DOI: 10.5061/dryad.s7h44j168
title: Metagenomic bins and biosynthetic gene clusters in gut bacteria of turtle ants

description: Cephalotes are herbivorous ants (&gt;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.
description: <b>Genomes and
 metagenomes analysis</b> The 14 genomes of cultured gut bacteria and 18 metagenomes of <i>Cephalotes</i> gut bacteria were obtained from JGI-IMG version 5.0 (Table S1 and S2 respectively) from the previous projects Gs0085494 (“<i>Cephalotes varians</i> microbial communities from the Florida Keys, USA”), Gs0114286 (“Symbiotic bacteria isolated from <i>Cephalotes varians</i>”), Gs0117930 (“<i>Cephalotes</i> ants gut microbiomes”) and Gs0118097 (“Symbiotic bacteria isolated from <i>Cephalotes rohweri</i>”). The 14 cultured isolate genomes are all part of the <i>Cephalotes</i> core microbiome: two <i>Cephaloticoccus</i> genomes (order: Opitutales, class: Opitutae; one genome from each ant host),  four <i>Ventosimonas</i> genomes (order: Pseudomonadales, class: Gammaproteobacteria; one genome from <i>C. varians</i> and three genomes from <i>C. rohweri</i>), six Burkholderiales genomes (class: Betaproteobacteria; four genomes from <i>C. varians</i> and two genomes from <i>C. rohweri</i>), one Rhizobiales genome (class: Alphaproteobacteria;  from <i>C. varians</i>), and one Xanthomonadales genome (class: Gammaproteobacteria; from <i>C. rohweri</i>). All these bacteria belong to the Proteobacteria phylum, except Opitutales which are part of the Verrucomicrobia phylum. The metagenomic data used in this study have two metagenomes from the same <i>C. varians </i>species. However, for the metagenome of <i>C. varians</i> PL010W the sequencing quality is very different from all the other metagenomes (number of reads, GC content) including <i>C. varians</i> PL005W, therefore it was excluded in our analysis. The metagenomes were analyzed via the software Anvi’o version 5.5 to sort the different bacterial families composing each metagenome into distinct bins. In this analysis, the fasta sequence of a metagenome is used to create a contig database and a profile database. Then, this contig database is visualized and bins are manually created to maximize completeness while minimizing contamination. Finally, the software CheckM version 1.1 was used to verify the completeness, contamination and strain homogeneity of each bin, and to identify the taxonomic lineage of each bin. <b>Bacterial biosynthetic gene clusters analysis</b> The bacterial biosynthetic gene clusters (BGCs) of each genome and each metagenomic bin were analyzed with antiSMASH version 5.0 with the following analysis options: strict detection, and activation of search for KnownClusterBlast, ClusterBlast, SubClusterBlast and Active site finder. BGCs smaller than 5kb were then filtered out of the data and were not included. The taxonomic classification of each cluster was verified to the genus level using the software Blast+. There was no identification conflict between CheckM and Blast+. NaPDos (https://npdomainseeker.sdsc.edu/, accessed July 2020) was used to classify the ketosynthase (KS) domain and condensation (C) domain sequences of NRP and PK retrieved from the genome and metagenome mining analysis and to infer the KS and C phylogenies.    
description: The data contain: (1) the metagenomic bins
 (name of the file: Chanson_et_al_Cephalotes_metagenomic_bins) in
 ".fasta" files. The file name corresponds to the name of the
 ant from which each metagenomic bin are associated. (2)
 the biosynthetic gene clusters detected in the genomes of culture isolate
 bacterial symbionts (name of the file:
 Chanson_et_al_Cephalotes_genomes_BGCs) in ".gbk" files. The file
 name corresponds to the name of the ants from which each BGC was
 obtained. (3) the biosynthetic gene clusters detected
 in the genomes of culture isolate bacterial symbionts (name of the file:
 Chanson_et_al_Cephalotes_genomes_BGCs) in ".gbk" files. The file
 name corresponds to the name of the ants from which each BGC was obtained
 follow by the number of the metagenoic bin containing the BGCs.