AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences

Abstract

Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood–Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se.

High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure

“…Bioperl (Stajich et al, 2002), NCBI-blast+ (Camacho et al, 2009), AcetoBase (Singh et al, 2019) OTU sequences is performed with the subsequent generation of a phylogenetic tree. The last step is data visualization, in which all the results generated in steps two and three are rendered in different plots and interactive graphs.…”

Profiling acetogenic community dynamics in anaerobic digesters - comparative analyses using next-generation sequencing and T-RFLP

“…The T-RFLP profile of FTHFS gene fragments was simulated using the reference nucleotide dataset retrieved from AcetoBase, which consists of ~6820 non-redundant full-length taxonomically annotated FTHFS nucleotide sequences (Singh et al 2019). A dataset of in silico (IS) PCR amplicons was generated by aligning the full-length FTHFS nucleotide reference dataset and FTHFS clone sequences generated in a previous study (Müller et al 2016).…”

“…However, few studies have specifically focused on acetogenic community dynamics or on developing a high-throughput method for reliable acetogenic community profiling (Singh et al 2020). Since acetogenesis is a physiological process, and not a phylogenetic characteristic, development of acetogen-specific 16S rRNA gene primers is practically impossible (Ljungdahl 1986; Drake 1994a; Lovell 1994; Lovell and Leaphart 2005; Drake, Gößner and Daniel 2008; Singh et al 2019, 2020). Therefore, established molecular analysis methods/pipelines based on the 16S rRNA gene cannot be used for analysis of the acetogenic community.…”

“…The Wood-Ljungdahl pathway (WLP) is a characteristic of acetogens (Drake 1994b; Peretó et al 1999; Lever 2012; Poehlein et al 2012) and the marker gene formyltetrahydrofolate synthetase (FTHFS) has been successfully used to decode the potential acetogenic community (Hori et al 2011; De Vrieze and Verstraete 2016; Müller et al 2016). While FTHFS is also present in the genome of non-acetogenic bacteria, sulphate-reducing bacteria and methanogens, still it has been successfully used for over two decades as the marker of choice in acetogenic community analysis (Ljungdahl 1986; Lovell, Przybyla and Ljungdahl 1990; Lovell and Leaphart 2005; Ohashi et al 2007; Drake, Gößner and Daniel 2008; Gagen et al 2010; Moestedt et al 2016; Schuchmann and Müller 2016; Singh et al 2019, 2020). Recently, we published a database (AcetoBase) (Singh et al 2019) and an analysis pipeline (AcetoScan) (Singh et al 2020), and successfully demonstrated proof-of-concept for targeting the potential acetogenic community in biogas reactor samples and unsupervised analysis of FTHFS AmpSeq data.…”

“…While FTHFS is also present in the genome of non-acetogenic bacteria, sulphate-reducing bacteria and methanogens, still it has been successfully used for over two decades as the marker of choice in acetogenic community analysis (Ljungdahl 1986; Lovell, Przybyla and Ljungdahl 1990; Lovell and Leaphart 2005; Ohashi et al 2007; Drake, Gößner and Daniel 2008; Gagen et al 2010; Moestedt et al 2016; Schuchmann and Müller 2016; Singh et al 2019, 2020). Recently, we published a database (AcetoBase) (Singh et al 2019) and an analysis pipeline (AcetoScan) (Singh et al 2020), and successfully demonstrated proof-of-concept for targeting the potential acetogenic community in biogas reactor samples and unsupervised analysis of FTHFS AmpSeq data. Our previous studies showed that AcetoBase and AcetoScan can be used for reliable monitoring of the acetogenic community in multiplexed samples in biogas reactors.…”