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Clinical Microbiology and Infection :... Jul 2012Most of the bacterial species that form part of the biosphere have never been cultivated. In this situation, a comprehensive study of bacterial communities requires the... (Review)
Review
Most of the bacterial species that form part of the biosphere have never been cultivated. In this situation, a comprehensive study of bacterial communities requires the utilization of non-culture-based methods, which have been named metagenomics. In this paper we review the use of different metagenomic techniques for understanding the effect of antibiotics on microbial communities, to synthesize new antimicrobial compounds and to analyse the distribution of antibiotic resistance genes in different ecosystems. These techniques include functional metagenomics, which serves to find new antibiotics or new antibiotic resistance genes, and descriptive metagenomics, which serves to analyse changes in the composition of the microbiota and to track the presence and abundance of already known antibiotic resistance genes in different ecosystems.
Topics: Anti-Bacterial Agents; Bacteria; Biota; Drug Resistance, Bacterial; Gastrointestinal Tract; Humans; Metagenome; Metagenomics
PubMed: 22647044
DOI: 10.1111/j.1469-0691.2012.03868.x -
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 -
Nature Oct 2023Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities. Exploration of this vast sequence space has been limited to...
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.
Topics: Cluster Analysis; Metagenome; Metagenomics; Proteins; Databases, Protein; Protein Conformation; Microbiology
PubMed: 37821698
DOI: 10.1038/s41586-023-06583-7 -
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 -
Clinical Microbiology and Infection :... Jul 2012The development of extensive sequencing methods has allowed metagenomic studies on the human gut microbiome to be carried out. This has tremendously increased our... (Review)
Review
The development of extensive sequencing methods has allowed metagenomic studies on the human gut microbiome to be carried out. This has tremendously increased our knowledge on gut microbiota composition and activity, allowing microbiota aberrations related to different diseases to be identified. These aberrations constitute targets for the development of probiotics directed to correct them. Probiotics are extensively used to modulate gut microbiota. Nevertheless, metagenomic studies on the effects of probiotics are still very scarce. In the near future, the use of metagenomics promises to expand our understanding of probiotic action.
Topics: Biota; Gastrointestinal Tract; Humans; Metagenome; Metagenomics; Probiotics
PubMed: 22647045
DOI: 10.1111/j.1469-0691.2012.03873.x -
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 -
Journal of Food Protection Mar 2022Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole genome sequencing. This approach is... (Review)
Review
ABSTRACT
Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole genome sequencing. This approach is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, next-generation sequencing is still anchored in the traditional laboratory practice of the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding and shotgun and long-read metagenomics, are part of the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed alongside current limitations and knowledge gaps and new opportunities arising from the use of this technology.
Topics: Food Safety; High-Throughput Nucleotide Sequencing; Metagenome; Metagenomics; Whole Genome Sequencing
PubMed: 34706052
DOI: 10.4315/JFP-21-301 -
Journal of Biotechnology Nov 2017Metagenomics has proven to be one of the most important research fields for microbial ecology during the last decade. Starting from 16S rRNA marker gene analysis for the... (Review)
Review
Metagenomics has proven to be one of the most important research fields for microbial ecology during the last decade. Starting from 16S rRNA marker gene analysis for the characterization of community compositions to whole metagenome shotgun sequencing which additionally allows for functional analysis, metagenomics has been applied in a wide spectrum of research areas. The cost reduction paired with the increase in the amount of data due to the advent of next-generation sequencing led to a rapidly growing demand for bioinformatic software in metagenomics. By now, a large number of tools that can be used to analyze metagenomic datasets has been developed. The Bielefeld-Gießen center for microbial bioinformatics as part of the German Network for Bioinformatics Infrastructure bundles and imparts expert knowledge in the analysis of metagenomic datasets, especially in research on microbial communities involved in anaerobic digestion residing in biogas reactors. In this review, we give an overview of the field of metagenomics, introduce into important bioinformatic tools and possible workflows, accompanied by application examples of biogas surveys successfully conducted at the Center for Biotechnology of Bielefeld University.
Topics: Anaerobiosis; Biofuels; Computational Biology; High-Throughput Nucleotide Sequencing; Metagenome; Metagenomics
PubMed: 28823476
DOI: 10.1016/j.jbiotec.2017.08.012