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1.
Genome Biol ; 24(1): 1, 2023 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-36609515

RESUMO

Binning aims to recover microbial genomes from metagenomic data. For complex metagenomic communities, the available binning methods are far from satisfactory, which usually do not fully use different types of features and important biological knowledge. We developed a novel ensemble binner, MetaBinner, which generates component results with multiple types of features by k-means and uses single-copy gene information for initialization. It then employs a two-stage ensemble strategy based on single-copy genes to integrate the component results efficiently and effectively. Extensive experimental results on three large-scale simulated datasets and one real-world dataset demonstrate that MetaBinner outperforms the state-of-the-art binners significantly.


Assuntos
Algoritmos , Microbiota , Microbiota/genética , Metagenoma , Genoma Microbiano , Metagenômica/métodos , Análise de Sequência de DNA
2.
Methods Mol Biol ; 2588: 75-89, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36418683

RESUMO

Since our chapter on genome sequencing using the GS-FLX pyrosequencer in the First Edition of this book, significant advances have been made in next-generation DNA sequencing (NGS) technology. Not only has the GS-FLX become extinct, but the more recent introduction and establishment of the so-called third-generation DNA sequencers by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) has revolutionized genomics yet again by generating ultra-long (>100,000 basepair) sequence reads concomitant with an incredible reduction in cost per sequenced basepair. Unfortunately, the ultra-high sequence yields of third-generation sequencers are compromised by their inherent sequencing error rates, prompting an alternative sequencing strategy, i.e., a hybrid sequencing strategy, which combines PacBio/ONT primary datasets with complementary datasets generated by mainstream short-read NGS platforms, e.g., Illumina or Ion Torrent. Although the concept of a hybrid sequencing strategy is not new, existing yields and accuracy of ultra-long and short-read sequencing technologies makes such a strategy achievable, resulting in complete genome sequences in one hit. In this chapter, we describe our updated laboratory and bioinformatic protocols that will allow the average research group to obtain complete oral microbial genome sequences assembled from a combination of DNA sequence data generated by NGS and third-generation platforms.


Assuntos
Genoma Microbiano , Sequenciamento de Nucleotídeos em Larga Escala , Sequência de Bases , Análise de Sequência de DNA/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Genômica
3.
Methods Mol Biol ; 2605: 103-131, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36520391

RESUMO

The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.


Assuntos
Hominidae , Homem de Neandertal , Animais , Humanos , DNA Antigo , Restos Mortais , Hominidae/genética , DNA/genética , Genoma Microbiano , Homem de Neandertal/genética , Análise de Sequência de DNA/métodos
4.
Methods Mol Biol ; 2605: 241-270, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36520398

RESUMO

Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial species occurring in our environment. However, despite the development of powerful bioinformatics approaches, full interpretation of the content of these genomes remains a difficult task. To address this challenge, the MicroScope platform has been developed. It is an integrated Web platform for management, annotation, comparative analysis, and visualization of microbial genomes ( https://mage.genoscope.cns.fr/microscope ). Launched in 2005, the platform has been under continuous development and provides analyzes for complete and ongoing genome projects together with metabolic network reconstruction and transcriptomic experiments allowing users to improve the understanding of gene functions. MicroScope platform is widely used by microbiologists from academia and industry all around the world for collaborative studies and expert annotation. It enables collaborative work in a rich comparative genomic context and improves community-based curation efforts. Here, we describe the protocol to follow for the integration and analysis of transcriptomics data in the Microscope platform. The chapter reviews each key step from the experimental design to the analysis and interpretation of the experiment data and results. The integration of transcriptomics data gives a dynamic view of the genome by allowing the users to improve the understanding of gene functions by interpreting them in the light of regulatory cell processes. Moreover, they can also contribute to the refinement of genome annotation through the discovery of new genes and help to fill metabolic gaps.


Assuntos
Software , Transcriptoma , Genômica/métodos , Biologia Computacional/métodos , Genoma Microbiano , Bases de Dados Genéticas , Anotação de Sequência Molecular
5.
Cell Host Microbe ; 30(11): 1501-1503, 2022 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-36356563

RESUMO

In this issue of Cell Host & Microbe, Millman et al. use bioinformatic and genetic approaches to discover 21 novel antiviral immune systems in prokaryotes. Remarkably, many of these systems bear homology to components of the human innate immune system, suggesting an evolutionary tie between prokaryotic and eukaryotic antiviral defenses.


Assuntos
Antivirais , Expedições , Humanos , Células Procarióticas , Células Eucarióticas , Genoma Microbiano
6.
Gigascience ; 112022 11 18.
Artigo em Inglês | MEDLINE | ID: mdl-36399059

RESUMO

BACKGROUND: Due to the importance of chicken production and the remarkable influence of the gut microbiota on host health and growth, tens of thousands of metagenome-assembled genomes (MAGs) have been constructed for the chicken gut microbiome. However, due to the limitations of short-read sequencing and assembly technologies, most of these MAGs are far from complete, are of lower quality, and include contaminant reads. RESULTS: We generated 332 Gb of high-fidelity (HiFi) long reads from the 5 chicken intestinal compartments and assembled 461 and 337 microbial genomes, of which 53% and 55% are circular, at the species and strain levels, respectively. For the assembled microbial genomes, approximately 95% were regarded as complete according to the "RNA complete" criteria, which requires at least 1 full-length ribosomal RNA (rRNA) operon encoding all 3 types of rRNA (16S, 23S, and 5S) and at least 18 copies of full-length transfer RNA genes. In comparison with the short-read-derived chicken MAGs, 384 (83% of 461) and 89 (26% of 337) strain-level and species-level genomes in this study are novel, with no matches to previously reported sequences. At the gene level, one-third of the 2.5 million genes in the HiFi-derived gene catalog are novel and cannot be matched to the short-read-derived gene catalog. Moreover, the HiFi-derived genomes have much higher continuity and completeness, as well as lower contamination; the HiFi-derived gene catalog has a much higher ratio of complete gene structures. The dominant phylum in our HiFi-assembled genomes was Firmicutes (82.5%), and the foregut was highly enriched in 5 genera: Ligilactobacillus, Limosilactobacillus, Lactobacillus, Weissella, and Enterococcus, all of which belong to the order Lactobacillales. Using GTDB-Tk, all 337 species-level genomes were successfully classified at the order level; however, 2, 35, and 189 genomes could not be classified into any known family, genus, and species, respectively. Among these incompletely classified genomes, 9 and 49 may belong to novel genera and species, respectively, because their 16S rRNA genes have identities lower than 95% and 97% to any known 16S rRNA genes. CONCLUSIONS: HiFi sequencing not only produced metagenome assemblies and gene structures with markedly improved quality but also recovered a substantial portion of novel genomes and genes that were missed in previous short-read-based metagenome studies. The novel genomes and species obtained in this study will facilitate gut microbiome and host-microbiota interaction studies, thereby contributing to the sustainable development of poultry resources.


Assuntos
Galinhas , Metagenoma , Animais , Galinhas/genética , RNA Ribossômico 16S/genética , Metagenômica , Genoma Microbiano
7.
Sci Data ; 9(1): 605, 2022 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-36207335

RESUMO

Jiaozhou Bay is a typical semi-enclosed bay with a temperate climate imposed by strong anthropogenic influence. To investigate microbial biodiversity and ecosystem services in this highly dynamic coastal environment, we conducted a monthly microbial survey spanning eight months at two stations in the bay and the open Yellow Sea starting in April 2015. This report provides a comprehensive inventory of amplicon sequences and environmental microbial genomes from this survey. In total, 2,543 amplicon sequence variants were obtained with monthly relative abundance profiles in three size fractions (>2.7 µm, 2.7-0.7 µm, and 0.7-0.22 µm). Shotgun metagenomes yielded 915 high-quality metagenome-assembled genomes with ≥50% completeness and ≤5% contamination. These environmental genomes comprise 27 bacterial and 5 archaeal phyla. We expect this comprehensive dataset will facilitate a better understanding of coastal microbial ecology.


Assuntos
Baías , Microbiota , Baías/microbiologia , China , Genoma Microbiano , Metagenoma , Oceanos e Mares
8.
Cell Host Microbe ; 30(11): 1556-1569.e5, 2022 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-36302390

RESUMO

Bacterial anti-phage systems are frequently clustered in microbial genomes, forming defense islands. This property enabled the recent discovery of multiple defense systems based on their genomic co-localization with known systems, but the full arsenal of anti-phage mechanisms remains unknown. We report the discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments. We identified multiple systems with domains involved in eukaryotic antiviral immunity, including those homologous to the ubiquitin-like ISG15 protein, dynamin-like domains, and SEFIR domains, and show their participation in bacterial defenses. Additional systems include domains predicted to manipulate DNA and RNA molecules, alongside toxin-antitoxin systems shown here to function in anti-phage defense. These systems are widely distributed in microbial genomes, and in some bacteria, they form a considerable fraction of the immune arsenal. Our data substantially expand the inventory of defense systems utilized by bacteria to counteract phage infection.


Assuntos
Bacteriófagos , Bacteriófagos/genética , Bactérias/genética , Genoma Microbiano , Genômica , Sistema Imunitário
10.
Bioinformatics ; 38(19): 4481-4487, 2022 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-35972375

RESUMO

MOTIVATION: Despite recent advancements in sequencing technologies and assembly methods, obtaining high-quality microbial genomes from metagenomic samples is still not a trivial task. Current metagenomic binners do not take full advantage of assembly graphs and are not optimized for long-read assemblies. Deep graph learning algorithms have been proposed in other fields to deal with complex graph data structures. The graph structure generated during the assembly process could be integrated with contig features to obtain better bins with deep learning. RESULTS: We propose GraphMB, which uses graph neural networks to incorporate the assembly graph into the binning process. We test GraphMB on long-read datasets of different complexities, and compare the performance with other binners in terms of the number of High Quality (HQ) genome bins obtained. With our approach, we were able to obtain unique bins on all real datasets, and obtain more bins on most datasets. In particular, we obtained on average 17.5% more HQ bins when compared with state-of-the-art binners and 13.7% when aggregating the results of our binner with the others. These results indicate that a deep learning model can integrate contig-specific and graph-structure information to improve metagenomic binning. AVAILABILITY AND IMPLEMENTATION: GraphMB is available from https://github.com/MicrobialDarkMatter/GraphMB. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Metagenoma , Metagenômica , Análise de Sequência de DNA/métodos , Metagenômica/métodos , Genoma Microbiano , Algoritmos
11.
Sci Data ; 9(1): 480, 2022 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-35933411

RESUMO

Cold seep microbial communities are fascinating ecosystems on Earth which provide unique models for understanding the living strategies in deep-sea distinct environments. In this study, 23 metagenomes were generated from samples collected in the Site-F cold seep field in South China Sea, including the sea water closely above the invertebrate communities, the cold seep fluids, the fluids under the invertebrate communities and the sediment column around the seep vent. By binning tools, we retrieved a total of 768 metagenome assembled genome (MAGs) that were estimated to be >60% complete. Of the MAGs, 61 were estimated to be >90% complete, while an additional 105 were >80% complete. Phylogenomic analysis revealed 597 bacterial and 171 archaeal MAGs, of which nearly all were distantly related to known cultivated isolates. In the 768 MAGs, the abundant Bacteria in phylum level included Proteobacteria, Desulfobacterota, Bacteroidota, Patescibacteria and Chloroflexota, while the abundant Archaea included Asgardarchaeota, Thermoplasmatota, and Thermoproteota. These results provide a dataset available for further interrogation of deep-sea microbial ecology.


Assuntos
Genoma Microbiano , Metagenoma , Microbiota , Archaea/genética , Bactérias/genética , Sedimentos Geológicos/microbiologia , Filogenia , RNA Ribossômico 16S/genética
12.
Cell ; 185(15): 2725-2738, 2022 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-35868276

RESUMO

Microbial culturing and meta-omic profiling technologies have significantly advanced our understanding of the taxonomic and functional variation of the human microbiome and its impact on host processes. The next increase in resolution will come by understanding the role of low-abundant and less-prevalent bacteria and the study of individual cell behaviors that underlie the complexity of microbial ecosystems. To this aim, single-cell techniques are being rapidly developed to isolate, culture, and characterize the genomes and transcriptomes of individual microbes in complex communities. Here, we discuss how these single-cell technologies are providing unique insights into the biology and behavior of human microbiomes.


Assuntos
Microbiota , Bactérias/genética , Genoma Microbiano , Interações entre Hospedeiro e Microrganismos , Humanos , Análise de Sequência de RNA , Análise de Célula Única
13.
Sci Data ; 9(1): 310, 2022 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-35710651

RESUMO

As a unique geographical transition zone, the estuary is considered as a model environment to decipher the diversity, functions and ecological processes of microbial communities, which play important roles in the global biogeochemical cycle. Here we used surface water metagenomic sequencing datasets to construct metagenome-assembled genomes (MAGs) from 30 subtropical estuaries at a large scale along South China. In total, 500 dereplicated MAGs with completeness ≥ 50% and contamination ≤ 10% were obtained, among which more than one-thirds (n = 207 MAGs) have a completeness ≥ 70%. These MAGs are dominated by taxa assigned to the phylum Proteobacteria (n = 182 MAGs), Bacteroidota (n = 110) and Actinobacteriota (n = 104). These draft genomes can be used to study the diversity, phylogenetic history and metabolic potential of microbiota in the estuary, which should help improve our understanding of the structure and function of these microorganisms and how they evolved and adapted to extreme conditions in the estuarine ecosystem.


Assuntos
Genoma Microbiano , Metagenoma , Microbiota , China , Estuários , Metagenômica
14.
ACS Synth Biol ; 11(6): 2134-2143, 2022 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-35584409

RESUMO

Mismatch tolerance, a cause of the off-target effect, impedes accurate genome editing with the CRISPR/Cas system. Herein, we observed that oligonucleotide-directed single-base substitutions could be rarely introduced in the microbial genome using CRISPR/Cpf1-mediated negative selection. Because crRNAs have the ability to recognize and discriminate among specific target DNA sequences, we systematically compared the effects of modified crRNAs with 3'-end nucleotide truncations and a single mismatch on the genomic cleavage activity of FnCpf1 inEscherichia coli. Five nucleotides could be maximally truncated at the crRNA 3'-end for the efficient cleavage of the DNA targets of galK and xylB in the cells. However, target cleavage in the genome was inefficient when a single mismatch was simultaneously introduced in the maximally 3'-end-truncated crRNA. Based on these results, we assumed that the maximally truncated crRNA-Cpf1 complex can distinguish between single-base-edited and unedited targets in vivo. Compared to other crRNAs with shorter truncations, maximally 3'-end-truncated crRNAs showed highly efficient single-base substitutions (>80%) in the DNA targets of galK and xylB. Furthermore, the editing efficiency for the 24 bases in both galK and xylB showed success rates of 79 and 50%, respectively. We successfully introduced single-nucleotide indels in galK and xylB with editing efficiencies of 79 and 62%, respectively. Collectively, the maximally truncated crRNA-Cpf1 complex could perform efficient base and nucleotide editing regardless of the target base location or mutation type; this system is a simple and efficient tool for microbial genome editing, including indel correction, at the single-nucleotide resolution.


Assuntos
Edição de Genes , Nucleotídeos , Sistemas CRISPR-Cas/genética , DNA/genética , Edição de Genes/métodos , Genoma Microbiano , Nucleotídeos/genética
16.
mSphere ; 7(3): e0007722, 2022 06 29.
Artigo em Inglês | MEDLINE | ID: mdl-35491842

RESUMO

The availability of public genomics data has become essential for modern life sciences research, yet the quality, traceability, and curation of these data have significant impacts on a broad range of microbial genomics research. While microbial genome databases such as NCBI's RefSeq database leverage the scalability of crowd sourcing for growth, genomics data provenance and authenticity of the source materials used to produce data are not strict requirements. Here, we describe the de novo assembly of 1,113 bacterial genome references produced from authenticated materials sourced from the American Type Culture Collection (ATCC), each with full genomics data provenance relating to bioinformatics methods, quality control, and passage history. Comparative genomics analysis of ATCC standard reference genomes (ASRGs) revealed significant issues with regard to NCBI's RefSeq bacterial genome assemblies related to completeness, mutations, structure, strain metadata, and gaps in traceability to the original biological source materials. Nearly half of RefSeq assemblies lack details on sample source information, sequencing technology, or bioinformatics methods. Deep curation of these records is not within the scope of NCBI's core mission in supporting open science, which aims to collect sequence records that are submitted by the public. Nonetheless, we propose that gaps in metadata accuracy and data provenance represent an "elephant in the room" for microbial genomics research. Effectively addressing these issues will require raising the level of accountability for data depositors and acknowledging the need for higher expectations of quality among the researchers whose research depends on accurate and attributable reference genome data. IMPORTANCE The traceability of microbial genomics data to authenticated physical biological materials is not a requirement for depositing these data into public genome databases. This creates significant risks for the reliability and data provenance of these important genomics research resources, the impact of which is not well understood. We sought to investigate this by carrying out a comparative genomics study of 1,113 ATCC standard reference genomes (ASRGs) produced by ATCC from authenticated and traceable materials using the latest sequencing technologies. We found widespread discrepancies in genome assembly quality, genetic variability, and the quality and completeness of the associated metadata among hundreds of reference genomes for ATCC strains found in NCBI's RefSeq database. We present a comparative analysis of de novo-assembled ASRGs, their respective metadata, and variant analysis using RefSeq genomes as a reference. Although assembly quality in RefSeq has generally improved over time, we found that significant quality issues remain, especially as related to genomic data and metadata provenance. Our work highlights the importance of data authentication and provenance for the microbial genomics community, and underscores the risks of ignoring this issue in the future.


Assuntos
Bases de Dados Genéticas , Genômica , Genoma Bacteriano , Genoma Microbiano , Reprodutibilidade dos Testes
17.
Bioinformatics ; 38(11): 2973-2979, 2022 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-35482530

RESUMO

MOTIVATION: Metagenomic binning aims to retrieve microbial genomes directly from ecosystems by clustering metagenomic contigs assembled from short reads into draft genomic bins. Traditional shotgun-based binning methods depend on the contigs' composition and abundance profiles and are impaired by the paucity of enough samples to construct reliable co-abundance profiles. When applied to a single sample, shotgun-based binning methods struggle to distinguish closely related species only using composition information. As an alternative binning approach, Hi-C-based binning employs metagenomic Hi-C technique to measure the proximity contacts between metagenomic fragments. However, spurious inter-species Hi-C contacts inevitably generated by incorrect ligations of DNA fragments between species link the contigs from varying genomes, weakening the purity of final draft genomic bins. Therefore, it is imperative to develop a binning pipeline to overcome the shortcomings of both types of binning methods on a single sample. RESULTS: We develop HiFine, a novel binning pipeline to refine the binning results of metagenomic contigs by integrating both Hi-C-based and shotgun-based binning tools. HiFine designs a strategy of fragmentation for the original bin sets derived from the Hi-C-based and shotgun-based binning methods, which considerably increases the purity of initial bins, followed by merging fragmented bins and recruiting unbinned contigs. We demonstrate that HiFine significantly improves the existing binning results of both types of binning methods and achieves better performance in constructing species genomes on publicly available datasets. To the best of our knowledge, HiFine is the first pipeline to integrate different types of tools for the binning of metagenomic contigs. AVAILABILITY AND IMPLEMENTATION: HiFine is available at https://github.com/dyxstat/HiFine. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Ecossistema , Metagenômica , Metagenômica/métodos , Metagenoma , Análise por Conglomerados , Genoma Microbiano , Algoritmos , Análise de Sequência de DNA/métodos
18.
Nat Prod Rep ; 39(6): 1172-1225, 2022 06 22.
Artigo em Inglês | MEDLINE | ID: mdl-35470828

RESUMO

Covering: up to the end of 2021Within the 2,5-dioxopiperazines-containing natural products, those generated from tryptophan allow further structural diversification due to the rich chemical reactivity of the indole heterocycle. The great variety of natural products, ranging from simple dimeric bispyrrolidinoindoline dioxopiperazines and tryptophan-derived dioxopiperazine/pyrrolidinoindoline dioxopiperazine analogs to complex polycyclic downstream metabolites containing transannular connections between the subunits, will be covered. These natural products are constructed by Nature using hybrid polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) assembly lines. Mining of microbial genome sequences has more recently allowed the study of the metabolic routes and the discovery of their hidden biosynthetic potential. The competition (ideally, also the combined efforts) between their isolation from the cultures of the producing microorganisms after global genome mining and heterologous expression and the synthetic campaigns, has more recently allowed the successful generation and structural confirmation of these natural products. Their biological activities as well as their proposed biogenetic routes and computational studies on biogenesis will also be covered.


Assuntos
Produtos Biológicos , Triptofano , Dicetopiperazinas , Genoma Microbiano , Peptídeo Sintases/metabolismo , Policetídeo Sintases/metabolismo , Triptofano/genética
20.
Microbiome ; 10(1): 33, 2022 02 16.
Artigo em Inglês | MEDLINE | ID: mdl-35172890

RESUMO

BACKGROUND: Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. RESULTS: We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric "MW-score" (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. CONCLUSION: METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC . Video abstract.


Assuntos
Genoma Microbiano , Microbiota , Humanos , Lagos , Metagenoma/genética , Metagenômica , Microbiota/genética
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