A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Ноя. 11, 2023

Abstract Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct large-scale excavation soil matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 metagenomes. We identify 16,530 21,077 species-level (SGBs) unknown SGBs (uSGBs), which expand archaeal bacterial diversity across the tree life. also illustrate pivotal role uSGBs in augmenting microbiome’s functional landscape intra-species diversity, providing large proportions 43,169 biosynthetic gene clusters 8545 CRISPR-Cas genes. Additionally, determine that contributed 84.6% previously unexplored viral-host associations catalogue. The catalogue provides useful genomic resource for further studies investigating resources.

Язык: Английский

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SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Янв. 31, 2024

Determining the taxonomy and relative abundance of microorganisms in metagenomic data is a foundational problem microbial ecology. To address limitations existing approaches, we developed ‘SingleM’, which estimates community composition using conserved regions within universal marker genes. SingleM accurately profiles complex communities known species, only tool that detects species without genomic representation, even those representing novel phyla. Given SingleM’s computational efficiency, applied it to 248,559 publicly available metagenomes show vast majority samples from marine, freshwater, sediment soil environments are dominated by lacking representation (median 75.0%). also provides way identify for recovery metagenome-assembled genomes lineages interest, can incorporate user-recovered into its reference database improve profiling resolution. Quantifying full diversity Bacteria Archaea shows genome databases far saturated.

Язык: Английский

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Acidophilic partial nitrification (pH<6) facilitates ultra-efficient short-flow nitrogen transformation: Experimental validation and genomic insights

Water Research, Год журнала: 2024, Номер 260, С. 121921 - 121921

Опубликована: Июнь 12, 2024

Язык: Английский

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Biogeographic patterns and drivers of soil viromes

Nature Ecology & Evolution, Год журнала: 2024, Номер 8(4), С. 717 - 728

Опубликована: Фев. 21, 2024

Язык: Английский

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Global patterns in the growth potential of soil bacterial communities

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Авг. 11, 2024

Despite the growing catalogue of studies detailing taxonomic and functional composition soil bacterial communities, life history traits those communities remain largely unknown. This study analyzes a global dataset metagenomes to explore environmental drivers growth potential, fundamental aspect history. We find that estimated from codon usage statistics, was highest in forested biomes lowest arid latitudes. indicates productivity generally reflects ecosystem globally. Accordingly, strongest predictors potential were indicators, such as distance equator, properties vary along gradients, pH carbon nitrogen ratios. also observe negatively correlated with relative abundances genes involved carbohydrate metabolism, demonstrating tradeoffs between resource acquisition bacteria. Overall, we identify macroecological patterns link rates cycling. The authors show latitudes, which

Язык: Английский

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Advances in lasso peptide discovery, biosynthesis, and function

Trends in Genetics, Год журнала: 2024, Номер 40(11), С. 950 - 968

Опубликована: Авг. 31, 2024

Язык: Английский

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Effects of Oasis Evolution on Soil Microbial Community Structure and Function in Arid Areas

Forests, Год журнала: 2025, Номер 16(2), С. 343 - 343

Опубликована: Фев. 14, 2025

Soil is an important link in the cycling of carbon, nitrogen, and other elements. The soil environment, especially water, nutrients, salts, undergoes profound changes process oasis evolution. As a key component ecosystem oasis, microbial communities are strongly influenced by environmental factors have feedback effects on them. However, response community structure function to evolution its mechanism still unclear. In this study, different land-use types, including cotton field (CF), orchard (OR), forest land (FL), waste (WL) sand (SL), were analyzed metagenomic sequencing. results showed that had highest water content, showing significant difference compared with types. Forest pH, also Among types degrees evolution, Pseudarthrobacter Actinomycetota dominant phyla, higher relative abundance. main metabolic pathways field, land, L-glutamine biosynthesis, ornithine cycle, nitrate reduction V. total salt, moisture available potassium physicochemical influencing microorganisms. This study will deepen our understanding role provide scientific basis for ecological restoration desertification control arid areas.

Язык: Английский

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Conserved immunomodulation and variation in host association by Xanthomonadales commensals in Arabidopsis root microbiota

Nature Plants, Год журнала: 2025, Номер unknown

Опубликована: Фев. 19, 2025

Язык: Английский

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The multi-kingdom microbiome catalog of the chicken gastrointestinal tract

Biosafety and Health, Год журнала: 2024, Номер 6(2), С. 101 - 115

Опубликована: Март 2, 2024

Chicken is an important food animal worldwide and plays role in human life by providing meat eggs. Despite recent significant advances gut microbiome studies, a comprehensive study of chicken bacterial, archaeal, viral genomes remains unavailable. In this study, we constructed multi-kingdom catalog (CMKMC), including 18,201 225 33,411 genomes, annotated over 6,076,006 protein-coding genes integrating 135 metagenomes publicly available metagenome-assembled (MAGs) from ten countries. We found that 812 240 MAGs our dataset were putative novel species genera, respectively, far beyond what was previously reported. The newly unclassified predominant Phyla Firmicutes_A (n = 263), followed Firmicutes 126), Bacteroidota 121), Proteobacteria 87). Most the classified species-level operational taxonomic units belong to Caudovirales. Approximately, 63.24 % viromes are predicted infect two or more hosts, complete circular viruses. Moreover, diverse auxiliary metabolic antibiotic resistance carried Together, CMKMC provides largest integrated date, functional insights into gastrointestinal tract microbiota, paves way for microbial interventions better health productivity.

Язык: Английский

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Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 31, 2024

Abstract The NCBI Sequence Read Archive (SRA) is the largest public repository of DNA sequencing data, containing most comprehensive snapshot Earth’s genetic diversity to date. As its size exceeds 50.0 petabases across >27 million datasets, entirety these data cannot be searched for sequences interest in a reasonable time. To drastically increase accessibility this we perform genome assembly over each SRA dataset using massively parallel cloud computing. resulting Logan assemblage assembled date, and believe will enable new-era accessible petabase-scale computational biology inquiry. We provide free unrestricted access disseminate datasets foster early adoption. illustrate usefulness align diverse set sequence queries all SRA, completing as little 11 hours.

Язык: Английский

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