Brittan S. Scales, M.P.H, Ph.D.
Highly skilled Bioinformatician and Microbiologist trained in Microbiome and NGS research
Research Interests
About
Publications
Microbiology, Genomics, and Clinical Significance of the Pseudomonas fluorescens Species Complex, an Unappreciated Colonizer of Humans
Clinical Microbiology Reviews / Oct 01, 2014
Scales, B. S., Dickson, R. P., LiPuma, J. J., & Huffnagle, G. B. (2014). Microbiology, Genomics, and Clinical Significance of the Pseudomonas fluorescens Species Complex, an Unappreciated Colonizer of Humans. Clinical Microbiology Reviews, 27(4), 927–948. https://doi.org/10.1128/cmr.00044-14
Changes in the Lung Microbiome following Lung Transplantation Include the Emergence of Two Distinct Pseudomonas Species with Distinct Clinical Associations
PLoS ONE / May 15, 2014
Dickson, R. P., Erb-Downward, J. R., Freeman, C. M., Walker, N., Scales, B. S., Beck, J. M., Martinez, F. J., Curtis, J. L., Lama, V. N., & Huffnagle, G. B. (2014). Changes in the Lung Microbiome following Lung Transplantation Include the Emergence of Two Distinct Pseudomonas Species with Distinct Clinical Associations. PLoS ONE, 9(5), e97214. https://doi.org/10.1371/journal.pone.0097214
The microbiome in wound repair and tissue fibrosis
The Journal of Pathology / Nov 29, 2012
Scales, B. S., & Huffnagle, G. B. (2012). The microbiome in wound repair and tissue fibrosis. The Journal of Pathology, 229(2), 323–331. Portico. https://doi.org/10.1002/path.4118
A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs
Journal of Leukocyte Biology / Jun 30, 2016
Scales, B. S., Dickson, R. P., & Huffnagle, G. B. (2016). A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs. Journal of Leukocyte Biology, 100(5), 943–950. https://doi.org/10.1189/jlb.3mr0316-106r
Vibrio Colonization Is Highly Dynamic in Early Microplastic-Associated Biofilms as Well as on Field-Collected Microplastics
Microorganisms / Dec 30, 2020
Kesy, K., Labrenz, M., Scales, B. S., Kreikemeyer, B., & Oberbeckmann, S. (2020). Vibrio Colonization Is Highly Dynamic in Early Microplastic-Associated Biofilms as Well as on Field-Collected Microplastics. Microorganisms, 9(1), 76. https://doi.org/10.3390/microorganisms9010076
Cross-Hemisphere Study Reveals Geographically Ubiquitous, Plastic-Specific Bacteria Emerging from the Rare and Unexplored Biosphere
mSphere / Jun 30, 2021
Scales, B. S., Cable, R. N., Duhaime, M. B., Gerdts, G., Fischer, F., Fischer, D., Mothes, S., Hintzki, L., Moldaenke, L., Ruwe, M., Kalinowski, J., Kreikemeyer, B., Pedrotti, M.-L., Gorsky, G., Elineau, A., Labrenz, M., & Oberbeckmann, S. (2021). Cross-Hemisphere Study Reveals Geographically Ubiquitous, Plastic-Specific Bacteria Emerging from the Rare and Unexplored Biosphere. MSphere, 6(3). https://doi.org/10.1128/msphere.00851-20
Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs
BMC Genomics / Dec 01, 2015
Scales, B. S., Erb-Downward, J. R., Huffnagle, I. M., LiPuma, J. J., & Huffnagle, G. B. (2015). Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs. BMC Genomics, 16(1). https://doi.org/10.1186/s12864-015-2261-2
Genome Sequences of 12 Pseudomonas lundensis Strains Isolated from the Lungs of Humans
Genome Announcements / Feb 15, 2018
Scales, B. S., Erb-Downward, J. R., Falkowski, N. R., LiPuma, J. J., & Huffnagle, G. B. (2018). Genome Sequences of 12 Pseudomonas lundensis Strains Isolated from the Lungs of Humans. Genome Announcements, 6(7). https://doi.org/10.1128/genomea.01461-17
Draft Genome Sequences of Five Pseudomonas fluorescens Subclade I and II Strains, Isolated from Human Respiratory Samples
Genome Announcements / Aug 27, 2015
Scales, B. S., Erb-Downward, J. R., LiPuma, J. J., & Huffnagle, G. B. (2015). Draft Genome Sequences of Five Pseudomonas fluorescens Subclade I and II Strains, Isolated from Human Respiratory Samples. Genome Announcements, 3(4). https://doi.org/10.1128/genomea.00837-15
Draft Genome Sequences of Seven Pseudomonas fluorescens Subclade III Strains Isolated from Cystic Fibrosis Patients
Genome Announcements / Feb 26, 2015
Scales, B. S., Erb-Downward, J. R., Huffnagle, I. M., LiPuma, J. J., & Huffnagle, G. B. (2015). Draft Genome Sequences of Seven Pseudomonas fluorescens Subclade III Strains Isolated from Cystic Fibrosis Patients. Genome Announcements, 3(1). https://doi.org/10.1128/genomea.01285-14
The Psychrotrophic Pseudomonas lundensis, a Non- aeruginosa Pseudomonad, Has a Type III Secretion System of the Ysc Family, Which Is Transcriptionally Active at 37°C
mBio / Feb 22, 2022
Ravi, K., Falkowski, N. R., Scales, B. S., Akulava, V. D., Valentovich, L. N., & Huffnagle, G. B. (2022). The Psychrotrophic Pseudomonas lundensis, a Non- aeruginosa Pseudomonad, Has a Type III Secretion System of the Ysc Family, Which Is Transcriptionally Active at 37°C. MBio, 13(1). https://doi.org/10.1128/mbio.03869-21
Expression of Concern: Alveolar Macrophages from Overweight/Obese Subjects with Asthma Demonstrate a Proinflammatory Phenotype
American Journal of Respiratory and Critical Care Medicine / Apr 01, 2015
Expression of Concern: Alveolar Macrophages from Overweight/Obese Subjects with Asthma Demonstrate a Proinflammatory Phenotype. (2015). American Journal of Respiratory and Critical Care Medicine, 191(7), e28–e28. https://doi.org/10.1164/rccm.1917eoc
Analysis of Culture-Dependent versus Culture-Independent Techniques for Identification of Bacteria in Clinically Obtained Bronchoalveolar Lavage Fluid
Journal of Clinical Microbiology / Oct 01, 2014
Dickson, R. P., Erb-Downward, J. R., Prescott, H. C., Martinez, F. J., Curtis, J. L., Lama, V. N., & Huffnagle, G. B. (2014). Analysis of Culture-Dependent versus Culture-Independent Techniques for Identification of Bacteria in Clinically Obtained Bronchoalveolar Lavage Fluid. Journal of Clinical Microbiology, 52(10), 3605–3613. https://doi.org/10.1128/jcm.01028-14
The Lung Microbiome Predicts Mortality and Response to Azithromycin in Lung Transplant Patients with Chronic Rejection
American Journal of Respiratory and Critical Care Medicine / Jan 25, 2024
Combs, M. P., Luth, J. E., Falkowski, N. R., Wheeler, D. S., Walker, N. M., Erb-Downward, J. R., Wakeam, E., Sjoding, M. W., Dunlap, D. G., Admon, A. J., Dickson, R. P., & Lama, V. N. (2024). The Lung Microbiome Predicts Mortality and Response to Azithromycin in Lung Transplant Patients with Chronic Rejection. American Journal of Respiratory and Critical Care Medicine. https://doi.org/10.1164/rccm.202308-1326oc
Next Steps for Confirming Bronchoalveolar Lavage Amlyase as an Useful Biomarker for Ventilator-Associated Pneumonia*
Critical Care Medicine / Jan 01, 2018
Royer, S., & Prescott, H. C. (2018). Next Steps for Confirming Bronchoalveolar Lavage Amlyase as an Useful Biomarker for Ventilator-Associated Pneumonia*. Critical Care Medicine, 46(1), 165–166. https://doi.org/10.1097/ccm.0000000000002783
Education
University of Michigan–Ann Arbor
Ph.D., Microbiology and Immunology / September, 2015
University of California, Berkeley
M.P.H, Infectious Diseases and Vaccinology / May, 2009
University of California, Los Angeles
B.S., Microbiology, Immunology & Molecular Genetics / April, 2006
Experience
ScaleAI
Ph.D. Production Expert, Coding/Math/Science / February, 2023 — March, 2024
Train a proprietary AI model on the subjects of coding, science, and math.
Leibniz Institute for Baltic Sea Research, Warnemünde (IOW)
Postdoctoral Researcher / July, 2018 — November, 2022
Principal researcher for two large international projects. Optimized protocols and pipelines for the sequencing of microbial sequences from mixed trophic aquatic environments. DNA extraction, PCR, molecular methods, NGS, bioinformatic analysis. Analysis and interpretation of targeted metabolomics data using HPLC-UV/Vis and MS. Data storage, organization, and maintenance. Created, organized, and maintained an extensive microbial culture collection. Coordinated international logistics with an inter-disciplinary team. Wrote progress reports and translated official documents between German and English. Presented results to interdisciplinary audiences at the local and international level. Published results in high-impact, peer-reviewed scientific research journals. Supervised and trained student interns and technicians. Prepared protocols and materials for a large, tran-Pacific research cruise. Oversaw day-to-day operations, making sure to maintain a high level of quality assurance.
University of Michigan, Department of Microbiology & Immunology
Postdoctoral Researcher / January, 2016 — June, 2018
Designed RNA-Seq experiments to track microbial gene expression in response to environmental conditions relevant to mammalian host infection. Performed RNA extraction protocols. Mapped phylogenetic relatedness of a new subclade of microorganisms using next-generation sequencing methods.
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