Anaerobic microbiomes can be used to recover the chemical energy in agroindustrial and municipal wastes as useful products. Here, we report a total of 109 draft metagenome-assembled genomes from a bioreactor-fed carbohydrate-rich dairy manure hydrolysate. Studying these genomes will aid us in deciphering the metabolic networks in anaerobic microbiomes.
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http://dx.doi.org/10.1128/mra.00292-22 | DOI Listing |
Phytopathology
January 2025
Virginia Polytechnic Institute and State University, School of Plant and Environmental Science, Blacksburg, Virginia, United States;
Diseases that affect the vascular system or the pith are of great economic impact since they can rapidly destroy the affected plants, leading to complete loss in production. Fast and precise identification is thus important to inform containment and management, but many identification methods are slow because they are culture-dependent and they do not reach strain resolution. Here we used culture-independent long-read metagenomic sequencing of DNA extracted directly from stems of two tomato samples that displayed wilt symptoms.
View Article and Find Full Text PDFBrief Bioinform
November 2024
Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via E. Orabona 4, 70126, Bari, Italy.
The advent of high-throughput sequencing (HTS) technologies unlocked the complexity of the microbial world through the development of metagenomics, which now provides an unprecedented and comprehensive overview of its taxonomic and functional contribution in a huge variety of macro- and micro-ecosystems. In particular, shotgun metagenomics allows the reconstruction of microbial genomes, through the assembly of reads into MAGs (metagenome-assembled genomes). In fact, MAGs represent an information-rich proxy for inferring the taxonomic composition and the functional contribution of microbiomes, even if the relevant analytical approaches are not trivial and still improvable.
View Article and Find Full Text PDFNat Microbiol
January 2025
River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, ENAC, Ecole Polytechnique Fédérale de Lausanne, Sion, Switzerland.
Glacier-fed streams (GFS) feature among Earth's most extreme aquatic ecosystems marked by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize in biofilms within them, but how they cope with such conditions is unknown. Here, leveraging 156 metagenomes from the Vanishing Glaciers project obtained from sediment samples in GFS from 9 mountains ranges, we report thousands of metagenome-assembled genomes (MAGs) encompassing prokaryotes, algae, fungi and viruses, that shed light on biotic interactions within glacier-fed stream biofilms.
View Article and Find Full Text PDFMicrobiol Resour Announc
December 2024
CIBIO, University of Trento, Trento, Italy.
We provide 309 quality-controlled bacterial metagenome-assembled genomes recovered from supragingival plaque metagenomes. Samples were collected from head and neck cancer patients following radiotherapy, so the recovered genomes can be useful to investigate the effects of oral cavity irradiation on oral microbiome members.
View Article and Find Full Text PDFMicrobiol Resour Announc
December 2024
China National Center for Bioinformation, Beijing, China.
We conducted metagenomic sequencing on a stool sample collected from urban-dwelling and obtained a metagenome-assembled genome of . Phylogenetic analysis revealed that this strain is closely related to the one isolated from dogs, forming a distinct clade separate from the reference genome.
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