Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering

Abstract

The human gut microbiota is a dense microbial ecosystem with extensive opportunities for bacterial contact-dependent processes such as conjugation and Type VI secretion system (T6SS)-dependent antagonism. In the gut Bacteroidales, two distinct genetic architectures of T6SS loci, GA1 and GA2, are contained on Integrative and Conjugative Elements (ICE). Despite intense interest in the T6SSs of the gut Bacteroidales, there is only a superficial understanding of their evolutionary patterns, and of their dissemination among Bacteroidales species in human gut communities. Here, we combine extensive genomic and metagenomic analyses to better understand their ecological and evolutionary dynamics. We identify new genetic subtypes, document extensive intrapersonal transfer of these ICE to Bacteroidales species within human gut microbiomes, and most importantly, reveal frequent population fixation of these newly armed strains in multiple species within a person. We further show the distribution of each of the distinct T6SSs in human populations and show there is geographical clustering. We reveal that the GA1 T6SS ICE integrates at a minimal recombination site leading to their integration throughout genomes and their frequent interruption of genes, whereas the GA2 T6SS ICE integrate at one of three different tRNA genes. The exclusion of concurrent GA1 and GA2 T6SSs in individual strains is associated with intact T6SS loci and with an ICE-encoded gene. By performing a comprehensive analysis of mobile genetic elements (MGE) in co-resident Bacteroidales species in numerous human gut communities, we identify 74 MGE that transferred to multiple Bacteroidales species within individual gut microbiomes. We further show that only three other MGE demonstrate multi-species spread in human gut microbiomes to the degree demonstrated by the GA1 and GA2 ICE. These data underscore the ubiquity and dissemination of mobile T6SS loci within Bacteroidales communities and across human populations.

Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters

“…Different conjugative elements are distinguished by different colors. The plasmid in the tree is a conjugative plasmid pMMCAT 69 . The ICE names are based on the ImmeDB database and the ICE_novel1 and 2 are newly identified ICEs that have not been included in the ImmeDB database.…”

Bacteroidetocins Target the Essential Outer Membrane Protein BamA of Bacteroidales Symbionts and Pathogens

“…5E ), despite coexisting with the Bd-B-positive B. thetaiotaomicron strain for nearly 9 years. To further evaluate if any Bacteroidales strains harboring Bd-A, Bd-B, or Bd-D have an alteration in the BamA sites shown in this study to confer resistance, we searched our Bacteroidales isolate collection of 1,434 sequenced genomes ( 21 ). We found 19 strains encoding either a Bd-A, Bd-B, or Bd-D peptide, and all BamA proteins of these strains contain the conserved aspartate, tryptophan, and asparagine residues shown in various Bacteroidales species to confer resistance when altered.…”

Presence and absence of type VI secretion systems in bacteria

“…Studies on the three T6SSs of Bacteroidales have suggested that T6SS-positive bacteria may play a role in the colonization of the human microbiome [57, 59]. Bacteroidales are a highly abundant order of microbes in the human gut microbiome, members of which have been reported to encode the T6SS from human samples worldwide [60]. Thus, T6SS-positive bacteria are highly abundant in host-associated communities, where they use the T6SS, among other things, to kill competing bacteria.…”

“…At the strain level, various presence/absence patterns can be observed, too. In Vibrio crassostreae , for example, some strains are T6SS-positive and others T6SS-negative (), as is the case with Bacteroides ovatus as well () [60, 80]. Indeed, intraspecific presence/absence variation of the T6SS was observed in all Bacteroides species analysed by García-Bayona and colleagues [60].…”