Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Nature Biotechnology, Год журнала: 2023, Номер 41(11), С. 1633 - 1644

Опубликована: Фев. 23, 2023

Abstract Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms most metagenomes. Here we present MetaPhlAn 4, which integrates information metagenome assemblies and isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference metagenome-assembled genomes, define unique marker genes 26,970 species-level genome bins, 4,992 them taxonomically unidentified at the species level. 4 explains ~20% reads in international human gut microbiomes >40% less-characterized environments such as rumen microbiome proves accurate than available alternatives on synthetic evaluations while also reliably quantifying with no cultured isolates. Application method to >24,500 metagenomes highlights previously undetected be strong biomarkers host conditions lifestyles mouse shows that even uncharacterized genetically profiled resolution single strains.

Язык: Английский

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Diversity and functional landscapes in the microbiota of animals in the wild

Science, Год журнала: 2021, Номер 372(6539)

Опубликована: Март 25, 2021

Animals in the wild are able to subsist on pathogen-infected and poisonous food show immunity various diseases. These may be due their microbiota, yet we have a poor understanding of animal microbial diversity function. We used metagenomics analyze gut microbiota more than 180 species wild, covering diverse classes, feeding behaviors, geographies, traits. Using de novo metagenome assembly, constructed functionally annotated database 5000 genomes, comprising 1209 bacterial which 75% unknown. The composition, diversity, functional content exhibit associations with taxonomy, diet, activity, social structure, life span. identify animals as largely untapped resource for discovery therapeutics biotechnology applications.

Язык: Английский

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Revisiting the role of Akkermansia muciniphila as a therapeutic bacterium

Gut Microbes, Год журнала: 2022, Номер 14(1)

Опубликована: Май 25, 2022

Despite a short history since its first isolation, Akkermansia muciniphila has been extensively studied in relation to effects on human metabolism. A recent intervention study also demonstrated that the bacterium is safe use for therapeutic purposes. The best-known of A. health and disease relate ability strengthen gut integrity, modulate insulin resistance, protect host from metabolic inflammation. further molecular mechanism, induction GLP-1 secretion through ICAM-2 receptor, was recently discovered with identification new bacterial protein produced by muciniphila. However, other studies have suggested detrimental role specific immune settings. Here, we evaluate molecular, mechanistic suggest some missing links be connected before organism should considered as next-generation biotherapeutic agent.

Язык: Английский

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Seasonal shift of the gut microbiome synchronizes host peripheral circadian rhythm for physiological adaptation to a low-fat diet in the giant panda

Cell Reports, Год журнала: 2022, Номер 38(3), С. 110203 - 110203

Опубликована: Янв. 1, 2022

Characteristics of the gut microbiome vary synchronously with changes in host diet. However, underlying effects these fluctuations remain unclear. Here, we performed fecal microbiota transplantation (FMT) diet-specific feces from an endangered mammal (the giant panda) into a germ-free mouse model. We demonstrated that butyrate-producing bacterium Clostridium butyricum was more abundant during shoot-eating season than leaf-eating season, congruent significant increase body mass. Following season-specific FMT, model resembled donor, and mice transplanted grew faster stored fat. Mechanistic investigations revealed butyrate extended upregulation hepatic circadian gene Per2, subsequently increasing phospholipid biosynthesis. Validation experiments further confirmed this causal relationship. This study seasonal shifts affect growth performance, facilitating deeper understanding host-microbe interactions wild mammals.

Язык: Английский

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Bioactive compounds for human and planetary health

Frontiers in Nutrition, Год журнала: 2023, Номер 10

Опубликована: Июль 17, 2023

Bioactive compounds found in edible plants and foods are vital for human planetary health, yet their significance remains underappreciated. These natural bioactives, as part of whole diets, ingredients, or supplements, can modulate multiple aspects health wellness. Recent advancements omic sciences computational biology, combined with the development Precision Nutrition, have contributed to convergence nutrition medicine, well more efficient affordable healthcare solutions that harness power food prevention therapy. Innovation this field is crucial feed a growing global population sustainably healthily. This requires significant changes our system, spanning agriculture, production, distribution consumption. As we facing pressing challenges, investing bioactive-based an opportunity protect biodiversity soils, waters, atmosphere, while also creating value consumers, patients, communities, stakeholders. Such research innovation targets include alternative proteins, such cellular agriculture plant-derived protein; extracts improve shelf-life preservatives; upcycling agricultural by-products reduce waste; alternatives synthetic fertilizers pesticides. Translational bioactives currently being developed at two levels, using systems-oriented approach. First, biological level, interplay between these host microbiome elucidated through omics research, big data artificial intelligence, accelerate both discovery validation. Second, ecosystem efforts focused on producing diverse nutrient-rich, flavorful, resilient, high-yield crops, educating consumers make informed choices benefit planet. Adopting system-oriented perspective helps: unravel intricate dynamic relationships nutrition, sustainability outcomes, harnessing nature promote wellbeing; foster sustainable ecosystem. Interdisciplinary collaboration needed new era practical food-based some most challenges humanity planet today.

Язык: Английский

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Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans

Science, Год журнала: 2024, Номер 383(6688)

Опубликована: Март 14, 2024

Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, main component plant fiber. However, evidence cellulose fermentation in human is scarce. We have identified ruminococcal species microbiota populations that assemble functional multienzymatic cellulosome structures capable degrading cell wall polysaccharides. One these species, which strongly associated with humans, likely originated ruminant and was subsequently transferred to gut, potentially during domestication where it underwent diversification diet-related adaptation through acquisition genes from other microbes. Collectively, are abundant widespread among ancient hunter-gatherers, rural but rare industrialized societies thus indicating potential disappearance response westernized lifestyle.

Язык: Английский

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Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries

Cell, Год журнала: 2024, Номер 187(17), С. 4554 - 4570.e18

Опубликована: Июль 8, 2024

Diet impacts human health, influencing body adiposity and the risk of developing cardiometabolic diseases. The gut microbiome is a key player in diet-health axis, but while its bacterial fraction widely studied, role micro-eukaryotes, including Blastocystis, underexplored. We performed global-scale analysis on 56,989 metagenomes showed that Blastocystis exhibits distinct prevalence patterns linked to geography, lifestyle, dietary habits. presence defined specific signature was positively associated with more favorable profiles negatively obesity (p < 1e-16) disorders altered ecology 1e-8). In diet intervention study involving 1,124 individuals, improvements quality were weight loss increases = 0.003) abundance 1e-7). Our findings suggest potentially beneficial for which may help explain personalized host responses downstream disease etiopathogenesis.

Язык: Английский

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Sequencing-based analysis of microbiomes

Nature Reviews Genetics, Год журнала: 2024, Номер 25(12), С. 829 - 845

Опубликована: Июнь 25, 2024

Язык: Английский

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Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Авг. 22, 2022

Abstract Metagenomic assembly enables novel organism discovery from microbial communities, but most metagenomes it can only capture few abundant organisms. Here, we present a method - MetaPhlAn 4 to integrate information both metagenome assemblies and isolate genomes for improved more comprehensive metagenomic taxonomic profiling. From curated collection of 1.01M prokaryotic reference metagenome-assembled genomes, defined unique marker genes 26,970 species-level genome bins, 4,992 them taxonomically unidentified at the species level. explains ∼20% reads in international human gut microbiomes >40% less-characterized environments such as rumen microbiome, proved accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application >24,500 highlighted previously undetected be strong biomarkers host conditions lifestyles mice microbiomes, showed that even uncharacterized genetically profiled resolution single strains. thus integrates novelty sensitivity fidelity reference-based analyses, providing efficient profiling enabling deeper microbiome biomarker detection.

Язык: Английский

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Advances in constraint-based modelling of microbial communities

Current Opinion in Systems Biology, Год журнала: 2021, Номер 27, С. 100346 - 100346

Опубликована: Май 21, 2021

Microbial communities are near universally present in nature. A wealth of meta-omics data has been gathered from numerous ecosystems, such as the human gut, ocean or soil. Constraint-based reconstruction and analysis is a valuable tool for contextualisation allows mechanistic prediction metabolic fluxes. Advances genome-scale multispecies modelling tools have enabled construction interrogation constraint-based models on microbiome scale spanning hundreds organisms. Here, we give comprehensive overview areas application these multiscale, strain- molecule-resolved models, discuss key works, which computational yielded novel biological knowledge. We show that can complement experimental approaches applications ecology, health, industry to environmental conservation.

Язык: Английский

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