Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes

Abstract

Shipworms play critical roles in recycling wood in the sea. Symbiotic bacteria supply enzymes that the organisms need for nutrition and wood degradation. Some of these bacteria have been grown in pure culture and have the capacity to make many secondary metabolites. However, little is known about whether such secondary metabolite pathways are represented in the symbiont communities within their hosts. In addition, little has been reported about the patterns of host-symbiont co-occurrence. Here, we collected shipworms from the United States, the Philippines, and Brazil and cultivated symbiotic bacteria from their gills. We analyzed sequences from 22 shipworm gill metagenomes from seven shipworm species and from 23 cultivated symbiont isolates. Using (meta)genome sequencing, we demonstrate that the cultivated isolates represent all the major bacterial symbiont species and strains in shipworm gills. We show that the bacterial symbionts are distributed among shipworm hosts in consistent, predictable patterns. The symbiotic bacteria harbor many gene cluster families (GCFs) for biosynthesis of bioactive secondary metabolites, only <5% of which match previously described biosynthetic pathways. Because we were able to cultivate the symbionts and to sequence their genomes, we can definitively enumerate the biosynthetic pathways in these symbiont communities, showing that ∼150 of ∼200 total biosynthetic gene clusters (BGCs) present in the animal gill metagenomes are represented in our culture collection. Shipworm symbionts occur in suites that differ predictably across a wide taxonomic and geographic range of host species and collectively constitute an immense resource for the discovery of new biosynthetic pathways corresponding to bioactive secondary metabolites. IMPORTANCE We define a system in which the major symbionts that are important to host biology and to the production of secondary metabolites can be cultivated. We show that symbiotic bacteria that are critical to host nutrition and lifestyle also have an immense capacity to produce a multitude of diverse and likely novel bioactive secondary metabolites that could lead to the discovery of drugs and that these pathways are found within shipworm gills. We propose that, by shaping associated microbial communities within the host, the compounds support the ability of shipworms to degrade wood in marine environments. Because these symbionts can be cultivated and genetically manipulated, they provide a powerful model for understanding how secondary metabolism impacts microbial symbiosis.

Shipworm symbiosis ecology-guided discovery of an antibiotic that kills colistin-resistant Acinetobacter

“…A previous systematic analysis of shipworm symbiont isolate genomes and animal gill metagenomes identified a NRPS BGC, where it was defined as "GCF_1", as being highly conserved in T. turnerae, and portions of the cluster were detected in all T. turnerae-containing shipworms. [8] Here, multigene BLAST analysis of 8 sequenced T. turnerae strains found this cluster to be ubiquitous (Figure 1A); however, the region including turD and turE appeared to be regularly disrupted in many of these strains. In correctly assembled sequences, this region contained two repeats of 6k bp in length that were 98% identical, while in the misassembled sequences this region was scrambled.…”

Assessing Biosynthetic Gene Cluster Diversity of Specialized Metabolites in the Conserved Gut Symbionts of Herbivorous Turtle Ants

“…To further evaluate the quality of the metagenomic data, we investigate the genomic similarity of each metagenomic bin to the cultured isolate genomes from C. rohweri and C. varians (seven strains from each ant species). We created a heatmap representing the gANI and the AF values as a proxy of the sequence similarity ( Supplementary Figure 4 and Supplementary Table 6 ; Altamia et al, 2020 ). The mapping of bins to cultured isolate genomes was considered successful if it met the gANI × AF > 80 threshold.…”

“…The AF is calculated by dividing the sum of the lengths of all BBH genes by the sum of the length of all the genes in genome 1. For AF, values higher than 0.5 are considered conspecifics ( Altamia et al, 2020 ).…”

“…Next, the contigs of each metagenomic bin were mapped to each cultured isolate genome from the corresponding host species using the bbmap.sh function in the BBMerge software version 38.22 ( Bushnell et al, 2017 ) with the following parameters: kfilter = 22, subfilter = 15, and maxindel = 80. These parameters were used in a similar study published recently ( Altamia et al, 2020 ). BBMap aligns contig sequences from each metagenomic bin (genome 1) and each cultured isolate genome (genome 2) and returns the percentage of contigs in genome 2 which were found in genome 1.…”

“…BGC studies often focus on the genomes of culturable strains from environmental bacteria ( Paulus et al, 2017 ; Crits-Christoph et al, 2018 ) or host-associated bacteria ( Kroiss et al, 2010 ; Beemelmanns et al, 2016 ) and contribute to the discovery of bioactive compounds for medicine. Mining of bacterial metagenomes has also been investigated from environmental samples ( Cuadrat et al, 2018 ), as well as bacterial communities associated within hosts ( Donia et al, 2011 ; Wilson and Piel, 2013 ; Altamia et al, 2020 ; Waterworth et al, 2020 ).…”