A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93T, was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93Twas capable of acetylenotrophic and diazotrophic growth, grew at 22–37 °C, pH 6.3–8.5 and in the presence of 10–45 g l−1NaCl. Phylogenetic analyses based on 16S rRNA gene sequencing showed that SFB93Trepresented a member of the genus
Journal editors have a large amount of power to advance open science in their respective fields by incentivising and mandating open policies and practices at their journals. The Data PASS Journal Editors Discussion Interface (JEDI, an online community for social science journal editors:
- PAR ID:
- 10491181
- Author(s) / Creator(s):
- ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »
- Publisher / Repository:
- Springer Science + Business Media
- Date Published:
- Journal Name:
- Research Integrity and Peer Review
- Volume:
- 9
- Issue:
- 1
- ISSN:
- 2058-8615
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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with highest 16S rRNA gene sequence similarities toSyntrophotalea DSM 3246T(96.6 %),Syntrophotalea acetylenica DSM 2380T(96.5 %), andSyntrophotalea carbinolica DSM 2394T(96.7 %). Genome sequencing revealed a genome size of 3.22 Mbp and a DNA G+C content of 53.4 %. SFB93Thad low genome-wide average nucleotide identity (81–87.5 %) and <70 % digital DNA–DNA hybridization value with other members of the genusSyntrophotalea venetiana . The phylogenetic position of SFB93Twithin the familySyntrophotalea and as a novel member of the genusSyntrophotaleaceae was confirmed via phylogenetic reconstruction based on concatenated alignments of 92 bacterial core genes. On the basis of the results of phenotypic, genotypic and phylogenetic analyses, a novel species,Syntrophotalea Syntrophotalea acetylenivorans sp. nov., is proposed, with SFB93T(=DSM 106009T=JCM 33327T=ATCC TSD-118T) as the type strain. -
A Gram-stain-negative, rod-shaped bacterial strain, designated
Vibrio floridensis IRLE0018 (=NRRL B-65642=NCTC 14661), was isolated from a cyanobacterial bloom along the Indian River Lagoon (IRL), a large and highly biodiverse estuary in eastern Florida (USA). The results of phylogenetic, biochemical, and phenotypic analyses indicate that this isolate is distinct from species of the genus with validly published names and is the closest relative to the emergent human pathogen,Vibrio . Here, we present the complete genome sequence ofVibrio vulnificus V. floridensis strain IRLE0018 (4 535 135 bp). On the basis of the established average nucleotide identity (ANI) values for the determination of different species (ANI <95 %), strain IRLE0018, with an ANI of approximately 92 % compared with its closest relative, , represents a novel species within the genusV. vulnificus . To our knowledge, this represents the first time this species has been described. The results of genomic analyses ofVibrio V. floridensis IRLE0018 indicate the presence of antibiotic resistance genes and several known virulence factors, however, its pathogenicity profile (e.g. survival in serum, phagocytosis avoidance) reveals limited virulence potential of this species in contrast to .V. vulnificus -
While recent efforts to catalogue Earth’s microbial diversity have focused upon surface and marine habitats, 12–20 % of Earth’s biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by
Betaproteobacteria, Gammaproteobacteria and , probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalentFirmicutes andBetaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. AnGammaproteobacteria in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling. -
Abstract Background The pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species.
Results Here we introduce PGV, a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering. Our experimental results demonstrate that PGV enables an intuitive, effective and interactive visualization of a pan-genome by providing a genome browser that can elucidate complex structural genomic variations.
Conclusions The PGV software can be installed via conda or downloaded from
https://github.com/ucrbioinfo/PGV . The companion PGV browser athttp://pgv.cs.ucr.edu can be tested using example bed tracks available from the GitHub page. -
Abstract Background Computational cell type deconvolution enables the estimation of cell type abundance from bulk tissues and is important for understanding tissue microenviroment, especially in tumor tissues. With rapid development of deconvolution methods, many benchmarking studies have been published aiming for a comprehensive evaluation for these methods. Benchmarking studies rely on cell-type resolved single-cell RNA-seq data to create simulated pseudobulk datasets by adding individual cells-types in controlled proportions.
Results In our work, we show that the standard application of this approach, which uses randomly selected single cells, regardless of the intrinsic difference between them, generates synthetic bulk expression values that lack appropriate biological variance. We demonstrate why and how the current bulk simulation pipeline with random cells is unrealistic and propose a heterogeneous simulation strategy as a solution. The heterogeneously simulated bulk samples match up with the variance observed in real bulk datasets and therefore provide concrete benefits for benchmarking in several ways. We demonstrate that conceptual classes of deconvolution methods differ dramatically in their robustness to heterogeneity with reference-free methods performing particularly poorly. For regression-based methods, the heterogeneous simulation provides an explicit framework to disentangle the contributions of reference construction and regression methods to performance. Finally, we perform an extensive benchmark of diverse methods across eight different datasets and find BayesPrism and a hybrid MuSiC/CIBERSORTx approach to be the top performers.
Conclusions Our heterogeneous bulk simulation method and the entire benchmarking framework is implemented in a user friendly package
https://github.com/humengying0907/deconvBenchmarking andhttps://doi.org/10.5281/zenodo.8206516 , enabling further developments in deconvolution methods.