Methanobrevibacter smithii cell variants in human physiology and pathology: a review

Heliyon, Год журнала: 2024, Номер unknown, С. e36742 - e36742

Опубликована: Сен. 1, 2024

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A metagenomic catalogue of the ruminant gut archaeome

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Ноя. 7, 2024

While the ruminant gut archaeome regulates microbiota and hydrogen balance, it is also a major producer of greenhouse gas methane. However, diversity within gastrointestinal tract (GIT) animals worldwide remains largely underexplored. Here, we construct catalogue 998 unique archaeal genomes recovered from GITs ruminants, utilizing 2270 metagenomic samples across 10 different species. Most (669/998 = 67.03%) belong to Methanobacteriaceae Methanomethylophilaceae (198/998 19.84%). We recover 47/279 previously undescribed at strain level with completeness >80% contamination <5%. investigate biogeography various ruminants demonstrate that compositional similarities vary significantly by breed location. The contains 42,691 protein clusters, clustering methanogenic pathway analysis reveal strain- host-specific dependencies among animals. find archaea potentially carry antibiotic metal resistance genes, mobile genetic elements, virulence factors, quorum sensors, complex viromes. Overall, this substantial repository for recourses, providing potential advancing our understanding ecology discovering strategies regulate methane production in ruminants. employing 2,270 species, authors archaeome, comprised nonredundant genomes, expanding knowledge on Archaea compositions, diversity, functions

Язык: Английский

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A global virome of methanogenic archaea highlights novel diversity and adaptations to the gut environment

Research Square (Research Square), Год журнала: 2023, Номер unknown

Опубликована: Фев. 9, 2023

Abstract Mobile genetic elements (MGEs), especially viruses, have a major impact on microbial communities. Methanogenic archaea play key environmental and economical roles, being the main producers of methane -a potent greenhouse gas an energy source. They are widespread in diverse anoxic artificial natural environments, including animal gut microbiomes. However, their viruses remain vastly unknown. Here, we carried out global investigation MGEs 3436 genomes metagenome-assembled covering all known diversity methanogens using newly assembled CRISPR database consisting 60,000 spacers methanogens, most extensive collection to date. We obtained 248 high-quality (pro)viral 63 plasmid sequences assigned hosts belonging nine orders methanogenic archaea, first Methanonatronarchaeales, Methanocellales Methanoliparales archaea. found novel arrays ‘ Ca. Methanomassiliicoccus intestinalis’ Methanomethylophilus’ with targeting small ssDNA Smacoviridae, supporting extending hypothesis interaction between smacoviruses associated Methanomassiliicoccales. Gene network analysis shows that encompass unique interconnected MGE repertoire, viral families head-tailed Caudoviricetes , but also icosahedral archaeal-specific pleomorphic, spherical, spindle (pro)viruses. reveal well-delineated modules for virus-host interaction, genome replication virion assembly, rich repertoire defense counter-defense systems suggesting highly dynamic complex interactions MGEs. identify potential conjugation composed VirB4, VirB5 VirB6 proteins encoded plasmids (pro)viruses Methanosarcinales, report Euryarchaeota. identified 15 new infecting Methanobacteriales, prominent microbiome. These encode large protein domains recognizing cleaving pseudomurein entry egress, convergent adaptation bacterial archaeal presence cell wall. Finally, highlight enrichment glycan-binding (immunoglobulin-like (Ig-like)/Flg_new) diversity-generating retroelements (DGRs) from gut-associated role host environments remarkable convergence phages bacteria. Our work represents important step toward characterization vast better understanding regulating communities globally development much-needed tools.

Язык: Английский

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3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors

Journal of Cheminformatics, Год журнала: 2023, Номер 15(1)

Опубликована: Авг. 28, 2023

Abstract Proteochemometric (PCM) modelling is a powerful computational drug discovery tool used in bioactivity prediction of potential candidates relying on both chemical and protein information. In PCM features are computed to describe small molecules proteins, which directly impact the quality predictive models. State-of-the-art descriptors, however, calculated from sequence neglect dynamic nature proteins. This can be computationally simulated with molecular dynamics (MD). Here, novel 3D descriptors (3DDPDs) were designed applied tasks As test case, publicly available G protein-coupled receptor (GPCR) MD data GPCRmd was used. GPCRs membrane-bound activated by hormones neurotransmitters, constitute an important target family for discovery. exist different conformational states that allow transmission diverse signals modified ligand interactions, among other factors. To translate MD-encoded two types 3DDPDs considered: one-hot encoded residue-specific (rs) embedding-like protein-specific (ps) 3DDPDs. The developed calculating distributions trajectory coordinates partial charges, applying dimensionality reduction, subsequently condensing them into vectors per residue or protein, respectively. benchmarked several against state-of-the-art non-dynamic descriptors. Our rs- ps3DDPDs outperformed regression using temporal split showed comparable performance random all classification tasks. Combinations did not result increased performance. Finally, power capture fluctuations mutant explored. results presented here show including information machine learning tasks, specifically prediction, open opportunities applications discovery, oncology.

Язык: Английский

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Realities of the consortium approach in Science: Sustainable enzymatic production of C1 chemicals from carbon dioxide

RSC Sustainability, Год журнала: 2024, Номер 2(11), С. 3264 - 3275

Опубликована: Янв. 1, 2024

This perspective reflects on the implementation of a multidisciplinary consortium project combining biological, chemical and computational sciences to discover develop new enzymes for carbon dioxide fixation.

Язык: Английский

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