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Nov 13, 2024 | 
nature.com | Arianna I Krinos |Natalie Cohen |Tatiana A. Rynearson |Frederik Schulz
AbstractMeta-omics is commonly used for large-scale analyses of microbial eukaryotes, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets.
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Aug 17, 2024 | 
biorxiv.org | Frederik Schulz |Université Laval |Thomas M Pitot
AbstractBackgroundLarge double-stranded DNA viruses of the phylum Nucleocytoviricota (Giant viruses; GVs) include the largest known viruses, both in terms of capsid and genome size and are associated with a wide range of eukaryotic hosts. The ones able to infect protists and algae have been shown to be the dominant orders of GVs in the environmental samples. These viruses encode for genes that may have significantly impacted biogeochemical cycling and host genome evolution.
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Jul 11, 2024 | 
journals.plos.org | George A Schaible |Zackary J. Jay |John B. Cliff |Frederik Schulz
Loading metrics Open Access Peer-reviewedResearch Article Citation: Schaible GA, Jay ZJ, Cliff J, Schulz F, Gauvin C, Goudeau D, et al. (2024) Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells. PLoS Biol 22(7): e3002638.
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Mar 15, 2024 | 
mdpi.com | Frederik Schulz |Jon H Hanf |Frederik Nikolai |Alexander A. Kugel
1. IntroductionThe case of non-alcoholic wine has one of its roots in the recent discourse surrounding the negative effects of alcohol consumption on health and society. According to the World Health Organization (WHO), there is a direct correlation between alcohol consumption and increased risks of liver diseases, various cancers, the accelerated spread of infectious diseases such as HIV and mental health disorders.
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Jan 5, 2024 | 
biorxiv.org | Jillian Myers |Frederik Schulz |Kevin R. Amses |Saleh Rahimlou
AbstractGiant viruses of the phylum Nucleocytoviricota have captured researchers' attention due to their increasingly recognized impacts on eukaryotic genome evolution. Their origins are hypothesized to predate or coincide with the diversification of eukaryotes and their natural hosts span the eukaryotic tree of life. But surprisingly, giant viruses have not been found in the fungal kingdom, though recent metagenomic work suggests a putative association.
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Nov 27, 2023 | 
biorxiv.org | Zackary J. Jay |John B. Cliff |Frederik Schulz |George A Schaible
AbstractConsortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single cell resolution.
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Sep 21, 2023 | 
nature.com | Antonio Pedro Camargo |Frederik Schulz |Yan Xu |Stephen Nayfach
AbstractIdentifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses.
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Sep 7, 2023 | 
mdpi.com | David Jones |Frederik Schulz |Simon Roux |Steven Brown
1. IntroductionThe review includes both a historical perspective and the current status of the solvent-producing clostridia. This encompasses the comparative genomic and phylogenetic analysis of clostridial species and a survey of prophages and R-type tailocins. In order to provide a general background context to the review, an updated historical account has been included.
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Aug 30, 2023 | 
mdpi.com | Frederik Schulz |Jon H Hanf |Hadi Farid |Frederik Nikolai
1. IntroductionBeverages are a central part of our daily diet. As new products enter the global beverage market every year, water; juices; soft drinks; and alcoholic beverages such as wine, beer, and spirits are no longer limited to a handful of brands and varieties. Due to their constant consumption, beverages have been the focus of nutrition research for years.
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Mar 16, 2023 | 
nature.com | Ramunas Stepanauskas |Frederik Schulz |Tanja Woyke |Emiley A Eloe-Fadrosh |Dengxun Lai |Zheng-Shuang Hua | +4 more
Compilation of MAGs and SAGsGenomes used in this study and their provenance are summarized in Supplementary Table 1. Newly generated MAGs originated from geothermal environments (Tengchong, Yunnan Province, China; Beatty, Nevada, USA; British Columbia, Canada; and Guaymas Basin, Mexico), freshwater lakes (Powell Lake, British Columbia, Canada; Lake Kivu, Rwanda; Lake Alinen Mustajärvi, Finland) and wastewater (Apeldoorn, the Netherlands).
