The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals its Role in Community Composition

Abstract

1While the composition of the human gut microbiome has been well defined, the forces 2 governing its assembly are poorly understood. Recently, prominent members of this 3 community from the order Bacteroidales were shown to possess the type VI secretion 4 system (T6SS), which mediates contact-dependent antagonism between Gram-negative 5 bacteria. However, the distribution of the T6SS in human gut microbiomes and its role 6have not yet been characterized. To address this challenge, we construct an extensive 7 catalog of T6SS effector/immunity (E-I) genes from three genetic architectures (GA1-3) 8 found in Bacteroidales genomes. We then use metagenomic analysis to assess the 9 abundances of these genes across a large set of gut microbiome samples. We find that 10 despite E-I diversity across reference strains, each individual microbiome harbors a 11 limited set of E-I genes representing a single E-I genotype. Importantly, for GA1-2, these 12 genotypes are not associated with a specific species, suggesting selection for 13 compatibility. GA3, in contrast, is restricted to B. fragilis, and its low diversity reflects a 14 single B. fragilis strain per sample. We further show that in infant microbiomes GA3 is 15 enriched and B. fragilis strains are replaced over time, suggesting competition for 16 dominance in developing microbiomes. Finally, we find a strong association between the 17 presence of GA3 and increased abundance of Bacteroides, indicating that this system 18 confers a selective advantage in vivo in Bacteroides rich ecosystems. Combined, our 19 findings provide the first comprehensive characterization of the T6SS landscape in the 20 human microbiome, implicating it in both intra-and inter-species interactions.

Effector loading onto the VgrG carrier activates type VI secretion system assembly

“…The type VI secretion system (T6SS) is a versatile secretion system that has been implicated in virulence, antagonism, nutrient acquisition, and horizontal gene transfer [1][2][3]. Contact-dependent interbacterial competition appears to be the major function of T6SS, a function that can influence the composition of microbial communities [4,5]. A T6SS machine resembles a contractile phage tail-like structure [6][7][8].…”

Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome

“…A comparison of these immunity sequences to available bacterial genomes revealed a clade matching cognate immunity genes in B. fragilis (i6:cI). Additionally, we found an i6 sequence homologous to i6:cIII in the genome of B. ovatus, which we previously found does not contain the cognate T6SS effector gene (6).…”

“…The density of bacteria in the mammalian gut microbiome can exceed 10 11 gm -1 ; therefore, overcoming contact-dependent interbacterial antagonism is likely a major hurdle to survival in this ecosystem (4,5). The type VI secretion system (T6SS) is a pathway predicted to be widely utilized by gut bacteria to mediate the delivery of toxic effector proteins to neighboring cells (6)(7)(8)(9). While kin cells are innately resistant to these effectors via cognate immunity proteins, it is unknown whether non-self cells in the gut can escape intoxication.…”

“…To identify potential mechanisms of defense against T6Sdelivered interbacterial effectors, we mined a large collection of shotgun metagenomic samples (n=553) from multiple studies of the human gut microbiome for sequences homologous to known immunity genes (table S1) (10)(11)(12). We first focused our efforts on Bacteroides fragilis, a bacterium belonging to the order Bacteroidales, which harbors a well described and diverse repertoire of effector and cognate immunity genes (table S2) (6,7,13). As expected for genes predicted to reside within the B. fragilis genome, sequences mapping to these immunity loci were detected at an abundance similar to that of B. fragilis species-specific marker genes in many microbiome samples ( Fig.…”

“…B. fragilis is typically found as a clonal population in the human gut microbiome, and recent studies suggest that this is in part due to active strain exclusion via the T6SS (6,16). However, in gnotobiotic mouse colonization experiments, certain B. fragilis strain pairs inexplicably co-exist (8).…”