A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation

Signal Transduction and Targeted Therapy, Journal Year: 2024, Volume and Issue: 9(1)

Published: Sept. 23, 2024

Language: Английский

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Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(16)

Published: April 9, 2024

Bacteriophages (phages) play critical roles in modulating microbial ecology. Within the human microbiome, factors influencing long-term coexistence of phages and bacteria remain poorly investigated. Saccharibacteria (formerly TM7) are ubiquitous members oral microbiome. These ultrasmall form episymbiotic relationships with their host impact physiology. Here, we showed that during surface-associated growth, a isolate (named TM7x) protects its bacterium, Schaalia odontolytica strain XH001) against lytic phage LC001 predation. RNA-Sequencing analysis identified XH001 gene cluster predicted functions involved biogenesis cell wall polysaccharides (CWP), whose expression is significantly down-regulated when forming symbiosis TM7x. Through genetic work, experimentally demonstrated this CWP on bacterial–phage interaction by affecting binding. In vitro coevolution experiments further heterogeneous populations TM7x-associated TM7x-free XH001, which display differential susceptibility to predation, promote coexistence. Our study highlights tripartite between episymbiont, phage. More importantly, present mechanism, i.e., episymbiont-mediated modulation bacteria, impacts predation contributes formation “source-sink” dynamics biofilm, promoting within

Language: Английский

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Recent advancements in bacterial anti-phage strategies and the underlying mechanisms altering susceptibility to antibiotics

Microbiological Research, Journal Year: 2025, Volume and Issue: 295, P. 128107 - 128107

Published: Feb. 21, 2025

Language: Английский

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First-ever ASM Global Research Symposium on Microbes in Human Health in Tsinghua, Beijing, China

mSphere, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 24, 2025

ABSTRACT The American Society for Microbiology Global Research Symposium on Microbes in Human Health, hosted partnership with Tsinghua University, was held Beijing, China, 25 to 27 September 2024. conference provided an international forum microbiologists from different disciplines present and discuss new findings. meeting covered a wide range of topics, spanning across bacteria, virus, fungi, hosts. This report summarizes the presentations emerging themes.

Language: Английский

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Mutations in Gordonia amarae mycolic acid biosynthetic pathway confer resistance to Patescibacteria parasite Mycosynbacter amalyticus

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 5, 2025

The obligate necrotrophic parasite, Candidatus Mycosynbacter amalyticus, a member of the Patescibacteria has been isolated from wastewater. Subsequent efforts have directed toward unravelling its biological lifecycle and attachment mechanism facilitating infection subsequent lysis Actinobacterial host, Gordonia amarae. Here, using electron cryo-tomography (CryoET), we reveal molecular anatomy parasitic amalyticus cells, uncovering an unusual process. Through laboratory-based evolution experiments, generated eleven slow-growing independent spontaneous amarae resistant mutants. Mycolic acids (MA) are key components outer cellular envelope G. other Actinobacteria, with MA being physical attribute implicated in associated wastewater foaming. CryoET genome sequencing exposed absence intact suite mutations predominantly occurring within pks13 pptT genes biosynthetic pathway. Our findings suggest that structural integrity is critical for Ca. to host.

Language: Английский

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Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: April 7, 2025

Abstract Background Candidate Phyla Radiation (CPR) represents a unique superphylum characterized by ultra-small cell size and symbiotic lifestyle. Although CPR bacteria have been identified in varied environments, their broader distribution, associations with hosts, ecological roles remain largely unexplored. To address these knowledge gaps, serpentinite-like environment was selected as simplified model system to investigate the communities hyperalkaline environments association hosts extreme conditions. Additionally, enzymatic activity, global evolution of CPR-derived genes encoding essential metabolites (e.g., folate or vitamin B 9 ) were analyzed assessed. Results In highly alkaline ecosystem (pH = 10.9–12.4), metagenomic analyses water sediment samples revealed that constituted 1.93–34.8% microbial communities. Metabolic reconstruction 12 high-quality metagenome-assembled genomes (MAGs) affiliated novel taxa from orders UBA6257, UBA9973, Paceibacterales suggests lack complete biosynthetic pathways for amino acids, lipids, nucleotides. Notably, commonly harbored associated cofactor biosynthesis metabolism, including dihydrofolate reductase ( folA ), serine hydroxymethyltransferase glyA methylenetetrahydrofolate folD ). two presumed auxotrophic incapable forming tetrahydrofolate (THF) due absence , potential some harboring genes. The functionality experimentally verified heterologous expression -deletion mutant Escherichia coli MG1655 Δ . Further assessment available n 4,581) proteins synthesis bioactive derivatives and/or genes) present 90.8% examined. It widespread metabolic complementarity between hosts. Conclusions This finding deepens our understanding mechanisms CPR-host symbiosis, providing insight into cofactor-dependent mutualistic interactions. Our observations suggest may contribute organisms indirectly influence biogeochemical processes.

Language: Английский

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The Subgingival Microbial Composition in Health and Periodontitis with Different Probing Depths

Microorganisms, Journal Year: 2025, Volume and Issue: 13(4), P. 930 - 930

Published: April 17, 2025

The differences in microbiota between periodontitis and health have been extensively studied; however, knowledge about how the shifts from shallow to deep periodontal pockets remains limited despite its clinical importance disease progres-sion management. Patients diagnosed with stage III commonly pre-sent varied probing depths (PD) within same oral cavity, reflecting localized severity. This study aims analyze microbiome of subgingival plaques at various PDs patients. Subgingival were collected sixteen healthy subjects (health group) pa-tients (PD 0–3 mm, PD 4–5 mm 6–9 groups). A total 64 plaque samples underwent 16S rRNA gene sequencing. group exhib-ited significantly higher alpha diversity than group, distinct microbial community structures observed patients, regardless depth. relative abundance specific genera differed notably states; Corynebacterium Cardiobacterium decreased, whereas Schaalia increased mm) group. Co-occurrence network analysis on species level revealed that had most complex interspecies interactions, followed by groups. These findings indicate significant variations mi-crobial diversity, composition, interactions associated periodon-tal severity, highlighting their potential relevance for diagnosis targeted therapeutic strategies.

Language: Английский

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9th International Conference on Clinical Metagenomics (ICCMg9): meeting report

Trends in Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

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Enhanced Phytopathogen Biofilm Control in the Soybean Phyllosphere by the Phoresy of Bacteriophages Hitchhiking on Biocontrol Bacteria

Environmental Science & Technology, Journal Year: 2025, Volume and Issue: unknown

Published: May 2, 2025

Phage-based biocontrol has shown notable advantages in protecting plants against pathogenic bacteria agricultural settings compared to chemical-based bactericides. However, the efficiency and scope of phage are limited by intrinsic properties phages. Here, we investigated pathogen biofilm eradication phyllosphere using phoresy system hitchhiking phages onto carrier bacteria. The efficiently removed soybean phyllosphere, reducing total biomass 58% phytopathogens 82% untreated control. Biofilm tests demonstrated a significant combined beneficial effect (Bliss independence model, CI < 1) as improved colonization 1.2-fold facilitated infection 1.4-fold. Transcriptomic analysis showed that significantly enhanced motility (e.g., fliC pilD genes) energy metabolism pgm pgk suppressed defense MSH3 FLS2 petB petC pathogens. Metabolomics revealed stimulated secretion metabolites flavonoid tropane alkaloid) could enhance stress response protection soybeans. Overall, on offers novel effective strategy for microbiome manipulation bacterial disease

Language: Английский

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Selecting Endogenous Promoters for Improving Biosynthesis of Squalene in Schizochytrium sp.

Biotechnology Journal, Journal Year: 2024, Volume and Issue: 19(10)

Published: Oct. 1, 2024

ABSTRACT Squalene (C 30 H 50 ) is an acyclic triterpenoid compound renowned for its myriad physiological functions, such as anticancer and antioxidative properties, rendering it invaluable in both the food pharmaceutical sectors. Due to natural resource constraints, microbial fermentation has emerged a prominent trend. Schizochytrium sp., known harbor intact mevalonate acid (MVA) pathway, possesses inherent capability biosynthesize squalene. However, there dearth of reported key genes MVA squalene synthesis pathways, along with associated promoter elements their modification. This study commenced by cloning characterizing 13 endogenous promoters derived from transcriptome sequencing data. Subsequently, five exhibiting varying expression intensities were chosen aforementioned pool facilitate overexpression synthase gene synthetase (SQS), pivotal pathway. Ultimately, transformed strain designated SQS‐3626, production 2.8 times greater than that wild‐type strain, was identified. Finally, optimization nitrogen source concentrations trace element contents medium conducted. Following 120 h fed‐batch fermentation, accumulated final yield SQS‐3626 reached 2.2 g/L.

Language: Английский

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