Flagellar genes are associated with the colonization persistence phenotype of theDrosophila melanogastermicrobiota

Abstract

In this work we use Drosophila melanogaster as a model to identify bacterial genes necessary for bacteria to colonize their hosts independent of the bulk flow of diet. Early work on this model system established that dietary replenishment drives the composition of the D. melanogaster gut microbiota, and subsequent research has shown that some bacterial strains can stably colonize, or persist with, the fly independent of dietary replenishment. Here we reveal transposon insertions in specific bacterial genes that influence the bacterial colonization persistence phenotype by using a gene association approach. We initially established that different bacterial strains persist at varying levels, independent of dietary replenishment. We then repeated the analysis with an expanded panel of bacterial strains and performed a metagenome wide association (MGWA) to identify distinct bacterial genes that are significantly correlated with the colonization level of persistent bacterial strains. Based on the MGWA, we tested if 44 bacterial transposon insertion mutants from 6 gene categories affect bacterial persistence with the flies. We identified that transposon insertions in four flagellar genes, one urea carboxylase gene, one phosphatidyl inositol gene, one bacterial secretion gene, and one antimicrobial peptide (AMP) resistance gene each significantly influenced the colonization of an Acetobacter fabarum strain with D. melanogaster. Follow-up experiments revealed that each flagellar mutant was non-motile, even though the wild-type strain was motile. Taken together, these results reveal transposon insertions in specific bacterial genes, including motility genes, are necessary for at least one member of the fly microbiota to persistently colonize the fly.

Humidity determines penetrance of a latitudinal gradient in genetic selection on the microbiota byDrosophila melanogaster

“…In the laboratory, we defined residents as microorganisms that colonized the flies after a 2 hour starvation period, and transients as the difference between microbial loads in starved flies and their unstarved, vial-matched siblings. There was a significant difference in the relative abundances of the resident and transient microbiota combined (unstarved flies) or resident bacteria only (starved flies), consistent with established work that a portion of the fly microbiota is transient (20, 21, 33, 34) (F 1, 389 = 13.19, R 2 = 0.03, p < 0.001, Fig. 4A, Table S7).…”

“…The starvation strategy eliminated transient microorganisms that could not persist for longer than the bulk flow of food, leaving behind resident microorganisms (e.g. (21, 34)). We estimated the abundance of the transient microorganisms in the flies as the difference between the average abundance of LAB and AAB in the unstarved and starved flies on a per-experiment basis (3 total experiments in time, each with 3 replicate vials of flies).…”

MprF-mediated immune evasion is necessary forLactiplantibacillus plantarumresilience inDrosophilagut during inflammation

“…Importantly, the other recent studies further support the role of MprF in microbiota persistence in the gut. For example, a metagenome-wide association (MGWA) study identified multiple bacterial genes, including mprF , that are significantly correlated with the level of colonization [69]. Subsequent analyses confirmed that an mprF transposon insertion mutant of Acetobacter fabarum showed decreased persistence within the flies [69].…”

“…For example, a metagenome-wide association (MGWA) study identified multiple bacterial genes, including mprF , that are significantly correlated with the level of colonization [69]. Subsequent analyses confirmed that an mprF transposon insertion mutant of Acetobacter fabarum showed decreased persistence within the flies [69]. However, it has not been tested whether this phenotype is due to mutant’s sensitivity to host AMPs.…”

The ecological relevance of flagellar motility in soil bacterial communities

“…In laboratory conditions, bacteria have been widely investigated for their ability to swim towards resources [11, 12], display quorum sensing [13], or swim away from toxins [14]. Several experimental studies show that the hydration level of surfaces generally predicts how easily bacteria can colonize a given surface [15], and that flagellar motility also predicts the temporal persistence of bacterial pathogens in host microbiomes [16]. The high energetic cost of powering the flagellar machinery is tightly linked to regulatory systems that control flagellar expression depending on the spatial proximity and quality of available resources (i.e., optimal foraging based on energetic constraints; [17–19]).…”