On Day 1 of European Galaxy Days, Mina Hojat Ansari presented FAIRYMAGS: A Galaxy Workflow for MAG Recovery Applied to Termite Microbiomes.
Read more: https://elixir-europe.org/how-we-work/scientific-programme/commissioned-services/science/bfsp/fairymags
@galaxyfreiburg
#termite #EGD2025 #microbiomes #workflow #genome_assembly #galaxyproject #workflows #metagenome #eosc #fair #open_science
Study show #extracellular_vesicles exchange #genetic information between #cells in the sea.
#horizonatal_gene_transfer #evolution #metagenome #peDNA
https://phys.org/news/2023-11-extracellular-vesicles-exchange-genetic-cells.html
Researchers led by Susanne Erdmann from the Max Planck Institute for Marine Microbiology in Bremen have looked at data that has so far been mostly discarded as contamination, revealing the previously underestimated role of extracellular vesicles (EVs) in exchanging genetic information between cells and highlighting their importance for the microbial community in the sea.
Always wondered how much #antibiotic #resistance is picked up just by international #travel.
Now we know, through this neat paper using whole-#metagenome #sequencing looking at effect on gut #microbiome. 1st fig below shows predicted antibiotic class resistance gene acquisition after travel.
So, how to prevent it? One thing is probably discouraging unnecessary #antibiotic consumption on holiday! (2nd fig).
#AMR #medicine #infectiousdiseases #MedMastodon #microbiology
https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(23)00147-7/fulltext?dgcid=raven_jbs_aip_email#%20
Background Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar. Results Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion. Conclusion Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.
Despite its toxicity to many organisms, including most prokaryotes, carbon monoxide (CO) is utilized by some aerobic and anaerobic prokaryotes. Hydrogenogenic CO utilizers employ carbon monoxide dehydrogenase (CODH) and energy-converting hydrogenase (ECH) to oxidize CO and reduce protons to produce H2. Those prokaryotes constitute a rare biosphere and are difficult to detect even with PCR amplification and with metagenomic analyses. In this study, anaerobic CO-enrichment cultures followed by construction of metagenome assembled genomes (MAGs) detected high-quality MAGs from potential hydrogenogenic CO utilizers. Of 32 MAGs constructed, 5 were potential CO utilizer harboring CODH genes. Of the five MAGs, two were classified into the genus Thermolithobacter on the basis of 16S rRNA sequence identity, related to Carboxydocella tharmautotrophica 41, with an average nucleotide identity (ANI) of approximately 72%. Additionally, two were related to Geoglobus acetivorans with ANI values ranging from 75 to 77% to G. acetivorans SBH6, and one MAG was identified as Desulfotomaculum kuznetsovii with an ANI > 96% to D. kuznetsovii DSM 6115. The two Thermolithobacter MAGs identified in this study contained CODH-ECH gene clusters, and were therefore identified as potential hydrogenogenic CO utilizers. However, these MAGs harbored three CODH gene clusters that showed distinct physiological functions in addition to CODH-ECH gene clusters. In total, the five potential CO utilizer MAGs contained sixteen CODH genes. Among those CODHs, four sets did not cluster with any known CODH protein sequences (with an identity of > 90%), and the CODH database was expanded.
According to the new #metagenome paper, #viruses / #phages of non-aquatic environments only outnumber cells by about two-fold (major capsid protein and universal SCGs used as markers). So the new estimation of virus/phage count might be far closer to cells. Interesting. #microbiology
It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa–200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ~13 fold and in plankton from marine and saline waters by ~2–4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.
The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics, but information regarding viral hosts is lost. This study presents iPHoP (integrated Phage-Host Prediction), a new tool that leverages multiple complementary approaches to maximize host prediction for metagenome-assembled virus genomes.
The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics, but information regarding viral hosts is lost. This study presents iPHoP (integrated Phage-Host Prediction), a new tool that leverages multiple complementary approaches to maximize host prediction for metagenome-assembled virus genomes.
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