Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.

Autor: Tong X; Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, People's Republic of China.; School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China., Luo D; School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China., Leung MHY; School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China., Lee JYY; School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China., Shen Z; School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China., Jiang W; Department of Applied Mathematics, School of Mathematics and Physics, Xi'an Jiaotong-Liverpool University, Suzhou, People's Republic of China., Mason CE; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA., Lee PKH; School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China. patrick.kh.lee@cityu.edu.hk.; Low-Carbon and Climate Impact Research Centre, City University of Hong Kong, Hong Kong SAR, China. patrick.kh.lee@cityu.edu.hk.
Jazyk: angličtina
Zdroj: Microbiome [Microbiome] 2024 Oct 17; Vol. 12 (1), pp. 198. Date of Electronic Publication: 2024 Oct 17.
DOI: 10.1186/s40168-024-01926-6
Abstrakt: Background: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.
Results: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.
Conclusions: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.
(© 2024. The Author(s).)
Databáze: MEDLINE
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