Intraspecies associations from strain-rich metagenome samples DOI Creative Commons
Evan B. Qu, Jacob S. Baker, Laura Markey

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 8, 2025

Abstract Genetically distinct strains of a species can vary widely in phenotype, reducing the utility species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all sample, current strain-resolved analysis methods face tradeoff: de novo genotyping approaches detect novel but struggle when applied to strain-rich low-coverage samples, while reference database work robustly across sample types are insensitive diversity. We present PHLAME, method that bridges this divide by combining advantages reference-based novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces probabilistic, mutation-based, framework accurately quantify from nearest reference. By applying publicly available human skin vaginal metagenomes, we uncover previously undetected clade coexisting species, geography, host age. The ability characterize intraspecies dynamics inaccessible environments will propel new mechanistic insights accumulating metagenomic data.

Language: Английский

Codiversification of gut microbiota with humans DOI
Taichi A. Suzuki, J. Liam Fitzstevens, Victor T. Schmidt

et al.

Science, Journal Year: 2022, Volume and Issue: 377(6612), P. 1328 - 1332

Published: Sept. 15, 2022

The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. question is whether such specificity arises from shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification host microbiota, we analyzed paired metagenomes genomes 1225 individuals Europe, Asia, Africa, including mothers children. Between countries, parallel was evident Moreover, displaying the strongest independently evolved traits characteristic dependency, reduced oxygen temperature sensitivity. These findings all point to importance understanding potential role population-specific microbiome-mediated disease phenotypes.

Language: Английский

Citations

132
Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes DOI Creative Commons
Matthew M. Carter, Matthew R. Olm, Bryan D. Merrill

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(14), P. 3111 - 3124.e13

Published: June 21, 2023

The gut microbiome modulates immune and metabolic health. Human data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers Tanzania comparative populations in Nepal California. We recovered 91,662 genomes bacteria, archaea, bacteriophages, eukaryotes, 44% which absent existing unified datasets. identified 124 gut-resident species vanishing highlighted distinct aspects related to situ replication rates, signatures selection, strain sharing. Industrialized microbes were found be enriched genes associated with oxidative stress, possibly a result adaptation inflammatory processes. This unparalleled view provides valuable resource, expands capable colonizing human gut, clarifies extensive perturbation induced by lifestyle.

Language: Английский

Citations

126
Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions DOI Creative Commons
Nguyễn Nhật Nam, Hoang Dang Khoa, Kieu The Loan Trinh

et al.

Foods, Journal Year: 2023, Volume and Issue: 12(11), P. 2140 - 2140

Published: May 25, 2023

Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase discoveries related to microbial world. Newly discovered microbiomes different ecologies provide meaningful information on diversity functions of microorganisms Earth. Therefore, results metagenomic studies new microbe-based applications human health, agriculture, food industry, among others. This review summarizes fundamental procedures recent advances bioinformatic tools. It also explores up-to-date study, plant research, environmental sciences, other fields. Finally, is powerful tool for studying world, it still numerous that are currently hidden awaiting discovery. this discusses future perspectives

Language: Английский

Citations

73
Host genetic regulation of human gut microbial structural variation DOI Creative Commons
Daria V. Zhernakova, Daoming Wang, Lei Liu

et al.

Nature, Journal Year: 2024, Volume and Issue: 625(7996), P. 813 - 821

Published: Jan. 3, 2024

Although the impact of host genetics on gut microbial diversity and abundance specific taxa is well established

Language: Английский

Citations

65
Critical role of the gut microbiota in immune responses and cancer immunotherapy DOI Creative Commons
Ze-Hua Li, Weixi Xiong, Liang Zhu

et al.

Journal of Hematology & Oncology, Journal Year: 2024, Volume and Issue: 17(1)

Published: May 14, 2024

The gut microbiota plays a critical role in the progression of human diseases, especially cancer. In recent decades, there has been accumulating evidence connections between and cancer immunotherapy. Therefore, understanding functional regulating immune responses to immunotherapy is crucial for developing precision medicine. this review, we extract insights from state-of-the-art research decipher complicated crosstalk among microbiota, systemic system, context Additionally, as can account immune-related adverse events, discuss potential interventions minimize these effects clinical application five microbiota-targeted strategies that precisely increase efficacy Finally, holds promising target immunotherapeutics, summarize current challenges provide general outlook on future directions field.

Language: Английский

Citations

41
Gut microbiota reshapes cancer immunotherapy efficacy: Mechanisms and therapeutic strategies DOI Creative Commons
Jindong Xie, Manqing Liu, Xinpei Deng

et al.

iMeta, Journal Year: 2024, Volume and Issue: 3(1)

Published: Jan. 1, 2024

Abstract Gut microbiota is essential for maintaining local and systemic immune homeostasis in the presence of bacterial challenges. It has been demonstrated that play contrasting roles cancer development as well anticancer immunity. Cancer immunotherapy, a novel therapy relies on stimulation host immunity, suffered from low responding rate incidence severe immune‐related adverse events (irAEs). Previous studies have diversity composition gut were associated with heterogeneity therapeutic effects. Therefore, alteration taxa can lead to improved clinical outcomes immunotherapy. In this review, we determine whether or microbiota‐derived metabolites are linked responses immunotherapy irAEs. Moreover, discuss various approaches improve efficacy reduce toxicities by modulating composition.

Language: Английский

Citations

35
Western diets and chronic diseases DOI
Timon E. Adolph, Herbert Tilg

Nature Medicine, Journal Year: 2024, Volume and Issue: 30(8), P. 2133 - 2147

Published: July 31, 2024

Language: Английский

Citations

32
Alistipes indistinctus-derived hippuric acid promotes intestinal urate excretion to alleviate hyperuricemia DOI Creative Commons
Yingxi Xu,

Ludi Liu,

Jiang-Yuan Zhu

et al.

Cell Host & Microbe, Journal Year: 2024, Volume and Issue: 32(3), P. 366 - 381.e9

Published: Feb. 26, 2024

Language: Английский

Citations

31
A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation DOI Creative Commons

Ziqi Ma,

Tao Zuo, Norbert Frey

et al.

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

Published: Sept. 23, 2024

Language: Английский

Citations

28
Host control of the microbiome: Mechanisms, evolution, and disease DOI Creative Commons
Jacob Wilde, Emma Slack, Kevin R. Foster

et al.

Science, Journal Year: 2024, Volume and Issue: 385(6706)

Published: July 18, 2024

Many species, including humans, host communities of symbiotic microbes. There is a vast literature on the ways these microbiomes affect hosts, but here we argue for an increased focus how hosts their microbiomes. Hosts exert control over symbionts through diverse mechanisms, immunity, barrier function, physiological homeostasis, and transit. These mechanisms enable to shape ecology evolution generate natural selection microbial traits that benefit host. Our result from perpetual tension between symbiont evolution, can leverage host's evolved abilities regulate microbiota prevent treat disease. The study will be central our ability both understand manipulate microbiotas better health.

Language: Английский

Citations

27