Department of Chemical Engineering, University of California, Santa Barbara, CA 93106.
Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Proc Natl Acad Sci U S A. 2021 May 4;118(18). doi: 10.1073/pnas.2019855118.
Anaerobic fungi (class Neocallimastigomycetes) thrive as low-abundance members of the herbivore digestive tract. The genomes of anaerobic gut fungi are poorly characterized and have not been extensively mined for the biosynthetic enzymes of natural products such as antibiotics. Here, we investigate the potential of anaerobic gut fungi to synthesize natural products that could regulate membership within the gut microbiome. Complementary 'omics' approaches were combined to catalog the natural products of anaerobic gut fungi from four different representative species: (), (), (), and (). In total, 146 genes were identified that encode biosynthetic enzymes for diverse types of natural products, including nonribosomal peptide synthetases and polyketide synthases. In addition, and genomes encoded seven putative bacteriocins, a class of antimicrobial peptides typically produced by bacteria. During standard laboratory growth on plant biomass or soluble substrates, 26% of total core biosynthetic genes in all four strains were transcribed. Across all four fungal strains, 30% of total biosynthetic gene products were detected via proteomics when grown on cellobiose. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of fungal supernatants detected 72 likely natural products from alone. A compound produced by all four strains of anaerobic fungi was putatively identified as the polyketide-related styrylpyrone baumin. Molecular networking quantified similarities between tandem mass spectrometry (MS/MS) spectra among these fungi, enabling three groups of natural products to be identified that are unique to anaerobic fungi. Overall, these results support the finding that anaerobic gut fungi synthesize natural products, which could be harnessed as a source of antimicrobials, therapeutics, and other bioactive compounds.
厌氧真菌（Neocallimastigomycetes 类）作为食草动物消化道中低丰度的成员而茁壮成长。厌氧肠道真菌的基因组特征较差，尚未广泛挖掘其生物合成酶用于抗生素等天然产物。在这里，我们研究了厌氧肠道真菌合成天然产物的潜力，这些产物可以调节肠道微生物组中的成员。采用互补的“组学”方法，从四个不同代表物种（）、（）、（）和（）中对厌氧肠道真菌的天然产物进行了编目。总共鉴定出 146 个基因，这些基因编码用于各种天然产物的生物合成酶，包括非核糖体肽合成酶和聚酮合酶。此外，和基因组编码了七种假定的细菌素，这是一类通常由细菌产生的抗菌肽。在标准的植物生物质或可溶性基质上的实验室生长过程中，所有四个菌株中总核心生物合成基因的 26%被转录。在所有四个真菌菌株中，当在纤维二糖上生长时，通过蛋白质组学检测到总生物合成基因的 30%。来自 的真菌上清液的液相色谱-串联质谱 (LC-MS/MS) 特征分析检测到 72 种可能的天然产物。从所有四种厌氧真菌菌株中产生的一种化合物被推测为与聚酮相关的 styrylpyrone baumin。分子网络定量了这些真菌之间串联质谱 (MS/MS) 图谱之间的相似性，能够识别出厌氧真菌特有的三组天然产物。总的来说，这些结果支持了厌氧肠道真菌合成天然产物的发现，这些天然产物可以作为抗生素、治疗剂和其他生物活性化合物的来源。
