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

Background:

The human gut microbiota (the hundreds of strains that colonize the gut in all individuals) has tremendous impact on our physiology. However, the precise rules and mechanisms mediating the exact composition of the gut microbiota remain mostly unclear. An emerging theme is bacterial warfare – the direct antagonism of growth or survival by competing microbial strains in close proximity. Of particular importance is the Type VI secretion system (T6SS), which mediates competition between multiple gram-negative species, including the well-studied Bacteroidetes phylum that is highly abundant and important in the human gut [Russell 2014, Wexler 2016]. T6SS inject toxic effectors into target bacteria, and bacteria protect themselves from self-poisoning using cognate immunity proteins. Previous work from the Mougous and Borenstein groups had identified the widespread presence of these T6SS effector-immunity pairs in human gut metagenomes, with notable compositional shifts between T6SS+ and T6SS- microbiomes [Verster and Ross 2017]. This paper extends on those prior findings to explore the breadth of immunity proteins and how their spread into different species may shape gut ecology.

 

Key Findings:

• T6SS immunity homologs are widespread through gut microbiomes even in the absence of B. fragilis.

The authors examine human gut metagenomes for sequences homologous to T6SS immunity proteins from Bacteroides fragilis. While effector sequence presence was well correlated with B. fragilis abundance, there were many samples with immunity sequences despite low or absent B. fragilis abundance. These orphan immunity genes were encoded by multiple different Bacteroides species, and included multiple clades of sequence homologs that were non-identical to the immunity gene in B. fragilis.

• Orphan immunity genes are in large gene clusters and provide active protection against T6SS warfare in vivo.

Two of the dominant clades of immunity genes were found encoded together in a gene cluster the authors named “AID-1” (acquired interbacterial defense 1) which was predicted to be on a mobile integrative and conjugative element. AID-1 systems also included homologs or pseudogenes of other T6SS immunity genes, and their gene products were capable of mediating protection against the cognate effectors, demonstrating that they encoded active immunity genes. In vitro and in vivo competition assays revealed that presence of the AID-1 system (in particular, the i6 and i7 homologs in the AID-1 system) enhanced fitness against cognate effector-expressing B. fragilis strains. Finally, B. ovatus strains with orphan immunity genes were more abundant in gut metagenomes than those without, suggesting active competitive fitness advantages in the human gut.

• rAID-1 systems mediating broad T6SS immunity are widespread and active within and beyond the Bacteroides.

AID-1 and similar systems were protective against B. fragilis-specific effectors, prompting the authors to search for immunity genes in B. fragilis against T6SS effectors produced by a different form of the T6SS not unique to B. fragilis. Indeed, many B. fragilis genomes contained gene clusters containing homologs of these immunity genes, associated with a tyrosine recombinase and integron sequences, leading the authors to name these “rAID-1” systems. rAID-1 systems did encode active immunity against cognate effectors, and were widespread through Bacteroidales genomes. Overall, this suggests that sharing of bacterial immunity genes is an important mechanism for survival and competition within many complex microbial communities, including the human gut.

 

Importance:

This work deepens our understanding of the ecological forces at play in the human gut microbiota and other complex microbial environments, illustrating how dominant a selective force bacterial warfare can be and new mechanisms by which immunity spreads. Additionally, the discovery of the AID-1/2 and rAID-1 systems provides a wealth of new candidate immunity genes and opportunities to further explore bacterial competition across a broader range of species (see below), which will be highly important in understanding the rules governing the human gut microbiota, a highly complex and variable ecosystem.

 

Moving Forward:

• In the samples with no B. fragilis but presence of immunity genes, is immunity maintained / selected for by a T6SS cognate effector expressed from another species, or by an alternative immunity gene in the same gene cluster against an alternative warfare system?
• It is very interesting that rAID-1 systems contain apparent immunity genes from a wide range of other bacterial orders, including gram-positives and gram-negatives. Are these immunity homologs active against a diverse range of bacterial warfare systems, and do they similarly predict fitness within complex communities? For example, do Bacteriodales encoding predicted Clostridiales immunity genes have higher abundance in Clostridiales-high microbial communities?
• Fig 4A depicts the immunity gene clusters from rAID-1 systems. The unknown genes within these clusters may be excellent candidates for discovering new bacterial warfare systems as probes for cognate effectors – analogous to the discovery of new anti-phage systems by exploring gene clusters co-localized with previously established phage defense systems [Doron and Melamed et al 2018]. This will be very exciting to see!

 

References:

• Russell, A.B. et al. A Type VI Secretion-Related Pathway in Bacteroidetes Mediates Interbacterial Antagonism. Cell Host & Microbe 16(2) 227-236 (2014)
• Wexler, A.G. et al. Human symbionts inject and neutralize antibacterial toxins to persist in the gut. PNAS 113(13) 3639-3644 (2016)
• Verster, A.J., Ross, B.D. et al. The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition. Cell Host & Microbe 22(3) 441-419 (2017)
• Doron, S., Melamed, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359(6379) eaar4120 (2018)

 

 

doi: https://doi.org/10.1242/prelights.6295

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