New approaches for metagenome assembly with short reads

Ayling, Martin; Clark, Matthew D.; Leggett, Richard M.

doi:10.1093/bib/bbz020

Cited by 141 publications

(110 citation statements)

References 81 publications

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“…Current methods of mining for cas genes in metagenome are based on the de-novo assembled contigs and binned genomes [6]. Assembling long contigs requires high coverage of the genomes so that the dominant microbes with low genomic heterogeneity and less repetitive regions are often more represented in de-novo assemblies [7]. Besides, the incomplete assembling of soil metagenomes generates shorter contigs, which makes cas gene annotation more problematic.…”

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confidence: 99%

Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming

Chai

Cole

et al. 2020

The ISME Journal

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There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus-host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16°C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus-host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.

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confidence: 99%

Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming

Chai

Cole

et al. 2020

The ISME Journal

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“…Recent studies have proposed metagenomic binning as a culture-independent method to extract genomes from samples (Albertsen, et al 2013: 533, Pasolli, et al 2019: 649-62.e20, Tully, et al 2018: 170203, Wang, et al 2019: 48). However, one of the main pitfalls of metagenomic binning is that metagenomic assemblers struggle to assemble contigs of closely related taxa, especially if the organisms are found in low abundance (Ayling, et al 2019). With knowledge now that strain-level variation occurs in species of the microbiome (Lloyd-Price, et al 2017: 61-6), targeted culture efforts are needed to confirm that strain variation observed in metagenomic data is not simply due to assembler bias.…”

Section: Discussionmentioning

confidence: 99%

The Gut Microbiota composition of Feral and Tamworth Pigs determined using High-Throughput Culturomics and Metagenomics Reveals Compositional Variations When Compared to the Commercial Breeds

Fenske

Ghimire

Antony

et al. 2019

Preprint

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Bacterial communities in the hindguts of pigs have a profound impact on health and disease. Yet very limited studies have been performed outside intensive swine farms to determine pig gut microbiome composition in natural populations. Feral pigs represent a unique situation where the microbiome structure can be observed outside the realm of modern agriculture. Additionally, Tamworth pigs that freely forage were included to characterize the microbiome structure of this rare breed. In this study, gut microbiome of feral and Tamworth pigs were determined using metagenomics and culturomics. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. In total, 46 distinct species were successfully isolated from 1000 colonies selected. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. Furthermore, the naturally raised Tamworth pig microbiome contained more number of antibiotic resistance genes when compared to feral pig microbiome. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function by assembling simple to complex microbiota communities in bioreactors or germfree animal models.

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“…MEGAHIT (version 1.2.9) [28], metaSPAdes (version 3.13.1) [29], Ray (version 2.3.1) [30] have been used to assemble short-reads into contigs. These tools were selected based on their popularity for assembling metagenomic reads [31].…”

Section: Assemblersmentioning

confidence: 99%

Assembling reads improves taxonomic classification of species

Tran

Phan

2020

Preprint

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Background: Most current metagenomic classifiers and profilers employ short reads to classify, bin and profile microbial genomes that are present in metagenomic samples. Many of these methods adopt techniques that aim to identify unique genomic regions of genomes so as to differentiate them. Because of this, short-read lengths might be suboptimal. Longer read lengths might improve the performance of classification and profiling. However, longer reads produced by current technology tend to have a higher rate of sequencing errors, compared to short reads. It is not clear if the trade-off between longer length versus higher sequencing errors will increase or decrease classification and profiling performance.Results: We compared performance of popular metagenomic classifiers on short reads and longer reads, which are assembled from the same short reads. When using a number of popular assemblers to assemble long reads from the short reads, we discovered that most classifiers made fewer predictions with longer reads and that they achieved higher classification performance on synthetic metagenomic data. Specifically, across most classifiers, we observed a significant increase in precision, while recall remained the same, resulting in higher overall classification performance. On real metagenomic data, we observed a similar trend that classifiers made fewer predictions. This suggested that they might have the same performance characteristics of having higher precision while maintaining the same recall with longer reads.Conclusions: This finding has two main implications. First, it suggests that classifying species in metagenomic environments can be achieved with higher overall performance simply by assembling short reads. This suggested that they might have the same performance characteristics of having higher precision while maintaining the same recall as shorter reads. Second, this finding suggests that it might be a good idea to consider utilizing long-read technologies in species classification for metagenomic applications. Current long-read technologies tend to have higher sequencing errors and are more expensive compared to short-read technologies. The trade-offs between the pros and cons should be investigated.

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New approaches for metagenome assembly with short reads

Cited by 141 publications

References 81 publications

Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming

Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming

The Gut Microbiota composition of Feral and Tamworth Pigs determined using High-Throughput Culturomics and Metagenomics Reveals Compositional Variations When Compared to the Commercial Breeds

Assembling reads improves taxonomic classification of species

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