Droplet microfluidics: unveiling the hidden complexity of the human microbiome

Lab on a Chip, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The human microbiome is vital for health. Droplet microfluidics offers a versatile toolbox research, enabling single-cell sequencing, cultivation, and functional analyses to deepen our understanding drive innovations.

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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Multi-Metagenome Analysis Unravels Community Collapse After Sampling and Hints the Cultivation Strategy of CPR Bacteria in Groundwater

Microorganisms, Journal Year: 2025, Volume and Issue: 13(5), P. 972 - 972

Published: April 24, 2025

Groundwater harbors phylogenetically diverse Candidate Phyla Radiation (CPR) bacteria, representing an ideal ecosystem for studying this microbial dark matter. However, no CPR strains have been successfully isolated from groundwater, severely limiting further research. This study employed a multi-metagenome approach, integrating time-resolved sampling, antibiotic/nutrient interventions, and correlation networks to unravel ecological roles in groundwater provide insights into their subsequent cultivation. Through 36 metagenomes system containing at least 68 phyla, we revealed the time-sensitive collapse of communities: total abundance plummeted 7.9% 0.15% within 48 h post-sampling, driven by competition with rapidly dividing non-CPR such as members Pseudomonadota. Ampicillin (100 mg/L) stabilized communities suppressing competitors, whereas low-nutrient conditions paradoxically reversed effect. Long-term enrichment (14 months) recovered 63 phyla (0.35% abundance), revealing survival resilience despite nutrient deprivation. Correlation prioritized Actinomyces, novel Acidimicrobiaceae genus, Aestuariivirga, Baekduia Caedimonadaceae potential partners, providing actionable targets co-culture trials. Here, propose recommendations spanning activation status, identification symbiotic optimization culture conditions, which bypass traditional blind cultivation are critical future efforts cultivate bacterial groundwater. Cultivating bacteria will contribute clarifying diversity, roles, evolutionary mechanisms, metabolic pathways, genetic potential.

Language: Английский

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Dietary Trials and Gut Candidate Phyla Radiation Bacteria: The Effect of Placebo on the Prevalence of Saccharibacteria in Healthy Armenian Women and Women with Familial Mediterranean Fever

AgriScience and Technology, Journal Year: 2024, Volume and Issue: unknown, P. 345 - 353

Published: Jan. 1, 2024

“Candidate Phyla Radiation” (CPR) bacteria, representing ~15 % of bacterial diversity and over 70 phyla, are extremely small bacteria that primarily survive in parasitic or symbiotic forms. CPR including Candidatus Brownbacteria, Hugbacteria, Saccharibacteria (formerly TM7), were first identified humans 2007. They linked to the microbiota healthy diseased individuals, being present oral cavity, gastrointestinal, reproductive tracts. such as Saccharibacteria, associated with dysbiotic conditions like periodontitis can act pathogens potential protectors against inflammatory damage caused by host-associated bacteria.This study aimed assess effect a placebo on gut Armenian women those Familial Mediterranean Fever (FMF) disease, condition high prevalence Armenia often disturbances. Stool samples analyzed using culture-independent, high-density DNA microarray method, statistical analyses performed Multibase 2015 Excel Add-in program (NumericalDynamics, Tokyo, Japan). Results indicate respond variably depending health status, some showing significant quantitative qualitative changes while others remained unchanged. In conclusion, this confirms presence both FMF. The distinct responses intestinal highlight importance placebo-controlled trials research. Furthermore, findings emphasize role gut-brain processes their implications disease.

Language: Английский

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