John Christian Gaby is a Microbiologist with the Genomics and Bioinformatics Research Unit of the United States Department of Agriculture. His research interests include microbial ecology, biological nitrogen fixation, metagenomics, and bioinformatics. He currently works on the development of machine learning models to predict prokaryotic phenotype from genome sequence data.


  • Microbial Ecology
  • Biological Nitrogen Fixation
  • Metagenomics
  • Bioinformatics


  • Ph.D., Microbiology, 2013

    Cornell University

  • B.S., Biology with Emphasis in Microbiology, 2002

    The University of Tennessee



Research Microbiologist Research Associate

Genomics and Bioinformatics Research Unit of the United States Department of Agriculture

2020 – Present Gainesville, FL, USA
Areas of focus include:

  • Genomics
  • Machine Learning
  • Sequence Graphs

Postdoctoral Researcher

The Norwegian University of Life Sciences (NMBU)

2016 – 2020 Ås, Norway
Areas of focus include:

  • Metagenomics
  • Metaproteomics
  • SSU rRNA Sequence Analysis
  • Microbiome Analysis in R
  • Illumina Sequencing
  • Anaerobic Digestion and Biogas Production
  • Intestinal Microbiomes

Postdoctoral Researcher

The Georgia Institute of Technology

2013 – 2016 Atlanta, GA, USA
Areas of focus include:

  • nifH Sequence Analysis
  • Design of an Ecological Field Survey
  • Isolation and Enrichment of Diazotrophs
  • Biological Nitrogen Fixation
  • Agroecosystems

Fulbright US Student Fellow

Corporación Corpogen

2011 – 2012 Bogotá, Colombia
Areas of focus include:

  • Denitrification
  • Páramo

Graduate Research Assistant

Cornell University

2005 – 2011 Ithaca, NY, USA
Areas of focus include:

  • nifH Database
  • Quantitative, Real-time PCR
  • Biological Nitrogen Fixation

Recent Publications

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Isolation and characterization of extracellular vesicles secreted in vitro by porcine microbiota

The secretion of extracellular vesicles, EVs, is a common process in both prokaryotic and eukaryotic cells for intercellular …

Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut

Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our …

Contingent Effects of Liming on N2O-Emissions Driven by Autotrophic Nitrification

Liming acidic soils is often found to reduce their N2O emission due to lowered N2O/(N2O + N2) product ratio of denitrification. Some …

Professional Development

Analysis of Multivariate Data from Ecology and Environmental Science, using PRIMER v6

Recent Posts

Create a Word List

In this blogpost, I use UNIX BASH shell commands to create an alphabetized list of unique words from the Spanish literary work Don …

Oslo Botanical Garden Photo Gallery

UF Field and Fork Farm Gardens Photo Gallery

Vigeland Gardens Photo Gallery

Prokaryotic Genome GC Content

In this blogpost, I explore the range of genome GC contents using a data table of 11,710 refseq prokaryotic genomes.


  • Gainesville, USA