Post-translational regulation of autophagy is involved in intra-microbiome suppression of fungal pathogens DOI Creative Commons
Jing Wang,

Chaoyun Xu,

Qiming Sun

et al.

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: June 6, 2021

Abstract Background Microbiome interactions are important determinants for ecosystem functioning, stability, and health. In previous studies, it was often observed that bacteria suppress potentially pathogenic fungal species part of the same plant microbiota; however, underlying microbe-microbe interplay remains mostly elusive. Here, we explored antagonistic fungus Fusarium graminearum bacterium Streptomyces hygroscopicus at molecular level. Both ubiquitous members healthy wheat under dysbiosis, causes devastating diseases. Results co-cultures, found alters acetylome leading to substantial induction autophagy . The secrets rapamycin inactivate target (TOR), which subsequently promotes degradation histone acetyltransferase Gcn5 through 26S proteasome. negatively regulates by acetylating autophagy-related protein Atg8 lysine site K13 blocking cellular relocalization Atg8. Thus, triggered reduce acetylation, resulting in F. Conclusions Autophagy homeostasis plays an essential role growth competition, as well virulence. Our work reveals a novel post-translational regulation initiated bacterial antibiotic. Rapamycin shown be powerful modulator bacteria–fungi with potential importance explaining microbial microbiomes. autophagic process provides possibilities targets biologically control pathogens.

Language: Английский

Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes DOI
Athina Gavriilidou, Satria A. Kautsar,

Nestor Zaburannyi

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(5), P. 726 - 735

Published: May 2, 2022

Language: Английский

Citations

204
Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils DOI Creative Commons
Yuanyuan Bao, Jan Dolfing,

Zhiying Guo

et al.

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: April 7, 2021

Abstract Background Microbial-driven decomposition of plant residues is integral to carbon sequestration in terrestrial ecosystems. Actinobacteria , one the most widely distributed bacterial phyla soils, are known for their ability degrade vitro. However, situ importance and specific activity across contrasting ecological environments not known. Here, we conducted three field experiments with buried straw combination microcosm 13 C-straw paddy soils under different soil fertility levels reveal ecophysiological roles residue decomposition. Results While accounting only 4.6% total abundance, encoded 16% abundance carbohydrate-active enzymes (CAZymes). The taxonomic functional compositions were, surprisingly, relatively stable during Slopes linear regression models between chemical composition Actinobacterial traits were flatter than those other groups at both local regional scales due holding genes encoding full set CAZymes, nitrogenases, antibiotic synthetases. Ecological co-occurrence network C-based metagenomic analyses indicated that degradation increased less fertile as links community members relative abundances decreasing fertility. Conclusions This study provided DNA-based evidence non-dominant plays a key role possess high proportions CAZymes group maintain presence terms roles. Their was more pronounced where possession interspecies interactions stood out more. Our work provides new angles understanding global cycling.

Language: Английский

Citations

186
Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces DOI
Kunkun Fan, Haiyan Chu, David J. Eldridge

et al.

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(1), P. 113 - 126

Published: Jan. 9, 2023

Language: Английский

Citations

98
Biosynthetic gene cluster profiling predicts the positive association between antagonism and phylogeny in Bacillus DOI Creative Commons
Liming Xia, Youzhi Miao,

A’li Cao

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Feb. 23, 2022

Understanding the driving forces and intrinsic mechanisms of microbial competition is a fundamental question in ecology. Despite well-established negative correlation between exploitation phylogenetic distance, process interference that exemplified by antagonism remains controversial. Here, we studied genus Bacillus, commonly recognized producer multifarious antibiotics, to explore role patterns biosynthetic gene clusters (BGCs) mediating relationship phylogeny. Comparative genomic analysis revealed positive association BGC distance distance. Antagonistic tests demonstrated inhibition phenotype positively correlated with both predicted especially for antagonistic strains possessing abundant BGCs. Mutant-based verification showed was dependent on BGCs specifically harbored strain. These findings highlight BGC-phylogeny coherence regulates congeneric which deepens our understanding force mechanism interactions.

Language: Английский

Citations

73
A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources DOI Creative Commons
Bin Ma, Caiyu Lu, Yiling Wang

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 11, 2023

Abstract Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct large-scale excavation soil matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 metagenomes. We identify 16,530 21,077 species-level (SGBs) unknown SGBs (uSGBs), which expand archaeal bacterial diversity across the tree life. also illustrate pivotal role uSGBs in augmenting microbiome’s functional landscape intra-species diversity, providing large proportions 43,169 biosynthetic gene clusters 8545 CRISPR-Cas genes. Additionally, determine that contributed 84.6% previously unexplored viral-host associations catalogue. The catalogue provides useful genomic resource for further studies investigating resources.

Language: Английский

Citations

59
Extreme summers impact cropland and grassland soil microbiomes DOI Creative Commons
Qicheng Bei, Thomas Reitz,

Beatrix Schnabel

et al.

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(10), P. 1589 - 1600

Published: July 7, 2023

The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond such disturbances. Here, metagenomics was used investigate effects future climate scenarios (+0.6 °C warming and altered precipitation) on during summers 2014-2019. Unexpectedly, Central Europe experienced heatwaves droughts 2018-2019, causing significant impacts structure, assembly, function microbiomes. Specifically, relative abundance Actinobacteria (bacteria), Eurotiales (fungi), Vilmaviridae (viruses) significantly increased in both cropland grassland. contribution homogeneous selection bacterial community assembly from 40.0% normal 51.9% summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), sporulation (spoIID, spoVK) were identified as potential contributors drought-enriched taxa, their expressions confirmed by metatranscriptomics 2022. impact further evident taxonomic profiles 721 recovered metagenome-assembled genomes (MAGs). Annotation contigs MAGs suggested that may have a competitive advantage due geosmin 2-methylisoborneol. Future caused similar pattern changes communities summers, but much lesser extent. Soil grassland showed greater resilience change than those cropland. Overall, this study provides comprehensive framework for understanding response

Language: Английский

Citations

48
Microbial secondary metabolites: advancements to accelerate discovery towards application DOI
Jaime Lorenzo N. Dinglasan, Hiroshi Otani, Drew T. Doering

et al.

Nature Reviews Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 17, 2025

Language: Английский

Citations

3
Cardiorenal syndrome: clinical diagnosis, molecular mechanisms and therapeutic strategies DOI
Bo Zhao, Xinrong Hu, Weidong Wang

et al.

Acta Pharmacologica Sinica, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

Language: Английский

Citations

3
zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters DOI Creative Commons
Rauf Salamzade, Patricia Q. Tran, Cody Martin

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(3)

Published: Jan. 24, 2025

Abstract Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai zol, which together enable large-scale comparative analysis of different types gene clusters mobile-genetic elements, such as biosynthetic (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts thousands genomes. First, allows the identification orthologous instances query cluster interest amongst database target Subsequently, zol enables reliable, context-specific ortholog groups for individual protein-encoding instances. In addition, performs functional annotation computes variety evolutionary statistics each inferred group. Importantly, in comparison tools visual exploration homologous relationships between clusters, can handle produce detailed reports that easy digest. To showcase apply them for: (i) longitudinal tracking virus metagenomes, (ii) performing population genetic investigations BGCs fungal species, (iii) uncovering trends virulence-associated genomes from diverse bacterial genus.

Language: Английский

Citations

2
Antimicrobial resistance in biofilms: Exploring marine actinobacteria as a potential source of antibiotics and biofilm inhibitors DOI Creative Commons

Nikky Goel,

Syeda Warisul Fatima, Sumit Kumar

et al.

Biotechnology Reports, Journal Year: 2021, Volume and Issue: 30, P. e00613 - e00613

Published: March 27, 2021

Antimicrobial resistance (AMR) is one of the serious global public health threats that require immediate action. With emergence new mechanisms in infection-causing microorganisms such as bacteria, fungi, and viruses, AMR threatens effective prevention treatment diseases caused by them. This has resulted prolonged illness, disability, death. It been predicted will lead to over ten million deaths 2050. The rapid spread multidrug-resistant bacteria also causing old antibiotics become ineffective. Among diverse factors contributing AMR, intrinsic biofilm development highlighted an essential facet. Moreover, biofilm-derived antibiotic tolerance leads recurrent chronic infections. Therefore, discovery novel bioactive molecules a potential solution can help combat AMR. To achieve this, sustained mining antimicrobial from actinobacteria, particularly marine be promising strategy. Given their vast diversity different habitats, extraordinary capacity actinobacteria tapped synthesize or for inhibition. Advanced screening strategies approaches field modern biochemical molecular biology used detect compounds. In view present review focuses on understanding some recent inhibit formation explores role sources inhibitor molecules.

Language: Английский

Citations

77