The human gut microbiome is a dynamic and densely populated microbial community that can provide important benefits to its host. Cooperation and competition for nutrients among its constituents only partially explain community composition and interpersonal variation. Notably, certain human-associated Bacteroidetes—one of two major phyla in the gut—also encode machinery for contact-dependent interbacterial antagonism, but its impact within gut microbial communities remains unknown. Here we report that prominent human gut symbionts persist in the gut through continuous attack on their immediate neighbors. Our analysis of just one of the hundreds of species in these communities reveals 12 candidate antibacterial effector loci that can exist in 32 combinations. Through the use of secretome studies, in vitro bacterial interaction assays and multiple mouse models, we uncover strain-specific effector/immunity repertoires that can predict interbacterial interactions in vitro and in vivo, and find that some of these strains avoid contact-dependent killing by accumulating immunity genes to effectors that they do not encode. Effector transmission rates in live animals can exceed 1 billion events per minute per gram of colonic contents, and multiphylum communities of human gut commensals can partially protect sensitive strains from these attacks. Together, these results suggest that gut microbes can determine their interactions through direct contact. An understanding of the strategies human gut symbionts have evolved to target other members of this community may provide new approaches for microbiome manipulation.

Summary Although gut microbiome composition is well defined, the mechanisms underlying community assembly remain poorly understood. Bacteroidales possess three genetic architectures (GA1–3) of the type VI secretion system (T6SS), an effector delivery pathway that mediates interbacterial competition. Here we define the distribution and role of GA1–3 in the human gut using metagenomic analysis. We find that adult microbiomes harbor limited effector and cognate immunity genes, suggesting selection for compatibility at the species (GA1, GA2) and strain (GA3) levels. Bacteroides fragilis GA3 is known to mediate potent inter-strain competition, and we observe GA3 enrichment among strains colonizing infant microbiomes, suggesting competition early in life. Additionally, GA3 is associated with increased Bacteroides abundance, indicating that this system confers an advantage in Bacteroides-rich ecosystems. Collectively, these analyses uncover the prevalence of T6SS-dependent competition and reveal its potential role in shaping human gut microbial composition.

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.

The human intestine harbors a highly complex microbial community; interpersonal variation in this community can impact pathogen susceptibility, metabolism, and other aspects of health. Here, we identified and characterized a commensal-targeting antibacterial protein encoded in the gut microbiome.

Previous research discovered hundreds of phylogenetically diverse soil bacteria with the capacity to grow on a wide range of antibiotics as their sole carbon source. Some of them are closely related to human pathogens. The purpose of this study is to evaluate whether there is a barrier that might prevent the penicillin catabolism genes from transferring from PE‐S1G‐1 to Acinetobacter baylyi strain ADP1. Due to its natural competence and its close relation to human pathogen Acinetobacter baumannii, ADP1 is an ideal model for this study. Natural transformation with genomic DNA of PE‐S1G‐1, phi29 elongation with primers to add short homologous DNA to the genomic DNA, and Sau3A genomic plasmid libraries were used to test this barrier. None of these methods mentioned above transformed ADP1 to be a strain with penicillin catabolism phenotype. Surprisingly, a recent research challenges the concept of bacteria subsisting on antibiotics and argues that the selective media used in the original study (SCS) contains 15 mg/L EDTA which could be the carbon source that sustains the growth of these “antibiotic‐eaters.” The hypothesis that these bacteria could subsist on EDTA is currently being tested.