About

Peter R. Girguis, Ph.D., is a Professor of Organismic and Evolutionary Biology at Harvard University. His research focuses on understanding the biology of organisms in their natural environments, particularly in extreme and understudied habitats. Girguis' work involves exploring the physiological, ecological, and evolutionary adaptations of organisms to their environments, often utilizing innovative technologies and interdisciplinary approaches to investigate life in extreme conditions.

Research topics

• Computer Science
• Computational biology
• Genetics
• Biology
• Evolutionary biology
• World Wide Web
• Data science
• Library science
• Astronomy
• Ecology

Selected publications

• Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

  Nature Microbiology · 2022 · 181 citations

  • Political Science
  • Computational biology
  • Biology

  Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

  PublisherOA PDFDOI

• Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites

  Proceedings of the National Academy of Sciences · 2021 · 27 citations

  • Environmental chemistry
  • Oceanography
  • Environmental science

  , and the presence of specific microbial lineages. Our data also suggest that other features, such as electrical conductance, rock particle size, and microbial community alpha diversity, may influence a sample's methanotrophic potential, but these factors did not demonstrate clear patterns with respect to methane oxidation rates. Based on the apparent pervasiveness within seep carbonates of microbial communities capable of performing anaerobic oxidation of methane, as well as the frequent occurrence of carbonates at seeps, we suggest that rock-hosted methanotrophy may be an important contributor to marine methane consumption.

  PublisherOA PDFDOI

• Author Correction: A genomic catalog of Earth’s microbiomes

  Nature Biotechnology · 2021 · 19 citations

  • Computer Science
  • Computational biology
  • Biology

  A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.

  PublisherOA PDFDOI

• A genomic catalog of Earth’s microbiomes

  Nature Biotechnology · 2020 · 963 citations

  • Biology
  • Evolutionary biology
  • Ecology

  The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

  PublisherOA PDFDOI

• Publisher Correction: A genomic catalog of Earth’s microbiomes

  Nature Biotechnology · 2020 · 26 citations

  • Computer Science
  • Computational biology
  • Biology

  An amendment to this paper has been published and can be accessed via a link at the top of the paper.

  PublisherOA PDFDOI

• Roadmap for naming uncultivated Archaea and Bacteria

  Nature Microbiology · 2020 · 157 citations

  • Biology
  • Evolutionary biology
  • Computational biology

  The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

  PublisherOA PDFDOI

• Genetic tool development in marine protists: emerging model organisms for experimental cell biology

  Nature Methods · 2020 · 172 citations

  • Biology
  • Evolutionary biology
  • Ecology

  Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

  DOI

Frequent coauthors

• Nathaniel W. Fortney

  University of Wisconsin–Madison

  6 shared

• Ghasem Hosseini Salekdeh

  Macquarie University

  6 shared

• Thomas Möck

  University of East Anglia

  6 shared

• Alvaro M. Plominsky

  University of California, San Diego

  6 shared

• Sarahi L. Garcia

  Carl von Ossietzky Universität Oldenburg

  6 shared

• Petr Baldrián

  Czech Academy of Sciences, Institute of Microbiology

  6 shared

• О. V. Shubenkova

  Limnological Institute

  6 shared

• Osvaldo Ulloa

  6 shared

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