-
Nature Communications Feb 2021Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes...
Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.
Topics: Animals; Bacteria; Female; Gastrointestinal Microbiome; Genes, Microbial; High-Throughput Nucleotide Sequencing; Metagenome; Metagenomics; Phylogeny; Species Specificity; Swine
PubMed: 33597514
DOI: 10.1038/s41467-021-21295-0 -
Molecular Biology and Evolution Dec 2021Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales....
Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.
Topics: Databases, Genetic; Genomics; Metagenome; Metagenomics; Molecular Sequence Annotation; Phylogeny; Software
PubMed: 34597405
DOI: 10.1093/molbev/msab293 -
Microbial Genomics Nov 2021Command-line annotation software tools have continuously gained popularity compared to centralized online services due to the worldwide increase of sequenced bacterial...
Command-line annotation software tools have continuously gained popularity compared to centralized online services due to the worldwide increase of sequenced bacterial genomes. However, results of existing command-line software pipelines heavily depend on taxon-specific databases or sufficiently well annotated reference genomes. Here, we introduce Bakta, a new command-line software tool for the robust, taxon-independent, thorough and, nonetheless, fast annotation of bacterial genomes. Bakta conducts a comprehensive annotation workflow including the detection of small proteins taking into account replicon metadata. The annotation of coding sequences is accelerated via an alignment-free sequence identification approach that in addition facilitates the precise assignment of public database cross-references. Annotation results are exported in GFF3 and International Nucleotide Sequence Database Collaboration (INSDC)-compliant flat files, as well as comprehensive JSON files, facilitating automated downstream analysis. We compared Bakta to other rapid contemporary command-line annotation software tools in both targeted and taxonomically broad benchmarks including isolates and metagenomic-assembled genomes. We demonstrated that Bakta outperforms other tools in terms of functional annotations, the assignment of functional categories and database cross-references, whilst providing comparable wall-clock runtimes. Bakta is implemented in Python 3 and runs on MacOS and Linux systems. It is freely available under a GPLv3 license at https://github.com/oschwengers/bakta. An accompanying web version is available at https://bakta.computational.bio.
Topics: Databases, Nucleic Acid; Genome, Bacterial; Metagenome; Metagenomics; Software
PubMed: 34739369
DOI: 10.1099/mgen.0.000685 -
DNA Research : An International Journal... Dec 2023Various microorganisms exist in environments, and each of them has its optimal growth temperature (OGT). The relationship between genomic information and OGT of each...
Various microorganisms exist in environments, and each of them has its optimal growth temperature (OGT). The relationship between genomic information and OGT of each species has long been studied, and one such study revealed that OGT of prokaryotes can be accurately predicted based on the fraction of seven amino acids (IVYWREL) among all encoded amino-acid sequences in its genome. Extending this discovery, we developed a 'Metagenomic Thermometer' as a means of predicting environmental temperature based on metagenomic sequences. Temperature prediction of diverse environments using publicly available metagenomic data revealed that the Metagenomic Thermometer can predict environmental temperatures with small temperature changes and little influx of microorganisms from other environments. The accuracy of the Metagenomic Thermometer was also confirmed by a demonstration experiment using an artificial hot water canal. The Metagenomic Thermometer was also applied to human gut metagenomic samples, yielding a reasonably accurate value for human body temperature. The result further suggests that deep body temperature determines the dominant lineage of the gut community. Metagenomic Thermometer provides a new insight into temperature-driven community assembly based on amino-acid composition rather than microbial taxa.
Topics: Humans; Thermometers; Metagenome; Metagenomics; Genomics
PubMed: 37940329
DOI: 10.1093/dnares/dsad024 -
Current Opinion in Virology Apr 2022Viruses are diverse biological entities that influence all life. Even with limited genome sizes, viruses can manipulate, drive, steal from, and kill their hosts. The... (Review)
Review
Viruses are diverse biological entities that influence all life. Even with limited genome sizes, viruses can manipulate, drive, steal from, and kill their hosts. The field of virus genomics, using sequencing data to understand viral capabilities, has seen significant innovations in recent years. However, with advancements in metagenomic sequencing and related technologies, the bottleneck to discovering and employing the virosphere has become the analysis of genomes rather than generation. With metagenomics rapidly expanding available data, vital components of virus genomes and features are being overlooked, with the issue compounded by lagging databases and bioinformatics methods. Despite the field moving in a positive direction, there are noteworthy points to keep in mind, from how software-based virus genome predictions are interpreted to what information is overlooked by current standards. In this review, we discuss conventions and ideologies that likely need to be revised while continuing forward in the study of virus genomics.
Topics: Genome, Viral; Metagenome; Metagenomics; Software; Viruses
PubMed: 35051682
DOI: 10.1016/j.coviro.2022.101200 -
Annual Review of Virology Sep 2022Over the past 20 years, our knowledge of virus diversity and abundance in subsurface environments has expanded dramatically through application of quantitative... (Review)
Review
Over the past 20 years, our knowledge of virus diversity and abundance in subsurface environments has expanded dramatically through application of quantitative metagenomic approaches. In most subsurface environments, viral diversity and abundance rival viral diversity and abundance observed in surface environments. Most of these viruses are uncharacterized in terms of their hosts and replication cycles. Analysis of accessory metabolic genes encoded by subsurface viruses indicates that they evolved to replicate within the unique features of their environments. The key question remains: What role do these viruses play in the ecology and evolution of the environments in which they replicate? Undoubtedly, as more virologists examine the role of viruses in subsurface environments, new insights will emerge.
Topics: Ecology; Metagenome; Metagenomics; Viruses
PubMed: 36173700
DOI: 10.1146/annurev-virology-093020-015957 -
The Lancet. Microbe Nov 2022Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases in humans, developing new... (Review)
Review
Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases in humans, developing new therapies, and finding preventive measures. Many studies have found significant associations between the microbiome and various diseases; however, Koch's classical postulates remind us about the importance of causative reasoning when considering the relationship between microbes and a disease manifestation. Although causal discovery in observational microbiome data faces many challenges, methodological advances in causal structure learning have improved the potential of data-driven prediction of causal effects in large-scale biological systems. In this Personal View, we show the capability of existing methods for inferring causal effects from metagenomic data, and we highlight ways in which the introduction of causal structures that are more flexible than existing structures offers new opportunities for causal reasoning. Our observations suggest that microbiome research can further benefit from tools developed in the past 5 years in causal discovery and learn from their applications elsewhere.
Topics: Humans; Microbiota; Metagenomics; Causality; Metagenome
PubMed: 36152674
DOI: 10.1016/S2666-5247(22)00186-0 -
Medical Mycology Journal 2023The human body is host to a large number of commensal microbial species such as bacteria, fungi, and viruses. Among these, the human mycobiome is often neglected as a... (Review)
Review
The human body is host to a large number of commensal microbial species such as bacteria, fungi, and viruses. Among these, the human mycobiome is often neglected as a potential cause of disease, as it is thought to be comparatively much less abundant and less diverse than the human bacteriome. Additionally, most fungi are not easily cultured, even in specific media. Hence, their study has been limited to date, mainly because of the unavailability of methods used for their detection. However, the utilization of a novel metagenomic methodology will enable the identification of well-characterized mycobiomes in several parts of the human body and broaden our knowledge of their contribution to human health and disease. In this article, we review the role of the human mycobiome in the gut, respiratory organs, skin, genital tract, and carcinogenesis, highlighting the correlations between the human mycobiome and mycobiome-associated diseases.
Topics: Humans; Mycobiome; Carcinogenesis; Knowledge; Metagenome; Metagenomics
PubMed: 37648499
DOI: 10.3314/mmj.23-002 -
Trends in Genetics : TIG Jan 2020While the human microbiome's structure and function have been extensively studied, its within-species genetic diversity is less well understood. However, genetic... (Review)
Review
While the human microbiome's structure and function have been extensively studied, its within-species genetic diversity is less well understood. However, genetic mutations in the microbiome can confer biomedically relevant traits, such as the ability to extract nutrients from food, metabolize drugs, evade antibiotics, and communicate with the host immune system. The population genetic processes by which these traits evolve are complex, in part due to interacting ecological and evolutionary forces in the microbiome. Advances in metagenomic sequencing, coupled with bioinformatics tools and population genetic models, facilitate quantification of microbiome genetic variation and inferences about how this diversity arises, evolves, and correlates with traits of both microbes and hosts. In this review, we explore the population genetic forces (mutation, recombination, drift, and selection) that shape microbiome genetic diversity within and between hosts, as well as efforts towards predictive models that leverage microbiome genetics.
Topics: Bacteria; Gastrointestinal Microbiome; Genetic Variation; Genetics, Population; Humans; Metagenome; Metagenomics; Microbiota
PubMed: 31780057
DOI: 10.1016/j.tig.2019.10.010 -
Genome Biology Apr 2021High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated... (Review)
Review
High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent and discuss methodological progress and perspectives in these areas.
Topics: Chromosomes; Computational Biology; Diploidy; Genomics; Haplotypes; High-Throughput Nucleotide Sequencing; Humans; Metagenome; Metagenomics; Polyploidy; Sequence Analysis, DNA
PubMed: 33845884
DOI: 10.1186/s13059-021-02328-9