Metagenomic bins and biosynthetic gene clusters in gut bacteria of turtle ants

Cephalotes are herbivorous ants (>115 species) feeding on
low-nitrogen food sources and they rely on gut symbionts to supplement
their diet in nutrients by recycling nitrogen food waste into amino acids.
These conserved gut symbionts, composed of five bacterial orders, have
been studied previously for their primary nitrogen metabolism, however
little is known about their ability to biosynthesize specialized
metabolites which can play a role in bacterial interactions between
communities living in close proximity in the gut. We investigated the
diversity of biosynthetic gene clusters (BGCs) producing specialized
metabolites in the genomes and metagenomes of conserved gut symbionts by
studying 17 Cephalotes species collected across several geographical
areas. Our results reveal that (1) mining metagenomes and genomes show
complementary results to retrieve BGCs especially when bacterial isolates
are difficult to culture, (2) the conserved gut symbionts involved in the
nutritional symbiosis have a large diversity of BGCs of different chemical
families, (3) the phylogenetic analysis of BGCs encoding the production of
arylpolyenes, non-ribosomal peptides (NRP), polyketides (PK), and
siderophores shows high similarity between BGCs of a single symbiont
across different ant host species, and between BGCs originated from
different bacterial orders within a single host species. Additionally, the
diversity of BGCs was found in four of the five conserved symbionts
co-occurring in the hindgut except for one major player (Opitutales)
localized alone in the midgut and lacking BGCs. This spatial isolation
prevents direct interaction of Opitutales with other symbionts and
suggesting that BGCs have an essential role for symbionts living in close
proximity. These findings together pave the way for studying the
mechanisms of BGCs conservation and evolution in gut symbionts genomes and
the role of bacterial specialized metabolites involved in multipartite
mutualism with Cephalotes turtle ants.