AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters

Abstract

AcetoBase is a public repository and database of formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial FTHFS nucleotide and protein sequences from genomes and metagenome-assembled genomes and of sequences generated by clone library sequencing. At its publication in 2019, AcetoBase (Version 1) was also the first database to establish connections between the FTHFS gene, the Wood–Ljungdahl pathway and 16S ribosomal RNA genes. Since the publication of AcetoBase, there have been significant improvements in the taxonomy of many bacterial lineages and accessibility/availability of public genomics and metagenomics data. The update to the AcetoBase reference database described here (Version 2) provides new sequence data and taxonomy, along with improvements in web functionality and user interface. The evaluation of this latest update by re-analysis of publicly accessible FTHFS amplicon sequencing data previously analysed with AcetoBase Version 1 revealed significant improvements in the taxonomic assignment of FTHFS sequences. Database URL: https://acetobase.molbio.slu.se

Co‐substrate composition is critical for enrichment of functional key species and for process efficiency during biogas production from cattle manure

“…The FTHFS analyses revealed some specialist bacterial taxa with potential for metabolic tasks such as degradation of complex plant material (family Lachnospiraceae ) (Beaumont et al, 2021 ; Koeck et al, 2015 ; Lebuhn et al, 2014 ; Suksong et al, 2019 ), known syntrophic acetate/propionate/butyrate‐oxidising bacteria ( Tepidanaerobacter , Syntrophomonas , etc.) (Singh & Schnürer, 2022 ) and proposed acetate/propionate‐oxidising bacteria (phylum Cloacimonadota and family Clostridiaceae , Peptococcaceae ) (Ahlert et al, 2016 ; Singh & Schnürer, 2022 ; Singh, Schnürer, & Westerholm, 2021 ; Westerholm et al, 2022 ). Specific changes in community profile in the control reactor and reactors with co‐substrates are further discussed below.…”

“…For the data analysis, raw paired‐end reads for forward and reverse sequence were concatenated in a single file and used as single‐end reads (with parameters ‐m 300, ‐n 150, ‐q 20, ‐t 1.0, ‐c 2, ‐e 1e‐30) as described elsewhere (Singh, Moestedt, et al, 2021 ). For taxonomic annotations, the AcetoBase database (v2.0) was used (Singh & Schnürer, 2022 ). The raw sequencing data have been submitted to the Sequence Read Archive (SRA) database at the National Center for Biotechnology Information (NCBI), under the study numbers PRJNA507984 (16S rRNA gene‐amplicon sequencing) and PRJNA873909 (FTHFS gene‐amplicon sequencing).…”

Potential of acetic acid to restore methane production in anaerobic reactors critically intoxicated by ammonia as evidenced by metabolic and microbial monitoring

“…On average, 65.5% of reads passed the quality control thresholds and the resulting read counts were normalized to 10,000 reads per sample for further comparative analyses. SAO and SPO were identified using blast against the Acetobase database [ 62 ] and using the 16S rRNA gene signatures of known SPOs [ 63 ], respectively. Matches with a sequence similarity of over 97% were retained as positive for both SAOs and SPOs.…”

The microbiology of Power-to-X applications

“…For instance,Westerholm et al 2011 studied the fhs gene diversity in a mesophilic laboratory-scale biogas reactor, the fhs gene abundance in natural and engineered environments was analyzed by qPCR(Xu et al 2009), and homoacetogenic activity during acidification in a thermophilic AD system was investigated targeting the fhs gene(Akuzawa et al 2011). More recently, fhs gene amplicon sequencing was used in microbiological surveillance of biogas plants(Singh et al 2020(Singh et al , 2021aSingh et al 2021b), and the fhs gene database AcetoBase was established(Singh et al 2019;Singh and Schnürer 2022).In the study of Braga Nan et al (2020), quantification of the FTHFS gene was performed by using qPCR to assess homoacetogenesis in batch cultures with seven different inocula fed with hydrogen but no clear correlation between acetic acid accumulation and copy number of the target gene was observed.…”