Understand and predict microbiome and resistome dynamics in response to perturbations across diverse populations and environments

A WashU Dissertation by: Manish Boolchandani (Dept. of Biology & Biomedical Sciences)

Abstract: Complex microbial communities are at the interface of human, animal and environment interconnected ecosystem, where they can move within and between these entities. These microbial communities are mostly beneficial, maintaining the host health and homeostatic state. However, these communities can also serve as reservoirs of antibiotic resistance (AR) genes that may disseminate to pathogen bacteria, compromising the treatment options. Like other microbial communities, human gut microbiome is highly dynamic and can get acutely perturbed with the changes in the habitat, diet, lifestyle and disease. A perturbed gut community structure has profound impact on the host health and physiology. Use of antibiotics in medical and animal sector, international travel to high infectious burden regions and occupational exposure at workplace like dairy farm or swine farm can significantly alter the microbiome structure and function. Thus, in this thesis, I aim to understand the ecological principles governing the microbiome structure in different habitats and their response to such perturbations. To accomplish this goal, I first developed and optimized the computational pipelines (PARFuMS, Resfams (v2), and resAnnotator) for high-throughput characterization of antibiotic resistance genes in diverse habitats. I then employed these methods along with other bioinformatics suites to understand the dynamics of human gut microbiota and the antibiotic resistant genes that it collectively encodes (the ‘resistome’) in response to perturbations such as international travel and swine farm exposures. Additionally, I studied wild and captive baboon populations to understand the impact of captivity and lifestyle changes associated with human contact on the changes in baboon’s microbiome and antibiotic resistome. To determine the impact of international travel and enteric infections on the gut microbial ecosystem, I have specifically focused on two international travel scenarios. In the first scenario, travelers from different countries, mainly the US and European nations, travel to one location i.e. Cusco, Peru, and in the second scenario, travelers from one country, Netherlands, travel to four different destinations viz. North Africa, East Africa, Southeastern Asia and Southern Asia. In the first scenario, I investigated the impact of travelers’ diarrhea (TD) on travelers’ gut microbiome and resistome, and the dynamics of these changes throughout travel and during specific diarrheal episodes. To this end, we assembled a cohort of 159 travelers visiting the Andean city of Cusco, Peru and applied next-generation sequencing techniques to 718 longitudinally-collected stool samples. I found that the gut microbiome composition of all travelers changed significantly during their stay, but the taxonomic diversity was stable. However, diarrhea disrupts this stability and results in an increased abundance of antibiotic resistance genes which remains high weeks after the diarrheal episode. I also identified several taxa that were differentially abundant between diarrheal and non-diarrheal samples, which were used to develop a classification model that can distinguish between the two sample types. In addition, we sequenced the genomes of 212 diarrheagenic Escherichia coli isolates, and found that isolates from travelers with diarrhea encoded more AR genes than those from healthy subjects. In summary, the gut microbiomes of international travelers’ was found to be surprisingly resilient against dysbiosis; however, they are susceptible to colonization by antibiotic resistant and multidrug-resistant bacteria, a risk that becomes more pronounced if they have travelers’ diarrhea. In the second scenario, I specifically studied the resistome dynamics among travelers to different high infectious burden regions by comparing their pre- and post-travel samples. The study showed that the destination shapes the travelers’ resistome, where travelers to a common destination share similar resistome post-travel compared to their pre-travel resistome. I also found that Southeastern Asia travelers acquired most AMR gene families compared to other travelers, and several high-risk AR genes (e.g. mcr-1, blaCTX-M-1) were borne on mobile genetic elements, highlighting the potential risk of global spread of the locally endemic AR genes. Indiscriminate use of antimicrobials brings agricultural workers at risk for potential long-term health effects from occupational exposure to AR microbes. To understand how exposure to such workplaces impact the gut resistome dynamics, I studied metagenomic samples from fourteen healthy students who visited the confined and controlled swine farms for three consecutive months and were sampled before-, during and after their visit in China. Longitudinal investigation showed extensive sharing of AR genes and microorganisms after exposure to the swine farm environment, along with several evidences of plasmid-associated AR genes that were borne on mobile genetic elements. The study also showed partial reversal of the microbiome and resistome shift within four to six-month period post-visit to the swine farms, attributing to the resiliency of the human gut microbiome. Although the antibiotics and the defense mechanisms adopted by bacteria to combat them are ancient, the spread of AR is steadily rising since the introduction of antibiotics in agriculture and medicine. To understand the impact of human exposure and how primate microbiota have changed in the antibiotic era, I investigated the resistome of wild and captive baboon population. I found expansion of resistome among captive baboons compared to the wild-type counterparts, and the captivity and lifestyle changes associated with human contact can lead to marked changes in the ecology of primate gut communities. In this thesis, I demonstrated the impact of different anthropogenic activities, like international travel and use of antibiotics in livestock farming on the microbiome and resistome of the host, and how these activities perturb the gut microbial ecosystem. Although each project demonstrates the resiliency of the microbiome and its ability to recover from the perturbed state, there are also long-term, indirect impact on the host physiology especially with the acquisition of AR genes upon exposure or enteric infections. I believe these studies lay ground with potential hypothesis that can be further tested with clinical intervention studies.

Citation or DOI: Boolchandani, Manish, “Understand and predict microbiome and resistome dynamics in response to perturbations across diverse populations and environments” (2021). Arts & Sciences Electronic Theses and Dissertations. 2360. https://openscholarship.wustl.edu/art_sci_etds/2360