Bacteria, the early form of life to develop on Earth, are present in most of the global habits, such as soil, water, clouds, acidic hot springs, and Earth’s crust etc. Among all possible habits, the microbial communities residing at the interface with large host organisms, such as human gut and around plant roots, represent two extremely complex ecological systems. The relatively stable coexistence of microbiota with their host implies the ecological significance of holobionts, the entity comprised of the macroscopic host and its associated microbiota.
We conducted three studies to investigate the relevance of symbionts to their host health and metabolism. In two studies regarding human gut, we addressed how medication use, improved diet, and exercise impact the gut microbiota. In the third study, we investigated the Brachypodium distachyon rhizosphere microbiota in multiple aspects including sampling scale (traditional vs. subscale), location on the root (root sections), within and between plant variations, and effect of inoculations.
The work presented here builds on three manuscripts:
MANUSCRIPT 1, “Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial”, is a study addressing the global concerns regarding the undesired effects of antibiotics use. We focused on the influence of antibiotics treatment on gut microbiota in early life. With the strength of randomized clinical trial (RCT) study design, we showed that azithromycin led to a reduction of alpha diversity and shift in microbial composition short after treatment (14 days). However, long-term (13-39 month) impact of azithromycin on gut microbiota composition was not observed. Our results alleviated concerns with respect to the adverse effects of antibiotics treatment on gut microbiota.
MANUSCRIPT 2, “Glucose-lowering medication and lifestyle intervention drive the gut microbiota in a similar direction: A randomized clinical trial”, is a study aiming to compare the effect of glucose-lowering medication treatment and lifestyle intervention on gut microbiota for patients with type 2 diabetes (T2D). We found that although both lifestyle intervention and medication treatment shifted the gut microbiota tremendously over a 12-month follow-up, these two therapies did not lead to different changes in taxonomic composition and functional potential of gut microbiota. We concluded that glucose-lowering medication especially metformin drives the gut microbiota of diabetic patients in parallel with the effect of lifestyle intervention.
MANUSCRIPT 3, “A glance into spatial and individual variability of rhizosphere microbiota”, is a study aiming to investigate the rhizosphere microbiota in different sampling scales. At the scale of a single root, we showed that rhizosphere microbiota are highly heterogeneous along root axis in alpha diversity, beta diversity, taxonomic composition, but also in the response to inoculation. Conversely, the traditional sampling scale by homogenizing the entire root system reduced the variance between replicates, giving higher reproducibility at the expense of not fully seeing the influence of inoculation on rhizosphere microbiota.