Biology subjects

Abram, F.

Publications and source records attributed to Abram, F..

5 recordsLinked to original sources

bioRxiv2021

Mining underutilized whole-genome sequencing projects to improve 16S rRNA databases

Current approaches to interpreting 16S rDNA amplicon data are hampered by several factors. Among these are database inaccuracy or incompleteness, sequencing error, and biased DNA/RNA extraction. Existing 16S rRNA databases source the majority of sequences from deposited amplicon sequences, draft genomes, and complete genomes. Most of the draft genomes available are assembled from short reads. However, repeated ribosomal regions are notoriously difficult to assemble well from short reads, and as a consequence the short-read-assembled 16S rDNA region may be an amalgamation of different loci within the genome. This complicates high-resolution community analysis, as a draft genomes 16S rDNA sequence may be a chimera of multiple loci; in such cases, the draft-derived sequences in a database may not represent a 16S rRNA sequence as it occurs in biology. We present Focus16, a pipeline for improving 16S rRNA databases by mining NCBIs Sequence Read Archive for whole-genome sequencing runs that could be reassembled to yield additional 16S rRNA sequences. Using riboSeed (a genome assembly tool for correcting rDNA misassembly), Focus16 provides a way to augment 16S rRNA databases with high-quality re-assembled sequences. In this study, we augmented the widely-used SILVA 16S rRNA database with the novel sequences disclosed by Focus16 and re-processed amplicon sequences from several benchmarking datasets with DADA2. Using this augmented SILVA database increased the number of amplicon sequence variants that could be assigned taxonomic annotations. Further, fine-scale classification was improved by revealing ambiguities. We observed, for example, that amplicon sequence variants (ASVs) may be assigned to a specific genus where Focus16-correction would indicate that the ASV is represented in two or more genera. Thus, we demonstrate that improvements can be made to taxonomic classification by incorporating these carefully re-assembled 16S rRNA sequences, and we invite the community to expand our work to augment existing 16S rRNA reference databases such as SILVA, GreenGenes, and RDP.

bioinformatics↗

bioRxiv2019

Organic soil amendment with Spent Mushroom Substrate results in fungal colonisation, alters bacterial-fungal co-occurrence patterns and improves plant productivity.

In agricultural systems based on organic fertilisers, the activity of prokaryotes and fungi is essential for degradation of complex substrates and release of nutrients for plant uptake. Understanding the dynamics of microbial communities in these systems is, therefore, desirable for designing successful management strategies aiming to optimise nutrient availability and to improve plant productivity. Of particular interest is how the microbial inoculum provided by an organic substrate persists in the soil and interacts with soil and plant microbiomes, as these processes may affect the long-term benefits of organic amendments. We aimed to investigate how these dynamics occurred in soil treated with stabilised spent mushroom substrate (SMS), a soil amendment rich in nutrients and complex organic matter. We carried out a 14 weeks soil trial to assess the plant growth promoting properties of the SMS and to monitor the successional processes of the resulting SMS-soil communities compared to a mineral amended control. Bacterial and fungal communities were analysed by high-throughput sequencing at both DNA and RNA (cDNA) levels. Using a combination of computational tools, including SourceTracker and Network analysis, we assessed the persistence of SMS-derived taxa in soil, and the changes in co-occurrence patterns and microbial community structure over time. Prokaryotic and fungal communities presented remarkably distinct trajectories following SMS treatment. The soil prokaryotic communities displayed higher levels of resilience to the changes introduced by SMS treatment and rapidly tended toward a soil-like profile, with low persistence of SMS-derived prokaryotes. In contrast, the SMS fungal community had greater success in soil colonisation during the time monitored. SMS treatment promoted an increase in the participation of fungi in the highly connected fraction of the active community, including fungal taxa of SMS origin. We observed the presence of highly connected microbial guilds, composed by fungal and bacterial taxa with reported capabilities of complex organic matter degradation. Many of these taxa were also significantly correlated with the organic matter content and plant yield, suggesting that these highly connected taxa may play key roles not only in the community structure, but also in the plant-soil system under organic fertilisation.

microbiology↗

bioRxiv2019

The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei.

Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeon Methanosarcina mazei. Pi-starved M. mazei cells increased transcript abundance of the PHO-regulated alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starved M. mazei cells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a >5.7-fold increase in ppk1 gene transcripts. Ppk1 expression in M. mazei thus appears not to be under classical PHO regulon control.

microbiology↗

bioRxiv2018

Easily phylotyping E. coli via the EzClermont web app and command-line tool.

The Clermont PCR method of phylotyping Escherichia coli has remained a useful classification scheme despite the proliferation of higher-resolution sequence typing schemes. We have implemented an in silico Clermont PCR method as both a web app and as a command-line tool to allow researchers to easily apply this phylotyping scheme to genome assemblies easily. Availability and ImplementationEzClermont is available as a web app at http://www.ezclermont.org. For local use, EzClermont can be installed with pip or installed from the source code at https://github.com/nickp60/ezclermont. All analysis was done with version 0.4.0. Contactn.waters4@nuigalway.ie, leighton.pritchard@strath.ac.uk Supplementary informationTable S1: test dataset; S2: validation dataset; S3: results.

bioinformatics↗

bioRxiv2017

riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions

The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only {approx}10% of sequencing projects have resulted in a closed genome. The most common repeated regions are those coding for ribosomal operons (rDNAs), which occur in a bacterial genome between 1 and 15 times, and are typically used as sequence markers to classify and identify bacteria. Here, we exploit conservation in the genomic context in which rDNAs occur across taxa to improve assembly of these regions relative to de novo sequencing by using the conserved nature of rDNAs across taxa and the uniqueness of their flanking regions within a genome. We describe a method to construct targeted pseudocontigs generated by iteratively assembling reads that map to a reference genomes rDNAs. These pseudocontigs are then used to more accurately assemble the newly-sequenced chromosome. We show that this method, implemented as riboSeed, correctly bridges across adjacent contigs in bacterial genome assembly and, when used in conjunction with other genome polishing tools, can assist in closure of a genome.

bioinformatics↗