LorDist: a novel method for calculating the distance based on functional data analysis with application to longitudinal microbial data
ABSTRACT Longitudinal human microbial data offer insights into microbiome dynamics over time. Traditional methods usually overlook temporal relationships among samples from the same subject. Here, we presented the Longitudinal Microbial Data Distance (LorDist) method, which uses functional data fitt...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2025-08-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01542-25 |
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| author | Xinhe Qi Menghan Zhang Tongqing Wei Jinran Lin Xingming Zhao Yin Yao Yueqing Hu Yan Zheng |
| author_facet | Xinhe Qi Menghan Zhang Tongqing Wei Jinran Lin Xingming Zhao Yin Yao Yueqing Hu Yan Zheng |
| author_sort | Xinhe Qi |
| collection | DOAJ |
| description | ABSTRACT Longitudinal human microbial data offer insights into microbiome dynamics over time. Traditional methods usually overlook temporal relationships among samples from the same subject. Here, we presented the Longitudinal Microbial Data Distance (LorDist) method, which uses functional data fitting to construct a distance matrix integrating information from the same subject at different time points. Simulation data showed that LorDist handled well up to 60% sparseness and worked robustly with various sequencing depths and time points. Empirical data analysis demonstrated that LorDist excels in capturing differences across subjects with longitudinal microbiome data. LorDist presented the potential of longitudinal microbial data in addressing temporal autocorrelation and distinguishing phenotypes.IMPORTANCELongitudinal analysis of the human microbiome is critical for understanding its dynamic role in health and disease. However, current analytical approaches struggle to address key challenges, such as data sparsity and irregular sampling, inherent to time-series microbiome studies. Here, we developed longitudinal microbial data distance (LorDist), an innovative method leveraging functional data analysis to model temporal microbial dynamics with enhanced precision. Compared to existing methods, LorDist consistently outperforms in discerning biologically meaningful group differences, even in highly sparse data sets or under fluctuating sequencing depths. Our findings demonstrate LorDist’s robust performance on real-world data sets involving inflammatory bowel disease and infant gut development. By explicitly preserving the temporal structure inherent in microbiome data, LorDist enables robust detection of subtle yet critical biological shifts, paving the way for improved diagnostics and personalized therapeutic strategies in microbiome science. |
| format | Article |
| id | doaj-art-9f3e2dd2292e42b4994c5fa39824ddd6 |
| institution | Kabale University |
| issn | 2165-0497 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj-art-9f3e2dd2292e42b4994c5fa39824ddd62025-08-20T03:44:01ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972025-08-0113810.1128/spectrum.01542-25LorDist: a novel method for calculating the distance based on functional data analysis with application to longitudinal microbial dataXinhe Qi0Menghan Zhang1Tongqing Wei2Jinran Lin3Xingming Zhao4Yin Yao5Yueqing Hu6Yan Zheng7State Key Laboratory of Genetics and Development of Complex Phenotypes, Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, Center for Evolutionary Biology, Fudan University, Shanghai, ChinaState Key Laboratory of Genetics and Development of Complex Phenotypes, Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, Center for Evolutionary Biology, Fudan University, Shanghai, ChinaSchool of Life Sciences, Fudan University, Shanghai, ChinaState Key Laboratory of Genetics and Development of Complex Phenotypes, Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, Center for Evolutionary Biology, Fudan University, Shanghai, ChinaResearch Institute of Intelligent Complex Systems, Fudan University, Shanghai, ChinaState Key Laboratory of Genetics and Development of Complex Phenotypes, Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, Center for Evolutionary Biology, Fudan University, Shanghai, ChinaState Key Laboratory of Genetics and Development of Complex Phenotypes, Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, Center for Evolutionary Biology, Fudan University, Shanghai, ChinaState Key Laboratory of Genetics and Development of Complex Phenotypes, Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, Center for Evolutionary Biology, Fudan University, Shanghai, ChinaABSTRACT Longitudinal human microbial data offer insights into microbiome dynamics over time. Traditional methods usually overlook temporal relationships among samples from the same subject. Here, we presented the Longitudinal Microbial Data Distance (LorDist) method, which uses functional data fitting to construct a distance matrix integrating information from the same subject at different time points. Simulation data showed that LorDist handled well up to 60% sparseness and worked robustly with various sequencing depths and time points. Empirical data analysis demonstrated that LorDist excels in capturing differences across subjects with longitudinal microbiome data. LorDist presented the potential of longitudinal microbial data in addressing temporal autocorrelation and distinguishing phenotypes.IMPORTANCELongitudinal analysis of the human microbiome is critical for understanding its dynamic role in health and disease. However, current analytical approaches struggle to address key challenges, such as data sparsity and irregular sampling, inherent to time-series microbiome studies. Here, we developed longitudinal microbial data distance (LorDist), an innovative method leveraging functional data analysis to model temporal microbial dynamics with enhanced precision. Compared to existing methods, LorDist consistently outperforms in discerning biologically meaningful group differences, even in highly sparse data sets or under fluctuating sequencing depths. Our findings demonstrate LorDist’s robust performance on real-world data sets involving inflammatory bowel disease and infant gut development. By explicitly preserving the temporal structure inherent in microbiome data, LorDist enables robust detection of subtle yet critical biological shifts, paving the way for improved diagnostics and personalized therapeutic strategies in microbiome science.https://journals.asm.org/doi/10.1128/spectrum.01542-25longitudinal microbial datafunctional data analysissparse data |
| spellingShingle | Xinhe Qi Menghan Zhang Tongqing Wei Jinran Lin Xingming Zhao Yin Yao Yueqing Hu Yan Zheng LorDist: a novel method for calculating the distance based on functional data analysis with application to longitudinal microbial data Microbiology Spectrum longitudinal microbial data functional data analysis sparse data |
| title | LorDist: a novel method for calculating the distance based on functional data analysis with application to longitudinal microbial data |
| title_full | LorDist: a novel method for calculating the distance based on functional data analysis with application to longitudinal microbial data |
| title_fullStr | LorDist: a novel method for calculating the distance based on functional data analysis with application to longitudinal microbial data |
| title_full_unstemmed | LorDist: a novel method for calculating the distance based on functional data analysis with application to longitudinal microbial data |
| title_short | LorDist: a novel method for calculating the distance based on functional data analysis with application to longitudinal microbial data |
| title_sort | lordist a novel method for calculating the distance based on functional data analysis with application to longitudinal microbial data |
| topic | longitudinal microbial data functional data analysis sparse data |
| url | https://journals.asm.org/doi/10.1128/spectrum.01542-25 |
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