EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Barbera, Pierre; Kozlov, Alexey M; Czech, Lucas; Morel, Benoît; Stamatakis, Alexandros

doi:10.1101/291658

Cited by 107 publications

(138 citation statements)

References 14 publications

Supporting

Mentioning

138

Contrasting

Order By: Relevance

“…Metagenomic functional abundances were predicted from 16S abundances using PICRUSt2 v2.1.0‐b (https://github.com/picrust/picrust2/wiki). Briefly, 16S ASVs inferred by DADA2 were aligned with HMMER (Eddy ) and placed in the provided reference tree using EPA‐ng and GAPPA (Barbera et al ). Gene family copy numbers were predicted for 16S as well as KEGG functions (i.e., EC and KO accessions) using Hidden State Prediction ( castor ; Louca and Doebeli ) based on 16S ASV abundances and phylogenetic proximity to reference taxa with available genomes.…”

Section: Methodsmentioning

confidence: 99%

Depth‐dependent detritus production in the sponge, Halisarca caerulea

Lesser

Mueller

Pankey

et al. 2019

Limnology & Oceanography

View full text Add to dashboard Cite

Sponges are important ecological and functional components of coral reefs. Recently, a new hypothesis about the functional ecology of sponges in organic matter recycling pathways, the sponge‐loop hypothesis, in which dissolved and particulate organic matter is taken up by sponges and shunted to higher trophic levels as detritus, has been proposed and demonstrated for shallow (< 30 m) cryptic species. However, support for this hypothesis at mesophotic depths (∼ 30–150 m) is lacking. Here, we examined detritus production, a prerequisite of the sponge loop pathway, in a reciprocal transplant experiment, using Halisarca caerulea from water depths of 10 and 50 m. Detritus production was significantly lower in mesophotic sponges compared to shallow samples of H. caerulea. Additionally, detritus production rates in transplanted sponges moved in the direction of rates observed for resident conspecifics. The microbiome of these sponge populations was also significantly different between shallow and mesophotic depths, and the microbial communities of the transplanted sponges also shifted in the direction of their new depth in 10 d largely driven by changes in Oxyphotobacteria, Acidimicrobiia, Nitrososphaeria, Nitrospira, Deltaproteobacteria, and Dadabacteriia. This occurred in an environment where the availability of both dissolved and particulate trophic resources changed significantly across the shallow to mesophotic depth gradient where these sponge populations were found. These results suggest that changes in sponge detritus production are primarily driven by differential quality and quantity of trophic resources, as well as their utilization by the sponge host, and its microbiome, along the shallow to mesophotic depth gradient.

show abstract

Section: Methodsmentioning

confidence: 99%

Depth‐dependent detritus production in the sponge, Halisarca caerulea

Lesser

Mueller

Pankey

et al. 2019

Limnology & Oceanography

View full text Add to dashboard Cite

show abstract

“…The abundance of the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology (KO) 53 in each sample was estimated by PICRUSt2. [54][55][56][57][58] In KEGG orthology set enrichment analysis (KOSEA), sets of KOs in the KEGG pathway database 53 were used as substitutes for sets of genes in the gene set enrichment analysis (GSEA). 59 See the Supporting Information Methods for details.…”

Section: Kyoto Encyclopedia Of Genes and Genomesmentioning

confidence: 99%

Meta‐Analysis of Gut Dysbiosis in Parkinson's Disease

et al. 2020

View full text Add to dashboard Cite

Background PD may begin with the intestinal accumulation of α‐synuclein fibrils, which can be causally associated with gut dysbiosis. The variability of gut microbiota across countries prevented us from identifying shared gut dysbiosis in PD. Objectives To identify gut dysbiosis in PD across countries. Methods We performed 16S ribosomal RNA gene sequencing analysis of gut microbiota in 223 patients with PD and 137 controls, and meta‐analyzed gut dysbiosis by combining our dataset with four previously reported data sets from the United States, Finland, Russia, and Germany. We excluded uncommon taxa from our analyses. For pathway analysis, we developed the Kyoto Encyclopedia of Genes and Genomes orthology set enrichment analysis method. Results After adjusting for confounding factors (body mass index, constipation, sex, age, and catechol‐O‐methyl transferase inhibitor), genera Akkermansia and Catabacter, as well as families Akkermansiaceae, were increased, whereas genera Roseburia, Faecalibacterium, and Lachnospiraceae ND3007 group were decreased in PD. Catechol‐O‐methyl transferase inhibitor intake markedly increased family Lactobacillaceae. Inspection of these bacteria in 12 datasets that were not included in the meta‐analysis revealed that increased genus Akkermansia and decreased genera Roseburia and Faecalibacterium were frequently observed across countries. Kyoto Encyclopedia of Genes and Genomes orthology set enrichment analysis revealed changes in short‐chain fatty acid metabolisms in our dataset. Conclusions We report that intestinal mucin layer‐degrading Akkermansia is increased and that short‐chain fatty acid–producing Roseburia and Faecalibacterium are decreased in PD across countries. © 2020 International Parkinson and Movement Disorder Society

show abstract

“…Next, a more stringent procedure was carried out, with the putative fish sequences extracted from this initial blast result subjected to a second blastn search, this time using our curated reference library of British Isles fishes as the blast database (same settings as the "nt" search but with '-word size 7'). The same reads were then run through the Evolutionary Placement Algorithm (EPA-ng v0.3.5, gappa v0.2.0; Barbera et al, 2018;Czech & Stamatakis, 2019…”

Section: Bioinformatic Processingmentioning

confidence: 99%

Non‐specific amplification compromises environmental DNA metabarcoding with COI

et al. 2019

View full text Add to dashboard Cite

Metabarcoding extra‐organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. Of critical consideration when designing experiments, and especially so when developing community standards and legislative frameworks, is the choice of genetic marker and primer set. Mitochondrial cytochrome c oxidase subunit I (COI), the standard DNA barcode marker for animals, with its extensive reference library, taxonomic discriminatory power and predictable sequence variation, is the natural choice for many metabarcoding applications. However, for targeting specific taxonomic groups in environmental samples, the utility of COI has yet to be fully scrutinized. Here, by using a case study of marine and freshwater fishes from the British Isles, we quantify the in silico performance of twelve primer pairs from four mitochondrial loci – COI, cytochrome b, 12S and 16S – in terms of reference library coverage, taxonomic discriminatory power and primer universality. We subsequently test in vitro four primer pairs – three COI and one 12S – for their specificity, reproducibility, and congruence with independent datasets derived from traditional survey methods at five estuarine and coastal sites around the English Channel and North Sea. Our results show that for aqueous extra‐organismal DNA at low template concentrations, both metazoan‐targeted and fish‐targeted COI primers perform poorly in comparison to 12S, exhibiting low levels of reproducibility due to non‐specific amplification of prokaryotic and non‐target eukaryotic DNAs. An ideal metabarcode would have an extensive reference library upon which custom primers could be designed, either for broad assessments of biodiversity, or taxon specific surveys. Such a database is available for COI, but low primer specificity hinders practical application, while conversely, 12S primers offer high specificity, but lack adequate references. The latter, however, can be mitigated by expanding the concept of DNA barcodes to include whole mitochondrial genomes generated by genome‐skimming existing tissue collections.

show abstract

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Cited by 107 publications

References 14 publications

Depth‐dependent detritus production in the sponge, Halisarca caerulea

Depth‐dependent detritus production in the sponge, Halisarca caerulea

Meta‐Analysis of Gut Dysbiosis in Parkinson's Disease

Non‐specific amplification compromises environmental DNA metabarcoding with COI

Contact Info

Product

Resources

About