Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(12), P. 829 - 845
Published: June 25, 2024
Language: Английский
Citations
22Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome
Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(7), P. 1884 - 1898
Published: June 12, 2024
Language: Английский
Citations
20Unraveling host regulation of gut microbiota through the epigenome–microbiome axis
Trends in Microbiology, Journal Year: 2024, Volume and Issue: 32(12), P. 1229 - 1240
Published: June 5, 2024
Recent studies of dynamic interactions between epigenetic modifications a host organism and the composition or activity its associated gut microbiota suggest an opportunity for to shape microbiome through alterations that lead changes in gene expression noncoding RNA activity. We use insights from microbiota-induced review potential epigenetically regulate microbiome, which bidirectional 'epigenome–microbiome axis' emerges. This axis embeds environmentally induced variation, may influence adaptive evolution host–microbe interactions. furthermore present our perspective on how epigenome–microbiome can be understood investigated within holo-omic framework with applications applied health food sciences.
Language: Английский
Citations
19Broadening oncological boundaries: the intratumoral microbiota
Trends in Microbiology, Journal Year: 2024, Volume and Issue: 32(8), P. 807 - 822
Published: Feb. 3, 2024
The microbiota of solid tumors was identified >100 years ago; however, heterogeneous composition and diversity have been revealed only recently. Growing evidence has suggested that several functional mechanisms the intratumoral affect tumorigenesis progression, suggesting is a promising biomarker for multiple cancers. low biomass poses major challenge to related research, thus necessitating use multiple-modality integrated framework resolve this dilemma. Advanced techniques such as single-cell sequencing provide significant clues, gradual optimization experiments culture-based methods enables deeper investigation underlying involved. In review, we outline current state research on describe challenges comprehensive strategies future research.
Language: Английский
Citations
18Revisiting the ecological significance, composition, and functions of plant microbiome: a review
New Zealand Journal of Crop and Horticultural Science, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 33
Published: Jan. 30, 2025
Plants have evolved alongside a diverse array of microorganisms, playing crucial roles in supporting plant growth and health. Considerable knowledge now exists regarding the composition dynamics microbiota, along with functional capabilities individual community members. Given significance microbiome challenges crop farming faces, there is pressing necessity to translate microbial techniques into practical applications. Various approaches enhance are available. However, success applying inoculants field often inconsistent, necessitating improvements. Farming practices genetic makeup can also impact microbiota functioning. Consequently, selecting suitable agronomic breeding strategies that plant-microbiome interactions becomes maximising benefits microbiota. To conclude, exploiting new generation inoculants, adopting microbiota-based farm management approaches, developing improved lines promising avenues optimise utilisation microbiome. This paper provides comprehensive review importance functions plant-associated microbes explains concepts use
Language: Английский
Citations
1A Multi‐Omics Meta‐Analysis of Rhizosphere Microbiome Reveals Growth‐Promoting Marker Bacteria at Different Stages of Legume Development
Plant Cell & Environment, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 14, 2025
ABSTRACT Plant‐microbe interactions have been studied extensively in legumes, but the influence of host developmental stages on its microbiome remains poorly understood. The rhizospheric region enriched with microbial diversity presents an optimal environment to investigate this relationship. We employed a multi‐omics meta‐analysis approach identify bacteria co‐existing legumes at different stages. data from eight legume species across various geographical locations, soil conditions and (vegetative, reproductive maturation) were included study. A total 10 stage‐specific marker identified found be positively associated plant growth phenotypes. functional profiling elucidated expression these bacterial genes, indicating active presence bacteria. Co‐expression network analysis revealed involvement gene clusters biological processes such as cobalt nitrogen metabolism. Further, pathway enrichment illustrated role metabolic pathways, biosynthesis secondary metabolites, biotin metabolism carbon fixation photosynthetic organisms. Our study positive relationship between plant, suggesting their crucial development that could further aid crop improvement strategies.
Language: Английский
Citations
1A metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass
Gut Microbes, Journal Year: 2024, Volume and Issue: 16(1)
Published: Feb. 29, 2024
The high background of host RNA poses a major challenge to metatranscriptome analysis human samples. Hence, metatranscriptomics has been mainly applied microbe-rich samples, while its application in tissues with low ratio microbial cells yet be explored. Since there is no computational workflow specifically designed for the taxonomic and functional this type we propose an effective strategy accurately characterize microbiome content. We experimentally generated synthetic samples well-characterized bacterial cell compositions, mimicking loads. These were used optimizing establishing controlled setting. Our results show that integration optimized Kraken 2/Bracken HUMAnN 3 content, enables accurate identification large number species false-positive rate, improving detection functions. effectiveness our was demonstrated simulated datasets, most importantly, gastric tissue specimens, thus providing proof concept applicability on mucosal gastrointestinal tract. use reliable approach content will expand understanding activity microbiome, uncovering critical interactions between health disease.
Language: Английский
Citations
6Interactions between microsporidia and other members of the microbiome
Journal of Eukaryotic Microbiology, Journal Year: 2024, Volume and Issue: unknown
Published: April 1, 2024
Abstract The microbiome is the collection of microbes that are associated with a host. Microsporidia intracellular eukaryotic parasites can infect most types animals. In last decade, there has been much progress to define relationship between microsporidia and microbiome. this review, we cover an increasing number reports suggesting common components in both invertebrates vertebrates. These infections range from mutualistic pathogenic, causing several physiological phenotypes, including death. Infection often causes disruption normal microbiome, increases decreases bacterial, fungal, viral, protozoan species being observed. This impact on occur through upregulation downregulation innate immunity as well morphological changes tissues interactions these microbes. Other microbes, particularly bacteria, inhibit have exploited control infections. bacteria function regulating immunity, secreting anti‐microsporidia compounds, and, engineered versions, expressing double‐stranded RNA targeting genes. We end review by discussing potential future directions further understand complex other members
Language: Английский
Citations
5Soil microbial ecology through the lens of metatranscriptomics
Soil Ecology Letters, Journal Year: 2023, Volume and Issue: 6(3)
Published: Dec. 28, 2023
Language: Английский
Citations
12Metatranscriptomics-guided discovery and characterization of a polyphenol-metabolizing gut microbial enzyme
Cell Host & Microbe, Journal Year: 2024, Volume and Issue: unknown
Published: Oct. 1, 2024
Language: Английский
Citations
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