Metagenome analysis using the Kraken software suite

Lu, Jennifer; Rincon, Natalia; Wood, Derrick E.; Breitwieser, Florian P.; Pockrandt, Christopher; Langmead, Ben; Salzberg, Steven L.; Steinegger, Martin

doi:10.1038/s41596-022-00738-y

Cited by 224 publications

(174 citation statements)

References 40 publications

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“…Metagenomic sequencing has provided great improvements in microbiome analysis by metagenomic experiments that can be broadly categorized as either microbiome experiments or pathogen identification experiments (Knight et al ., 2018; Lu et al ., 2022). In microbiome experiments, researchers focus on describing what is present in a given sample.…”

Section: Introductionmentioning

confidence: 99%

Centrifuge+: improving metagenomic analysis upon Centrifuge

Liu

Ren

et al. 2023

Preprint

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Accurate abundance estimation of species is essential for metagenomic analysis. Although many methods have been developed for classification of metagenomic data and abundance estimation of species, the abundance estimation of species remains challenging due to the ambiguous reads that align equally well to more than one genome. Here, we present Centrifuge+, which introduces unique mapping rate to describe the influence of similarities among species in the reference database when analyzing ambiguous reads. In contrast to the popular Centrifuge, Centrifuge+ improved the accuracy of abundance estimation on simulated reads from 4278 complete prokaryotic genomes.

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Section: Introductionmentioning

confidence: 99%

Centrifuge+: improving metagenomic analysis upon Centrifuge

Liu

Ren

et al. 2023

Preprint

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“…In the current study, the raw sequencing data was obtained from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) project (PRJEB32731), and applied to a processing pipeline (https://github.com/Gibbons-Lab/pipelines). Briefly, the obtained FASTQ files were processed using the fastp (version 0.23.2) tool 65 to filter and trim the reads, and taxonomic abundance was obtained using the Kraken 2 (version 2.1.2) and Bracken (version 2.6.0) tools 66 with the Kraken 2 default database (based on NCBI RefSeq). The final collapsed taxonomic table across the samples consisted of 4,669, 1,225, 354, 167, 76, and 35 taxa for species, genus, family, order, class, and phylum, respectively.…”

Section: Methodsmentioning

confidence: 99%

Multiomic Body Mass Index signatures in blood reveal clinically relevant population heterogeneity and variable responses to a healthy lifestyle intervention

Watanabe

Wilmanski

Diener

et al. 2022

Preprint

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Multiomic profiling is useful in characterizing heterogeneity of both health and disease states. Obesity exerts profound metabolic perturbation in individuals and is a risk factor for multiple chronic diseases. Here, we report a global atlas of cross-sectional and longitudinal changes associated with Body Mass Index (BMI) across 1,100+ blood analytes, as well as their correspondence to host genome and fecal microbiome composition, from a cohort of 1,277 individuals enrolled in a wellness program. Machine learning-based models predicting BMI from blood multiomics captured heterogeneous states of both metabolic and gut microbiome health better than classically measured BMI, suggesting that multiomic data can provide deeper insight into host physiology. Moreover, longitudinal analyses identified variable trajectories of BMI in response to a lifestyle intervention, depending on the analyzed omics platform; metabolomics-based BMI decreased to a greater extent than actual BMI, while proteomics-based BMI exhibited greater resistance. Our analysis further elucidated blood analyte-analyte associations which were significantly modified by obesity and partially reversed in the metabolically obese population through the program. Altogether, our findings provide an atlas of the gradual blood perturbations accompanying obesity and serve as a valuable resource for robustly characterizing metabolic health and identifying actionable targets for obesity.

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“…Unexpectedly, the brain tissue displayed exceptional high abundance of the family Mycobacteriaceae, representing more than 80% of the total microbial metagenomic reads (Fig. 2C, Additional file 2: Figure S2) [11][12][13].…”

Section: Metagenomic Analysis Did Not Reveal Any Treponema Genomes Bu...mentioning

confidence: 99%

A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland

et al. 2023

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Background In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case. Results Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy’s bone lesion and high mercury concentrations. Conclusions The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.

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Metagenome analysis using the Kraken software suite

Cited by 224 publications

References 40 publications

Centrifuge+: improving metagenomic analysis upon Centrifuge

Centrifuge+: improving metagenomic analysis upon Centrifuge

Multiomic Body Mass Index signatures in blood reveal clinically relevant population heterogeneity and variable responses to a healthy lifestyle intervention

A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland

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