Search Results - "Pedro Belda-Ferre"

The human oral metaproteome reveals potential biomarkers for caries disease by Belda-Ferre, Pedro, Williamson, James, Simón-Soro, Áurea, Artacho, Alejandro, Jensen, Ole N., Mira, Alex

“…Tooth decay is considered the most prevalent human disease worldwide. We present the first metaproteomic study of the oral biofilm, using different mass…”
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Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea by Zhu, Qiyun, Mai, Uyen, Pfeiffer, Wayne, Janssen, Stefan, Asnicar, Francesco, Sanders, Jon G., Belda-Ferre, Pedro, Al-Ghalith, Gabriel A., Kopylova, Evguenia, McDonald, Daniel, Kosciolek, Tomasz, Yin, John B., Huang, Shi, Salam, Nimaichand, Jiao, Jian-Yu, Wu, Zijun, Xu, Zhenjiang Z., Cantrell, Kalen, Yang, Yimeng, Sayyari, Erfan, Rabiee, Maryam, Morton, James T., Podell, Sheila, Knights, Dan, Li, Wen-Jun, Huttenhower, Curtis, Segata, Nicola, Smarr, Larry, Mirarab, Siavash, Knight, Rob

“…Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of…”
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Microbiota diversity and gene expression dynamics in human oral biofilms by Benítez-Páez, Alfonso, Belda-Ferre, Pedro, Simón-Soro, Aurea, Mira, Alex

“…Micro-organisms inhabiting teeth surfaces grow on biofilms where a specific and complex succession of bacteria has been described by co-aggregation tests and…”
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The oral metagenome in health and disease by Belda-Ferre, Pedro, Alcaraz, Luis David, Cabrera-Rubio, Raúl, Romero, Héctor, Simón-Soro, Aurea, Pignatelli, Miguel, Mira, Alex

“…The oral cavity of humans is inhabited by hundreds of bacterial species and some of them have a key role in the development of oral diseases, mainly dental…”
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High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County by Karthikeyan, Smruthi, Ronquillo, Nancy, Belda-Ferre, Pedro, Alvarado, Destiny, Javidi, Tara, Longhurst, Christopher A, Knight, Rob

“…Large-scale wastewater surveillance has the ability to greatly augment the tracking of infection dynamics especially in communities where the prevalence rates…”
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Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities by Gonzalez, Juan M, Portillo, Maria C, Belda-Ferre, Pedro, Mira, Alex

“…The microbial world has been shown to hold an unimaginable diversity. The use of rRNA genes and PCR amplification to assess microbial community structure and…”
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Human Skin, Oral, and Gut Microbiomes Predict Chronological Age by Huang, Shi, Haiminen, Niina, Carrieri, Anna-Paola, Hu, Rebecca, Jiang, Lingjing, Parida, Laxmi, Russell, Baylee, Allaband, Celeste, Zarrinpar, Amir, Vázquez-Baeza, Yoshiki, Belda-Ferre, Pedro, Zhou, Hongwei, Kim, Ho-Cheol, Swafford, Austin D, Knight, Rob, Xu, Zhenjiang Zech

“…Human gut microbiomes are known to change with age, yet the relative value of human microbiomes across the body as predictors of age, and prediction robustness…”
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Streptococcus dentisani sp. nov., a novel member of the mitis group by Camelo-Castillo, Anny, Benítez-Páez, Alfonso, Belda-Ferre, Pedro, Cabrera-Rubio, Raúl, Mira, Alex

“…Genomic, taxonomic and biochemical studies were performed on two strains of α-haemolytic streptococci that showed them to be clustered with major members of…”
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A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities by Shaffer, Justin P, Marotz, Clarisse, Belda-Ferre, Pedro, Martino, Cameron, Wandro, Stephen, Estaki, Mehrbod, Salido, Rodolfo A, Carpenter, Carolina S, Zaramela, Livia S, Minich, Jeremiah J, Bryant, MacKenzie, Sanders, Karenina, Fraraccio, Serena, Ackermann, Gail, Humphrey, Gregory, Swafford, Austin D, Miller-Montgomery, Sandrine, Knight, Rob

“…One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused…”
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Detection of transient bacteraemia following dental extractions by 16S rDNA pyrosequencing: a pilot study by Benítez-Páez, Alfonso, Álvarez, Maximiliano, Belda-Ferre, Pedro, Rubido, Susana, Mira, Alex, Tomás, Inmaculada

“…The current manuscript aims to determine the prevalence, duration and bacterial diversity of bacteraemia following dental extractions using conventional…”
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Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome by Huang, Shi, Jiang, Shuaiming, Huo, Dongxue, Allaband, Celeste, Estaki, Mehrbod, Cantu, Victor, Belda-Ferre, Pedro, Vázquez-Baeza, Yoshiki, Zhu, Qiyun, Ma, Chenchen, Li, Congfa, Zarrinpar, Amir, Liu, Yang-Yu, Knight, Rob, Zhang, Jiachao

“…Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts…”
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A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria by Leão, Tiago, Wang, Mingxun, Moss, Nathan, da Silva, Ricardo, Sanders, Jon, Nurk, Sergey, Gurevich, Alexey, Humphrey, Gregory, Reher, Raphael, Zhu, Qiyun, Belda-Ferre, Pedro, Glukhov, Evgenia, Whitner, Syrena, Alexander, Kelsey L, Rex, Robert, Pevzner, Pavel, Dorrestein, Pieter C, Knight, Rob, Bandeira, Nuno, Gerwick, William H, Gerwick, Lena

“…Microbial natural products are important for the understanding of microbial interactions, chemical defense and communication, and have also served as an…”
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SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment by Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., Allard, Sarah M.

“…Abstract Background SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial…”
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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy by Zhu, Qiyun, Huang, Shi, Gonzalez, Antonio, McGrath, Imran, McDonald, Daniel, Haiminen, Niina, Armstrong, George, Vázquez-Baeza, Yoshiki, Yu, Julian, Kuczynski, Justin, Sepich-Poore, Gregory D, Swafford, Austin D, Das, Promi, Shaffer, Justin P, Lejzerowicz, Franck, Belda-Ferre, Pedro, Havulinna, Aki S, Méric, Guillaume, Niiranen, Teemu, Lahti, Leo, Salomaa, Veikko, Kim, Ho-Cheol, Jain, Mohit, Inouye, Michael, Gilbert, Jack A, Knight, Rob

“…We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference…”
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Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load by Marotz, Clarisse, Morton, James T, Navarro, Perris, Coker, Joanna, Belda-Ferre, Pedro, Knight, Rob, Zengler, Karsten

“…Evaluating microbial community composition through next-generation sequencing has become increasingly accessible. However, metagenomic sequencing data sets…”
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Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment by Minich, Jeremiah J, Ali, Farhana, Marotz, Clarisse, Belda-Ferre, Pedro, Chiang, Leslie, Shaffer, Justin P, Carpenter, Carolina S, McDonald, Daniel, Gilbert, Jack, Allard, Sarah M, Allen, Eric E, Knight, Rob, Sweeney, Daniel A, Swafford, Austin D

“…Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical…”
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Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution by Brennan, Caitriona, Salido, Rodolfo A, Belda-Ferre, Pedro, Bryant, MacKenzie, Cowart, Charles, Tiu, Maria D, González, Antonio, McDonald, Daniel, Tribelhorn, Caitlin, Zarrinpar, Amir, Knight, Rob

“…Next-generation sequencing technologies have enabled many advances across diverse areas of biology, with many benefiting from increased sample size. Although…”
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Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies by Brennan, Caitriona, Belda-Ferre, Pedro, Zuffa, Simone, Charron-Lamoureux, Vincent, Mohanty, Ipsita, Ackermann, Gail, Allaband, Celeste, Ambre, Madison, Boyer, Tara, Bryant, MacKenzie, Cantrell, Kalen, Gonzalez, Antonio, McDonald, Daniel, Salido, Rodolfo A, Song, Se Jin, Wright, Gillian, Dorrestein, Pieter C, Knight, Rob

“…Large-scale studies are essential to answer questions about complex microbial communities that can be extremely dynamic across hosts, environments, and time…”
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Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights by Oles, Renee E, Carrillo Terrazas, Marvic, Loomis, Luke R, Hsu, Chia-Yun, Tribelhorn, Caitlin, Belda-Ferre, Pedro, Ea, Allison C, Bryant, MacKenzie, Young, Jocelyn A, Carrow, Hannah C, Sandborn, William J, Dulai, Parambir S, Sivagnanam, Mamata, Pride, David, Knight, Rob, Chu, Hiutung

“…is a Gram-negative commensal bacterium commonly found in the human colon, which differentiates into two genomospecies termed divisions I and II. Through a…”
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Mining virulence genes using metagenomics by Belda-Ferre, Pedro, Cabrera-Rubio, Raúl, Moya, Andrés, Mira, Alex

“…When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for…”
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