Article
Biochemical Research Methods
Jennifer Mattock, Mick Watson
Summary: We compared single- and multi-coverage binning on the same set of samples and found that multi-coverage binning outperformed single-coverage binning by identifying contaminant contigs and chimeric bins that other approaches missed. Although resource expensive, multi-coverage binning should always be prioritized as it generates higher quality and less contaminated bins. This study demonstrates the superiority of the multi-coverage binning approach in analyzing multi-sample metagenomic datasets.
Article
Biochemical Research Methods
Zhenmiao Zhang, Chao Yang, Werner Pieter Veldsman, Xiaodong Fang, Lu Zhang
Summary: This paper comprehensively evaluates 19 commonly used assembly tools on metagenomic sequencing datasets from simulation, mock communities, and human gut microbiomes. It finds that long-read assemblers generate high contig contiguity but fail to reveal some medium- and high-quality metagenome-assembled genomes (MAGs). Linked-read assemblers obtain the highest number of overall near-complete MAGs from the human gut microbiomes. Hybrid assemblers using both short- and long-read sequencing are promising methods to improve both total assembly length and the number of near-complete MAGs. The paper also discusses the running time and memory consumption of these assembly tools and provides practical guidance for selecting them.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Carlo Ferravante, Domenico Memoli, Domenico Palumbo, Paolo Ciaramella, Antonio Di Loria, Ylenia D'Agostino, Giovanni Nassa, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz, Giorgio Giurato
Summary: HOME-BIO is a comprehensive pipeline for metagenomics data analysis, comprising three independent analytical modules designed for an inclusive analysis of large NGS datasets. It is a powerful and easy-to-use tool that can be run by users with limited computational expertise, allowing in-depth analyses and customization according to specific user needs.
BMC BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Zoe Yandle, Gabriel Gonzalez, Michael Carr, Jelle Matthijnssens, Cillian De Gascun
Summary: This study developed an unbiased methodology using Oxford Nanopore Technology (ONT) sequencing to obtain whole-genome sequences (WGS) of Rotavirus A (RVA) from clinical samples. The developed protocol generated 146 near-complete RVA WGS out of the 157 RVA-positive clinical samples, with high quality and accuracy. The protocol can be extended to other viral agents in other sample types.
JOURNAL OF VIROLOGICAL METHODS
(2023)
Article
Microbiology
Veronica Roman-Reyna, Enora Dupas, Sophie Cesbron, Guido Marchi, Sara Campigli, Mary Ann Hansen, Elizabeth Bush, Melanie Prarat, Katherine Shiplett, Melanie L. Lewis Ivey, Joy Pierzynski, Sally A. Miller, Francesca Peduto Hand, Marie-Agnes Jacques, Jonathan M. Jacobs
Summary: Xylella fastidiosa (Xf) is a globally distributed plant-pathogenic bacterium, and conventional diagnostics are limited by known sequences and detection limits. The authors developed a metagenomics pipeline for affordable and fast Xf detection, showing versatility in different plant hosts and DNA extraction methods. This pipeline can be used for early detection of Xf and potentially extended to other plant-pathogen interactions.
Article
Biochemistry & Molecular Biology
Ioanna Kalvari, Eric P. Nawrocki, Nancy Ontiveros-Palacios, Joanna Argasinska, Kevin Lamkiewicz, Manja Marz, Sam Griffiths-Jones, Claire Toffano-Nioche, Daniel Gautheret, Zasha Weinberg, Elena Rivas, Sean R. Eddy, Robert D. Finn, Alex Bateman, Anton Petrov
Summary: Rfam is a database of RNA families with 3444 families, each represented by a multiple sequence alignment of known RNA sequences and a covariance model for searching additional members. Recent developments focused on improving data quality and coverage, adding new families like microRNAs, viral and bacterial RNAs through expert collaborations. The database saw significant growth with 759 new families added in Rfam 14, along with new features such as the Rfam Cloud family curation system.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Virology
Rachel L. Tulloch, Karan Kim, Chisha Sikazwe, Alice Michie, Rebecca Burrell, Edward C. Holmes, Dominic E. Dwyer, Philip N. Britton, Jen Kok, John-Sebastian Eden
Summary: The RAPIDprep assay is a simple and fast protocol for diagnosing infections within 24 hours of sample collection by sequencing ribosomal RNA-depleted total RNA. It effectively depletes human and microbial rRNA and amplifies genomic yield without the need for nucleic acid quantification or quality assessment. This assay can detect known and undiagnosed pathogens, providing valuable information for molecular epidemiological investigations and vaccine design.
Article
Biology
Alex Mas-Sandoval, Nathaniel S. Pope, Knud Nor Nielsen, Isin Altinkaya, Matteo Fumagalli, Thorfinn Sand Korneliussen
Summary: This study presents a new method for accurately estimating the multidimensional joint site frequency spectrum based on low-coverage sequencing data. The method is computationally efficient and storage-saving compared to previous implementations, and its accuracy has been validated using data from a fungal pathogen.
Article
Biochemistry & Molecular Biology
Xiaoli Yu, Jiayin Zhou, Wen Song, Mengzhao Xu, Qiang He, Yisheng Peng, Yun Tian, Cheng Wang, Longfei Shu, Shanquan Wang, Qingyun Yan, Jihua Liu, Qichao Tu, Zhili He
Summary: Shotgun metagenome sequencing has opened up a new way to deepen our understanding of sulfur cycling microbial communities, but accurate analysis of these microbial communities remains technically challenging due to low coverage and inaccurate definition of sulfur cycling gene families in public databases.
MOLECULAR ECOLOGY RESOURCES
(2021)
Letter
Immunology
Zhongqiu Teng, Yan Shi, Yao Peng, Huayi Zhang, Xia Luo, Xinchang Lun, Lianxu Xia, Yuanhai You, Zhenpeng Li, Wen Zhang, Ying Zhang, Shicun Dong, Wentao Guo, Biao Kan, Bo Pang, Jianguo Xu, Aiping Qin
Summary: A case of Ricke ttsia sibirica subspecies sibirica BJ-90 infection in China was identified through metagenomic analysis of an eschar biopsy specimen, with a seroprevalence of spotted fever group Ricke ttsia at approximately 17.4% among the local population. This report emphasizes the threat of rickettsioses to public health in the Qinghai-Tibet Plateau.
EMERGING INFECTIOUS DISEASES
(2021)
Article
Biotechnology & Applied Microbiology
Pablo Aja-Macaya, Soraya Rumbo-Feal, Margarita Poza, Angelina Canizares, Juan A. A. Vallejo, German Bou
Summary: A new method for extraction and enrichment of genomic MPXV DNA was developed, which significantly improved the sequencing efficiency and trustworthiness of the consensus sequences. Enriched samples contained a higher percentage of MPXV reads compared to non-enriched samples, leading to more accurate and cost-effective diagnosis of contagious diseases.
Article
Biochemical Research Methods
Jeremy Fan, Steven Huang, Samuel D. Chorlton
Summary: BugSeq is a novel and highly accurate metagenomic classifier for nanopore reads, evaluated on simulated data, mock microbial communities, and real clinical samples. Compared to existing tools, BugSeq shows superior accuracy and run times, especially in producing higher concordance with microbiological culture and qPCR results in samples from patients with lower respiratory tract infections.
BMC BIOINFORMATICS
(2021)
Article
Immunology
Hyo Lim Hong, Laure Flurin, Matthew J. Thoendel, Matthew J. Wolf, Matthew P. Abdel, Kerryl E. Greenwood-Quaintance, Robin Patel
Summary: This study compared the performance of 16S rRNA gene-based targeted metagenomic sequencing (tNGS) and shotgun metagenomic sequencing (sNGS) in detecting and identifying pathogens in sonicate fluid from failed total hip arthroplasty (THA) and total knee arthroplasty (TKA). The study found that tNGS had a higher positive percent agreement with sonicate fluid culture compared to sNGS, and detected potential pathogens in culture-negative PJIs. The study concludes that tNGS is a potential diagnostic tool for identifying PJI pathogens in sonicate fluid, with similar performance characteristics to sNGS.
CLINICAL INFECTIOUS DISEASES
(2023)
Review
Public, Environmental & Occupational Health
Yulian Li, Wentao Bian, Shiping Wu, Jie Zhang, Dan Li
Summary: This meta-analysis evaluated the performance of mNGS in diagnosing tuberculosis and found that it has high sensitivity and can rapidly diagnose Mycobacterium tuberculosis. Various factors, such as sample types, study types, and sample sizes, may contribute to heterogeneity. In a population with a 10% prevalence rate, the accuracy of sensitivity reached 94%.
FRONTIERS IN PUBLIC HEALTH
(2023)
Article
Medicine, General & Internal
Huiyu Xi, Lishuai Zhang, Bo Xu, Haiyang Liu, Suyan Li
Summary: This article reports a case of ocular inflammation caused by Brucella, successfully diagnosed using mNGS technology. Despite the low incidence of Brucella in non-epidemic areas, it should still be considered as a possible pathogen. mNGS technology can aid in early diagnosis and treatment of difficult-to-diagnose ocular infections.
FRONTIERS IN MEDICINE
(2022)
Article
Microbiology
Patricia Apura, Victor de Lorenzo, Cecilia M. Arraiano, Esteban Martinez-Garcia, Sandra C. Viegas
Summary: The study revealed that different ribonucleases play specific roles in the physiology and environmental adaptation of the soil bacterium Pseudomonas putida KT2440. The absence of each ribonuclease led to distinct effects on growth, motility, and morphology of the organism, indicating species-specific regulatory functions and post-transcriptional adaptation mechanisms utilized by P. putida in facing hostile environments.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Sofia Fraile, Maria Briones, Monica Revenga-Parra, Victor de Lorenzo, Encarnacion Lorenzo, Esteban Martinez-Garcia
Summary: Gram-negative bacteria have complex outer membrane structures that make designing reliable bacterial coatings challenging. In this study, ectopic expression of a fibrinogen-specific nanobody on Pseudomonas putida cells enabled the formation of a bacterial monolayer strongly bound to an antigen-coated support. This approach has potential for engineering specific bacterial coverings on target surfaces.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Raul A. Donoso, Daniela Ruiz, Carla Garate-Castro, Pamela Villegas, Jose Eduardo Gonzalez-Pastor, Victor de Lorenzo, Bernardo Gonzalez, Danilo Perez-Pantoja
Summary: The study revealed the natural function of self-sufficient cytochrome P450 members in the CYP116B subfamily, demonstrating their significant role in degrading 2-hydroxyphenylacetic acid. This provides valuable insights for the development of cytochrome P450-based biocatalytic processes.
MICROBIAL BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Jonathan Tellechea-Luzardo, Leanne Hobbs, Elena Velazquez, Lenka Pelechova, Simon Woods, Victor de Lorenzo, Natalio Krasnogor
Summary: The advance in gene synthesis and editing techniques, along with integration of life science research with informatics, IoT, and automation, are bringing full-stack biotechnology platforms for cell line programming closer to reality. These platforms will increase the speed of biological product production and consumption, making traceability, transparency, and trustworthiness essential for engineered cell lines and their processes.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Elena Velazquez, Yamal Al-Ramahi, Jonathan Tellechea-Luzardo, Natalio Krasnogor, Victor de Lorenzo
Summary: Research demonstrates that by improving targetron technology, exogenous sequences can be successfully inserted into the genomes of Gram-negative bacteria. Through the establishment of a series of standardized vectors and the combination of CRISPR/Cas9-facilitated counterselection, successful intron-mediated DNA delivery in bacteria was achieved, and P. putida microorganism was successfully tagged.
ACS SYNTHETIC BIOLOGY
(2021)
Editorial Material
Biotechnology & Applied Microbiology
Victor de Lorenzo
Summary: Our current era is marked by awareness of climate change, environmental deterioration, global pandemics, and inequalities between developed and underdeveloped countries, with a recognition of the crucial role of microorganisms in the functioning of the biosphere. To address these challenges, it is important to engage in multi-faceted discussions involving politics, technology, and science, utilizing advanced microbial biotechnology tools.
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Pablo Nikel, Ilaria Benedetti, Nicolas T. Wirth, Victor de Lorenzo, Belen Calles
Summary: The potential of regulatory nodes from different bacteria as parts for expression cargoes was examined. The performance of these expression devices, assembled within the same plasmid backbone, was analyzed in Escherichia coli. The study revealed differences in their capacity, expression noise, inducibility, and ON/OFF ratios due to the arrangement of functional DNA segments. This research resulted in a collection of formatted expression cargoes without cross talk, providing choices for users and improving interoperability of specific constructs.
MICROBIAL BIOTECHNOLOGY
(2022)
Review
Biology
Victor de Lorenzo
Summary: Contemporary synthetic biology and biotechnologies provide tools and strategies for addressing climate change, but the challenge lies in delivering these technologies to various dimensions of time and space. Environmental Galenics (EG) refers to the science and technology of releasing designed biological agents into deteriorated ecosystems to achieve safe and effective recovery. EG also involves using microorganism carriers and horizontal gene transfer channels to spread beneficial activities.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Elena Velazquez, Beatriz Alvarez, Luis Angel Fernandez, Victor de Lorenzo
Summary: This study exploited the ability of T7 RNA polymerase fusions with cytosine deaminases to induce C -> T changes in specific DNA segments of Pseudomonas putida KT2440. By introducing CdA-RNAP(T7) fusions into test strains, the researchers achieved specific mutagenesis of DNA segments. It was found that the absence of uracil-DNA glycosylase significantly increased mutagenic rates, and the most active variant, pmCDA1, caused extensive mutations.
MICROBIAL BIOTECHNOLOGY
(2022)
Editorial Material
Microbiology
Victor de Lorenzo
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Pavel Dvorak, Teca Calcagno Galvao, Katharina Pflueger-Grau, Alice M. Banks, Victor de Lorenzo, Jose I. Jimenez
Summary: The biodegradative capacity of bacteria is influenced by water availability. The activity and specificity of the transcriptional regulator XylR in the biodegradation of m-xylene were examined when water potential was manipulated. Water limitation led to increased effector specificity, which could be counteracted by external addition of glycine betaine. XylR variants were unaffected by water potential and the conformational changes in the A domain and effector-binding pocket were suggested by AlphaFold prediction.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
Juhyun Kim, Victor de Lorenzo, Angel Goni-Moreno
Summary: Experimental evidence shows that the differential pressure experienced by cells in the middle versus the periphery of a colony affects their growth rate and spatial direction, ultimately shaping the colony's form.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2023)
Article
Biochemical Research Methods
Angeles Hueso-Gil, Belen Calles, Viïctor de Lorenzo
Summary: The inner physicochemical heterogeneity of bacterial cells leads to three-dimensional variations of resources, which has been exploited in adjusting parameters for optogenetic control of biofilm formation in Pseudomonas putida. A superactive variant of PleD diguanylate cyclase was inserted into the chromosome of wild-type and biofilm-deficient P. putida. Random chromosomal insertions enable sampling the intracellular milieu for optimal resources that deliver a preset phenotypic specification.
ACS SYNTHETIC BIOLOGY
(2023)
Editorial Material
Biotechnology & Applied Microbiology
Victor de Lorenzo, Kenneth Timmis
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Biology
Adrian Lopez-Garcia, Alejandro Saborio-Montero, Monica Gutierrez-Rivas, Raquel Atxaerandio, Idoia Goiri, Aser Garcia-Rodriguez, Jose A. Jimenez-Montero, Carmen Gonzalez, Javier Tamames, Fernando Puente-Sanchez, Magdalena Serrano, Rafael Carrasco, Cristina Ovilo, Oscar Gonzalez-Recio
Summary: This study analyzed the whole rumen metagenome to understand the role of rumen microbes in methane emissions. The results show a subtle association between methane production and overall microbiota composition, with certain genera and KEGGs significantly associated with methane production. High methane emissions are linked to higher relative abundance of ciliates and fungi, while low emissions are associated with bacteria.
