MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

Kang, Dongwan; Li, Feng; Kirton, Edward; Thomas, Ashleigh; Egan, Rob; An, Hong; Zhong, Wang

doi:10.7717/peerj.7359

Cited by 2,337 publications

(1,533 citation statements)

References 24 publications

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“…For the L04 strain, we investigated how a non-curated MAG that was generated by binning the contigs from the assembly of short Illumina reads without any further bin-refinement step (SR-L04 hereafter), compared to the L04 hybrid genome. To do this, the contigs previously assembled from Illumina reads were binned using two different tools -metabat2 (Kang et al, 2019) and maxbin2 (Wu et al, 2016) -and the results were combined using binning_refiner from metawrap (Song and Thomas, 2017;Uritskiy et al, 2018). The total size of SR-L04 was 3.13 Mb and it was comprised of 398 contigs with an average length of 7854 bp (Table 1).…”

Section: A Mag Generated From Short Reads Is Highly Fragmented But Acmentioning

confidence: 99%

Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses

Caceres

Lewis

Homa

et al. 2019

Preprint

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Asgard archaea is a recently proposed superphylum currently comprised of five recognised phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota and Helarchaeota. Members of this group have been identified based on culture-independent approaches with several metagenome-assembled genomes (MAGs) reconstructed to date. However, most of these genomes consist of several relatively small contigs, and, until recently, no complete Asgard archaea genome is yet available. Large scale phylogenetic analyses suggest that Asgard archaea represent the closest archaeal relatives of eukaryotes. In addition, members of this superphylum encode proteins that were originally thought to be specific to eukaryotes, including components of the trafficking machinery, cytoskeleton and endosomal sorting complexes required for transport (ESCRT). Yet, these findings have been questioned on the basis that the genome sequences that underpin them were assembled from metagenomic data, and could have been subjected to contamination and other assembly artefacts. Even though several lines of evidence indicate that the previously reported findings were not affected by these issues, having access to high-quality and preferentially fully closed Asgard archaea genomes is needed to definitively close this debate. Current long-read sequencing technologies such as Oxford Nanopore allow the generation of long reads in a high-throughput manner making them suitable for their use in metagenomics. Although the use of long reads is still limited in this field, recent analyses have shown that it is feasible to obtain complete or nearcomplete genomes of abundant members of mock communities and metagenomes of various level of complexity. Here, we show that long read metagenomics can be successfully applied to obtain near-complete genomes of low-abundant members of complex communities from sediment samples. We were able to reconstruct six MAGs from different Lokiarchaeota lineages that show high completeness and low fragmentation, with one of them being a nearcomplete genome only consisting of three contigs. Our analyses confirm that the eukaryote-like features previously associated with Lokiarchaeota are not the result of contamination or assembly artefacts, and can indeed be found in the newly reconstructed genomes.Recent advances in long-read DNA sequencing technologies have made long read-based metagenomic sequencing efforts a feasible option (Hao et al., 2018;Nicholls et al., 2019). Long DNA sequencing reads improve the ability to resolve repetitive regions of sequences in de novo assembly, improving the contiguity of genomic assemblies. In metagenomes, repetitive sequences can be present within a single genome, as well as within several genomes that share similar regions (e.g., closely related strains, horizontally transferred genes). Therefore, if reads are long enough to span across repetitive regions, and also cover regions that are unique to a particular genome, their inclusion in metagenome assemblies can help to separate the genomic sequenc...

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Section: A Mag Generated From Short Reads Is Highly Fragmented But Acmentioning

confidence: 99%

Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses

Caceres

Lewis

Homa

et al. 2019

Preprint

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“…The co-assembled contigs were de-replicated using cd-hit v4.6.8 [16] with a 0.98 identity cutoff (-c 0.98), the dereplicated contigs were renamed and were used as references for read recruitment with bwa v0.7.15 [17] and the following metagenomic binning. MetaWRAP v1.1 [18] was used to bin contigs via MetaBAT v2.12.1 [19], CONCOCT v1.0.0 [20], and MaxBin2 [21] with a minimum length cutoff of 2 kb. The resulting bins were further refined within MetaWRAP without filtering for completion (-c 0) and allowing high contamination (-x 10000).…”

Section: Dna Extraction Sequencing Assembly and Metagenome-assemblementioning

confidence: 99%

Benchmarking metagenomic marine microbial growth prediction from codon usage bias and peak-to-trough ratios

Long

Hou

Ignacio‐Espinoza

et al. 2019

Preprint

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Growth rates are fundamental to all organisms and essential for characterizing microbial ecologies. Despite this, we do not know the instantaneous nor maximum growth rates of most naturally-occurring microorganisms. Recent reports indicate DNA replication rates can be estimated from metagenomic coverage, and maximum growth rates can be estimated from genomic characteristics. We tested these approaches with native marine bacteria (<0.6 um size fraction) as 10% inoculum grown in unamended virus-free seawater from the San Pedro Channel, California. This allowed microbial growth without grazing and with greatly reduced viral infection. At multiple time points up to 48 h, we sampled for cell abundances and metagenomic analyses. We generated 101 unique Metagenome-assembled genomes (MAGs) including α , β , and γ Proteobacteria, Flavobacteria, Actinobacteria, Verrucomicrobia, MarineGroup A/SAR406, MGII archaea, and others. We tracked the growth of each as the fraction of total metagenomic reads mapped to each MAG normalized with length, completeness, and total cell counts. Some MAGs did not grow appreciably, but those we could estimate had growth rates ranging from 0.08 to 5.99 d -1 ; these are the first reported growth rates for several of the groups.These metagenome-determined growth rates, which often changed within experiments, were compared to (a) DNA replication estimates from the 'peak-to-trough' ratio (PTR) as determined by three different approaches, and (b) maximum growth rates predicted from codon usage bias (CUB). For the large majority of taxa, observed growth rates were not correlated to PTR indices (r ~ -0.26 -0.08), with exceptions being rapidly growing Oceanospirillales and Saccharospirillaceae (r ~ 0.63 -0.92). However, CUB was moderately well correlated to observed maximum growth rates (r = 0.57). This suggests that maximum growth rates can be reasonably well-estimated from genomic information alone, but current PTR approaches poorly predict actual growth of most marine planktonic bacteria in unamended seawater.

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“…Binning was performed using two approaches: (1) binning the POLA 5/15 13C metagenome with CONCOCT [34] and bin refinement in Anvi'o [35]. (2) pooling contigs longer than 5kbp from all four naphthaleneenriched metagenomes, dereplicating them with cd-hit at 99% id [36,37] and binning them using a combination of MaxBin2 [38], CONCOCT [34] and MetaBAT2 [39]. These bins were combined, refined and reassembled using the MetaWRAP pipeline [40].…”

Section: Metagenomic Sequencing Analysismentioning

confidence: 99%

Metagenomics and stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

Sieradzki

Morando

Fuhrman

2019

Preprint

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Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs): toxic and recalcitrant components of crude oil as well as byproducts of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by low chronic inputs can respond to an acute pollution. We investigated the diversity and functional potential of a similar seed community in the Port of Los Angeles, a chronically polluted site, using stable isotope probing with naphthalene, deep-sequenced metagenomes and carbon incorporation rate measurements at the port and in two sites further into the San Pedro Channel. We show a switch in the composition of the PAH degrading community from diverse early-responding generalists to late-blooming specialized degraders. This switch demonstrates the ability of the local seed community of degraders at the Port of LA to incorporate carbon from PAHs independently of a labile-hydrocarbon degrading succession. We were able to directly show that assembled genomes belonged to naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in any of those genomes and even when combining genes from the entire microbial community. We use metabolic pathways identified in those genomes to generate metagenomic-based recommendations for future optimization of PAHs bioremediation.

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MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

Cited by 2,337 publications

References 24 publications

Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses

Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses

Benchmarking metagenomic marine microbial growth prediction from codon usage bias and peak-to-trough ratios

Metagenomics and stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

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