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Articles by Brian A. Firek
Identification and genetic characterization of megabase-scale plasmids of Enterobacteriaceae
Abstract Humans and animals are ubiquitously colonized by Enterobacteriaceae, including both commensals and clinically significant pathogens. Here, we report 21 complete Enterobacteriaceae megaplasmid genomes of up to 1.58 Mbp in length spanning two major clades that are highly divergent from previously described plasmids. Of these, three were reconstructed from isolates of Escherichia coli and Shigella flexneri; others were potentially hosted by species of Citrobacter and Enterobacter.
Correction: The salivary microbiota of patients with acute lower respiratory tract infection-A multicenter cohort study
Loading metrics The Supporting Information files (S1–S4 Figs, S1 Table, and S1–S3 Appendices) are uploaded incorrectly. Please view the correct S1–S4 Figs, S1 Table, and S1–S3 Appendices below. Supporting information Taxonomic families appear along the and points are distributed along the X-axis according to effect size. Size of point indicates mean relative abundance of each family.
Infant gut DNA bacteriophage strain persistence during the first 3 years of life
Highlights • Infant gut phageome has adult-like diversity by age 3, retaining 9% of initial phages • Maternally transmitted phage strains are more likely to persist in the infant gut • Genetic code expansion may contribute to DNA phage gut persistence • Phages encoding diversity-generating retroelements increase as infants mature Summary Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain.
Disruption of the microbiota across multiple body sites in critically ill children
Matthew B. Rogers1, Brian Firek1, Min Shi2, Andrew Yeh1, Rachel Brower-Sinning1, Victoria Aveson1, Brittany L. Kohl3, Anthony Fabio4, Joseph A. Carcillo3,5 & Michael J. Morowitz6 Microbiome volume 4, Article number: 66 (2016) Cite this article 2789 Accesses 24 Citations 23 Altmetric Metrics details Abstract Background Despite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients.
Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria
Abstract Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants. We performed genome-resolved metagenomic analysis of 1163 fecal samples from premature infants to identify microbial features predictive of NEC. Features considered include genes, bacterial strain types, eukaryotes, bacteriophages, plasmids, and growth rates.
The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms
The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms Brandon Brooks, Matthew R Olm, Brian A. Firek, Robyn Baker, David Geller-McGrath, Sophia R. Reimer, Karina R. Soenjoyo, Jennifer S. Yip, Dylan Dahan, Brian C. Thomas, Michael J. Morowitz, Jillian F. Banfield bioRxiv 315689; doi: https://doi.org/10.1101/315689
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