ORCID Profile
0000-0001-6831-4557
Current Organisations
Shenzhen University
,
Amsterdam University Medical Centers
,
University of Hawai'i at Manoa
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Cold Spring Harbor Laboratory
Date: 15-08-2019
DOI: 10.1101/735696
Abstract: Microbial organisms inhabit virtually all environments and encompass a vast biological ersity. The pan-genome concept aims to facilitate an understanding of ersity within defined phylogenetic groups. Hence, pan-genomes are increasingly used to characterize the strain ersity of prokaryotic species. To understand the interdependency of pan-genome features (such as numbers of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pan-genomes for 155 phylogenetically erse species using 7000 high-quality genomes. We show that many pan-genome features such as functional ersity and core genome nucleotide ersity are correlated to each other. Further, habitat flexibility as approximated by species ubiquity is associated with several pan-genome features, particularly core genome size. In general, environment had a stronger impact on pan-genome features than phylogenetic signal. Similar environmental preferences led to convergent evolution of pan-genomic features in distant phylogenetic clades. For ex le, the soil environment promotes expansion of pan-genome size, while host-associated habitats lead to its reduction.
Publisher: Springer Science and Business Media LLC
Date: 04-03-2019
DOI: 10.1038/S41467-019-08844-4
Abstract: Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites).
Publisher: Frontiers Media SA
Date: 12-06-2014
Publisher: Elsevier BV
Date: 09-2015
DOI: 10.1016/J.NBD.2015.06.016
Abstract: The pathological role of zinc in Alzheimer's disease (AD) is not yet fully elucidated, but there is strong evidence that zinc homeostasis is impaired in the AD brain and that this contributes to disease pathogenesis. In this study we examined the effects of zinc on the proteolysis of synthetic Apolipoprotein E (ApoE), a protein whose allelic variants differentially contribute to the onset rogression of disease. We have demonstrated that zinc promotes the proteolysis (using plasma kallikrein, thrombin and chymotrypsin) of synthetic ApoE in an isoform-specific way (E4>E2 and E3), resulting in more ApoE fragments, particularly for ApoE4. In the absence of exogenous proteases there was no effect of metal modulation on either lipidated or non-lipidated ApoE isoforms. Thus, increased zinc in the complex milieu of the ageing and AD brain could reduce the level of normal full-length ApoE and increase other forms that are involved in neurodegeneration. We further examined human plasma s les from people with different ApoE genotypes. Consistent with previous studies, plasma ApoE levels varied according to different genotypes, with ApoE2 carriers showing the highest total ApoE levels and ApoE4 carriers the lowest. The levels of plasma ApoE were not affected by either the addition of exogenous metals (copper, zinc or iron) or by chelation. Taken together, our study reveals that zinc may contribute to the pathogenesis of AD by affecting the proteolysis of ApoE, which to some extent explains why APOE4 carriers are more susceptible to AD.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-05-2015
Abstract: Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional ersity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans s les from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched s les, containing ,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that % of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
Publisher: Oxford University Press (OUP)
Date: 28-10-2023
DOI: 10.1093/NAR/GKAD943
Publisher: Cold Spring Harbor Laboratory
Date: 16-12-2020
DOI: 10.1101/2020.12.16.422776
Abstract: Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genomes remains a formidable challenge. We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of in idual contigs using a genome’s full complement of genes. GUNC complements existing approaches by targeting previously underdetected types of contamination: we conservatively estimate that 5.7% of genomes in GenBank, 5.2% in RefSeq, and 15-30% of pre-filtered ‘high quality’ metagenome-assembled genomes in recent studies are undetected chimeras. GUNC provides a fast and robust tool to substantially improve prokaryotic genome quality. Source code (GPLv3+): rp-bork/gunc
Publisher: Springer Science and Business Media LLC
Date: 20-10-2013
DOI: 10.1038/NMETH.2693
Abstract: To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal s les, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at www.bork.embl.de/software/mOTU/.
Publisher: Oxford University Press (OUP)
Date: 24-10-2019
DOI: 10.1093/NAR/GKZ1002
Abstract: Microbiology depends on the availability of annotated microbial genomes for many applications. Comparative genomics approaches have been a major advance, but consistent and accurate annotations of genomes can be hard to obtain. In addition, newer concepts such as the pan-genome concept are still being implemented to help answer biological questions. Hence, we present proGenomes2, which provides 87 920 high-quality genomes in a user-friendly and interactive manner. Genome sequences and annotations can be retrieved in idually or by taxonomic clade. Every genome in the database has been assigned to a species cluster and most genomes could be accurately assigned to one or multiple habitats. In addition, general functional annotations and specific annotations of antibiotic resistance genes and single nucleotide variants are provided. In short, proGenomes2 provides threefold more genomes, enhanced habitat annotations, updated taxonomic and functional annotation and improved linkage to the NCBI BioS le database. The database is available at progenomes.embl.de/.
Publisher: Springer Science and Business Media LLC
Date: 15-12-2021
DOI: 10.1038/S41586-021-04233-4
Abstract: Microbial genes encode the majority of the functional repertoire of life on earth. However, despite increasing efforts in metagenomic sequencing of various habitats
No related grants have been discovered for Daniel R. Mende.