KEMET – A python tool for KEGG Module evaluation and microbial genome annotation expansion

Palù, Matteo; Basile, Arianna; Zampieri, Guido; Treu, Laura; Rossi, Alessandro; Morlino, Maria Silvia; Campanaro, Stefano

doi:10.1016/j.csbj.2022.03.015

Cited by 21 publications

(11 citation statements)

References 27 publications

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“…Proteinencoding genes were predicted using Prodigal (v2.6.2) with default parameters and associated with KEGG IDs using EggNOG (v2.0.1-1) and Diamond (v0.9.22.123). KEGG IDs were associated with the corresponding KEGG modules to determine their completeness values by using an in-house developed pipeline [26]. Additional gene finding and annotation was performed on the five dominant MAGs by Rapid Annotation using Subsystem Technology (RAST) to order genes into subsystems, subcategories and categories, according to the SEED classification by sequence attribution to protein families (FIGfams) [27].…”

Section: Genome-centric Metagenomics and Statisticsmentioning

confidence: 99%

“…Additional gene finding and annotation was performed on the five dominant MAGs by Rapid Annotation using Subsystem Technology (RAST) to order genes into subsystems, subcategories and categories, according to the SEED classification by sequence attribution to protein families (FIGfams) [27]. To obtain the most complete possible annotation regarding genes responsible for exopolysaccharide biosynthesis, a targeted investigation was performed using Hidden Markov Models (HMM) search implemented in KEMET [26]. The software was used with the option --fixed_ko_list and the dedicated ko list (Supplementary Dataset S1) was manually defined starting from SEED classifications.…”

Section: Genome-centric Metagenomics and Statisticsmentioning

confidence: 99%

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Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation

et al. 2022

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Background Carbon fixation through biological methanation has emerged as a promising technology to produce renewable energy in the context of the circular economy. The anaerobic digestion microbiome is the fundamental biological system operating biogas upgrading and is paramount in power-to-gas conversion. Carbon dioxide (CO2) methanation is frequently performed by microbiota attached to solid supports generating biofilms. Despite the apparent simplicity of the microbial community involved in biogas upgrading, the dynamics behind most of the interspecies interaction remain obscure. To understand the role of the microbial species in CO2 fixation, the biofilm generated during the biogas upgrading process has been selected as a case study. The present work investigates via genome-centric metagenomics, based on a hybrid Nanopore-Illumina approach the biofilm developed on the diffusion devices of four ex situ biogas upgrading reactors. Moreover, genome-guided metabolic reconstruction and flux balance analysis were used to propose a biological role for the dominant microbes. Results The combined microbiome was composed of 59 species, with five being dominant (> 70% of total abundance); the metagenome-assembled genomes representing these species were refined to reach a high level of completeness. Genome-guided metabolic analysis appointed Firmicutes sp. GSMM966 as the main responsible for biofilm formation. Additionally, species interactions were investigated considering their co-occurrence in 134 samples, and in terms of metabolic exchanges through flux balance simulation in a simplified medium. Some of the most abundant species (e.g., Limnochordia sp. GSMM975) were widespread (~ 67% of tested experiments), while others (e.g., Methanothermobacter wolfeii GSMM957) had a scattered distribution. Genome-scale metabolic models of the microbial community were built with boundary conditions taken from the biochemical data and showed the presence of a flexible interaction network mainly based on hydrogen and carbon dioxide uptake and formate exchange. Conclusions Our work investigated the interplay between five dominant species within the biofilm and showed their importance in a large spectrum of anaerobic biogas reactor samples. Flux balance analysis provided a deeper insight into the potential syntrophic interaction between species, especially Limnochordia sp. GSMM975 and Methanothermobacter wolfeii GSMM957. Finally, it suggested species interactions to be based on formate and amino acids exchanges.

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Section: Genome-centric Metagenomics and Statisticsmentioning

confidence: 99%

Section: Genome-centric Metagenomics and Statisticsmentioning

confidence: 99%

Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation

et al. 2022

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“…The taxonomy of MAGs was determined using GTDB‐Tk (v1.7.0; Chaumeil et al 2020) and their functionality estimated using Bakta (v1.1; Schwengers et al 2021), and EggNogMapper (v.2.1.2; Huerta‐Cepas et al 2019). We used GapMind (Price et al 2020), KEMET (Palù et al 2022), and AMRFinderPlus (Feldgarden et al 2021) to estimate amino acid pathways, KEGG module completeness, and antibiotic resistance genes, respectively. In total, we generated 9472 prokaryotic genomic bins.…”

Section: Methodsmentioning

confidence: 99%

Unexpected functional diversity of stream biofilms within and across proglacial floodplains despite close spatial proximity

Michoud,

Kohler,

Peter

et al. 2023

Limnology & Oceanography

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High‐mountain streams are particularly vulnerable to climate change because they intimately interface with the cryosphere. As glaciers shrink and snowpack diminishes, proglacial streams will eventually shift from being glacier‐fed to streams fed by groundwater, snowmelt and precipitation. This shift will affect both the flow regime and physico‐chemical characteristics of streams, possibly also the structure and function of their benthic microbiome. Here, we applied genome‐resolved metagenomics to benthic biofilms from glacier‐fed streams and their groundwater‐fed tributaries within three proglacial floodplains in the Swiss Alps. Despite the close spatial proximity between both stream types, their microbiome structure differed consistently for both prokaryotes and eukaryotes. The glacier‐fed stream microbiome was taxonomically and functionally less diverse than its groundwater‐fed counterpart, and had smaller genomes, but with conservation of the central metabolic functions primarily related to nitrogen and sulfur cycling. Consequently, much higher functional variability was associated with the microbiome of tributary streams, mainly due to abundant genes involved in the transport and degradation of organic matter. Our findings suggest that glacier shrinkage will cause shifts in the functioning of benthic microbiomes of proglacial floodplains with yet unknown consequences for downstream biogeochemistry.

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“…Briefly, KEGG orthologs in genomes were identified by BlastKOALA ( Kanehisa et al, 2016 ) and KofamKOALA ( Aramaki et al, 2020 ) online. 1 Pathway comparisons were performed by KEMET with default parameters ( Palu et al, 2022 ). Pfam domains ( Mistry et al, 2021 ) of proteins were further analyzed by Interproscan (v5.54–87.0) ( Jones et al, 2014 ) with in a local searching mode.…”

Section: Methodsmentioning

confidence: 99%

Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris

et al. 2023

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Green sulfur bacteria (GSB) are a distinct group of anoxygenic phototrophic bacteria that are found in many ecological niches. Prosthecochloris, a marine representative genus of GSB, was found to be dominant in some coral skeletons. However, how coral-associated Prosthecochloris (CAP) adapts to diurnal changing microenvironments in coral skeletons is still poorly understood. In this study, three Prosthecochloris genomes were obtained through enrichment culture from the skeleton of the stony coral Galaxea fascicularis. These divergent three genomes belonged to Prosthecochloris marina and two genomes were circular. Comparative genomic analysis showed that between the CAP and non-CAP clades, CAP genomes possess specialized metabolic capacities (CO oxidation, CO2 hydration and sulfur oxidation), gas vesicles (vertical migration in coral skeletons), and cbb3-type cytochrome c oxidases (oxygen tolerance and gene regulation) to adapt to the microenvironments of coral skeletons. Within the CAP clade, variable polysaccharide synthesis gene clusters and phage defense systems may endow bacteria with differential cell surface structures and phage susceptibility, driving strain-level evolution. Furthermore, mobile genetic elements (MGEs) or evidence of horizontal gene transfer (HGT) were found in most of the genomic loci containing the above genes, suggesting that MGEs play an important role in the evolutionary diversification between CAP and non-CAP strains and within CAP clade strains. Our results provide insight into the adaptive strategy and population evolution of endolithic Prosthecochloris strains in coral skeletons.

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KEMET – A python tool for KEGG Module evaluation and microbial genome annotation expansion

Cited by 21 publications

References 27 publications

Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation

Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation

Unexpected functional diversity of stream biofilms within and across proglacial floodplains despite close spatial proximity

Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris

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