-
Bioresource Technology Jan 2022Anaerobic digestion (AD) is a technique that can be used to treat high concentrations of various organic wastes using a consortium of functionally diverse microorganisms... (Review)
Review
Anaerobic digestion (AD) is a technique that can be used to treat high concentrations of various organic wastes using a consortium of functionally diverse microorganisms under anaerobic conditions. Methane gas, a beneficial by-product of the AD process, is a renewable energy source that can replace fossil fuels following purification. However, detailed functional roles and metabolic interactions between microbial populations involved in organic waste removal and methanogenesis are yet to be known. Recent metagenomic approaches based on advanced high-throughput sequencing techniques have enabled the exploration of holistic microbial taxonomy and functionality of complex microbial populations involved in the AD process. Gene-centric and genome-centric analyses based on metagenome-assembled genomes are a platform that can be used to study the composition of microbial communities and their roles during AD. This review looks at how these up-to-date metagenomic analyses can be applied to promote our understanding and improved the development of the AD process.
Topics: Anaerobiosis; Bioreactors; Metagenome; Metagenomics; Methane
PubMed: 34813924
DOI: 10.1016/j.biortech.2021.126350 -
Scientific Data Oct 2023Biofloc technology is increasingly recognised as a sustainable aquaculture method. In this technique, bioflocs are generated as microbial aggregates that play pivotal...
Biofloc technology is increasingly recognised as a sustainable aquaculture method. In this technique, bioflocs are generated as microbial aggregates that play pivotal roles in assimilating toxic nitrogenous substances, thereby ensuring high water quality. Despite the crucial roles of the floc-associated bacterial (FAB) community in pathogen control and animal health, earlier microbiota studies have primarily relied on the metataxonomic approaches. Here, we employed shotgun sequencing on eight biofloc metagenomes from a commercial aquaculture system. This resulted in the generation of 106.6 Gbp, and the reconstruction of 444 metagenome-assembled genomes (MAGs). Among the recovered MAGs, 230 were high-quality (≥90% completeness, ≤5% contamination), and 214 were medium-quality (≥50% completeness, ≤10% contamination). Phylogenetic analysis unveiled Rhodobacteraceae as dominant members of the FAB community. The reported metagenomes and MAGs are crucial for elucidating the roles of diverse microorganisms and their functional genes in key processes such as nitrification, denitrification, and remineralization. This study will contribute to scientific understanding of phylogenetic diversity and metabolic capabilities of microbial taxa in aquaculture environments.
Topics: Animals; Aquaculture; Bacteria; Metagenome; Metagenomics; Microbiota; Phylogeny
PubMed: 37848477
DOI: 10.1038/s41597-023-02622-0 -
Microbiome Apr 2018The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as...
BACKGROUND
The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as metagenomics; in particular, the recent advances in sequencing technologies have enabled researchers to study even the most complex communities. Metagenome analysis, the assignment of sequences to taxonomic and functional entities, however, remains a tedious task: large amounts of data need to be processed. There are a number of approaches addressing particular aspects, but scientific questions are often too specific to be answered by a general-purpose method.
RESULTS
We present MGX, a flexible and extensible client/server-framework for the management and analysis of metagenomic datasets; MGX features a comprehensive set of adaptable workflows required for taxonomic and functional metagenome analysis, combined with an intuitive and easy-to-use graphical user interface offering customizable result visualizations. At the same time, MGX allows to include own data sources and devise custom analysis pipelines, thus enabling researchers to perform basic as well as highly specific analyses within a single application.
CONCLUSIONS
With MGX, we provide a novel metagenome analysis platform giving researchers access to the most recent analysis tools. MGX covers taxonomic and functional metagenome analysis, statistical evaluation, and a wide range of visualizations easing data interpretation. Its default taxonomic classification pipeline provides equivalent or superior results in comparison to existing tools.
Topics: Database Management Systems; Metagenome; Metagenomics; Microbiota; Reproducibility of Results; User-Computer Interface; Workflow
PubMed: 29690922
DOI: 10.1186/s40168-018-0460-1 -
Communications Biology Oct 2023Assembly of reads from metagenomic samples is a hard problem, often resulting in highly fragmented genome assemblies. Metagenomic binning allows us to reconstruct...
Assembly of reads from metagenomic samples is a hard problem, often resulting in highly fragmented genome assemblies. Metagenomic binning allows us to reconstruct genomes by re-grouping the sequences by their organism of origin, thus representing a crucial processing step when exploring the biological diversity of metagenomic samples. Here we present Adversarial Autoencoders for Metagenomics Binning (AAMB), an ensemble deep learning approach that integrates sequence co-abundances and tetranucleotide frequencies into a common denoised space that enables precise clustering of sequences into microbial genomes. When benchmarked, AAMB presented similar or better results compared with the state-of-the-art reference-free binner VAMB, reconstructing ~7% more near-complete (NC) genomes across simulated and real data. In addition, genomes reconstructed using AAMB had higher completeness and greater taxonomic diversity compared with VAMB. Finally, we implemented a pipeline Integrating VAMB and AAMB that enabled improved binning, recovering 20% and 29% more simulated and real NC genomes, respectively, compared to VAMB, with moderate additional runtime.
Topics: Metagenome; Genome, Microbial; Metagenomics; Cluster Analysis; Benchmarking
PubMed: 37865678
DOI: 10.1038/s42003-023-05452-3 -
Methods in Molecular Biology (Clifton,... 2021Assembly of metagenomic sequence data into microbial genomes is of critical importance for disentangling community complexity and unraveling the functional capacity of...
Assembly of metagenomic sequence data into microbial genomes is of critical importance for disentangling community complexity and unraveling the functional capacity of microorganisms. The rapid development of sequencing technology and novel assembly algorithms have made it possible to reliably reconstruct hundreds to thousands of microbial genomes from raw sequencing reads through metagenomic assembly. In this chapter, we introduce a routinely used metagenomic assembly workflow including read quality filtering, assembly, contig/scaffold binning, and postassembly check for genome completeness and contamination. We also describe a case study to reconstruct near-complete microbial genomes from metagenomes using our workflow.
Topics: Databases, Genetic; High-Throughput Nucleotide Sequencing; Metagenome; Metagenomics; Phylogeny; Research Design; Sequence Analysis, DNA; Software; Workflow
PubMed: 33961222
DOI: 10.1007/978-1-0716-1099-2_9 -
Medecine Sciences : M/S Nov 2016After more than one and a half century, i.e. since Louis Pasteur work on microbes, fermentation, and diseases, biological science has made a giant step in bacteria... (Review)
Review
After more than one and a half century, i.e. since Louis Pasteur work on microbes, fermentation, and diseases, biological science has made a giant step in bacteria knowledge. Thanks to an ultra-powerful "microscope", i.e. ultra-fast DNA sequencing, scientists have been able to read and group within a catalog over the last decade, the gene code of bacteria, i.e. the metagenome at the surface of our epithelia. More recently, live bacteria within adipose tissue, defining a tissue microbiota, as well as bacterial fragments such as DNA within the liver, the brain and the blood have been identified. Metagenomic analyses from large cohorts of patients have uncovered tight correlations between bacterial genes within our intestine and mouth and diseases such as metabolic diseases, diabetes, obesity, some liver diseases, kidney and heart failure as well as vascular diseases. Some causal mechanisms have been proposed in rodents and can set the soil for novel therapeutic strategies that could interfere with both the microbes and the corresponding host targets.
Topics: Animals; Gastrointestinal Tract; Humans; Metabolic Diseases; Metagenome; Metagenomics; Microbiota
PubMed: 28008835
DOI: 10.1051/medsci/20163211010 -
Microbiology Spectrum Apr 2022The reproductive tract metagenome plays a significant role in the various reproductive system functions, including reproductive cycles, health, and fertility. One of the...
The reproductive tract metagenome plays a significant role in the various reproductive system functions, including reproductive cycles, health, and fertility. One of the major challenges in bovine vaginal metagenome studies is host DNA contamination, which limits the sequencing capacity for metagenomic content and reduces the accuracy of untargeted shotgun metagenomic profiling. This is the first study comparing the effectiveness of different host depletion and DNA extraction methods for bovine vaginal metagenomic samples. The host depletion methods evaluated were slow centrifugation (Soft-spin), NEBNext Microbiome DNA Enrichment kit (NEBNext), and propidium monoazide (PMA) treatment, while the extraction methods were DNeasy Blood and Tissue extraction (DNeasy) and QIAamp DNA Microbiome extraction (QIAamp). Soft-spin and QIAamp were the most effective host depletion method and extraction methods, respectively, in reducing the number of cattle genomic content in bovine vaginal samples. The reduced host-to-microbe ratio in the extracted DNA increased the sequencing depth for microbial reads in untargeted shotgun sequencing. Bovine vaginal samples extracted with QIAamp presented taxonomical profiles which closely resembled the mock microbial composition, especially for the recovery of Gram-positive bacteria. Additionally, samples extracted with QIAamp presented extensive functional profiles with deep coverage. Overall, a combination of Soft-spin and QIAamp provided the most robust representation of the vaginal microbial community in cattle while minimizing host DNA contamination. In addition to the host tissue collected during the sampling process, bovine vaginal samples are saturated with large amounts of extracellular DNA and secreted proteins that are essential for physiological purposes, including the reproductive cycle and immune defense. Due to the high host-to-microbe genome ratio, which hampers the sequencing efficacy for metagenome samples and the recovery of the actual metagenomic profiles, bovine vaginal samples cannot benefit from the full potential of shotgun sequencing. This is the first investigation on the most effective host depletion and extraction methods for bovine vaginal metagenomic samples. This study demonstrated an effective combination of host depletion and extraction methods, which harvested higher percentages of 16S rRNA genes and microbial reads, which subsequently led to a taxonomical profile that resembled the actual community and a functional profile with deeper coverage. A representative metagenomic profile is essential for investigating the role of the bovine vaginal metagenome for both reproductive function and susceptibility to infections.
Topics: Animals; Cattle; DNA; Female; Metagenome; Metagenomics; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 35404108
DOI: 10.1128/spectrum.00412-21 -
The ISME Journal Jan 2021Growth rates are central to understanding microbial interactions and community dynamics. Metagenomic growth estimators have been developed, specifically codon usage bias...
Growth rates are central to understanding microbial interactions and community dynamics. Metagenomic growth estimators have been developed, specifically codon usage bias (CUB) for maximum growth rates and "peak-to-trough ratio" (PTR) for in situ rates. Both were originally tested with pure cultures, but natural populations are more heterogeneous, especially in individual cell histories pertinent to PTR. To test these methods, we compared predictors with observed growth rates of freshly collected marine prokaryotes in unamended seawater. We prefiltered and diluted samples to remove grazers and greatly reduce virus infection, so net growth approximated gross growth. We sampled over 44 h for abundances and metagenomes, generating 101 metagenome-assembled genomes (MAGs), including Actinobacteria, Verrucomicrobia, SAR406, MGII archaea, etc. We tracked each MAG population by cell-abundance-normalized read recruitment, finding growth rates of 0 to 5.99 per day, the first reported rates for several groups, and used these rates as benchmarks. PTR, calculated by three methods, rarely correlated to growth (r ~-0.26-0.08), except for rapidly growing γ-Proteobacteria (r ~0.63-0.92), while CUB correlated moderately well to observed maximum growth rates (r = 0.57). This suggests that current PTR approaches poorly predict actual growth of most marine bacterial populations, but maximum growth rates can be approximated from genomic characteristics.
Topics: Archaea; Bacteria; Benchmarking; Metagenome; Metagenomics
PubMed: 32939027
DOI: 10.1038/s41396-020-00773-1 -
Chinese Medical Journal Oct 2022
Topics: Humans; Virome; Bacteriophages; Feces; Metagenome; Metagenomics
PubMed: 36583859
DOI: 10.1097/CM9.0000000000002382 -
Progress in Molecular Biology and... 2022Recent advances in sequencing technologies, experimental protocols and approaches in data generation and analysis have enabled us to investigate the human microbiome at...
Recent advances in sequencing technologies, experimental protocols and approaches in data generation and analysis have enabled us to investigate the human microbiome at an unprecedented level of resolution. The current chapter aims to provide an understanding of the different computational and bioinformatic strategies adopted to answer the different questions of a typical microbiome investigation and how the upstream DNA sequencing methodologies can affect this. The chapter enlist the state-of-the-art in metagenomic data analysis along with the available strategies to perform an integrated investigation of the human microbiome along with other data layers.
Topics: Humans; High-Throughput Nucleotide Sequencing; Microbiota; Metagenome; Metagenomics; Computational Biology
PubMed: 36270681
DOI: 10.1016/bs.pmbts.2022.06.027