Becker Daniela, Popp Denny, Bonk Fabian, Kleinsteuber Sabine, Harms Hauke, Centler Florian
UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr 15, 04318 Leipzig, Germany.
IAV GmbH, Kauffahrtei 23-25, 09120 Chemnitz, Germany.
Microorganisms. 2023 Feb 7;11(2):420. doi: 10.3390/microorganisms11020420.
Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species-15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes.
使用宏基因组分析微生物群落是了解厌氧消化（AD）微生物群落组成结构和功能联系的有力方法。基于Illumina平台的短读长测序方法会产生高度碎片化的宏基因组，而长读长测序则能得到更连续的组装结果。为了评估这两种测序方法的混合方法的性能，我们比较了五个AD微生物群落样本产生的宏基因组组装基因组（MAG）。这些样本取自以不同进料方式（连续和不连续）和有机负荷率（OLR）进料短链脂肪酸的反应器。在所有进料方式下都显示出较高的相对丰度，但在较高的OLR下丰度大幅降低，此时 取而代之。不同进料方式和OLR的反应器之间细菌群落组成差异很大。然而，无论进料方式和OLR如何，功能潜力相似。使用纳米孔长读长和Illumina MiSeq读长的混合测序方法改善了组装统计数据，包括N50值增加（平均从32 kbp增加到1740 kbp）和最长重叠群长度增加（平均从94 kbp增加到1898 kbp）。混合方法还导致高质量MAG的比例更高，并产生了五个潜在的环状基因组，而仅使用基于MiSeq的重叠群则未产生环状基因组。最后，重建了27个混合MAG，其中18个代表潜在的新物种——其中15个是细菌物种。在途径分析过程中，选定的MAG显示出相似的丁酸降解基因模式，可能代表新的丁酸降解细菌。在宏基因组分析中添加长读长所展示的优势使得混合方法在处理复杂微生物群落时成为更可取的选择。
