Publications by authors named "J J Burckhardt"

Article Synopsis
  • Characterizing microbial communities is essential for understanding their complexity and diversity, typically using PCR assays for DNA detection and quantification, but designing specific primers has been challenging.* -
  • The introduction of Phylogenetically Unique Primers in Python (PUPpy) allows for the automated design of specific primers for microbial groups, using straightforward inputs and offering an easy-to-use interface.* -
  • PUPpy-designed primers have demonstrated 100% specificity in tests, enabling precise detection and absolute quantification of microbial abundance, outperforming traditional methods like 16S rRNA and shotgun sequencing in defined communities.*
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Tropini and Burckhardt introduce inoviruses and discuss how they are unique amongst bacteriophages.

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Changes to gut environmental factors such as pH and osmolality due to disease or drugs correlate with major shifts in microbiome composition; however, we currently cannot predict which species can tolerate such changes or how the community will be affected. Here, we assessed the growth of 92 representative human gut bacterial strains spanning 28 families across multiple pH values and osmolalities . The ability to grow in extreme pH or osmolality conditions correlated with the availability of known stress response genes in many cases, but not all, indicating that novel pathways may participate in protecting against acid or osmotic stresses.

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Background: Bacteriophages in the family Inoviridae, or inoviruses, are under-characterized phages previously implicated in bacterial pathogenesis by contributing to biofilm formation, immune evasion, and toxin secretion. Unlike most bacteriophages, inoviruses do not lyse their host cells to release new progeny virions; rather, they encode a secretion system that actively pumps them out of the bacterial cell. To date, no inovirus associated with the human gut microbiome has been isolated or characterized.

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Examining natural selection in wild populations is challenging, but crucial to understanding many ecological and evolutionary processes. Additionally, in hybridizing populations, natural selection may be an important determinant of the eventual outcome of hybridization. We characterized several components of relative fitness in hybridizing populations of Yellowstone cutthroat trout and rainbow trout in an effort to better understand the prolonged persistence of both parental species despite predictions of extirpation.

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