The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards
Abstract Background High-throughput sequencing has revolutionized environmental microbiome research, providing both quantitative and qualitative insights into nucleic acid targets in the environment. The resulting microbial composition (community structure) data are essential for environmental analy...
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| Format: | Article |
| Language: | English |
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BMC
2025-01-01
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| Series: | Microbiome |
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| Online Access: | https://doi.org/10.1186/s40168-024-02009-2 |
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| author | Chunxiao Wang Yu Yang Xiaoqing Xu Dou Wang Xianghui Shi Lei Liu Yu Deng Liguan Li Tong Zhang |
| author_facet | Chunxiao Wang Yu Yang Xiaoqing Xu Dou Wang Xianghui Shi Lei Liu Yu Deng Liguan Li Tong Zhang |
| author_sort | Chunxiao Wang |
| collection | DOAJ |
| description | Abstract Background High-throughput sequencing has revolutionized environmental microbiome research, providing both quantitative and qualitative insights into nucleic acid targets in the environment. The resulting microbial composition (community structure) data are essential for environmental analytical microbiology, enabling characterization of community dynamics and assessing microbial pollutants for the development of intervention strategies. However, the relative abundances derived from sequencing impede comparisons across samples and studies. Results This review systematically summarizes various absolute quantification (AQ) methods and their applications to obtain the absolute abundance of microbial cells and genetic elements. By critically comparing the strengths and limitations of AQ methods, we advocate the use of cellular internal standard-based high-throughput sequencing as an appropriate AQ approach for studying environmental microbiome originated from samples of complex matrices and high heterogeneity. To minimize ambiguity and facilitate cross-study comparisons, we outline essential reporting elements for technical considerations, and provide a checklist as a reference for environmental microbiome research. Conclusions In summary, we propose absolute microbiome quantification using cellular internal standards for environmental analytical microbiology, and we anticipate that this approach will greatly benefit future studies. Video Abstract Graphical Abstract |
| format | Article |
| id | doaj-art-72eeb6e5fccb40fd9ff21d28fa3c3ef8 |
| institution | Kabale University |
| issn | 2049-2618 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj-art-72eeb6e5fccb40fd9ff21d28fa3c3ef82025-02-02T12:33:57ZengBMCMicrobiome2049-26182025-01-0113111810.1186/s40168-024-02009-2The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standardsChunxiao Wang0Yu Yang1Xiaoqing Xu2Dou Wang3Xianghui Shi4Lei Liu5Yu Deng6Liguan Li7Tong Zhang8Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong KongAbstract Background High-throughput sequencing has revolutionized environmental microbiome research, providing both quantitative and qualitative insights into nucleic acid targets in the environment. The resulting microbial composition (community structure) data are essential for environmental analytical microbiology, enabling characterization of community dynamics and assessing microbial pollutants for the development of intervention strategies. However, the relative abundances derived from sequencing impede comparisons across samples and studies. Results This review systematically summarizes various absolute quantification (AQ) methods and their applications to obtain the absolute abundance of microbial cells and genetic elements. By critically comparing the strengths and limitations of AQ methods, we advocate the use of cellular internal standard-based high-throughput sequencing as an appropriate AQ approach for studying environmental microbiome originated from samples of complex matrices and high heterogeneity. To minimize ambiguity and facilitate cross-study comparisons, we outline essential reporting elements for technical considerations, and provide a checklist as a reference for environmental microbiome research. Conclusions In summary, we propose absolute microbiome quantification using cellular internal standards for environmental analytical microbiology, and we anticipate that this approach will greatly benefit future studies. Video Abstract Graphical Abstracthttps://doi.org/10.1186/s40168-024-02009-2Absolute quantificationMicrobiomeEnvironmental analytical microbiologyCellular internal standardStandardization |
| spellingShingle | Chunxiao Wang Yu Yang Xiaoqing Xu Dou Wang Xianghui Shi Lei Liu Yu Deng Liguan Li Tong Zhang The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards Microbiome Absolute quantification Microbiome Environmental analytical microbiology Cellular internal standard Standardization |
| title | The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards |
| title_full | The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards |
| title_fullStr | The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards |
| title_full_unstemmed | The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards |
| title_short | The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards |
| title_sort | quest for environmental analytical microbiology absolute quantitative microbiome using cellular internal standards |
| topic | Absolute quantification Microbiome Environmental analytical microbiology Cellular internal standard Standardization |
| url | https://doi.org/10.1186/s40168-024-02009-2 |
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