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Salinity Drives Functional and Taxonomic Diversities in Global Water Metagenomes

ABSTRACT: A tight association between microbial function and taxonomy is the basis of functional prediction based on taxonomy, but such associations have been controversial in water biomes largely due to the probable prevalence of functional redundancy. However, previous studies on this topic used a relatively coarse resolution of ecosystem functioning, potentially inflating the estimated functional redundancy. Thus, a comprehensive evaluation of the association between high-resolution functional traits and taxonomic diversity obtained from fresh and saline water metagenomic data is urgently needed. Here, we examined 938 functionally and taxonomically annotated water metagenomes obtained worldwide to scrutinize the connection between function and taxonomy, and to identify the key driver of water metagenomes function or taxonomic composition at a global scale. We found that pairwise similarity of function was significantly associated with taxonomy, though taxonomy had higher global dissimilarity than function. Classification into six water biomes resulted in greater variation in taxonomic compositions than functional profiles, as the key regulating factor was salinity. Fresh water microbes harbored distinct functional and taxonomic structures from microbes in saline water biomes, despite that taxonomy was more susceptible to gradient of geography and climate than function. In summary, our results find a significant relationship between taxonomic diversity and microbial functioning in global water metagenomes, although microbial taxonomic compositions vary to a larger extent than functional profiles in aquatic ecosystems, suggesting the possibility and necessity for functional prediction of microorganisms based on taxonomy in global aquatic ecosystems.

SUBMITTER: Chen H

PROVIDER: S-EPMC8591284 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:ObjectivesThis study aimed to identify colorectal cancer (CRC)-associated phylogenetic and functional bacterial features by a large-scale metagenomic sequencing and develop a binomial classifier to accurately distinguish between CRC patients and healthy individuals.MethodsWe conducted shotgun metagenomic analyses of fecal samples from a ZhongShanMed discovery cohort of 121 CRC and 52 controls and SouthernMed validation cohort of 67 CRC and 44 controls. Taxonomic profiling and quantification were performed by direct sequence alignment against genome taxonomy database (GTDB). High-quality reads were also aligned to IGC datasets to obtain functional profiles defined by Kyoto Encyclopedia of Genes and Genomes (KEGG). A least absolute shrinkage and selection operator (LASSO) classifier was constructed to quantify risk scores of probability of disease and to discriminate CRC from normal for discovery, validation, Fudan, GloriousMed, and HongKong cohorts.ResultsA diverse spectrum of bacterial and fungi species were found to be either enriched (368) or reduced (113) in CRC patients (q<0.05). Similarly, metabolic functions associated with biosynthesis and metabolism of amino acids and fatty acids were significantly altered (q<0.05). The LASSO regression analysis of significant changes in the abundance of microbial species in CRC achieved areas under the receiver operating characteristic curve (AUROCs) of 0.94 and 0.91 in the ZhongShanMed and SouthernMed cohorts, respectively. A further analysis of Fudan, GloriousMed, and HK cohorts using the same classification model also demonstrated AUROC of 0.80, 0.78, and 0.91, respectively. Moreover, major CRC-associated bacterial biomarkers identified in this study were found to be coherently enriched or depleted across 10 metagenomic sequencing studies of gut microbiota.ConclusionA coherent signature of CRC-associated bacterial biomarkers modeled on LASSO binomial classifier maybe used accurately for early detection of CRC.

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Salinity Drives Functional and Taxonomic Diversities in Global Water Metagenomes

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