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

Signal Transduction and Targeted Therapy, Год журнала: 2024, Номер 9(1)

Опубликована: Сен. 23, 2024

Язык: Английский

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

Microbiological Research, Год журнала: 2025, Номер 295, С. 128107 - 128107

Опубликована: Фев. 21, 2025

Язык: 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, Год журнала: 2024, Номер 121(16)

Опубликована: Апрель 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

Язык: Английский

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

Biotechnology Journal, Год журнала: 2024, Номер 19(10)

Опубликована: Окт. 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.

Язык: Английский

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

Trends in Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Язык: 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, Год журнала: 2025, Номер unknown

Опубликована: Май 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

Язык: Английский

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Beyond genomics in Patescibacteria: A trove of unexplored biology packed into ultrasmall bacteria

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(51)

Опубликована: Дек. 12, 2024

Patescibacteria, also known as the Candidate Phyla Radiation, are a diverse clade of largely uncultivated, small bacteria that comprise significant proportion all bacterial diversity. The few members have been cultivated exhibit fascinating life cycle in which they grow obligate epibionts on surface host bacteria. In this Perspective, we make case study these unique, divergent, and poorly characterized organisms represents an exciting frontier microbiology. This burgeoning field has already achieved several critical breakthroughs, including metagenomic sequence-based reconstructions metabolic biosynthetic capabilities Patescibacteria development generalizable strategies for their cultivation genetic manipulation. We argue advances, among others, should pave way toward molecular understanding complex interactions undoubtedly underpin relationship between hosts.

Язык: Английский

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

mSphere, Год журнала: 2025, Номер unknown

Опубликована: Фев. 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.

Язык: Английский

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

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Март 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.

Язык: Английский

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

Microbiome, Год журнала: 2025, Номер 13(1)

Опубликована: Апрель 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.

Язык: Английский

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