Data_Sheet_2_Thousands of Novel Endolysins Discovered in Uncultured Phage Genomes.FASTA

<p>Bacteriophages express endolysins toward the end of their replication cycle to degrade the microbial cell wall from within, allowing viral progeny to be released. Endolysins can also degrade the prokaryotic cell wall from the outside, thus have potential to be used for biotechnological and medical purposes. Multiple endolysins have been identified within the genomes of isolated phages, but their diversity in uncultured phages has been overlooked. We used a bioinformatics pipeline to identify novel endolysins from nearly 200,000 uncultured viruses. We report the discovery of 2,628 putative endolysins, many of which displayed novel domain architectures. In addition, several of the identified proteins are predicted to be active against genera that include pathogenic bacteria. These discoveries enhance the diversity of known endolysins and are a stepping stone for developing medical and biotechnological applications that rely on bacteriophages, the most diverse biological entities on Earth.</p

Table_1_Thousands of Novel Endolysins Discovered in Uncultured Phage Genomes.XLSX

<p>Bacteriophages express endolysins toward the end of their replication cycle to degrade the microbial cell wall from within, allowing viral progeny to be released. Endolysins can also degrade the prokaryotic cell wall from the outside, thus have potential to be used for biotechnological and medical purposes. Multiple endolysins have been identified within the genomes of isolated phages, but their diversity in uncultured phages has been overlooked. We used a bioinformatics pipeline to identify novel endolysins from nearly 200,000 uncultured viruses. We report the discovery of 2,628 putative endolysins, many of which displayed novel domain architectures. In addition, several of the identified proteins are predicted to be active against genera that include pathogenic bacteria. These discoveries enhance the diversity of known endolysins and are a stepping stone for developing medical and biotechnological applications that rely on bacteriophages, the most diverse biological entities on Earth.</p

Data_Sheet_3_Thousands of Novel Endolysins Discovered in Uncultured Phage Genomes.ZIP

<p>Bacteriophages express endolysins toward the end of their replication cycle to degrade the microbial cell wall from within, allowing viral progeny to be released. Endolysins can also degrade the prokaryotic cell wall from the outside, thus have potential to be used for biotechnological and medical purposes. Multiple endolysins have been identified within the genomes of isolated phages, but their diversity in uncultured phages has been overlooked. We used a bioinformatics pipeline to identify novel endolysins from nearly 200,000 uncultured viruses. We report the discovery of 2,628 putative endolysins, many of which displayed novel domain architectures. In addition, several of the identified proteins are predicted to be active against genera that include pathogenic bacteria. These discoveries enhance the diversity of known endolysins and are a stepping stone for developing medical and biotechnological applications that rely on bacteriophages, the most diverse biological entities on Earth.</p

Image_1_Thousands of Novel Endolysins Discovered in Uncultured Phage Genomes.PDF

<p>Bacteriophages express endolysins toward the end of their replication cycle to degrade the microbial cell wall from within, allowing viral progeny to be released. Endolysins can also degrade the prokaryotic cell wall from the outside, thus have potential to be used for biotechnological and medical purposes. Multiple endolysins have been identified within the genomes of isolated phages, but their diversity in uncultured phages has been overlooked. We used a bioinformatics pipeline to identify novel endolysins from nearly 200,000 uncultured viruses. We report the discovery of 2,628 putative endolysins, many of which displayed novel domain architectures. In addition, several of the identified proteins are predicted to be active against genera that include pathogenic bacteria. These discoveries enhance the diversity of known endolysins and are a stepping stone for developing medical and biotechnological applications that rely on bacteriophages, the most diverse biological entities on Earth.</p

Tropical Aquatic Archaea Show Environment-Specific Community Composition

<div><p>The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II <i>Euryarchaeota</i> was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV <i>Euryarchaeota</i> dominated freshwaters. Group III <i>Euryarchaeota</i>, a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria.</p> </div

Sediment Phylogenetic archaeal tree.

<p>Reference sequences from GenBank (<b>in bold</b>). OTUs were defined by using a distance level of 3% by using the furthest neighbor algorithm in MOTHUR. The tree topology is based on maximum likelihood and bootstrap analysis was performed with 1000 replications. Bootstrap value <50 are not shown.</p

Map of the studied site and the nine sampled locations.

<p>IG1 – Parnaioca water spring; IG2 – Parnaioca river; IG5 – mangrove; IG3 – Parnaioca beach; IG7 – Aventureiros beach; IG8 – Meros; SedIG – sediment from mangrove channel; SedL – Leste lagoon entrance; SedS – Sul lagoon entrance.</p

Venn diagram at 97% identity.

<p>A: Seawater, B: Freshwater, C: Sediment. IG1 – Parnaioca water spring; IG2 – Parnaioca river; IG5 – mangrove; IG3 – Parnaioca beach; IG7 – Aventureiros beach; IG8 – Meros; SedIG –mangrove channel; Leste – Leste lagoon center; Sul - Sul lagoon entrance. Asterisks shown for ∫-LIBSHUFF comparisons with p value >0.0001.</p

Freshwater Phylogenetic archaeal tree.

<p>Reference sequences from GenBank (<b>in bold</b>). OTUs were defined by using a distance level of 3% by using the furthest neighbor algorithm in MOTHUR. The tree topology is based on maximum likelihood and bootstrap analysis was performed with 1000 replications. Bootstrap value <50 are not shown.</p

Match between archaeal communities in freshwater, seawater and sediment libraries.

<p>Principal coordinates plots (PCoA) were generated using the pair wise unweighted UniFrac distances. Freshwater samples in circles, marine samples in squares, and sediments in triangles. Parnaioca Spring (green triangle); Parnaioca river (green circle); Mangrove water (green square); Parnaioca beach (blue triangle); Aventureiros beach (blue circle); Meros Island (blue square); SedIg (red triangle); SedLeste (red circle); SedSul (red square).</p