Rahimlou Saleh, Amend Anthony S, James Timothy Y
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA.
Pacific Biosciences Research Center, University of Hawaii at Mānoa, Honolulu, Hawai'i, USA.
mBio. 2025 Jun 11;16(6):e0114225. doi: 10.1128/mbio.01142-25. Epub 2025 May 19.
The fungus is the most prevalent member of the human skin mycobiota, known for its lipid dependence and inability to synthesize long-chain fatty acids. exhibits remarkable niche breadth, inhabiting soils, dust, as well as various marine environments from polar regions to deep-sea vents. The consistent presence of in marine habitats, including those associated with marine animals, suggests that the fungus is able to grow and play a fundamental role in marine ecosystems. In this study, we explored metagenomic sequences from the Sequence Read Archive database to investigate the presence, distribution, and origins of species within marine ecosystems, with the goal of assembling genomes. Using various search methods, we found that up to 10% of the shotgun and amplicon data sets analyzed contained sequences. However, the relative abundance of in each data set was low, and there was a strong correlation between human and sequences in marine environments, consistent with contamination. From the most -rich data sets, we attempted to generate metagenome-assembled genomes. However, contigs together showed low genome completeness levels, with a maximum of 2.2% in a sample. Phylogenetic analysis identified the contigs as closely related to human-associated and , along with and , which were the most prevalent species across all studied environments. Our data suggest that many observations of in the environment are derived from human sources and that widespread contamination confounds the exploration of diversity and ecological role in the marine environment.
is the singular fungus most associated with humans. It colonizes mammalian skin and requires host-derived fatty acids to grow. Widespread sequencing of environmental DNA surprisingly showed that is also ubiquitous outside of mammalian hosts. is frequently found in marine habitats where it is associated with corals, deep sea vents, diatoms, and more. Given its widespread presence, we reasoned that public metagenomic data could be used to assemble a genome sequence of an uncultured marine . However, we found that was ubiquitous but never abundant in marine samples and that the few metagenomes we could assemble were consistent with recent human introduction. We also found that the presence of human DNA in sequencing data sets is strongly correlated with the presence of DNA, and while not ruling out the growth and survival of in marine habitats, they suggest widespread contamination of public data with .
该真菌是人类皮肤微生物群中最普遍的成员，以其对脂质的依赖性和无法合成长链脂肪酸而闻名。它具有显著的生态位广度，栖息于土壤、灰尘以及从极地地区到深海热液喷口的各种海洋环境中。该真菌在包括与海洋动物相关的栖息地在内的海洋生境中持续存在，这表明它能够生长并在海洋生态系统中发挥重要作用。在本研究中，我们探索了序列读取存档数据库中的宏基因组序列，以调查海洋生态系统中该真菌物种的存在、分布和起源，目标是组装该真菌的基因组。使用各种搜索方法，我们发现分析的鸟枪法和扩增子数据集中高达10%包含该真菌的序列。然而，每个数据集中该真菌的相对丰度较低，并且海洋环境中人类和该真菌序列之间存在很强的相关性，这与污染一致。从最丰富的数据集出发，我们试图生成宏基因组组装基因组。然而，这些重叠群共同显示出较低的基因组完整性水平，在一个样本中最高为2.2%。系统发育分析确定这些重叠群与人类相关的该真菌以及其他物种密切相关，这些物种是所有研究环境中最普遍的物种。我们的数据表明，环境中该真菌的许多观察结果都来自人类来源，广泛的污染混淆了对其在海洋环境中的多样性和生态作用的探索。
该真菌是与人类关联最密切的单一真菌。它定殖于哺乳动物皮肤，需要宿主来源的脂肪酸才能生长。环境DNA的广泛测序令人惊讶地表明，该真菌在哺乳动物宿主之外也无处不在。它经常在与珊瑚、深海热液喷口、硅藻等相关的海洋栖息地中被发现。鉴于其广泛存在，我们推断公共宏基因组数据可用于组装未培养的海洋该真菌的基因组序列。然而，我们发现该真菌在海洋样本中无处不在但从不丰富，并且我们能够组装的少数宏基因组与近期人类引入一致。我们还发现测序数据集中人类DNA的存在与该真菌DNA的存在密切相关，虽然不排除该真菌在海洋栖息地中的生长和存活，但它们表明公共数据被该真菌广泛污染。
