Article
Biochemistry & Molecular Biology
Silvio Weging, Andreas Gogol-Doring, Ivo Grosse
Summary: kASA is a tool based on k-mer, capable of efficiently identifying and profiling metagenomic DNA or protein sequences with high sensitivity and precision. Custom algorithms and data structures optimized for external memory storage enable a full-scale taxonomic analysis on various devices.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Tara N. Furstenau, Tsosie Schneider, Isaac Shaffer, Adam J. Vazquez, Jason Sahl, Viacheslav Fofanov
Summary: With the growth of sequence databases and sequencing datasets, traditional alignment methods are no longer suitable for taxonomic classification of metagenomic reads. Existing methods sacrifice either speed or accuracy. To address this issue, a flexible new method called MTSv has been designed to balance efficiency and accuracy.
Article
Biochemistry & Molecular Biology
Georges P. Schmartz, Pascal Hirsch, Jeremy Amand, Jan Dastbaz, Tobias Fehlmann, Fabian Kern, Rolf Mueller, Andreas Keller
Summary: Despite improvements in taxonomic profiling tools, metagenomic assembly and genomic binning remain important in metagenomic analysis workflows. The tool BusyBee Web implements a composition-based binning method, capable of handling both assembled contigs and nanopore generated reads. It now offers comprehensive visualizations, allows for differential analysis of samples, and offers plasmid sequence checking using PLSDB as a reference database. Additionally, it provides an API and a Python package for automated access.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Food Science & Technology
Cansu Celik Dogan, Hafize Tugba Yuksel Dolgun, Serkan Ikiz, Sukru Kirkan, Ugur Parin
Summary: The fermented liquid industry is growing worldwide due to its health benefits. Our study contributes to the debate on whether industrially manufactured fermented liquids meet their claims by analyzing pathogens and beneficial bacteria through a metagenomic analysis technique. Potential probiotic bacteria and plant growth-promoting bacteria were identified in these liquids. These findings suggest the need for evaluation of their potential applications for long-term food hygiene and human health effects.
Article
Biochemical Research Methods
Hongxuan Zhai, Julia Fukuyama
Summary: K-mer-based distances are often used to describe differences between communities in metagenome sequencing studies. In this paper, we show a strong relationship between k-mer-based distances and phylogenetically-informed beta-diversity measures. Our results allow for phylogenetically-informed analyses using only k-mer data and provide insight into one class of phylogenetically-informed beta-diversity measures.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Timothy Chappell, Shlomo Geva, James M. Hogan, David Lovell, Andrew Trotman, Dimitri Perrin
Summary: We propose a novel approach for the Metagenomic Geolocation Challenge that utilizes random projection of sample reads. This approach directly uses k-mer composition to characterize samples, eliminating the computationally demanding step of aligning reads to microbial reference sequences. Our findings demonstrate that k-mer representations carry sufficient information to determine the origin of metagenomic samples and that this reference-free approach requires less computation compared to previous methods.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Modupe O. Coker, Rebecca M. Lebeaux, Anne G. Hoen, Yuka Moroishi, Diane Gilbert-Diamond, Erika F. Dade, Thomas J. Palys, Juliette C. Madan, Margaret R. Karagas
Summary: Several studies have shown that body mass index is strongly associated with differences in gut microbiota, but the relationship between body weight and oral microbiota is less clear especially in young children. The aim of this study was to evaluate the association between child growth and the saliva microbiome. The study found that within-sample diversity was inversely related to body mass measurements while community composition was not associated, and certain taxa were consistently associated with growth.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Sarah K. Highlander, Jason M. Wood, John D. Gillece, Megan Folkerts, Viacheslav Fofanov, Tara Furstenau, Nitin K. Singh, Lisa Guan, Arman Seuylemezian, James N. Benardini, David M. Engelthaler, Kasthuri Venkateswaran, Paul S. Keim
Summary: The National Aeronautics and Space Administration (NASA) has been using various techniques, including whole metagenomic sequencing, to study the microbial burden of spacecraft. They found that different analysis tools and methods generated different results in terms of taxonomic identification and functional assignment of the microorganisms. The study also revealed that the microbial diversity varied among different cleanroom samples, with vacuum particles being the most diverse and wipe samples being the least diverse. Functional annotation suggested that many identified microorganisms have the ability to grow in nutrient-limited environments.
Article
Multidisciplinary Sciences
Matteo Ciciani, Michele Demozzi, Eleonora Pedrazzoli, Elisabetta Visentin, Laura Pezze, Lorenzo Federico Signorini, Aitor Blanco-Miguez, Moreno Zolfo, Francesco Asnicar, Antonio Casini, Anna Cereseto, Nicola Segata
Summary: By developing a computational pipeline, researchers can accurately predict and isolate Cas9 nucleases targeting specific sequences, including using mutated sequences as PAM. This approach will be instrumental in generating a repertoire of Cas9 nucleases responding to any PAM requirement.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Eun Seob Lim, Jin Ju Kim, Woo Jun Sul, Joo-Sung Kim, Bomin Kim, Hun Kim, Ok Kyung Koo
Summary: The study identified dominant bacterial genera on kitchen surfaces, observed seasonal changes in bacterial ratios, identified the fan as a main source of outdoor air contamination, and noted microbial flow associated with food spoilage during food preparation.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Wei-Te Lei, Kai-Yao Huang, Jhih-Hua Jhong, Chia-Hung Chen, Shun-Long Weng
Summary: The study found that the characteristics of infant gut microbiota are influenced by feeding types and vitamin D supplementation, especially vitamin D can modulate infant gut microbiota by increasing the proportion of probiotics in breastfed infants.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Nathalia Caroline de Oliveira Melo, Amanda Cuevas-Sierra, Edwin Fernandez-Cruz, Victor de la O, Jose Alfredo Martinez
Summary: Gut microbiota plays a crucial role in maintaining the homeostasis of the gastrointestinal tract, and it has been increasingly recognized as potential biomarkers for metabolic health. The abundance and diversity of fecal microbial community are associated with various disorders, and they can also reflect the nutritional composition of food intake and dietary patterns. Therefore, gut microbial composition could serve as a reliable and precise alternative to subjective questionnaires in evaluating dietary interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Physics, Applied
Phuong H. L. Nguyen, Shimon Rubin, Pulak Sarangi, Piya Pal, Yeshaiahu Fainman
Summary: Surface-enhanced Raman spectroscopy combined with post-processing machine learning methods is used to enhance the analysis of molecular and chemical composition of DNA molecules. In this work, the inhomogeneous broadening caused by increasing adenine concentration is investigated, and one-dimensional and two-dimensional chemical composition classification models are developed for single stranded DNA sequences. Furthermore, a reservoir computing chemical composition classification scheme is proposed, which shows improved performance without relying on manual feature identification.
APPLIED PHYSICS LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Grzegorz Janusz, Andrzej Mazur, Anna Pawlik, Dorota Kolodynska, Bogdan Jaroszewicz, Anna Marzec-Grzadziel, Piotr Koper
Summary: Deadwood plays a crucial role in forest ecology, and the degradation and carbon assimilation of deadwood are carried out by fungi and bacteria. This study investigated the abundance and distribution of microbial taxa in dead spruce logs and the soil below over a 50-year period. The results showed differences in microbial diversity and relative abundance between the samples from 1974 and 2014, with certain taxa being more predominant in each time period.
Article
Plant Sciences
Sashuang Sun, Ning Liang, Zhiyu Zuo, David Parsons, Julien Morel, Jiang Shi, Zhao Wang, Letan Luo, Lin Zhao, Hui Fang, Yong He, Zhenjiang Zhou
Summary: This study aimed to provide an effective image analysis method for clover detection and botanical composition estimation in clover-grass mixture fields. Transfer learning methods, including DeepLab V3+, SegNet, and FCN-8s, were used to detect clover fractions, with results showing that the BPNN model outperformed the MLR model in terms of BC estimation, with lower root mean square error values.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Infectious Diseases
Ingo Riederer, Daniella Areas Mendes-da-Cruz, Guilherme Cordenonsi da Fonseca, Mariela Natacha Gonzalez, Otavio Brustolini, Cassia Rocha, Guilherme Loss, Joseane Biso de Carvalho, Mariane Talon Menezes, Lidiane Menezes Souza Raphael, Alexandra Gerber, Myrna Cristina Bonaldo, Gillian Butler-Browne, Vincent Mouly, Vinicius Cotta-de-Almeida, Wilson Savino, Ana Tereza Ribeiro de Vasconcelos
Summary: This study investigated the mechanisms of Zika virus infection in human skeletal muscle using an in vitro model. The research found that myoblasts are permissive to ZIKV infection, while myotubes control viral replication. Gene expression profiling revealed differences between infected myoblasts and myotubes, with the latter showing pathways related to antiviral and innate immune responses. This study sheds light on potential antiviral mechanisms against ZIKV infection in skeletal muscle.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Microbiology
Ana Valesca Fernandes Gilson Silva, Diego Menezes, Filipe Romero Rebello Moreira, Octavio Alcantara Torres, Paula Luize Camargos Fonseca, Rennan Garcias Moreira, Hugo Jose Alves, Vivian Ribeiro Alves, Tania Maria de Resende Amaral, Adriano Neves Coelho, Julia Maria Saraiva Duarte, Augusto Viana da Rocha, Luiz Gonzaga Paula de Almeida, Joao Locke Ferreira de Araujo, Hilton Soares de Oliveira, Nova Jersey Claudio de Oliveira, Camila Zolini, Josy Hubner de Sousa, Elizangela Goncalves de Souza, Rafael Marques de Souza, Luciana de Lima Ferreira, Alexandra Lehmkuhl Gerber, Ana Paula de Campos Guimaraes, Paulo Henrique Silva Maia, Fernanda Martins Marim, Lucyene Miguita, Cristiane Campos Monteiro, Tuffi Saliba Neto, Fabricia Soares Freire Pugedo, Daniel Costa Queiroz, Damares Nigia Alborguetti Cuzzuol Queiroz, Luciana Cunha Resende-Moreira, Franciele Martins Santos, Erika Fernanda Carlos Souza, Carolina Moreira Voloch, Ana Tereza Vasconcelos, Renato Santana de Aguiar, Renan Pedra de Souza
Summary: This study conducted epidemiological monitoring using diverse strategies to describe the initial stages of the COVID-19 pandemic in Betim City, Brazil. The results revealed the prevalence of the virus, risk factors for positivity, and multiple viral introductions.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biology
Emma J. Griffiths, Ruth E. Timme, Catarina Ines Mendes, Andrew J. Page, Nabil-Fareed Alikhan, Dan Fornika, Finlay Maguire, Josefina Campos, Daniel Park, Idowu B. Olawoye, Paul E. Oluniyi, Dominique Anderson, Alan Christoffels, Anders Goncalves da Silva, Rhiannon Cameron, Damion Dooley, Lee S. Katz, Allison Black, Ilene Karsch-Mizrachi, Tanya Barrett, Anjanette Johnston, Thomas R. Connor, Samuel M. Nicholls, Adam A. Witney, Gregory H. Tyson, Simon H. Tausch, Amogelang R. Raphenya, Brian Alcock, David M. Aanensen, Emma Hodcroft, William W. L. Hsiao, Ana Tereza R. Vasconcelos, Duncan R. MacCannell
Summary: PHA4GE is a global coalition working to improve openness, interoperability, and consistency in public health microbial bioinformatics. They have developed a SARS-CoV-2 contextual data specification package to support data collection and harmonization in public biorepositories.
Article
Genetics & Heredity
Wentai Ma, Jing Yang, Haoyi Fu, Chao Su, Caixia Yu, Qihui Wang, Ana Tereza Ribeiro de Vasconcelos, Georgii A. Bazykin, Yiming Bao, Mingkun Li
Summary: This study analyzed the viral genome of the Omicron variant and found it to have numerous mutations, especially in the Spike gene. These mutations may affect the replication, infectivity, and antigenicity of SARS-CoV-2. The Omicron variant has 53 mutations compared to its closest sequences in public databases, many of which are rare. Strengthening global genomic surveillance and data sharing is crucial for detecting and tracking the source of new variants.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Microbiology
Allan C. de Azevedo-Martins, Kary Ocana, Wanderley de Souza, Ana Tereza Ribeiro de Vasconcelos, Marta M. G. Teixeira, Erney P. Camargo, Joao M. P. Alves, Maria Cristina M. Motta
Summary: The symbiotic relationship between trypanosomatids and bacteria involves extensive metabolic exchanges, with the bacteria providing essential metabolic pathways for the protozoan. An in-silico study found that most genes involved in glycerophospholipid production are only present in the Symbiont Harboring Trypanosomatids (SHTs) and not in the bacteria. The bacterium has specific sequences and genes related to phosphatidylglycerol and phosphatidic acid production, which likely enhance SHT phosphatidic acid production. Phylogenetic analysis suggests that enzymes involved in the glycerophospholipid pathway have eukaryotic characteristics, indicating no gene transfers from the bacterium to the SHT nucleus. Overall, the data indicate that the symbiont plays a limited role in glycerophospholipid production, acquiring most of these molecules from the SHT.
Article
Public, Environmental & Occupational Health
Ronaldo da Silva Francisco Junior, Luiz G. P. de Almeida, Alessandra P. Lamarca, Liliane Cavalcante, Yasmmin Martins, Alexandra L. Gerber, Ana Paula de C. Guimaraes, Ricardo Barbosa Salviano, Fernanda Leitao dos Santos, Thiago Henrique de Oliveira, Isabelle Vasconcellos de Souza, Erika Martins de Carvalho, Mario Sergio Ribeiro, Silvia Carvalho, Flavio Dias da Silva, Marcio Henrique de Oliveira Garcia, Leandro Magalhaes de Souza, Cristiane Gomes da Silva, Caio Luiz Pereira Ribeiro, Andrea Cony Cavalcanti, Claudia Maria Braga de Mello, Amilcar Tanuri, Ana Tereza R. Vasconcelos
Summary: This study reports the first case of intra-host SARS-CoV-2 recombination between the variants of concern AY.33 (Delta) and P.1 (Gamma) during coinfection. By analyzing sequencing reads that contain lineage-defining mutations from both variants, the researchers identified six recombinant regions in the SARS-CoV-2 genome within a sample, four in the spike gene and two in the nucleocapsid gene. This represents a potential threat to public health management during the COVID-19 pandemic due to the emergence of viruses with recombinant phenotypes.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Pediatrics
Ronaldo da Silva Francisco Junior, Guilherme Loss de Morais, Joseane Biso de Carvalho, Cristina dos Santos Ferreira, Alexandra Lehmkuhl Gerber, Ana Paula de C. Guimaraes, Flavia Anisio Amendola, Fernanda Pinto-Mariz, Zilton Farias Meira de Vasconcelos, Ekaterini Simoes Goudouris, Ana Tereza Ribeiro de Vasconcelos
Summary: Our report highlights the importance of whole-exome sequencing (WES) in patients with known inborn errors of immunity, but uncommon clinical presentations. We identified a rare hemizygous missense variant in the BTK gene and a gain-of-function mutation in TGF beta 1, indicating a more complex genetic landscape underlying X-linked agammaglobulinemia (XLA) and bronchiolitis obliterans. This personalized understanding of the genetic basis may have implications for potential treatments and prognosis.
Article
Microbiology
Aline Parolin Calarga, Marco Tulio Pardini Gontijo, Luiz Gonzaga Paula de Almeida, Ana Tereza Ribeiro de Vasconcelos, Leandro Costa Nascimento, Taise Marongio Cotrim de Moraes Barbosa, Thalita Mara de Carvalho Perri, Silvia Regina dos Santos, Monique Ribeiro Tiba-Casas, Eneida Goncalves Lemes Marques, Cleide Marques Ferreira, Marcelo Brocchi
Summary: This study characterizes the antimicrobial-resistant phenotype of non-typhoidal S. enterica strains isolated from human infections in Sao Paulo, Brazil over a 20-year period. The findings reveal that a small percentage of isolates show multidrug resistance and pathogenic phenotypes, and contain antimicrobial resistance genes that could potentially be disseminated among other bacterial strains.
BRAZILIAN JOURNAL OF MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Dandara Cassu-Corsi, Fernanda F. Santos, Rodrigo Cayo, Willames M. B. S. Martins, Carolina S. Nodari, Luiz G. P. Almeida, Rafael A. Martins, Roberto J. Carvalho da Silva, Ana Tereza R. Vasconcelos, Antonio C. C. Pignatari, Ana C. Gales
Summary: This study sequenced Neisseria gonorrhoeae isolates collected in Sao Paulo, Brazil and identified different sequence types and resistance mutations. The results contribute to the understanding of N. gonorrhoeae strains circulating in the region.
Article
Infectious Diseases
Ana Paula Streling, Rodrigo Cayo, Carolina S. Nodari, Luiz G. P. Almeida, Felipe Bronze, Andre Valencio Siqueira, Adriana P. Matos, Vitor Oliveira, Ana Tereza R. Vasconcelos, Marcelo F. M. Marcondes, Ana Cristina Gales
Summary: Pseudomonas aeruginosa is often associated with life-threatening infections due to its intrinsic and acquired antimicrobial mechanisms, including different types of beta-lactamases. The study found that OXA-488 has a higher catalytic efficiency for benzylpenicillin and imipenem compared to OXA-50, although its carbapenemase activity is considered weak. Additionally, OXA-488 and OXA-494 have increased affinity for penicillins, contributing to improved catalytic efficiency against ampicillin.
MICROBIAL DRUG RESISTANCE
(2022)
Article
Virology
Dalal Nour, Rayane Rafei, Alessandra P. Lamarca, Luiz G. P. de Almeida, Marwan Osman, Mohamad Bachar Ismail, Hassan Mallat, Atika Berry, Gwendolyne Burfin, Quentin Semanas, Laurence Josset, Hamad Hassan, Fouad Dabboussi, Bruno Lina, Philippe Colson, Ana Tereza R. Vasconcelos, Monzer Hamze
Summary: This study provides a retrospective genomic surveillance of the SARS-CoV-2 pandemic in Lebanon, revealing the dominance of four different lineages and the role of Lebanon as a dispersal center for lineage B.1.398. The district of Tripoli in Lebanon was identified as a significant source of dispersal within the country. These findings highlight the potential role of developing countries in the emergence of new variants.
Article
Multidisciplinary Sciences
Douglas Terra Machado, Otavio Jose Bernardes Brustolini, Yasmmin Cortes Martins, Marco Antonio Grivet Mattoso Maia, Ana Tereza Ribeiro de Vasconcelos
Summary: DEGRE is a user-friendly tool that considers fixed and random effects on individuals in the experimental design of RNA-Seq research to infer differentially expressed genes (DEGs). It preprocesses the data and applies generalized linear mixed models (GLMMs) to provide inference for DEGs. This tool efficiently removes genes that could impact the inference and offers improved assessment measures in cases with higher biological variability.
Article
Biology
Rafael Mina Piergiorge, Ronaldo da Silva Francisco Junior, Ana Tereza Ribeiro de Vasconcelos, Cintia Barros Santos-Reboucas
Summary: This study identified a complex ceRNA network involved in late-onset AD and highlighted the Fragile X Messenger Ribonucleoprotein 1 (FMR1) as a driver gene in this network. The findings enhance our understanding of ceRNA regulatory pathways in AD and provide potential targets for early biomarkers and therapeutic interventions.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Guilherme C. da Fonseca, Liliane T. F. Cavalcante, Otavio J. Brustolini, Paula M. Luz, Debora C. Pires, Emilia M. Jalil, Eduardo M. Peixoto, Beatriz Grinsztejn, Valdilea G. Veloso, Sandro Nazer, Carlos A. M. Costa, Daniel A. M. Villela, Guilherme T. Goedert, Cleber V. B. D. Santos, Nadia C. P. Rodrigues, Fernando do Couto Motta, Marilda Mendonca Siqueira, Lara E. Coelho, Claudio J. Struchiner, Ana Tereza R. Vasconcelos
Summary: This article investigates the impact of the Gamma and Delta variants of SARS-CoV-2 on the host immune system, finding that Delta can more effectively activate the IFN-I response, while Gamma evades the host immune system by inhibiting the interferon response pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Letter
Virology
Alessandra P. Lamarca, Luiz G. P. de Almeida, Ronaldo da Silva Francisco, Liliane Cavalcante, Douglas Terra Machado, Otavio Brustolini, Alexandra L. Gerber, Ana Paula de C. Guimaraes, Cintia Policarpo, Gleidson da Silva de Oliveira, Lidia Theodoro Boullosa, Isabelle Vasconcellos de Souza, Erika Martins de Carvalho, Mario Sergio Ribeiro, Silvia Carvalho, Flavio Dias da Silva, Marcio Henrique de Oliveira Garcia, Leandro Magalhaes de Souza, Cristiane Gomes Da Silva, Caio Luiz Pereira Ribeiro, Andrea Cony Cavalcanti, Claudia Maria Braga de Mello, Amilcar Tanuri, Ana Tereza R. Vasconcelosa
JOURNAL OF VIROLOGY
(2022)