Promoting Microbiome Workforce Development with KBase

Discover the potential of student research with Microbiology Resource Announcements and KBase—where education meets innovation.

The Issue: to better harness the power of microbes for the benefit of our planet's health and sustainability, we need a deeper understanding of microbiome development, composition, and function. Achieving this goal requires equitable scientific training to support a diverse workforce and empower the next generation of researchers in open microbiome science.

Why This Matters: providing educators with inclusive, ready-to-use, and budget-friendly teaching resources is crucial. These resources engage a diverse group of students, encouraging them to ask important scientific questions while generating open and FAIR (findable, accessible, interoperable, and reusable) data.

About This Collection: this collection showcases announcements of microbial isolate genomes and metagenome-assembled genomes (MAGs) produced by undergraduate students and educators in the Microbiomes in Computational Research Opportunities Network (MICROnet). MICROnet, a program from the U.S. Department of Energy (DOE) Systems Biology Knowledgebase (KBase) platform, offers an open, accessible, and modular scientific workflow. This workflow is standardized, reproducible, and ready to be integrated into existing microbiology and bioinformatics courses.

Featured Articles in This Collection

• Open AccessBacteriologyAnnouncementMicrobiol Resour AnnouncArticle13 Aug 2024

  Genome sequence of Methylobacterium fujisawaense strain C14, isolated from concrete

  • E. Anders Kiledal,
  • Iz Moxley,
  • Olga Shevchenko,
  • Jennifer L. Goff,
  • Julia A. Maresca

  Strain C14 was isolated from concrete prepared using materials and a mix design from the Delaware Department of Transportation and weathered outside at the University of Delaware (39°40'48.2"N 75°45'00.0"W) from 2 May 2013 to 17 August 2014 (1). As other Methylobacterium spp. are genetically tractable (2), we sequenced the C14 genome to facilitate tool development for engineering isolates from concrete.
• Open AccessEnvironmental MicrobiologyAnnouncementMicrobiol Resour AnnouncArticle13 Aug 2024

  Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures

  • Jennifer L. Goff,
  • Chris Hahn,
  • Rebecca A. Ingrassia,
  • Chanistha Tiyapun,
  • Gray G. Waldschmidt,
  • Emma R. Smith,
  • Miranda N. Marini,
  • Olga Shevchenko,
  • Julia A. Maresca

  Organofluorine compounds are persistent environmental contaminants, and microbial biodegradation has been proposed as a remediation strategy (1, 2). Here, we isolated four bacterial strains after enrichment on perfluorooctanoic acid (PFOA) or fluoroacetic acid (MFA).
• Open AccessMicrobial EcologyAnnouncementMicrobiol Resour AnnouncArticle18 Jul 2024

  High-quality draft genome sequence of Paenibacillus sp. RC80, a candidate for biofuel production

  • Gabriella Rizzo,
  • Mallory Choudoir,
  • Rachel Simoes,
  • Nipuni Dayarathne,
  • Kristen M. DeAngelis

  The identification of RC80 as a potentially novel species within the Paenibacillus genus hints at the vast reservoir of untapped soil microbial diversity, offering tantalizing prospects for biotechnological applications, particularly in the realm of biofuel production (1). Therefore, we sequenced a bacterial genome isolated from temperate forest soil (2) to understand the genetic profile of this novel species and its potential for biofuel production.
• Open AccessEnvironmental MicrobiologyAnnouncementMicrobiol Resour AnnouncArticle16 Nov 2023

  Complete genome sequence of Bacillus thuringiensis strain RC340, isolated from a temperate forest soil sample in New England

  • Brendan Sullivan,
  • Claire E. Kitzmiller,
  • Wyatt C. Tran,
  • Mallory Choudoir,
  • Rachel Simoes,
  • Nipuni Dayarathne,
  • Kristen M. DeAngelis

  Soil microenvironments are highly competitive, and bacteria challenge one another for the limited resources available. B. thuringiensis has several mechanisms to gain a competitive advantage including bacteriocin production and antimicrobial resistance (AMR) proteins (1). Soil warming may induce the prevalence of AMR genes (2), so the focus of our genomics analysis was gene signatures of bacitracin resistance mechanisms.
• Open AccessMicrobial EcologyAnnouncementMicrobiol Resour AnnouncArticle16 Nov 2023

  Draft genome sequence of Paenibacillus sp. strain RC67, an isolate from a long-term forest soil warming experiment in Petersham, Massachusetts

  • Wyatt C. Tran,
  • Brendan Sullivan,
  • Claire E. Kitzmiller,
  • Mallory Choudoir,
  • Rachel Simoes,
  • Nipuni Dayarathne,
  • Kristen M. DeAngelis

  Soil microbes mediate nutrient cycling, but it remains elusive how climate warming impacts microorganisms and their metabolism. The ongoing Harvard Forest soil warming experiment investigates the influence of warming temperature on soils (1). Paenibacillus sp. strain RC67 was isolated from the Harvard Forest in Petersham, Massachusetts and sequenced to understand the impact of warmer climate on soil bacterial genomes. The genome sequence indicates that this isolate is a novel bacterial species belonging to the Paenibacillus genus.
• Open AccessEnvironmental MicrobiologyAnnouncementMicrobiol Resour AnnouncArticle19 Sep 2023

  High-quality genomes of Paenibacillus spp. RC334 and RC343, isolated from a long-term forest soil warming experiment

  • Claire E. Kitzmiller,
  • Wyatt C. Tran,
  • Brendan Sullivan,
  • Florencia Cortez,
  • Mallory Choudoir,
  • Rachel Simoes,
  • Nipuni Dayarathne,
  • Kristen M. DeAngelis

  Soil microbes have the potential to mitigate the impact of global warming, but we don’t understand how they respond to long-term warming (1, 2). We sequenced bacterial genomes isolated from the Harvard Forest soil warming experiment (2) to understand the genetic profile of these novel species.
• Open AccessEnvironmental MicrobiologyAnnouncementMicrobiol Resour AnnouncArticle15 Feb 2024

  Five draft genome assemblies from Bacillaceae isolated from a degraded wetland environment

  • Anna L. McLoon,
  • Prince Ackaah Asante,
  • Thomas Anderson,
  • Kellyanne Cahill,
  • Delana Cochrane,
  • Keira Cohen,
  • Jaylene German,
  • Christian M. Hrubes,
  • Isabella LaCroix,
  • Killian McNamee,
  • Anna Mossakowski,
  • Aidan M. Nichter,
  • Jessica L. Pepe,
  • Andrew T. Schofield

  Wetland environments play critical roles in the terrestrial carbon and water cycles, and microbial communities are key players in ecosystem function (1). Endospore-forming bacteria in the Bacillaceae family are metabolically and genomically diverse soil heterotrophs that influence plant health and nutrient cycling, and produce diverse natural products that influence bacterial and non-bacterial species in their environment (2).
• Open AccessEnvironmental MicrobiologyAnnouncementMicrobiol Resour AnnouncArticle19 Oct 2023

  Complete genome sequence of Bradyrhizobium NP1, isolated from forest soil

  • Trevor Fisher,
  • Francesca Durmazolu,
  • Kristen M. DeAngelis,
  • Maureen A. Morrow

  The diverse genus Bradyrhizobium is predicted to contain approximately 800 species (1) and includes non-symbiotic species that dominate forest soil (2). Bradyrhizobium NP1 was isolated from the Prospect Hill long-term warming experiment (3) at the Harvard Forest Long-Term Ecological Research site in Petersham, MA (42.54–72.18). In May 2021, organic horizon soil was collected from a heated plot and stored at 4°C until use. In August 2021, soil was plated on dilute nutrient broth supplemented with ammonium nitrate (Table 1) and incubated at room temperature (22°C). NP1 was a slow-growing colony that appeared after 10 weeks and thus was chosen for analysis.
• Open AccessEnvironmental MicrobiologyAnnouncementMicrobiol Resour AnnouncArticle24 Jan 2023

  Draft Metagenome-Assembled Genome Sequence of a Novel Citricoccus Species from Agricultural Soil in Western Colorado

  • Paul O’Toole,
  • Rebecca A. Daly,
  • Reza Keshavarz Afshar,
  • Michael Shaffer,
  • Kelly C. Wrighton,
  • Bridget B. McGivern

  Members of the genus Citricoccus are recognized as salt-tolerant soil microorganisms. Here, we report the metagenome-assembled genome sequence of a novel Citricoccus species recovered from untilled, surface agricultural soils in western Colorado.
• Open AccessBacteriologyAnnouncementMicrobiol Resour AnnouncArticle17 Nov 2022

  Draft Genome Sequences for 6 Isolates of Endospore-Forming Class Bacilli Species Isolated from Soil from a Suburban, Wooded, Developed Space

  • Anna L. McLoon,
  • Thomas T. Awad,
  • Molly F. Bogardus,
  • Meredith G. Buono,
  • Kaitlyn A. Devine,
  • Rebecca M. Draper,
  • Brianna Femenella,
  • Hannah M. Gallagher,
  • Laura A. Morelock,
  • Mishal Razi,
  • Jacqueline R. Rennick,
  • Abigail K. Sheridan,
  • Righlee J. Thibault,
  • Katie L. Touchette,
  • Grace E. Zuchowski

  Here, we report draft genome sequences of Bacillus pseudomycoides SC107, Rossellomorea sp. SC111, Peribacillus frigoritolerans SC112, Priestia megaterium SC114, Paenibacillus sp. SC116, and Lysinibacillus fusiformis SC117, isolated from a campus wooded ...
• Open AccessEnvironmental MicrobiologyAnnouncementMicrobiol Resour AnnouncArticle15 Sep 2022

  Draft Metagenome-Assembled Genome Sequences of Three Novel Ammonia-Oxidizing Nitrososphaera Strains Recovered from Agricultural Soils in Western Colorado

  • Arsen Yerlan,
  • Rebecca A. Daly,
  • Reza Keshavarz Afshar,
  • Michael Shaffer,
  • Kelly C. Wrighton,
  • Bridget B. McGivern

  Microbial nitrification is critical to nitrogen loss from agricultural soils. Here, we report three thaumarchaeotal metagenome-assembled genomes (MAGs) representing a new species of Nitrososphaera. These genomes expand the representation of archaeal ...
• Open AccessEnvironmental MicrobiologyAnnouncementMicrobiol Resour AnnouncArticle8 Jul 2021

  Draft Genome Sequence of Staphylococcus succinus Strain GN1, Isolated from a Basement Floor in Milwaukee, WI

  • Grant P. Nickolson,
  • Nasim Maghboli Balasjin,
  • Christopher W. Marshall

  A strain of Staphylococcus succinus was sampled from the floor of the basement of a house and isolated in an undergraduate classroom in Milwaukee, WI. Here, we report the draft genome sequence of this strain.
• Open AccessAnnouncementMicrobiol Resour AnnouncArticle10 Dec 2020

  Draft Genome Sequence of a Terrestrial Planctomycete, Singulisphaera sp. Strain GP187, Isolated from Forest Soil

  • Maureen A. Morrow,
  • Grace Pold,
  • Kristen M. DeAngelis

  Here, we present the draft genome sequence of a novel species of the genus Singulisphaera (phylum Planctomycetes, family Isosphaeraceae) isolated from soil. Singulisphaera sp. strain GP187 has a relatively large mobilome and numerous novel genes that may ...