Unveiling microbial diversity: harnessing long-read sequencing technology

Agustinho, Daniel P.; Fu, Yilei; Menon, Vipin K.; Metcalf, Ginger A.; Treangen, Todd J.; Sedlazeck, Fritz J.

doi:10.1038/s41592-024-02262-1

Cited by 11 publications

(2 citation statements)

References 129 publications

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“…Bacterial long-reads data, which start to emerge to look at bacterial structural variation [39], might help us better understand this discrepancy between the short-reads data the assembled datasets. In any case, there seems to be a higher proportion of individuals carrying the PUL in Korea and Japan than in China, as well as three times more reads blasting against the PUL (reflecting the abundance of PUL-positive bacterial strains) in positive individuals from Korea and Japan compared to China.…”

Section: Discussionmentioning

confidence: 99%

The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations

Mathieu

Touvrey

Poulet

et al. 2023

Preprint

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The human gut microbiota can acquire new catabolic functions by integrating genetic material coming from bacteria associated to the food. The most illustrative example is the acquisition of genes by the gut microbiota of Asian populations coming from marine bacteria living at the surface of algae incorporated in diet. In order to interrogate the pace of acquisition of algal polysaccharide utilizing loci (PUL) and their diffusion rate inside populations, we investigated the PUL dedicated to degradation of porphyran, the main polysaccharide of the red algae Porphyra sp. used to prepare maki-sushi. We demonstrated that both methylated and unmethylated fractions were catabolized without the help of external enzymes. The PUL organization was conserved in several Bacteroidetes strains, highlighting lateral transfers inside the microbiota, but we point out various conserved mutations, deletion and insertions. Geographic distribution of the variants showed that specific mutation and recombination events appeared independently in geographically distant populations.

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Section: Discussionmentioning

confidence: 99%

The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations

Mathieu

Touvrey

Poulet

et al. 2023

Preprint

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“…Long-read sequencing can overcome many of the challenges associated with metagenome assembly (Kolmogorov et al 2020; Feng et al 2022; Albertsen 2023; Benoit et al 2023; Agustinho et al 2024). The most popular long-read sequencing platforms are those produced by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT).…”

Section: Introductionmentioning

confidence: 99%

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods

Portik,

Feng,

Benoit

et al. 2024

Preprint

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Long-read metagenomic sequencing is a powerful approach for cataloging the microbial diversity present in complex microbiomes, including the human gut microbiome. We performed a deep-sequencing experiment using PacBio HiFi reads to obtain metagenome-assembled genomes (MAGs) from a pooled human gut microbiome. We performed long-read metagenome assembly using two methods (hifiasm-meta, metMDBG), used improved bioinformatic and proximity ligation binning strategies to cluster contigs and identify MAGs, and developed a novel framework to compare and consolidate MAGs (pb-MAG-mirror). We found proximity ligation binning yielded more MAGs than bioinformatic binning, but our novel comparison framework resulted in higher MAG yields than either binning strategy individually. In total, from 255 Gbp of total HiFi data we produced 595 total MAGs (including 175 high-quality MAGs) using hifiasm-meta, and 547 total MAGs (including 277 high-quality MAGs) with metaMDBG. Hifiasm-meta assembled almost twice as many strain-level MAGs as metaMDBG (246 vs. 156), but both assembly methods produced up to five strains for a species. Approximately 85% of the MAGs were assigned to known species, but we recovered >35 high-quality MAGs that represent uncultured diversity. Based on strict similarity scores, we found 125 MAGs were unequivocally shared across the assembly methods at the strain level, representing ~22% of the total MAGs recovered per method. Finally, we detected more total viral sequences in the metaMDBG assembly versus the hifiasm-meta assembly (~6,700 vs. ~4,500). Overall, we find the use of HiFi sequencing, improved metagenome assembly methods, and complementary binning strategies is highly effective for rapidly cataloging microbial genomes in complex microbiomes.

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Mapping the Environmental Microbiome

Lim

2024

Reference Module in Life Sciences

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Unveiling microbial diversity: harnessing long-read sequencing technology

Cited by 11 publications

References 129 publications

The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations

The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods

Mapping the Environmental Microbiome

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