Characterization of the infant gut microbiota mobilome

Abstract

The human gut is densely populated with a wide diversity of bacteria. These bacteria can serve as a reservoirs for multiple Antibiotic Resistance (AR) genes that in turn are associated with wide range of Mobile Genetic Elements (MGEs). The mobilome is the collection of MGEs such as plasmids, transposons and integrons that are main contributors to Horizontal Gene Transfer (HGT). The distribution and association of the mobilome in the developing gut microbiota of infants remains largely unexplored. Therefore, the main aim of this thesis is to study the prevalence, association and characterization of plasmids and integrons that were de novo assembled and detected in the developing gut microbiota of full term and preterm infants. From our study, we detected a diverse mobilome (potentially MGES) of conjugative plasmids and integrons. The MGEs that were de novo assembled from the shotgun metagenome data, especially conjugative plasmids harboured various AR and virulence gene factors. The integrons that are non-mobile genetic elements were closely associated with conjugative plasmids. These plasmids especially IncF and IncI conjugative plasmids were in-turn associated with the Enterobacteriaceae family. In addition to this, the de novo assembled plasmid-related contigs depicted a potential multireplicon status with shared and integrated IncF variants and shared plasmids between IncF and IncI plasmids. In total, we have de novo assembled 7 different IncF and IncI1 conjugative plasmids from different cohorts. We also detected a strong correlation with the mobilome and microbiota taxonomy. We detected a significant strong association with the abundance of conjugative plasmids and different Operational Taxonomic Units (OTUs) related to Enterobacteriaceae. Overall, the persistence patterns of the conjugative plasmids between the different time periods of the different cohorts were surprisingly consistent. Lastly, we isolated and characterised the functional attributes of strains carrying conjugative plasmids. We de novo assembled IncI and IncF plasmids and we demonstrated the mobility of these plasmids in vitro. We detected a mobile IncI plasmid and a non-mobile IncF plasmid, both carrying multidrug resistance genes. In addition, we also characterised a bacteriocin-producing IncFII/IncFIB conjugative plasmid from the strains. Taken together, our results provide information on the prevalence and persistence of conjugative plasmids and integrons in three longitudinal cohorts. In addition, we characterised the functional attributes and demonstrated transmission of the conjugative plasmids to other strains. These results reveal the innate ability of the mobilome to adapt to selective pressures in gut microbiota, in addition to spread among different bacteria.

Den humane tarmen er kolonisert av et stort antall bakterier. Disse bakteriene kan tjene som et reservoar for antibiotikaresistente gener som igjen er forbundet med et stort utvalg av mobile genetiske elementer. Mobilomet består av en samling mobile genetiske elementer som plasmider, transposoner og integroner, og representerer de viktigste bidragsyterne til horisontal genoverføring. Distribusjonen og assosiasjonen av mobilomet i forbindelse med utviklingen av tarmmikrobiota hos spedbarn er fortsatt lite kjent. Hovedmålet med denne oppgaven var derfor å studere forekomsten, assosiasjonen, samt å karakterisere plasmider og integroner som ble de novo sammenstilt og detektert i tarm hos for tidlig og normalfødte spedbarn.