1
|
Nuhamunada M, Mohite OS, Phaneuf P, Palsson B, Weber T. BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets. Nucleic Acids Res 2024; 52:5478-5495. [PMID: 38686794 PMCID: PMC11162802 DOI: 10.1093/nar/gkae314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome mining of bacterial pangenomes. BGCFlow incorporates several genome analytics and mining tools grouped into five common stages of analysis such as: (i) data selection, (ii) functional annotation, (iii) phylogenetic analysis, (iv) genome mining, and (v) comparative analysis. Furthermore, BGCFlow provides easy configuration of different projects, parallel distribution, scheduled job monitoring, an interactive database to visualize tables, exploratory Jupyter Notebooks, and customized reports. Here, we demonstrate the application of BGCFlow by investigating the phylogenetic distribution of various biosynthetic gene clusters detected across 42 genomes of the Saccharopolyspora genus, known to produce industrially important secondary/specialized metabolites. The BGCFlow-guided analysis predicted more accurate dereplication of BGCs and guided the targeted comparative analysis of selected RiPPs. The scalable, interoperable, adaptable, re-entrant, and reproducible nature of the BGCFlow will provide an effective novel way to extract the biosynthetic knowledge from the ever-growing genomic datasets of biotechnologically relevant bacterial species.
Collapse
Affiliation(s)
- Matin Nuhamunada
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Omkar S Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Patrick V Phaneuf
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Bernhard O Palsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| |
Collapse
|
2
|
De La Cruz KF, Townsend EC, Alex Cheong JZ, Salamzade R, Liu A, Sandstrom S, Davila E, Huang L, Xu KH, Wu SY, Meudt JJ, Shanmuganayagam D, Gibson ALF, Kalan LR. The porcine skin microbiome exhibits broad fungal antagonism. Fungal Genet Biol 2024; 173:103898. [PMID: 38815692 DOI: 10.1016/j.fgb.2024.103898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/02/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
The skin and its microbiome function to protect the host from pathogen colonization and environmental stressors. In this study, using the Wisconsin Miniature Swine™ model, we characterize the porcine skin fungal and bacterial microbiomes, identify bacterial isolates displaying antifungal activity, and use whole-genome sequencing to identify biosynthetic gene clusters encoding for secondary metabolites that may be responsible for the antagonistic effects on fungi. Through this comprehensive approach of paired microbiome sequencing with culturomics, we report the discovery of novel species of Corynebacterium and Rothia. Further, this study represents the first comprehensive evaluation of the porcine skin mycobiome and the evaluation of bacterial-fungal interactions on this surface. Several diverse bacterial isolates exhibit potent antifungal properties against opportunistic fungal pathogens in vitro. Genomic analysis of inhibitory species revealed a diverse repertoire of uncharacterized biosynthetic gene clusters suggesting a reservoir of novel chemical and biological diversity. Collectively, the porcine skin microbiome represents a potential unique source of novel antifungals.
Collapse
Affiliation(s)
- Karinda F De La Cruz
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Elizabeth C Townsend
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States; Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - J Z Alex Cheong
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States
| | - Rauf Salamzade
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States
| | - Aiping Liu
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Evelin Davila
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; National Summer Undergraduate Research Project, University of Arizona, Tucson, AZ, United States
| | - Lynda Huang
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Kayla H Xu
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Sherrie Y Wu
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Jennifer J Meudt
- Department of Animal & Dairy Sciences, University of Wisconsin, Madison, WI, United States; Center for Biomedical Swine Research & Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Dhanansayan Shanmuganayagam
- Department of Animal & Dairy Sciences, University of Wisconsin, Madison, WI, United States; Center for Biomedical Swine Research & Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Angela L F Gibson
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Lindsay R Kalan
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
| |
Collapse
|
3
|
Rahman MS, Shimul MEK, Parvez MAK. Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains. PLoS One 2024; 19:e0299588. [PMID: 38718091 PMCID: PMC11078359 DOI: 10.1371/journal.pone.0299588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 02/13/2024] [Indexed: 05/12/2024] Open
Abstract
Corynebacterium glutamicum is a non-pathogenic species of the Corynebacteriaceae family. It has been broadly used in industrial biotechnology for the production of valuable products. Though it is widely accepted at the industrial level, knowledge about the genomic diversity of the strains is limited. Here, we investigated the comparative genomic features of the strains and pan-genomic characteristics. We also observed phylogenetic relationships among the strains based on average nucleotide identity (ANI). We found diversity between strains at the genomic and pan-genomic levels. Less than one-third of the C. glutamicum pan-genome consists of core genes and soft-core genes. Whereas, a large number of strain-specific genes covered about half of the total pan-genome. Besides, C. glutamicum pan-genome is open and expanding, which indicates the possible addition of new gene families to the pan-genome. We also investigated the distribution of biosynthetic gene clusters (BGCs) among the strains. We discovered slight variations of BGCs at the strain level. Several BGCs with the potential to express novel bioactive secondary metabolites have been identified. Therefore, by utilizing the characteristic advantages of C. glutamicum, different strains can be potential applicants for natural drug discovery.
Collapse
Affiliation(s)
- Md. Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
- Department of Genetic Engineering and Biotechnology, Bioinformatics and Microbial Biotechnology Laboratory, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Ebrahim Khalil Shimul
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
- Department of Genetic Engineering and Biotechnology, Bioinformatics and Microbial Biotechnology Laboratory, Jashore University of Science and Technology, Jashore, Bangladesh
| | | |
Collapse
|
4
|
Jensen RO, Schulz F, Roux S, Klingeman DM, Mitchell WP, Udwary D, Moraïs S, Reynoso V, Winkler J, Nagaraju S, De Tissera S, Shapiro N, Ivanova N, Reddy TBK, Mizrahi I, Utturkar SM, Bayer EA, Woyke T, Mouncey NJ, Jewett MC, Simpson SD, Köpke M, Jones DT, Brown SD. Phylogenomics and genetic analysis of solvent-producing Clostridium species. Sci Data 2024; 11:432. [PMID: 38693191 PMCID: PMC11063209 DOI: 10.1038/s41597-024-03210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024] Open
Abstract
The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.
Collapse
Affiliation(s)
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | | | | | | | | | - Nicole Shapiro
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Sagar M Utturkar
- Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Edward A Bayer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California Merced, Life and Environmental Sciences, Merced, CA, USA
| | - Nigel J Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | | | - David T Jones
- Department of Microbiology, University of Otago, Dunedin, New Zealand.
| | | |
Collapse
|
5
|
Swaney MH, Henriquez N, Campbell T, Handelsman J, Kalan LR. Skin-associated Corynebacterium amycolatum shares cobamides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.28.591522. [PMID: 38712214 PMCID: PMC11071462 DOI: 10.1101/2024.04.28.591522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The underlying interactions that occur to maintain skin microbiome composition, function, and overall skin health are largely unknown. Often, these types of interactions are mediated by microbial metabolites. Cobamides, the vitamin B12 family of cofactors, are essential for metabolism in many bacteria, but are only synthesized by a small fraction of prokaryotes, including certain skin-associated species. Therefore, we hypothesize that cobamide sharing mediates skin community dynamics. Preliminary work predicts that several skin-associated Corynebacterium species encode de novo cobamide biosynthesis and that their abundance is associated with skin microbiome diversity. Here, we show that commensal Corynebacterium amycolatum produces cobamides and that this synthesis can be tuned by cobalt limitation. To demonstrate cobamide sharing by C. amycolatum, we employed a co-culture assay using an E. coli cobamide auxotroph and show that C. amycolatum produces sufficient cobamides to support E. coli growth, both in liquid co-culture and when separated spatially on solid medium. We also generated a C. amycolatum non-cobamide-producing strain (cob-) using UV mutagenesis that contains mutated cobamide biosynthesis genes cobK and cobO and confirm that disruption of cobamide biosynthesis abolishes support of E. coli growth through cobamide sharing. Our study provides a unique model to study metabolite sharing by microorganisms, which will be critical for understanding the fundamental interactions that occur within complex microbiomes and for developing approaches to target the human microbiota for health advances.
Collapse
Affiliation(s)
- M H Swaney
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI, USA
| | - N Henriquez
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
| | - T Campbell
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
| | - J Handelsman
- Wisconsin Institute for Discovery, Madison, WI, USA
- Department of Plant Pathology, University of Wisconsin, Madison, WI, USA
| | - L R Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, CAN
- David Braley Centre for Antibiotic Discovery, Hamilton, ON, CAN
| |
Collapse
|
6
|
Ahmed N, Joglekar P, Deming C, Lemon KP, Kong HH, Segre JA, Conlan S. Genomic characterization of the C. tuberculostearicum species complex, a prominent member of the human skin microbiome. mSystems 2023; 8:e0063223. [PMID: 38126779 PMCID: PMC10790575 DOI: 10.1128/msystems.00632-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/05/2023] [Indexed: 12/23/2023] Open
Abstract
IMPORTANCE Amplicon sequencing data combined with isolate whole genome sequencing have expanded our understanding of Corynebacterium on the skin. Healthy human skin is colonized by a diverse collection of Corynebacterium species, but Corynebacterium tuberculostearicum predominates on many skin sites. Our work supports the emerging idea that C. tuberculostearicum is a species complex encompassing several distinct species. We produced a collection of genomes that help define this complex, including a potentially new species we term Corynebacterium hallux based on a preference for sites on the feet, whole-genome average nucleotide identity, pangenomic analysis, and growth in skin-like media. This isolate collection and high-quality genome resource set the stage for developing engineered strains for both basic and translational clinical studies.
Collapse
Affiliation(s)
- Nashwa Ahmed
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Payal Joglekar
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Clayton Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - NISC Comparative Sequencing ProgramBarnabasBeatrice B.BlackSeanBouffardGerard G.BrooksShelise Y.CrawfordJuyunMarfaniHollyDekhtyarLyudmilaHanJoelHoShi-LingLegaspiRichelleMaduroQuino L.MasielloCatherine A.McDowellJennifer C.MontemayorCasandraMullikinJames C.ParkMorganRiebowNancy L.SchandlerKarenSchmidtBrianSisonChristinaStantripopSirintornThomasJames W.ThomasPamela J.VemulapalliMeghanaYoungAlice C.
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Division of Infectious Diseases, Texas Children’s Hospital, Baylor College of Medicine, Houston, Texas, USA
- Cutaneous Microbiome and Inflammation Section, NIAMS, NIH, Bethesda, Maryland, USA
| | - Katherine P. Lemon
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Division of Infectious Diseases, Texas Children’s Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - Heidi H. Kong
- Cutaneous Microbiome and Inflammation Section, NIAMS, NIH, Bethesda, Maryland, USA
| | - Julie A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| |
Collapse
|
7
|
Siems K, Runzheimer K, Rebrosova K, Etzbach L, Auerhammer A, Rehm A, Schwengers O, Šiler M, Samek O, Růžička F, Moeller R. Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis. Front Microbiol 2023; 14:1272734. [PMID: 37840735 PMCID: PMC10570620 DOI: 10.3389/fmicb.2023.1272734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction Staphylococcus capitis naturally colonizes the human skin but as an opportunistic pathogen, it can also cause biofilm-associated infections and bloodstream infections in newborns. Previously, we found that two strains from the subspecies S. capitis subsp. capitis produce yellow carotenoids despite the initial species description, reporting this subspecies as non-pigmented. In Staphylococcus aureus, the golden pigment staphyloxanthin is an important virulence factor, protecting cells against reactive oxygen species and modulating membrane fluidity. Methods In this study, we used two pigmented (DSM 111179 and DSM 113836) and two non-pigmented S. capitis subsp. capitis strains (DSM 20326T and DSM 31028) to identify the pigment, determine conditions under which pigment-production occurs and investigate whether pigmented strains show increased resistance to ROS and temperature stress. Results We found that the non-pigmented strains remained colorless regardless of the type of medium, whereas intensity of pigmentation in the two pigmented strains increased under low nutrient conditions and with longer incubation times. We were able to detect and identify staphyloxanthin and its derivates in the two pigmented strains but found that methanol cell extracts from all four strains showed ROS scavenging activity regardless of staphyloxanthin production. Increased survival to cold temperatures (-20°C) was detected in the two pigmented strains only after long-term storage compared to the non-pigmented strains. Conclusion The identification of staphyloxanthin in S. capitis is of clinical relevance and could be used, in the same way as in S. aureus, as a possible target for anti-virulence drug design.
Collapse
Affiliation(s)
- Katharina Siems
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Katharina Runzheimer
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Katarina Rebrosova
- Department of Microbiology, Faculty of Medicine, Masaryk University and St. Anne’s University Hospital, Brno, Czechia
| | - Lara Etzbach
- Institute of Nutritional and Food Sciences, Food Sciences, University of Bonn, Bonn, Germany
| | - Alina Auerhammer
- Institute of Nutritional and Food Sciences, Food Sciences, University of Bonn, Bonn, Germany
| | - Anna Rehm
- Department of Algorithmic Bioinformatics, Justus Liebig University Giessen, Giessen, Germany
| | - Oliver Schwengers
- Department of Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Martin Šiler
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Filip Růžička
- Department of Microbiology, Faculty of Medicine, Masaryk University and St. Anne’s University Hospital, Brno, Czechia
| | - Ralf Moeller
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| |
Collapse
|
8
|
Salamzade R, Tran P, Martin C, Manson AL, Gilmore MS, Earl AM, Anantharaman K, Kalan LR. zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544063. [PMID: 37333121 PMCID: PMC10274777 DOI: 10.1101/2023.06.07.544063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements (MGEs), such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous or homologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of protein-encoding ortholog groups for individual genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of statistics for each inferred ortholog group. These programs are showcased through application to: (i) longitudinal tracking of a virus in metagenomes, (ii) discovering novel population-genetic insights of two common BGCs in a fungal species, and (iii) uncovering large-scale evolutionary trends of a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.
Collapse
Affiliation(s)
- Rauf Salamzade
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Patricia Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Freshwater and Marine Science Doctoral Program, University of Wisconsin-Madison, WI, USA
| | - Cody Martin
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Abigail L. Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S. Gilmore
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
9
|
Tran TH, Roberts AQ, Escapa IF, Gao W, Segre JA, Kong HH, Conlan S, Kelly MS, Lemon KP. Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543719. [PMID: 37333201 PMCID: PMC10274666 DOI: 10.1101/2023.06.05.543719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. Based on the prevalence of these species, at least two likely coexist in the nasal microbiota of 82% of adults. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the functional protein repertoire and metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the U.S. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution across Africa and North America. All four species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent (core) compared to the accessory genome of each species indicating limited strain-level variability in metabolic capacity. Moreover, core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in the Botswanan clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.
Collapse
Affiliation(s)
- Tommy H. Tran
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ari Q. Roberts
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Isabel F. Escapa
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Julie A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Katherine P. Lemon
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|