YAMB: metagenome binning using nonlinear dimensionality reduction and density-based clustering

Korzhenkov, Aleksei A.

doi:10.1101/521286

Cited by 5 publications

(4 citation statements)

References 14 publications

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“…Binning of metagenomic contigs was performed by Concoct ( 37 ), Metabat2 ( 38 ) and Maxbin 2.0 ( 39 ) algorithms, implemented in Metawrap pipeline ( 40 ). Additional binning was performed with in-house developed pyYamb binning tool ( 41 ). Bin refinement of obtained bin sets was performed with DAS Tool package ( 42 ).…”

Section: Methodsmentioning

confidence: 99%

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Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts

Sharko,

Mazloum,

Krotova

et al. 2024

Front. Vet. Sci.

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IntroductionIt has been recognized that capripoxvirus infections have a strong cutaneous tropism with the manifestation of skin lesions in the form of nodules and scabs in the respective hosts, followed by necrosis and sloughing off. Considering that the skin microbiota is a complex community of commensal bacteria, fungi and viruses that are influenced by infections leading to pathological states, there is no evidence on how the skin microbiome is affected during capripoxvirus pathogenesis.MethodsIn this study, shotgun metagenomic sequencing was used to investigate the microbiome in pox lesions from hosts infected with lumpy skin disease virus and sheep pox virus.ResultsThe analysis revealed a high degree of variability in bacterial community structures across affected skin samples, indicating the importance of specific commensal microorganisms colonizing individual hosts. The most common and abundant bacteria found in scab samples were Fusobacterium necrophorum, Streptococcus dysgalactiae, Helcococcus ovis and Trueperella pyogenes, irrespective of host. Bacterial reads belonging to the genera Moraxella, Mannheimia, Corynebacterium, Staphylococcus and Micrococcus were identified.DiscussionThis study is the first to investigate capripox virus-associated changes in the skin microbiome using whole-genome metagenomic profiling. The findings will provide a basis for further investigation into capripoxvirus pathogenesis. In addition, this study highlights the challenge of selecting an optimal bioinformatics approach for the analysis of metagenomic data in clinical and veterinary practice. For example, direct classification of reads using a kmer-based algorithm resulted in a significant number of systematic false positives, which may be attributed to the peculiarities of the algorithm and database selection. On the contrary, the process of de novo assembly requires a large number of target reads from the symbiotic microbial community. In this work, the obtained sequencing data were processed by three different approaches, including direct classification of reads based on k-mers, mapping of reads to a marker gene database, and de novo assembly and binning of metagenomic contigs. The advantages and disadvantages of these techniques and their practicality in veterinary settings are discussed in relation to the results obtained.

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Section: Methodsmentioning

confidence: 99%

“…algorithms, implemented in Metawrap pipeline (40). Additional binning was performed with in-house developed pyYamb binning tool (41). Bin refinement of obtained bin sets was performed with DAS Tool package (42).…”

Section: De Novo Assembly Metagenomic Binning and Phylogenetic Analysismentioning

confidence: 99%

Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts

Sharko,

Mazloum,

Krotova

et al. 2024

Front. Vet. Sci.

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“…Parameters for data normalization and perplexity selection were based on the Rtsne.r script in YAMB 62 .…”

Section: Rtsne Analysismentioning

confidence: 99%

The polyketide to fatty acid transition in the evolution of animal lipid metabolism

Lin,

Li,

Krug

et al. 2024

Nat Commun

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Animals synthesize simple lipids using a distinct fatty acid synthase (FAS) related to the type I polyketide synthase (PKS) enzymes that produce complex specialized metabolites. The evolutionary origin of the animal FAS and its relationship to the diversity of PKSs remain unclear despite the critical role of lipid synthesis in cellular metabolism. Recently, an animal FAS-like PKS (AFPK) was identified in sacoglossan molluscs. Here, we explore the phylogenetic distribution of AFPKs and other PKS and FAS enzymes across the tree of life. We found AFPKs widely distributed in arthropods and molluscs (>6300 newly described AFPK sequences). The AFPKs form a clade with the animal FAS, providing an evolutionary link bridging the type I PKSs and the animal FAS. We found molluscan AFPK diversification correlated with shell loss, suggesting AFPKs provide a chemical defense. Arthropods have few or no PKSs, but our results indicate AFPKs contributed to their ecological and evolutionary success by facilitating branched hydrocarbon and pheromone biosynthesis. Although animal metabolism is well studied, surprising new metabolic enzyme classes such as AFPKs await discovery.

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“…The parameters for data normalization and perplexity selection were set up based on the Rtsne.r script in YAMB 59 .…”

Section: Rtsne Analysismentioning

confidence: 99%

The polyketide to fatty acid transition in the evolution of animal lipid metabolism

Lin

Krug

et al. 2023

Preprint

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Lipids are crucial to all life, but the biochemical origins of many animal lipids remain unclear. We unveil a previously uncharacterized class of enzymes that is widely occurring in animals, and responsible for producing elaborate lipid- and polyketide-like compounds. These enzymes, the animal FAS-like PKSs (AFPKs), share a common ancestor with the animal fatty acid synthase, which produces the fats needed for animal survival, providing a plausible evolutionary bridge between the drug-like polyketides and the fatty acids. Vertebrates lack AFPKs, but excepting the placental mammals contain PKSs. In contrast, molluscs and arthropods contain abundant AFPKs, correlated with their rich polyketide chemistry. Molluscan AFPKs are associated with a lack of other defenses, consistent with the hypothesis that AFPKs provide a chemical defense for some lineages. By contrast, shelled molluscs (physically defended) generally contain PKSs instead. Arthropods have few PKSs, likely originating in parasites or recent horizontal gene transfer, but their abundant AFPKs potentially contributed to their ecological and evolutionary success. Although animal metabolism is well studied, surprising new metabolic enzyme classes still await discovery and may be unrecognized drivers of hyperdiverse animal radiations including gastropods, beetles and spiders.

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YAMB: metagenome binning using nonlinear dimensionality reduction and density-based clustering

Cited by 5 publications

References 14 publications

Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts

Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts

The polyketide to fatty acid transition in the evolution of animal lipid metabolism

The polyketide to fatty acid transition in the evolution of animal lipid metabolism

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