Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(8), P. 1326 - 1339

Published: June 7, 2023

Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial archaeal members complex biogas-producing microbial communities. In present study, microbiomes three industrial-scale biogas digesters, each fed with different substrates, were analysed using machine-learning guided genome-centric metagenomics framework complemented metatranscriptome data. This data permitted us to elucidate relationship abundant core methanogenic communities their syntrophic partners. total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, assembled 16 S rRNA gene profiles these nrMAGs showed that phylum Firmicutes possessed highest copy number, while representatives domain had lowest. Further investigation anaerobic characteristic alterations over time but remained specific plant. The relative abundance various microorganisms revealed by metagenome was independent from corresponding activity Archaea considerably higher than expected abundance. We 51 in all plant abundances. microbiome correlated main chemical fermentation parameters, no individual parameter emerged predominant shaper community composition. Various interspecies H2/electron transfer mechanisms assigned hydrogenotrophic methanogens plants ran on agricultural biomass wastewater. Analysis methanogenesis pathways most active metabolic pathways.

Language: Английский

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Terabase-Scale Coassembly of a Tropical Soil Microbiome

Microbiology Spectrum, Journal Year: 2023, Volume and Issue: 11(4)

Published: June 13, 2023

Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is assembly, the computational reconstruction genome sequences from microbial communities. “Coassembly” metagenomic sequence data, which multiple samples assembled together, enables more complete detection genomes an environment than “multiassembly,” individually.

Language: Английский

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Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(2)

Published: Feb. 20, 2024

Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide prominent example microbial ecosystem engineer that is currently unculturable. They occur in low abundance natural sediments, but due to their capability long-distance electron transport, they exert disproportionately large impact on biogeochemistry environment. Current available marine cable are highly fragmented incomplete, hampering elucidation unique electrogenic physiology. Here, we present pipeline combines Nanopore long-read Illumina short-read shotgun sequencing. Starting from clonal enrichment bacterium, recovered circular metagenome-assembled genome (5.09 Mbp size), which represents novel bacterium species proposed name Candidatus Electrothrix scaldis. The closed contains 1109 identified genes, including key metabolic enzymes not previously described incomplete bacteria. We examined detail factors leading closure. Foremost, native, non-amplified long reads crucial resolve many repetitive regions within bacteria, by analysing whole assembly, found strain diversity insights approaches presented here could help achieve closure other keystone complex environmental samples at abundance.

Language: Английский

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Advancing metagenome-assembled genome-based pathogen identification: unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: 12(6)

Published: April 30, 2024

ABSTRACT Oxford Nanopore sequencing is one of the high-throughput technologies that facilitates reconstruction metagenome-assembled genomes (MAGs). This study aimed to assess potential long-read assembly algorithms in enhance MAG-based identification bacterial pathogens using both simulated and mock communities. Simulated communities were generated mimic those on fresh spinach surface water. Long reads produced R9.4.1+SQK-LSK109 R10.4 + SQK-LSK112, with 0.5, 1, 2 million reads. The included multidrug-resistant Salmonella enterica serotypes Heidelberg, Montevideo, Typhimurium community individually or combination, as well Pseudomonas aeruginosa water community. Real data sets ZymoBIOMICS HMW DNA Standard also studied. A bioinformatic pipeline (MAGenie, freely available at https://github.com/jackchen129/MAGenie ) combines metagenome assembly, taxonomic classification, sequence extraction was developed reconstruct draft MAGs from assemblies. Five assemblers evaluated based a series genomic analyses. Overall, Flye outperformed other assemblers, followed by Shasta, Raven, Unicycler, while Canu performed least effectively. In some instances, extracted sequences resulted provided locations structures antimicrobial resistance genes mobile genetic elements. Our showcases viability utilizing for precise phylogenetic inference, demonstrated consistent alignment topology between reference genome sequences. more effective most cases than R10.4+SQK-LSK112, greater depths generally led accurate results. IMPORTANCE By examining diverse communities, particularly housing multiple serotypes, this holds significance uncovering improve (MAG)-based pathogen through sequencing. research demonstrates stands out promising avenue boosting precision identification, thus advancing development robust surveillance measures. findings support ongoing endeavors fine-tune within complex metagenomic samples.

Language: Английский

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Visualizing metagenomic and metatranscriptomic data: A comprehensive review

Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 23, P. 2011 - 2033

Published: May 3, 2024

The fields of Metagenomics and Metatranscriptomics involve the examination complete nucleotide sequences, gene identification, analysis potential biological functions within diverse organisms or environmental samples. Despite vast opportunities for discovery in metagenomics, sheer volume complexity sequence data often present challenges processing visualization. This article highlights critical role advanced visualization tools enabling effective exploration, querying, these complex datasets. Emphasizing importance accessibility, categorizes various visualizers based on their intended applications utility empowering bioinformaticians non-bioinformaticians to interpret derive insights from meta-omics effectively.

Language: Английский

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