Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms

Olm, Matthew R.; West, Patrick T.; Brooks, Brandon; Firek, Brian; Baker, Robyn; Morowitz, Michael J.; Banfield, Jillian F.

doi:10.1186/s40168-019-0638-1

Cited by 66 publications

(48 citation statements)

References 90 publications

(101 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The K-mer-based classifier, EukRep, was developed to accomplish this separation (West et al 2018) . Although eukaryote genome recovery from metagenomes is increasingly reported (Quandt et al 2015;Mosier et al 2016;Olm et al 2019) , to our knowledge, none have been extensively curated or completed.…”

Section: Case Studies Illustrating the Curation Of Draft Magsmentioning

confidence: 99%

Accurate and Complete Genomes from Metagenomes

Chen

Anantharaman

Shaiber

et al. 2019

Preprint

Self Cite

127

View full text Add to dashboard Cite

51Genomes are an integral component of the biological information about an organism and, logically, the more 52 complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were 53 reconstructed from pure (monoclonal) cultures and the first reported sequences were manually curated to 54 completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights 55 for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as 56 community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation 57 by obtaining metagenome-assembled genomes (MAGs), but gaps, local assembly errors, chimeras and 58 contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome 59 curation to improve and in some cases achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few 60 CMAGs have been generated, although notably some are from very complex systems such as soil and 61 sediment. Through analysis of ~7000 published complete bacterial isolate genomes, we verify the value of 62 cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. 63Interestingly, analysis of cumulative GC skew identified potential mis-assemblies in some reference genomes 64 of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could 65 be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary 66 analyses can be based on very high-quality genomes. 67 68 69 70 2017), and even human blood (Moustafa et al. 2017) amenable to shotgun metagenomic surveys and recovery 87 of MAGs. Although incomplete, draft MAGs represent a major advance over knowing nothing about the genes 88 and pathways present in an organism, and led to the discovery of new metabolisms. For example, the complete 89 oxidation of ammonia to nitrate via nitrite (i.e., comammox) was determined by the detection of necessary 90 genes in a single MAG (Daims et al. 2015; van Kessel et al. 2015). MAGs are often derived from uncultivated 91 organisms that can be quite distantly related to any isolated species, which is a clear advantage of MAGs 92 (Becraft et al. 2017; Garg et al. 2019). For this reason, genome-resolved metagenomics has been critical for 93 more comprehensive descriptions of bacterial and archaeal diversity and the overall topology of the Tree of 94

show abstract

Section: Case Studies Illustrating the Curation Of Draft Magsmentioning

confidence: 99%

Accurate and Complete Genomes from Metagenomes

Chen

Anantharaman

Shaiber

et al. 2019

Preprint

Self Cite

127

View full text Add to dashboard Cite

show abstract

“…[1]), viruses (e.g. [2]) and, more recently, eukaryotes [3]. Obtaining eukaryotic metagenome-assembled genomes requires very deep sequencing, given their large genome sizes and typically low relative abundances.…”

Section: Introductionmentioning

confidence: 99%

The use of taxon-specific reference databases compromises metagenomic classification

2020

View full text Add to dashboard Cite

A recent article in BMC Genomics describes a new bioinformatics tool, HumanMycobiomeScan, to classify fungal taxa in metagenomic samples. This tool was used to characterize the gut mycobiome of hunter-gatherers and Western populations, resulting in the identification of a range of fungal species in the vast majority of samples. In the HumanMycobiomeScan pipeline, sequence reads are mapped against a reference database containing fungal genome sequences only. We argue that using reference databases comprised of a single taxonomic group leads to an unacceptably high number of false-positives due to: (i) mapping to conserved genetic regions in reference genomes, and (ii) sequence contamination in the assembled reference genomes. To demonstrate this, we replaced the HumanMycobiomeScan's fungal reference database with one containing genome sequences of amphibians and reptiles and re-analysed their case study. The classification pipeline recovered all species present in the reference database, revealing turtles (Geoemydidae), bull frogs (Pyxicephalidae) and snakes (Colubridae) as the most abundant herpetological taxa in the human gut. We also re-analysed their case study using a kingdom-agnostic pipeline. This revealed that while the gut of hunter-gatherers and Western subjects may be colonized by a range of microbial eukaryotes, only three fungal families were retrieved. These results highlight the pitfalls of using taxonspecific reference databases for metagenome classification, even when they are comprised of curated whole genome data. We propose that databases containing all domains of life provide the most suitable option for metagenomic species profiling, especially when targeting microbial eukaryotes.

show abstract

“…Contrary to metatranscriptomics, metagenomics yields coding and noncoding sequences, which can facilitate linking genes to species if sequencing depth is large enough to assemble large parts of fungal genomes (e.g. Olm et al 2019).…”

Section: Discussionmentioning

confidence: 99%

Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities – a proof of concept under laboratory conditions

et al. 2019

View full text Add to dashboard Cite

High-throughput sequencing (HTS) enables the generation of large amounts of genome sequence data at a reasonable cost. Organisms in mixed microbial communities can now be sequenced and identified in a culture-independent way, usually using amplicon sequencing of a DNA barcode. Bulk RNA-seq (metatranscriptomics) has several advantages over DNA-based amplicon sequencing: it is less susceptible to amplification biases, it captures only living organisms, and it enables a larger set of genes to be used for taxonomic identification. Using a model mock community comprising 17 fungal isolates, we evaluated whether metatranscriptomics can accurately identify fungal species and subspecies in mixed communities. Overall, 72.9% of the RNA transcripts were classified, from which the vast majority (99.5%) were correctly identified at the species level. Of the 15 species sequenced, 13 were retrieved and identified correctly. We also detected strain-level variation within the Cryptococcus species complexes: 99.3% of transcripts assigned to Cryptococcus were classified as one of the four strains used in the mock community. Laboratory contaminants and/or misclassifications were diverse, but represented only 0.44% of the transcripts. Hence, these results show that it is possible to obtain accurate species-and strain-level fungal identification from metatranscriptome data as long as taxa identified at low abundance are discarded to avoid false-positives derived from contamination or misclassifications. This study highlights both the advantages and current challenges in the application of metatranscriptomics in clinical mycology and ecological studies.

show abstract

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms

Cited by 66 publications

References 90 publications

Accurate and Complete Genomes from Metagenomes

Accurate and Complete Genomes from Metagenomes

The use of taxon-specific reference databases compromises metagenomic classification

Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities – a proof of concept under laboratory conditions

Contact Info

Product

Resources

About