Mapping of the benzoate metabolism by human gut microbiome indicates food-derived metagenome evolution

Abstract

Sodium benzoate is one of the widely used food preservatives and its metabolism in the human body has been studied only with the host perspective. Despite the human gut microbiome being considered as a virtual human organ, its role in benzoate metabolism is yet to be elucidated. The current study uses a multi-omic approach to rationalize the role of human gut microbes in benzoate metabolism. Microbial diversity analysis with multiple features synchronously indicates the dominance of Bacteroidetes followed by Firmicutes, Actinobacteria, and Proteobacteria. Metagenomic exploration highlights the presence of benzoate catabolic protein features. These features were mapped on to the aerobic and anaerobic pathways of benzoate catabolism. Benzoate catabolism assays identified statistically significant metabolites (P < 0.05) associated with the protocatechuate branch of the beta-ketoadipate pathway of the benzoate metabolism. Analysis of the 201 human gut metagenomic datasets across diverse populations indicates the omnipresence of these features. Enrichment of the benzoate catabolic protein features in human gut microbes rationalizes their role in benzoate catabolism, as well as indicates food-derived microbiome evolution.

Ageing and rejuvenation models reveal changes in key microbial communities associated with healthy ageing

“…4h ). Benzoate is a well-known antibacterial agent [ 51 ], and a recent study revealed that its catabolic pathways exist in human gut metagenomic datasets [ 52 ], and antimicrobial food additives induce enrichment of their catabolic pathways at the metagenomic level [ 53 ]. Likewise, we may argue that rejuvenated mice are more resistant to benzoate than aged mice.…”

Culture-Independent Exploration of the Hypersaline Ecosystem Indicates the Environment-Specific Microbiome Evolution

“…However, a majority of these studies were primarily focused on determining the phylogenetic affiliation of the residing microbes (Naghoni et al, 2017) and provide very limited information about the microbiome functioning (Sorokin and Kuenen, 2005). Metagenomics allows direct access to the genetic content of the microbiome to describe its composition and physiological functions (Ahmed et al, 2018;Yadav et al, 2021). Therefore, metagenomics was used to study the Sambhar Lake microbiome's adaptation, survival, and physiological functions in such a harsh environment.…”

“…In addition to the abovementioned feature, several protein features were identified especially for the quorum sensing and chemotaxis with a possible role in the microbial communication and growth of biofilms, as described by various studies (Waters and Bassler, 2005). Merely the presence of protein features could not confirm their functions, hereby a translation approach like metabolomics could be used to decode functional metabolic pathways by metabolite profiling (Yadav et al, 2020(Yadav et al, , 2021. Identification of metabolites associated with adaptive physiology, as well as with general cell physiology confirms their functions in the lake microbiome (Supplementary Table 8).…”

“…The Sambhar Lake water was centrifuged at 14,000 revs min −1 for 10 min to collect microbial pellet. The microbial pellet was quenched with 60% aqueous methanol solution (−48 • C) and processed for metabolite extraction (Yadav et al, 2021). Highperformance liquid chromatography coupled to quadrupole-time of flight mass spectrometry (HPLC/Q-TOF MS), possessing an Exion LC system integrated with X-500 QTOF (SCIEX Technology, United States) was used to obtain the metabolic profiles in the filtered supernatant.…”

“…Exploration of the salt lake microbiome will enrich the understanding of microbiome functioning in nutrient-deprived extreme conditions (Naghoni et al, 2017). Metagenomics and metabolomics are the pioneer culture-independent tools to explore the untapped microbial world to unveil microbiome genetic composition and functional metabolic pathways (Ahmed et al, 2018;Yadav et al, 2020Yadav et al, , 2021. Metagenomic exploration of the freshwater, alkaline, and saline water ecosystem has identified unique inhabitants and their unique genetic machinery (Poli et al, 2017).…”