Pedro Belda-Ferre

Accomplished PhD level scientist with an extensive publication track record in the microbiome space. Expertise in NGS and method development, applied to a variety of research topics, ranging from probiotic development, gnotobiotic animal models, clinical diagnostics and high-throughput highly automated sequencing protocols.

Research Expertise

Microbial Ecology

Human Microbiome

Bioinformatics

Ecology, Evolution, Behavior and Systematics

Microbiology

Genetics

Biotechnology

Microbiology (medical)

Infectious Diseases

Molecular Biology

Modeling and Simulation

Physiology

Biochemistry

Computer Science Applications

Genetics (clinical)

Biomedical Engineering

Applied Microbiology and Biotechnology

Bioengineering

Molecular Medicine

Pharmaceutical Science

Drug Discovery

Analytical Chemistry

Instrumentation

Fluid Flow and Transfer Processes

Process Chemistry and Technology

Parasitology

Virology

Environmental Chemistry

Epidemiology

Internal Medicine

Health Policy

Public Health, Environmental and Occupational Health

Environmental Engineering

Health, Toxicology and Mutagenesis

Pollution

Atmospheric Science

Geochemistry and Petrology

Space and Planetary Science

Immunology

Immunology and Allergy

About

I am a Microbiologist and bioinformatician with over 14 years of experience in the fields of Human Microbiome, Next-Generation Sequencing, Bioinformatics, Microbiology and High-throughput, High-complexity and CLIA laboratories. I am currently a Sr Scientist at Element Biosciences, developing new NGS workflows for the AVITI platform, enabling new applications for customers. Previously, I served as Senior Manager of R&D at Helix, one of the key decision driver in a medium-size start-up NGS population genomics company. I helped with bridging wet and dry lab expertise to develop high-throughput pipelines using liquid handling and automation robots, including Echo 550, Mosquito LV, EpMotion, Biomek 4000, Multiflo FX and Bravo platforms. Through my professional experience, I have published 40 peer-reviewed publications and a pharmacology book chapter, with over 2604 citations (h-index 21).

Legacy Map

Publications

The oral metagenome in health and disease

The ISME Journal

Healthy infants harbor intestinal bacteria that protect against food allergy

Nature Medicine

Global chemical effects of the microbiome include new bile-acid conjugations

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

Nature Communications

SARS-CoV-2 infection dynamics and genomic surveillance reveals early variant transmission in urban wastewater

Microbiota diversity and gene expression dynamics in human oral biofilms

A Tissue-Dependent Hypothesis of Dental Caries

Caries Research

Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities

Identifying a healthy oral microbiome through metagenomics

Clinical Microbiology and Infection

Streptococcus dentisani sp. nov., a novel member of the mitis group

International Journal of Systematic and Evolutionary Microbiology

High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County

Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information

Genome Research

Human Skin, Oral, and Gut Microbiomes Predict Chronological Age

The human oral metaproteome reveals potential biomarkers for caries disease

Detection of Transient Bacteraemia following Dental Extractions by 16S rDNA Pyrosequencing: A Pilot Study

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Emergence of an early SARS-CoV-2 epidemic in the United States

Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers

The ISME Journal

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome

Enhancing untargeted metabolomics using metadata-based source annotation

Nature Biotechnology

Mining Virulence Genes Using Metagenomics

A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria

Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV-2

Chemical Proportionality within Molecular Networks

Analytical Chemistry

Gut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis

Streptococcus dentisani sp. nov., a novel member of the mitis group

International Journal of Systematic and Evolutionary Microbiology

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

The Microbiome and Its Potential for Pharmacology

Concepts and Principles of Pharmacology

What’s LPS Got to Do with It? A Role for Gut LPS Variants in Driving Autoimmune and Allergic Disease

Cell Host & Microbe

Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load

Handwashing and Detergent Treatment Greatly Reduce SARS-CoV-2 Viral Load on Halloween Candy Handled by COVID-19 Patients

A Synthesis-Based Reverse Metabolomics Approach for the Discovery of Chemical Structures from Humans and Animals.

Bacterial and Chemical Evidence of Coastal Water Pollution from the Tijuana River in Sea Spray Aerosol

Environmental Science & Technology

Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) screening among symptom-free healthcare workers

Infection Control & Hospital Epidemiology

Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs

A Sensitive, Rapid, and Portable CasRx-based Diagnostic Assay for SARS-CoV-2

Reference data based insights expand understanding of human metabolomes

Implementation of Practical Surface SARS-CoV-2 Surveillance in School Settings

Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools

The Lancet Regional Health - Americas

SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp.

SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp

Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence

Semi-Automated Extraction of Viral RNA using the Omega Bio-tek Mag-Bind Viral DNA/RNA 96 Kit for SARS-CoV-2 Detection v1

High-throughput Wastewater SARS-CoV-2 Detection Pipeline v1

Emergence of an early SARS-CoV-2 epidemic in the United States

Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation

Nature Biotechnology

Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution

Pangenome comparison ofBacteroides fragilisgenomospecies unveil genetic diversity and ecological insights

Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings

Correction to: Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers

The ISME Journal

Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings

Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

Associations between SARS-CoV-2 and bacteria in the hospital environment

A candidate probiotic evolves rapidly and convergently but affects microbiomes differently

Reference data-set driven metabolomics

Universal adaptive evolution strategy of probiotic Lactobacillus plantarum to gut selection pressure from humans, mice and zebrafish

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

Ecological and Evolutionary Alterations in Graves’ Disease Gut Microbiome Reveal Specific Diagnostic Biomarkers

Marine Bacteria Affect Saccharide Enrichment in Sea Spray Aerosol during a Phytoplankton Bloom

ACS Earth and Space Chemistry

Non-Targeted Metabolomics Enables the Prioritization and Tracking of Anthropogenic Pollutants in Coastal Seawater

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment

Faculty Opinions recommendation of Global chemical effects of the microbiome include new bile-acid conjugations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature

Food allergy is associated with altered epithelial gene expression driven by early life dysbiosis

The Journal of Immunology

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