Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains
ABSTRACT Corynebacterium species, integral to the healthy human upper respiratory tract (URT) microbiota, remain underexplored in microbial genomics for their potential to promote respiratory health and exclude pathobionts. This genomic study investigated the diversity and capacity for natural produ...
Saved in:
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2025-06-01
|
| Series: | mSphere |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msphere.00258-25 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849434686200217600 |
|---|---|
| author | Ashley L. Cunningham Ilya Y. Zhbannikov Rachel Myers Tommy H. Tran Wei Gao Katherine P. Lemon Jhoanna N. Aquino Jillian H. Hurst Joon Won Yoon Patrick C. Seed Matthew S. Kelly |
| author_facet | Ashley L. Cunningham Ilya Y. Zhbannikov Rachel Myers Tommy H. Tran Wei Gao Katherine P. Lemon Jhoanna N. Aquino Jillian H. Hurst Joon Won Yoon Patrick C. Seed Matthew S. Kelly |
| author_sort | Ashley L. Cunningham |
| collection | DOAJ |
| description | ABSTRACT Corynebacterium species, integral to the healthy human upper respiratory tract (URT) microbiota, remain underexplored in microbial genomics for their potential to promote respiratory health and exclude pathobionts. This genomic study investigated the diversity and capacity for natural product synthesis within these species, as indicated by their biosynthetic gene clusters (BGCs). We aimed to map and quantify the BGC diversity in a contemporary collection of Corynebacterium strains, representative of their prevalence in the respiratory microbiota, and to elucidate intra- and interspecies variation in BGC content. The outcomes of this research could reveal key factors in maintaining the ecological balance of the upper respiratory tract and identify novel antimicrobial agents targeting respiratory pathobionts. Employing an in silico approach, we analyzed the biosynthetic potential of respiratory strains of non-diphtheriae Corynebacterium species and their reference genomes through genome sequencing and antiSMASH6 analysis. Among 161 genomes, we identified 672 BGCs, 495 of which were unique, including polyketide synthase, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, and siderophore families. To understand how this biosynthetic capacity compared to other respiratory bacteria, we then downloaded genomes from eight species that are associated with the URT and conducted BGC searches. We found that despite their compact genomes, Corynebacterium species possess a multitude of predicted BGCs, exceeding the diversity of natural product BGCs identified in multiple other respiratory bacteria. This research lays the foundation for future functional genomics studies on the role of Corynebacterium species in the respiratory microbiome and the discovery of novel therapeutics derived from this bacterial genus.IMPORTANCEBacterial secondary metabolites, produced by enzymes encoded by biosynthetic gene clusters, are ecologically important for bacterial communication and competition in nutrient-scarce environments and are a historically rich source of antibiotics and other medications. Human-associated Corynebacterium species, abundant in the healthy upper respiratory tract, are understudied despite evidence of their roles in promoting human health and preventing pathobiont colonization. Through genome mining of a large collection of Corynebacterium strains isolated from the human respiratory tract and publicly available genomes of other respiratory bacteria, our study suggests that Corynebacterium species have a high biosynthetic capacity and are predicted to harbor a wide range of biosynthetic gene cluster families. These findings substantially expand current knowledge regarding the production of secondary metabolites by human-associated Corynebacterium species. Our study also lays the foundations for understanding how Corynebacterium species interact in the healthy human upper respiratory tract and the potential for discovering novel biotherapeutics. |
| format | Article |
| id | doaj-art-6a7e9bb5ea3b4e6f8b81011f0d5a445f |
| institution | Kabale University |
| issn | 2379-5042 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSphere |
| spelling | doaj-art-6a7e9bb5ea3b4e6f8b81011f0d5a445f2025-08-20T03:26:33ZengAmerican Society for MicrobiologymSphere2379-50422025-06-0110610.1128/msphere.00258-25Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strainsAshley L. Cunningham0Ilya Y. Zhbannikov1Rachel Myers2Tommy H. Tran3Wei Gao4Katherine P. Lemon5Jhoanna N. Aquino6Jillian H. Hurst7Joon Won Yoon8Patrick C. Seed9Matthew S. Kelly10Department of Pediatrics, Northwestern University, Chicago, Illinois, USADepartment of Medicine Clinical Research Unit, Duke University, Durham, North Carolina, USADepartment of Medicine Clinical Research Unit, Duke University, Durham, North Carolina, USAAlkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USAThe Forsyth Institute (Microbiology), Cambridge, Massachusetts, USAAlkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USADivision of Pediatric Infectious Diseases, Duke University, Durham, North Carolina, USADivision of Pediatric Infectious Diseases, Duke University, Durham, North Carolina, USADepartment of Pediatrics, Northwestern University, Chicago, Illinois, USADepartment of Pediatrics, Northwestern University, Chicago, Illinois, USADivision of Pediatric Infectious Diseases, Duke University, Durham, North Carolina, USAABSTRACT Corynebacterium species, integral to the healthy human upper respiratory tract (URT) microbiota, remain underexplored in microbial genomics for their potential to promote respiratory health and exclude pathobionts. This genomic study investigated the diversity and capacity for natural product synthesis within these species, as indicated by their biosynthetic gene clusters (BGCs). We aimed to map and quantify the BGC diversity in a contemporary collection of Corynebacterium strains, representative of their prevalence in the respiratory microbiota, and to elucidate intra- and interspecies variation in BGC content. The outcomes of this research could reveal key factors in maintaining the ecological balance of the upper respiratory tract and identify novel antimicrobial agents targeting respiratory pathobionts. Employing an in silico approach, we analyzed the biosynthetic potential of respiratory strains of non-diphtheriae Corynebacterium species and their reference genomes through genome sequencing and antiSMASH6 analysis. Among 161 genomes, we identified 672 BGCs, 495 of which were unique, including polyketide synthase, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, and siderophore families. To understand how this biosynthetic capacity compared to other respiratory bacteria, we then downloaded genomes from eight species that are associated with the URT and conducted BGC searches. We found that despite their compact genomes, Corynebacterium species possess a multitude of predicted BGCs, exceeding the diversity of natural product BGCs identified in multiple other respiratory bacteria. This research lays the foundation for future functional genomics studies on the role of Corynebacterium species in the respiratory microbiome and the discovery of novel therapeutics derived from this bacterial genus.IMPORTANCEBacterial secondary metabolites, produced by enzymes encoded by biosynthetic gene clusters, are ecologically important for bacterial communication and competition in nutrient-scarce environments and are a historically rich source of antibiotics and other medications. Human-associated Corynebacterium species, abundant in the healthy upper respiratory tract, are understudied despite evidence of their roles in promoting human health and preventing pathobiont colonization. Through genome mining of a large collection of Corynebacterium strains isolated from the human respiratory tract and publicly available genomes of other respiratory bacteria, our study suggests that Corynebacterium species have a high biosynthetic capacity and are predicted to harbor a wide range of biosynthetic gene cluster families. These findings substantially expand current knowledge regarding the production of secondary metabolites by human-associated Corynebacterium species. Our study also lays the foundations for understanding how Corynebacterium species interact in the healthy human upper respiratory tract and the potential for discovering novel biotherapeutics.https://journals.asm.org/doi/10.1128/msphere.00258-25upper respiratory tractbacteriocinswhole-genome sequencinghuman microbiotamicrobiomebiosynthetic gene clusters |
| spellingShingle | Ashley L. Cunningham Ilya Y. Zhbannikov Rachel Myers Tommy H. Tran Wei Gao Katherine P. Lemon Jhoanna N. Aquino Jillian H. Hurst Joon Won Yoon Patrick C. Seed Matthew S. Kelly Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains mSphere upper respiratory tract bacteriocins whole-genome sequencing human microbiota microbiome biosynthetic gene clusters |
| title | Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains |
| title_full | Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains |
| title_fullStr | Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains |
| title_full_unstemmed | Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains |
| title_short | Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains |
| title_sort | genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory corynebacterium strains |
| topic | upper respiratory tract bacteriocins whole-genome sequencing human microbiota microbiome biosynthetic gene clusters |
| url | https://journals.asm.org/doi/10.1128/msphere.00258-25 |
| work_keys_str_mv | AT ashleylcunningham genomeminingidentifiesadiversityofnaturalproductbiosyntheticcapacityinhumanrespiratorycorynebacteriumstrains AT ilyayzhbannikov genomeminingidentifiesadiversityofnaturalproductbiosyntheticcapacityinhumanrespiratorycorynebacteriumstrains AT rachelmyers genomeminingidentifiesadiversityofnaturalproductbiosyntheticcapacityinhumanrespiratorycorynebacteriumstrains AT tommyhtran genomeminingidentifiesadiversityofnaturalproductbiosyntheticcapacityinhumanrespiratorycorynebacteriumstrains AT weigao genomeminingidentifiesadiversityofnaturalproductbiosyntheticcapacityinhumanrespiratorycorynebacteriumstrains AT katherineplemon genomeminingidentifiesadiversityofnaturalproductbiosyntheticcapacityinhumanrespiratorycorynebacteriumstrains AT jhoannanaquino genomeminingidentifiesadiversityofnaturalproductbiosyntheticcapacityinhumanrespiratorycorynebacteriumstrains AT jillianhhurst genomeminingidentifiesadiversityofnaturalproductbiosyntheticcapacityinhumanrespiratorycorynebacteriumstrains AT joonwonyoon genomeminingidentifiesadiversityofnaturalproductbiosyntheticcapacityinhumanrespiratorycorynebacteriumstrains AT patrickcseed genomeminingidentifiesadiversityofnaturalproductbiosyntheticcapacityinhumanrespiratorycorynebacteriumstrains AT matthewskelly genomeminingidentifiesadiversityofnaturalproductbiosyntheticcapacityinhumanrespiratorycorynebacteriumstrains |