Investigating the gut bacteria structure and function of hibernating bats through 16S rRNA high-throughput sequencing and culturomics
ABSTRACT The gut microbiota of bats is vital for their roles in health and the ecosystem, yet studies on hibernating bats in southwest China, particularly in the unique karst landscape of Guizhou, are limited. We captured three hibernating bat species—Pipistrellus (PB), Rhinolophus (RB), and Myotis...
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| Language: | English |
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American Society for Microbiology
2025-05-01
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| Series: | mSystems |
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| Online Access: | https://journals.asm.org/doi/10.1128/msystems.01463-24 |
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| author | Jian Zhou Ying Liu Tao Gu Jingzhu Zhou Fengming Chen Shijun Li |
| author_facet | Jian Zhou Ying Liu Tao Gu Jingzhu Zhou Fengming Chen Shijun Li |
| author_sort | Jian Zhou |
| collection | DOAJ |
| description | ABSTRACT The gut microbiota of bats is vital for their roles in health and the ecosystem, yet studies on hibernating bats in southwest China, particularly in the unique karst landscape of Guizhou, are limited. We captured three hibernating bat species—Pipistrellus (PB), Rhinolophus (RB), and Myotis (MB)—in Liping County, collecting rectal samples for 16S rRNA amplicon sequencing. Data processing involved Trimmomatic, Flash, and Qiime2 for operational taxonomic unit (OTU) standardization and species annotation via the Greengenes database. Differential abundance was analyzed using LEfSe, and diversity metrics were assessed through alpha and beta diversity analyses. The RB group was predominantly composed of Proteobacteria (80.99%), while MB and PB exhibited diverse compositions with significant OTU richness (729 in MB). Notable genera included Hafnia and Yersinia in RB and Cosenzaea myxofaciens in MB. High proportions of unclassified taxa were observed, particularly in RB (83.81%). Functional predictions indicated metabolic pathways, with a significant representation of human diseases in PB. Culturomics revealed the successful cultivation of Huaxiibacter chinensis and Enterobacter chengduensis from bats for the first time and appears to have identified a new bacterium that is likely closely related to Clostridium paraputrificum.IMPORTANCEOur research reveals significant differences in the composition and diversity of the gut microbiota among three bat groups (PB, MB, and RB) from Guizhou. While Proteobacteria predominates in all groups, its abundance varies. Notably, the high richness of operational taxonomic units (OTUs) in the MB group suggests a more diverse microbial ecosystem, underscoring the complex interactions between species diversity, diet, gut microbiota, and overall ecological dynamics in bats. Furthermore, the substantial presence of unknown bacterial species in their intestines highlights the critical importance of cultivation-based approaches. The presence of specific taxa may have potential health implications for both bats and humans. These findings emphasize the need for further investigations into the functional roles of these microbiota and their contributions to host health. Future research should focus on longitudinal studies to elucidate these intricate interactions. |
| format | Article |
| id | doaj-art-e4818d91128246a691ea4f9ebe87bbc3 |
| institution | OA Journals |
| issn | 2379-5077 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj-art-e4818d91128246a691ea4f9ebe87bbc32025-08-20T01:52:31ZengAmerican Society for MicrobiologymSystems2379-50772025-05-0110510.1128/msystems.01463-24Investigating the gut bacteria structure and function of hibernating bats through 16S rRNA high-throughput sequencing and culturomicsJian Zhou0Ying Liu1Tao Gu2Jingzhu Zhou3Fengming Chen4Shijun Li5School of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou, ChinaGuizhou Center for Disease Control and Prevention, Guiyang, Key Laboratory of Microbio and Infectious Disease Prevention and Control in Guizhou Province, Guiyang, Guizhou, ChinaSchool of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou, ChinaGuizhou Center for Disease Control and Prevention, Guiyang, Key Laboratory of Microbio and Infectious Disease Prevention and Control in Guizhou Province, Guiyang, Guizhou, ChinaGuizhou Center for Disease Control and Prevention, Guiyang, Key Laboratory of Microbio and Infectious Disease Prevention and Control in Guizhou Province, Guiyang, Guizhou, ChinaSchool of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou, ChinaABSTRACT The gut microbiota of bats is vital for their roles in health and the ecosystem, yet studies on hibernating bats in southwest China, particularly in the unique karst landscape of Guizhou, are limited. We captured three hibernating bat species—Pipistrellus (PB), Rhinolophus (RB), and Myotis (MB)—in Liping County, collecting rectal samples for 16S rRNA amplicon sequencing. Data processing involved Trimmomatic, Flash, and Qiime2 for operational taxonomic unit (OTU) standardization and species annotation via the Greengenes database. Differential abundance was analyzed using LEfSe, and diversity metrics were assessed through alpha and beta diversity analyses. The RB group was predominantly composed of Proteobacteria (80.99%), while MB and PB exhibited diverse compositions with significant OTU richness (729 in MB). Notable genera included Hafnia and Yersinia in RB and Cosenzaea myxofaciens in MB. High proportions of unclassified taxa were observed, particularly in RB (83.81%). Functional predictions indicated metabolic pathways, with a significant representation of human diseases in PB. Culturomics revealed the successful cultivation of Huaxiibacter chinensis and Enterobacter chengduensis from bats for the first time and appears to have identified a new bacterium that is likely closely related to Clostridium paraputrificum.IMPORTANCEOur research reveals significant differences in the composition and diversity of the gut microbiota among three bat groups (PB, MB, and RB) from Guizhou. While Proteobacteria predominates in all groups, its abundance varies. Notably, the high richness of operational taxonomic units (OTUs) in the MB group suggests a more diverse microbial ecosystem, underscoring the complex interactions between species diversity, diet, gut microbiota, and overall ecological dynamics in bats. Furthermore, the substantial presence of unknown bacterial species in their intestines highlights the critical importance of cultivation-based approaches. The presence of specific taxa may have potential health implications for both bats and humans. These findings emphasize the need for further investigations into the functional roles of these microbiota and their contributions to host health. Future research should focus on longitudinal studies to elucidate these intricate interactions.https://journals.asm.org/doi/10.1128/msystems.01463-24hibernating batsgut bacteriahigh-throughput sequencingculturomics16S rRNA |
| spellingShingle | Jian Zhou Ying Liu Tao Gu Jingzhu Zhou Fengming Chen Shijun Li Investigating the gut bacteria structure and function of hibernating bats through 16S rRNA high-throughput sequencing and culturomics mSystems hibernating bats gut bacteria high-throughput sequencing culturomics 16S rRNA |
| title | Investigating the gut bacteria structure and function of hibernating bats through 16S rRNA high-throughput sequencing and culturomics |
| title_full | Investigating the gut bacteria structure and function of hibernating bats through 16S rRNA high-throughput sequencing and culturomics |
| title_fullStr | Investigating the gut bacteria structure and function of hibernating bats through 16S rRNA high-throughput sequencing and culturomics |
| title_full_unstemmed | Investigating the gut bacteria structure and function of hibernating bats through 16S rRNA high-throughput sequencing and culturomics |
| title_short | Investigating the gut bacteria structure and function of hibernating bats through 16S rRNA high-throughput sequencing and culturomics |
| title_sort | investigating the gut bacteria structure and function of hibernating bats through 16s rrna high throughput sequencing and culturomics |
| topic | hibernating bats gut bacteria high-throughput sequencing culturomics 16S rRNA |
| url | https://journals.asm.org/doi/10.1128/msystems.01463-24 |
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