Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life
The default removal of low-abundance (rare) taxa from microbial community analyses may lead to an incomplete picture of the taxonomic and functional microbial potential within the human habitat. Publicly available shotgun metagenomics data of healthy children and children with cystic fibrosis (CF) w...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S200103702100516X |
| _version_ | 1797978309576884224 |
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| author | Marie-Madlen Pust Burkhard Tümmler |
| author_facet | Marie-Madlen Pust Burkhard Tümmler |
| author_sort | Marie-Madlen Pust |
| collection | DOAJ |
| description | The default removal of low-abundance (rare) taxa from microbial community analyses may lead to an incomplete picture of the taxonomic and functional microbial potential within the human habitat. Publicly available shotgun metagenomics data of healthy children and children with cystic fibrosis (CF) were reanalysed to study the development of the rare species biosphere, which was here defined by either the 15th, 25th or 35th species abundance percentile. We found that healthy children contained an age-independent network of abundant (core) and rare species with both entities being essential in maintaining the network structure. The protein sequence usage for more than 100 bacterial metabolic pathways differed between the core and rare species biosphere. In CF children, the background structure was underdeveloped and random forest bootstrapping based on all constituents of the early airway metagenome and host-associated factors indicated that rare taxa were the most important variables in deciding whether a child was healthy or suffered from the life-limiting CF disease. Attempts failed to make the age-independent CF network as robust as the healthy structure when an increasing number of bacterial taxa from the healthy network was incorporated into the CF structure by computer-based model simulations. However, the transfer of a key combination of taxa from the healthy to the CF network structure with high species diversity and low species dominance, correlated with a more robust CF network and a topological approximation of CF and healthy graph structures. Rothia mucilaginosa, Streptococci and rare species were essential in improving the underdeveloped CF network. |
| first_indexed | 2024-04-11T05:20:35Z |
| format | Article |
| id | doaj.art-b5131196a4a5473792fa34162fd4b26a |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:20:35Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-b5131196a4a5473792fa34162fd4b26a2022-12-24T04:50:54ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-0120175186Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human lifeMarie-Madlen Pust0Burkhard Tümmler1Department of Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, GermanyCorresponding author at: Department of Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany.; Department of Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, GermanyThe default removal of low-abundance (rare) taxa from microbial community analyses may lead to an incomplete picture of the taxonomic and functional microbial potential within the human habitat. Publicly available shotgun metagenomics data of healthy children and children with cystic fibrosis (CF) were reanalysed to study the development of the rare species biosphere, which was here defined by either the 15th, 25th or 35th species abundance percentile. We found that healthy children contained an age-independent network of abundant (core) and rare species with both entities being essential in maintaining the network structure. The protein sequence usage for more than 100 bacterial metabolic pathways differed between the core and rare species biosphere. In CF children, the background structure was underdeveloped and random forest bootstrapping based on all constituents of the early airway metagenome and host-associated factors indicated that rare taxa were the most important variables in deciding whether a child was healthy or suffered from the life-limiting CF disease. Attempts failed to make the age-independent CF network as robust as the healthy structure when an increasing number of bacterial taxa from the healthy network was incorporated into the CF structure by computer-based model simulations. However, the transfer of a key combination of taxa from the healthy to the CF network structure with high species diversity and low species dominance, correlated with a more robust CF network and a topological approximation of CF and healthy graph structures. Rothia mucilaginosa, Streptococci and rare species were essential in improving the underdeveloped CF network.http://www.sciencedirect.com/science/article/pii/S200103702100516XHuman airway metagenomeRare speciesGraph kernelsRandom forestMicrobiome development |
| spellingShingle | Marie-Madlen Pust Burkhard Tümmler Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life Computational and Structural Biotechnology Journal Human airway metagenome Rare species Graph kernels Random forest Microbiome development |
| title | Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life |
| title_full | Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life |
| title_fullStr | Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life |
| title_full_unstemmed | Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life |
| title_short | Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life |
| title_sort | bacterial low abundant taxa are key determinants of a healthy airway metagenome in the early years of human life |
| topic | Human airway metagenome Rare species Graph kernels Random forest Microbiome development |
| url | http://www.sciencedirect.com/science/article/pii/S200103702100516X |
| work_keys_str_mv | AT mariemadlenpust bacteriallowabundanttaxaarekeydeterminantsofahealthyairwaymetagenomeintheearlyyearsofhumanlife AT burkhardtummler bacteriallowabundanttaxaarekeydeterminantsofahealthyairwaymetagenomeintheearlyyearsofhumanlife |