Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources

• Published in: Microorganisms (Basel) 2023-02, Vol.11 (2), p.420
• Main Authors: Becker, Daniela, Popp, Denny, Bonk, Fabian, Kleinsteuber, Sabine, Harms, Hauke, Centler, Florian
• Format: Article
• Language: English
• Subjects: Abundance; Alternative energy sources; Anaerobic bacteria; Anaerobic digestion; Anaerobic microorganisms; Bacteria; Biodegradation; Biogas; Bioreactors; Carbon; Carbon dioxide; Carbon sources; Chemical oxygen demand; Chemical properties; Community composition; Degradation; DNA sequencing; Environmental aspects; Fatty acids; Feeding regimes; Genetic aspects; Genetic testing; Genomes; Hydrogen; Identification and classification; Loading rate; metagenome-assembled genomes; Metagenomics; methanogenic pathways; Microbial activity; Microbial colonies; Microbiological research; Microbiomes; Microorganisms; New species; Nucleotide sequencing; Organic loading; Oxidation; Reactors; Relative abundance; Statistical analysis; syntrophic acetate oxidation; syntrophic butyrate oxidation; syntrophic propionate oxidation
• ISSN: 2076-2607; 2076-2607
• 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.