HUMANN-based system to identify benzimidazole fungicides using multi-synchronous fluorescence spectra: An ensemble approach

Araujo, Carmen Paz Suárez; Báez, Patricio García; Rodríguez, Álvaro Sánchez; Rodríguez, José Juan Santana

doi:10.1007/s00216-009-2654-7

Cited by 10 publications

(2 citation statements)

References 32 publications

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“…In addition, the HMP Unified Metabolic Analysis Network (HUMAnN2) was used to determine the metabolic contributions within the samples. The HUMAnN2 pipeline involved mapping of the metagenomic reads against the KEGG database and MetaCyc pathway database [18][19][20][21]. As a pure culture was used as a negative control, any reads other than S.flexneri observed in subsequent DNA sequencing results were regarded as contamination and screened out of downstream analysis proportionally.…”

Section: Sequence Data Processingmentioning

confidence: 99%

Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study

Cheng

Liu

et al. 2020

Emerging Microbes & Infections

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The lung microbiome plays an important role in the pathophysiological processes associated with pulmonary tuberculosis (PTB). However, only a few studies using 16S rDNA amplicon sequencing have been reported, and the interactions between Mycobacterium tuberculosis (MTB) and the lung microbiome remain poorly understood. Patients with respiratory symptoms and imaging abnormalities compatible with tuberculosis (TB) were enrolled. We analyzed the lung microbiome in bronchoalveolar lavage (BAL) samples from 30 MTB-positive (MTB+) subjects and 30 MTB negative (MTB-) subjects by shotgun metagenomic sequencing. Alpha diversity tended to be lower in the MTB+ group than in the MTB-group. There was a significant difference in beta diversity between the MTB+ and MTB-subjects. MTB+ lung samples were dominated by MTB, while MTB-samples were enriched with Streptococcus, Prevotella, Nesseria, Selenomonas and Bifidobacterium, which more closely resemble the microbial composition of a healthy lung. Network analysis suggested that MTB could greatly impact the microbial community structure. MTB+ and MTB-communities showed distinct functional signatures. Fungal communities were also found to be associated with the presence or absence of MTB. Furthermore, it was confirmed that 16S rDNA amplicon sequencing underrepresents Mycobacterium. This pilot study is the first to explore the interplay between MTB and the host microbiome by using metagenomic sequencing. MTB dominates the lung microbiome of MTB+ subjects, while MTB-subjects have a Streptococcus-enriched microbiome. The 16S approach underrepresents Mycobacterium and is not the best way to study the TB-associated microbiome.

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Section: Sequence Data Processingmentioning

confidence: 99%

Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study

Cheng

Liu

et al. 2020

Emerging Microbes & Infections

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“…Metagenomic sequencing data allows one to examine the taxonomic composition of the microbial community (23)(24)(25). More importantly, it further enables protein family profiling (26)(27)(28) and metabolic pathway reconstruction (29,30). This information is critical to unlocking the functional potential of the microbial community and elucidating its interactions with the environment.…”

Section: Introductionmentioning

confidence: 99%

Integrated de novo Gene Prediction and Peptide Assembly of Metagenomic Sequencing Data

Thippabhotla

Liu

Yooseph

et al. 2021

Preprint

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Metagenomics is the study of all genomic content presented in given microbial communities. Metagenomic functional analysis aims to quantify protein families and reconstruct metabolic pathways from the metagenome. It plays a central role in understanding the interaction between the microbial community and its host or environment. De novo functional analysis, which allows the discovery of novel protein families, remains challenging for high-complexity communities. There are currently three main approaches for recovering novel genes or proteins: de novo nucleotide assembly, gene calling, and peptide assembly. Unfortunately, their informational connection and dependency have been overlooked, and each has been formulated as an independent problem. In this work, we develop a sophisticated workflow called integrated Metagenomic Protein Predictor (iMPP), which leverages the informational dependencies for better de novo functional analysis. iMPP contains three novel modules: a hybrid assembly graph generation module, a graph-based gene calling module, and a peptide assembly-based refinement module. iMPP significantly improved the existing gene calling sensitivity on unassembled fragmented reads, achieving a 92% - 97% recall rate at a high precision level (>90%). iMPP further allowed for more sensitive and accurate peptide assembly, recovering more reference proteins and delivering more hypothetical protein sequences. The high performance of iMPP can provide a more comprehensive and unbiased view of the microbial communities under investigation. iMPP is freely available from https://github.com/Sirisha-t/iMPP.

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XV International Symposium on Luminescence Spectrometry – Biophysical and Analytical Aspects, Extended Abstracts, 19‐22 June 2012, Barcelona,Spain ‐ (ISLS 2012)

2012

Luminescence

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Figure 1. Comparison of (a) QuEChERS and (b) MIP methodologies for fluoroquinolone analysis in milk samples. Fluorescence properties of new substituted thieno [3, 2-b] indole derivatives and their electrosynthesized oligomersFigure 2. IL-DLLME conditions for the analysis of OTA in wines by capillary HPLC-LIF.Abstract Luminescence 2012; 27: 534-572 /journal/luminescence 536 2. Kosata B, Kozmik V, Svoboda J, Novotna V, Vanek P, Glogarova M. Novel liquid crystals based on [1]benzothieno[3,2-b][1] benzothiophene. Liq Cryst 2003;30:603. 3. Aaron JJ, Mezlova M, Capochichi M, Svoboda J, Brochon J-C, Guiot E. Fluorescence properties of new fused thieno-indoles and their conducting oligomers. Evidence for an heavy atom quenching effect. Luminescence 2006;21:330. 4. Lô Ch, Adenier A, Chane Ching KI, Maurel F, Aaron JJ, Kosata B, Svoboda J. A novel fluorescent conducting polymer:poly[1thiophen-2-yl) benzothieno[3,2-b] benzothiophene]. Electrosynthesis, characterization and optical properties. J Synth Met 2006;156:256. 5. Lô Ch, Adenier A, Maurel F, Aaron JJ, Kosmik V, Svoboda J. Electrochemical, spectral and theoretical studies of two new methyl -thieno [3,2-b] benzothiophenes and their polymers electrosynthesized in organic and micellar media. Synth. Met. 2008;158:6. 6. Lô Ch, Aaron JJ, Kozmík V, Svoboda J, Brochon J-C, Na Li. Comparative study of the electrochemical, optical and photophysical properties of new substituted thieno[3,2-b]benzothiophenes and their oligomers. J. Fluoresc 2010;20:1037.Comparison of the classical and laser photo-induced fluorescence methods for the determination of some phenylurea pesticides

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HUMANN-based system to identify benzimidazole fungicides using multi-synchronous fluorescence spectra: An ensemble approach

Cited by 10 publications

References 32 publications

Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study

Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study

Integrated de novo Gene Prediction and Peptide Assembly of Metagenomic Sequencing Data

XV International Symposium on Luminescence Spectrometry – Biophysical and Analytical Aspects, Extended Abstracts, 19‐22 June 2012, Barcelona,Spain ‐ (ISLS 2012)

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