Finding a niche

This post was written by Sean Gibbons, a Post-Doctoral Associate with Eric Alm at MIT

The field of invasion ecology attempts to understand how and why certain species are able to invade or colonize territory outside of their native ranges. Human shipping and transportation activities have greatly increased the dispersal of animal and plant species across the planet. This great mixing event has led to an enormous increase in the number of invasive organisms, which threaten ecosystems around the world: from zebra mussels in the Great Lakes to the cane toad in Australia. However, most introduced species are unable to compete with locally adapted organisms. It is difficult to predict which organisms will succeed in a new ecosystem, or which ecosystems are more or less susceptible to invaders.

Wouldn't want this guy colonizing your gut...

Wouldn’t want this guy colonizing your gut…

Determining the colonization potential of an introduced species is a fundamental question for land managers and ecologists. Colonization of microbes is also an important issue for healthcare and the human microbiome. The probiotic industry has grown up around the idea that we can add living bacteria to the gut ecosystem to promote health. However, the scientific consensus so far is that most probiotics do not reliably alter the microbiome. In fact, most probiotics are washed out of the gut after a few days. The transient presence of probiotics, like Lactobacillus species, can influence host health, but another approach is to design probiotics that persist as microbial therapeutics in the gut ecosystem for indefinite periods of time.

Maldonado-Gómez and colleagues, in a recent paper in Cell Host & Microbe, used metagenomic data from a human cohort to predict features important for persistence of an introduced probiotic. They fed a specific strain of Bifidobacterium longum – a species commonly found in the human gut – to 23 volunteers for several days. The authors tracked the abundance of this strain in stool samples for several weeks after stopping the probiotic treatments. They found that the probiotic strain persisted for over 150 days in 7 patients. In addition to the abundance of the probiotic, the authors tracked the overall bacterial community composition and functional gene content in stool. Patient data revealed strong predictors of stable colonization. First, the initial presence of indigenous B. longum strains in a patient’s gut community was negatively associated with colonization. The presence of these related strains appeared to inhibit colonization, likely due to competition for a common set of resources. Second, the authors found that the presence of a suite of carbohydrate-utilization genes was negatively associated with colonization. These functional genes were present in the probiotic’s genome, but were not necessarily present in patients who harbored indigenous B. longum strains. Thus, the probiotic was able to stably colonize an individual if its ecological niche was vacant. There was no evidence that the introduced strain could invade and displace organisms that were already established in its niche.

Colonization of an introduced probiotic requires niche vacancy.

Colonization of an introduced probiotic requires niche vacancy.

This study is an important proof of concept for the rational design of microbial therapeutics and shows that there is hope for being able to tailor these therapeutics to each individual’s microbiome. It also shows the amazing potential for using the gut as a model system for studying the mechanisms behind colonization of introduced species in ecological communities. Increasing niche saturation (the use of all available resources) and ecological diversity in the gut may be an effective means of preventing unwanted colonization or invasion by pathogenic organisms. Indeed, greater niche saturation and diversity have been shown to prevent invasions in macro-scale ecosystems.

At the end of their paper, Maldonado-Gómez and colleagues discuss the next frontier in the design of medical-grade microbial therapeutics. They suggest that microbial colonization of the gut can be achieved more generally by incorporating a dietary a substrate that only the therapeutic microbe has access to. These substrates are known as ‘prebiotics’, and prebiotic/microbe cocktails are called ‘synbiotics.’ Synbiotics might allow for stable, colonization of the gut. The development of stable synbiotic systems could allow for the maintenance of beneficial species that produce natural metabolites positively associated with host health (for instance, butyrate), or drugs made by genetically engineered organisms.