Comparative Genome Analysis of Megasphaera sp. Reveals Niche Specialization and Its Potential Role in the Human Gut

Abstract

With increasing number of novel bacteria being isolated from the human gut ecosystem, there is a greater need to study their role in the gut ecosystem and their effect on the host health. In the present study, we carried out in silico genome-wide analysis of two novel Megasphaera sp. isolates NM10 (DSM25563) and BL7 (DSM25562), isolated from feces of two healthy individuals and validated the key features by in vitro studies. The analysis revealed the general metabolic potential, adaptive features and the potential effects of these isolates on the host. The comparative genome analysis of the two human gut isolates NM10 and BL7 with ruminal isolate Megasphaera elsdenii (DSM20460) highlighted the differential adaptive features for their survival in human gut. The key findings include features like bile resistance, presence of various sensory and regulatory systems, stress response systems, membrane transporters and resistance to antibiotics. Comparison of the “glycobiome” based on the genomes of the ruminal isolate with the human gut isolates NM10 and BL revealed the presence of diverse and unique sets of Carbohydrate-Active enzymes (CAZymes) amongst these isolates, with a higher collection of CAZymes in the human gut isolates. This could be attributed to the difference in host diet and thereby the environment, consequently suggesting host specific adaptation in these isolates. In silico analysis of metabolic potential predicted the ability of these isolates to produce important metabolites like short chain fatty acids (butyrate, acetate, formate, and caproate), vitamins and essential amino acids, which was further validated by in vitro experiments. The ability of these isolates to produce important metabolites advocates for a potential healthy influence on the host. Further in vivo studies including transcriptomic and proteomic analysis will be required for better understanding the role and impact of these Megasphaera sp. isolates NM10 and BL7 on the human host.

Stability and Resilience of Oral Microcosms Toward Acidification and Candida Outgrowth by Arginine Supplementation

“…Butyrate in the oral cavity is suggested to play a role in the development of periodontal disease [56,57]. Members of the genus Megasphaera are known to produce butyrate [58,59]. In our study, the relative abundance of OTU18 (Megasphaera) correlated with the concentration of butyrate, while OTU16 (Neisseria) appeared to be negatively related to butyrate (Fig.…”

ACI‐1 beta‐lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages

“…Examining the remaining three cases of aci1 found in gut metagenomes that were not hosted within A. intestini , two were from short uninformative scaffolds likely from Megasphaera elsdenii 14‐14 , a Negativicute mostly detected in the rumen but also known to occur within the human gut (Shetty et al ., ; Bag et al ., ). The other case is from Veillonella magna , a Negativicute previously identified in swine intestines (Kraatz and Taras, ).…”

Effects of Acarbose on the Gut Microbiota of Prediabetic Patients: A Randomized, Double-blind, Controlled Crossover Trial

“…It was also noted that some species of Megasphaera , which also thrived following acarbose treatment, could produce a larger amount of succinic acid by glucose fermentation [28]. In addition, a higher amount of complex carbohydrate-utilizing genes present in the human gut isolates that contained Megasphaera , including glycosyl hydrolase and amylomaltase [29], suggest that it may play a key role in the utilization of carbohydrates that cannot be directly degraded and utilized by the human digestive system, including the non-digested carbohydrates in acarbose-treated individuals. Megasphaera could potentially transform carbohydrates into SCFAs, including butyrate, formate, acetate, valerate, and caproate, which is beneficial for Lactobacillus growth.…”