Genomic characteristics and phylogenetic relationships of Cutibacterium acnes breast milk isolates
Abstract Background Cutibacterium acnes is one of the most commonly found microbes in breast milk. However, little is known about the genomic characteristics of C. acnes isolated from breast milk. In this study, the sequencing and assembly results of 10 C. acnes isolates from breast milk were compar...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-01-01
|
| Series: | BMC Microbiology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12866-024-03717-3 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841544939048009728 |
|---|---|
| author | Jiaqi Sun Guoxuan Hang Huimin Lv Yu Li Qiujie Song Zhi Zhong Zhihong Sun Wenjun Liu |
| author_facet | Jiaqi Sun Guoxuan Hang Huimin Lv Yu Li Qiujie Song Zhi Zhong Zhihong Sun Wenjun Liu |
| author_sort | Jiaqi Sun |
| collection | DOAJ |
| description | Abstract Background Cutibacterium acnes is one of the most commonly found microbes in breast milk. However, little is known about the genomic characteristics of C. acnes isolated from breast milk. In this study, the sequencing and assembly results of 10 C. acnes isolates from breast milk were compared with the genomic data of 454 strains downloaded from NCBI, and the characteristics of breast milk isolates from various perspectives, including phylogeny, genomic characteristics, virulence genes, drug resistance genes, and carbohydrate utilization, were elucidated. Results The findings of this study revealed no differences between the breast milk isolates and other isolates in terms of genomic features, phylogenetic relationships, virulence, and resistance-related genes. However, breast milk-derived isolates exhibited significantly lower copies of the carbohydrate metabolic enzyme genes GT5 and GT51 (P < 0.05) and a higher copy number of the GH31 gene (P < 0.05) than others. C. acnes primarily consists of three genetic branches (A, B, and C), which correspond to the three subspecies of C. acnes (C. acnes subsp. elongatum, C. acnes subsp. defendens, C. acnes subsp. acnes). The genetic differences between branches B and C were smaller than that between branch A. Branches A and B carry a higher number of copies of carbohydrate enzymes, including CE1, CE10, GH3, and CBM32 than branch C. Branches B and C possess the carbohydrate enzymes PL8 and GH23, which are absent in branch A. Core genes, core intergenic regions, and concatenated sequences of core genes and core intergenic regions were compared to construct a phylogenetic tree, and it was found that core intergenic regions could be used to describe phylogenetic relationships. Conclusions It is therefore speculated that the C. acnes in breast milk originates from the nipple or breast surface. This study provides a novel genetic basis for genetic differentiation of C. acnes isolates from breast milk. |
| format | Article |
| id | doaj-art-d798bb86475949a49526b76d7b30a5fe |
| institution | Kabale University |
| issn | 1471-2180 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj-art-d798bb86475949a49526b76d7b30a5fe2025-01-12T12:10:11ZengBMCBMC Microbiology1471-21802025-01-0125111110.1186/s12866-024-03717-3Genomic characteristics and phylogenetic relationships of Cutibacterium acnes breast milk isolatesJiaqi Sun0Guoxuan Hang1Huimin Lv2Yu Li3Qiujie Song4Zhi Zhong5Zhihong Sun6Wenjun Liu7Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural UniversityKey Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural UniversityKey Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural UniversityKey Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural UniversityKey Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural UniversityKey Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural UniversityKey Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural UniversityKey Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural UniversityAbstract Background Cutibacterium acnes is one of the most commonly found microbes in breast milk. However, little is known about the genomic characteristics of C. acnes isolated from breast milk. In this study, the sequencing and assembly results of 10 C. acnes isolates from breast milk were compared with the genomic data of 454 strains downloaded from NCBI, and the characteristics of breast milk isolates from various perspectives, including phylogeny, genomic characteristics, virulence genes, drug resistance genes, and carbohydrate utilization, were elucidated. Results The findings of this study revealed no differences between the breast milk isolates and other isolates in terms of genomic features, phylogenetic relationships, virulence, and resistance-related genes. However, breast milk-derived isolates exhibited significantly lower copies of the carbohydrate metabolic enzyme genes GT5 and GT51 (P < 0.05) and a higher copy number of the GH31 gene (P < 0.05) than others. C. acnes primarily consists of three genetic branches (A, B, and C), which correspond to the three subspecies of C. acnes (C. acnes subsp. elongatum, C. acnes subsp. defendens, C. acnes subsp. acnes). The genetic differences between branches B and C were smaller than that between branch A. Branches A and B carry a higher number of copies of carbohydrate enzymes, including CE1, CE10, GH3, and CBM32 than branch C. Branches B and C possess the carbohydrate enzymes PL8 and GH23, which are absent in branch A. Core genes, core intergenic regions, and concatenated sequences of core genes and core intergenic regions were compared to construct a phylogenetic tree, and it was found that core intergenic regions could be used to describe phylogenetic relationships. Conclusions It is therefore speculated that the C. acnes in breast milk originates from the nipple or breast surface. This study provides a novel genetic basis for genetic differentiation of C. acnes isolates from breast milk.https://doi.org/10.1186/s12866-024-03717-3Cutibacterium acnesGenomicsBreast milkCarbohydrate enzymes |
| spellingShingle | Jiaqi Sun Guoxuan Hang Huimin Lv Yu Li Qiujie Song Zhi Zhong Zhihong Sun Wenjun Liu Genomic characteristics and phylogenetic relationships of Cutibacterium acnes breast milk isolates BMC Microbiology Cutibacterium acnes Genomics Breast milk Carbohydrate enzymes |
| title | Genomic characteristics and phylogenetic relationships of Cutibacterium acnes breast milk isolates |
| title_full | Genomic characteristics and phylogenetic relationships of Cutibacterium acnes breast milk isolates |
| title_fullStr | Genomic characteristics and phylogenetic relationships of Cutibacterium acnes breast milk isolates |
| title_full_unstemmed | Genomic characteristics and phylogenetic relationships of Cutibacterium acnes breast milk isolates |
| title_short | Genomic characteristics and phylogenetic relationships of Cutibacterium acnes breast milk isolates |
| title_sort | genomic characteristics and phylogenetic relationships of cutibacterium acnes breast milk isolates |
| topic | Cutibacterium acnes Genomics Breast milk Carbohydrate enzymes |
| url | https://doi.org/10.1186/s12866-024-03717-3 |
| work_keys_str_mv | AT jiaqisun genomiccharacteristicsandphylogeneticrelationshipsofcutibacteriumacnesbreastmilkisolates AT guoxuanhang genomiccharacteristicsandphylogeneticrelationshipsofcutibacteriumacnesbreastmilkisolates AT huiminlv genomiccharacteristicsandphylogeneticrelationshipsofcutibacteriumacnesbreastmilkisolates AT yuli genomiccharacteristicsandphylogeneticrelationshipsofcutibacteriumacnesbreastmilkisolates AT qiujiesong genomiccharacteristicsandphylogeneticrelationshipsofcutibacteriumacnesbreastmilkisolates AT zhizhong genomiccharacteristicsandphylogeneticrelationshipsofcutibacteriumacnesbreastmilkisolates AT zhihongsun genomiccharacteristicsandphylogeneticrelationshipsofcutibacteriumacnesbreastmilkisolates AT wenjunliu genomiccharacteristicsandphylogeneticrelationshipsofcutibacteriumacnesbreastmilkisolates |