescue attempts (dietary changes, faecal transplants, pre~ and probiotics) may return the microbial carpet to normal.

This paper acutely highlights the shortcomings of taking a reductionist view to the application of single strain or species probiotic therapy as an exclusive approach in clinical practice. The authors instead lead us to at least step back and consider the enormity of the "garden" within our gastrointestinal tract and to give us a glimmer of understanding as to how the microbial universe within might be influenced through treatments, all of which are based upon a plant-based diet.

Salient quotes from the paper herald a warning for those who rely on just single species or strain of probiotic bacteria to restore the legions of microbial partners inhabiting our GI tract:  

"The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time - especially during disease and early development. Viewing the microbiota from an ecological perspective (Page 1) could provide insight into how to promote health by targeting this microbial community in clinical treatments." and, "just like gardeners, we must learn what conditions promote the health of desired species and exclude undesirable weeds." 

"Understanding how the microbiota varies across the human population, and correlating this variability with specific microbial functions, could very well be the next emerging phase toward truly personalized medicine".


  1.  Lozupone CA, Stombaugh JI, Gordon JI, et al. Diversity, stability and resilience of the human gut microbiota. Nature 2012;489(7415):220-230. [Full Text]


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Andrew Whitfield-Cook

Andrew is a registered nurse of 32 years, with more than 20 years experience in the natural medicine industry. Andrew is curious about, well, everything! He delights in interviewing specialist clinicians and researchers about their work and how the practical use of nutritional and herbal medicines, and physical therapies, may improve patient health.
His interests include gastroenterology, immunology and oncology. Andrew has a deep responsibility to impart the efficacious use plus the relevant safety aspects of integrative medicine to natural medicine practitioners.