Circular genome maps of five putative circoviruses directly recovered from metagenomic data of <i>M</i>. <i>molossus</i> and <i>D</i>. <i>rotundus</i> bat feces and their phylogenetic relationships with other representative members of the <i>Circoviridae</i> family.

<p>(A) The inversely arranged open-reading frames encoding the putative replication-associated protein (REP) and capsid protein (CAP) are shown in green and blue boxes, respectively. The genome organization was determined with Geneious R9. (B) The phylogenetic analysis is based on the REP protein sequences (alignment of 109 amino acids). The blue arrows indicate the five REP sequences of bat-sourced circoviruses obtained in the present study. The tree was inferred using the Bayesian method with the blosum62 model. Sequence identifiers include the NCBI accession number and the isolate name. Posterior probabilities of the Bayesian analysis (>50%) are shown next to each node. The scale bar indicates amino acid substitutions per site.</p

Heatmap based on the viral-associated contigs of 51 families of insect, phage, plant/protozoan and vertebrate viruses in each pooled sample.

<p>Location information is provided above each column (Caves F and M for <i>D</i>. <i>rotundus</i>, Urban and Forest for <i>M</i>. <i>molossus</i>). The names of the viral families are presented in alphabetical order in the middle. The boxes colored from green to dark red represent the number of contigs observed. Contigs varied between 1 and 450 for the saliva samples and between 1 and 1465 for feces. The scales are given for each type of sample.</p

Phylogenetic analysis of the complete L1 protein sequence (alignment of 459 amino acids) directly obtained from the metagenomic data of pooled fecal samples of <i>M</i>. <i>molossus</i> with other representative members of the <i>Papillomaviridae</i> family.

<p>The tree was inferred using the Bayesian method with the WAG + G model. Sequence identifiers include the NCBI accession number. The blue arrows indicate the bat-sourced papillomavirus sequence obtained in the present study. Posterior probabilities of the Bayesian analysis (>50%) are shown next to each node. The scale bar indicates amino acid substitutions per site.</p

Bioinformatic analysis pipeline for the 3,722,219 assembled contigs, based on Baker <i>et al</i>. [45].

<p>(A) Contigs assembled from both normalized and non-normalized sequence reads by two <i>de novo</i> assemblers (SPAdes and Velvet) were consolidated by sequential comparisons (numbered shadowed areas) and removal of duplicate sequences (red arrows). (B) Centroids subjected to sequential BLAST comparison and manually controlled taxonomic classification to identify viral sequences. Proportion of sequences assembled from feces (red) and saliva swabs (blue) are shown in the stacked chart for each species depending on habitats (caves F and M for <i>D</i>. <i>rotundus</i> and Urban and Forest for <i>M</i>. <i>molossus</i>). (C) Column charts represent the distribution of contig matches (per pooled samples and overall) and the distribution of vertebrate-related viral families by bat species and habitats.</p

Characteristics of the sampling sites and number of collected feces and saliva samples for <i>Molossus molossus</i> and <i>Desmodus rotundus</i>.

<p>Characteristics of the sampling sites and number of collected feces and saliva samples for <i>Molossus molossus</i> and <i>Desmodus rotundus</i>.</p

Phylogenetic analysis of partial sequences of the <i>pol</i> s region (alignment of 107 amino acids) directly obtained from the metagenomic data of pooled fecal samples of <i>M</i>. <i>molossus</i> with other representative members of the <i>Spumavirus</i> genus.

<p>The tree was inferred using the Bayesian method with the WAG + G model. Sequence identifiers include the NCBI accession number and the isolate name. The blue arrows indicate the sequence of bat-sourced spumavirus obtained in the present study. Posterior probabilities of the Bayesian analysis (>50%) are shown next to each node. The scale bar indicates amino acid substitutions per site.</p

Phylogenetic analysis of partial <i>pol</i> gene sequences (alignment of 951 nucleotides) directly obtained from the metagenomic data of pooled fecal samples of <i>M</i>. <i>molossus</i> with other representative members of the <i>Herpesviridae</i> family.

<p>The tree was inferred using the Bayesian method with the GTR + G + I model. Sequence identifiers include the NCBI accession number and the isolate name. The blue arrows indicate the bat-sourced herpesvirus obtained in the present study. Posterior probabilities of the Bayesian analysis (>50%) are shown next to each node. The scale bar indicates amino acid substitutions per site.</p

Phylogenetic analysis of partial RdRp protein sequences (alignment of 341 amino acids) directly obtained from the metagenomic data of pooled fecal samples of <i>M</i>. <i>molossus</i> with other representative members of the <i>Nairoviridae</i> family.

<p>The tree was inferred using the Bayesian method with the WAG + G model. Sequence identifiers include the NCBI accession number and the isolate name. The blue arrows indicate the bat-sourced nairovirus sequence obtained in the present study. Posterior probabilities of the Bayesian analysis (>50%) are shown next to each node. The scale bar indicates amino acid substitutions per site.</p

Phylogenetic analysis of partial <i>capsid</i> gene sequences (alignment of 299 nucleotides).

<p>The tree was inferred using the Bayesian method with the GTR + G + I model. Novel sequences generated in this study are shown in bold. Sequence identifiers include the strain ID and the NCBI accession number. The major clades representing the different LRV1 genotypes identified (A–F) as well as the clades of LRV1 isolates from <i>L</i>. <i>(V</i>.<i>) guyanensis</i> (<i>Lg</i>) or <i>L</i>. <i>(V</i>.<i>) braziliensis</i> (<i>Lb</i>) parasites are labeled. Posterior probabilities of the Bayesian analysis (>90%) are shown next to each node. The scale bar indicates nucleotide sequence divergence among sequences.</p

Epidemiological features of the 20 patients with ACL, <i>Leishmania</i> species identification and characteristics of the 24 LRV1 strains sequenced.

<p>Epidemiological features of the 20 patients with ACL, <i>Leishmania</i> species identification and characteristics of the 24 LRV1 strains sequenced.</p