Genomic and physiological analyses of an indigenous strain, Enterococcus faecium 17OM39

Abstract

The human gut microbiome plays a crucial role in human health and efforts need to be done for cultivation and characterisation of bacteria with potential health benefits. Here, we isolated a bacterium from a healthy Indian adult faeces and investigated its potential as probiotic. The cultured bacterial strain 17OM39 was identified as Enterococcus faecium by 16S rRNA gene sequencing. The strain 17OM39 exhibited tolerance to acidic pH, showed antimicrobial activity and displayed strong cell surface traits such as hydrophobicity and autoaggregation capacity. The strain was able to tolerate bile salts and showed bile salt hydrolytic (BSH) activity, exopolysaccharide production and adherence to human HT-29 cell line. Importantly, partial haemolytic activity was detected and the strain was susceptible to the human serum. Genomics investigation of strain 17OM39 revealed the presence of diverse genes encoding for proteolytic enzymes, stress response systems and the ability to produce essential amino acids, vitamins and antimicrobial compound Bacteriocin-A. No virulence factors and plasmids were found in this genome of the strain 17OM39. Collectively, these physiological and genomic features of 17OM39 confirm the potential of this strain as a candidate probiotic.

Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains

“…The NPNP group had two strains: NRRL B-2354 and 64/3 [25, 26]. The probiotic group had the marketed strain T110 [9] and strain 17OM39 isolated from healthy human gut [31]. …”

“…The carbohydrate metabolism was abundant in probiotic group while later in the pathogenic group (Fig. 3), this can be been attributed to the properties of probiotic strains to utilize various carbohydrates [31], while the pathogenic group had higher abundance of replication and recombination genes known to be associated with a large number of mobile elements [1, 2]. Comparison of accessory genes between probiotic and pathogenic group helped in identifying two manganese-containing catalase gene, which provide resistance to hydrogen peroxide present in human GIT [40–42].…”

“…Overall, the pathogenic group of E. faecium was found to have higher prevalence of antibiotic resistance genes; a factor that contributes to the challenge of selecting therapeutic measures. The probiotic group was devoid of any major clinically relevant antibiotic resistance [9, 31]. …”

Functional and Comparative Genomics of Niche-Specific Adapted ActinomycetesKocuria rhizophilaStrain D2 Isolated from Healthy Human Gut

“…Three self-declared healthy volunteers were selected with consent prior to collection of the samples. We immediately transported the collected faecal samples to the lab at 4°C and processed for isolation of faecal bacteria within 6 h. Faecal samples (1g) were transferred to 9 ml of sterile saline (0.85% sodium chloride, Sigma) and mixed well (50). The serial dilutions were subsequently prepared in sterile saline, and appropriate dilutions of the samples plated on Nutrient Agar (HiMedia, Mumbai, India).…”

“…Plates were incubated at 37°C for 48 h under aerobic condition. Glycerol [20% (v/v)] stocks were prepared to preserve the isolated pure cultures and froze at −80°C (50).…”