Genomic and Biochemical Characterization of Bifidobacterium pseudocatenulatum JCLA3 Isolated from Human Intestine

Abstract

Bifidobacteria have been investigated due to their mutualistic microbe–host interaction with humans throughout their life. This work aims to make a biochemical and genomic characterization of Bifidobacterium pseudocatenulatum JCLA3. By multilocus analysis, the species of B. pseudocatenulatum JCLA3 was established as pseudocatenulatum. It contains one circular genome of 2,369,863 bp with G + C content of 56.6%, no plasmids, 1937 CDSs, 54 tRNAs, 16 rRNAs, 1 tmRNA, 1 CRISPR region, and 401 operons predicted, including a CRISPR-Cas operon; it encodes an extensive number of enzymes, which allows it to utilize different carbohydrates. The ack gene was found as part of an operon formed by xfp and pta genes. Two genes of ldh were found at different positions. Chromosomally encoded resistance to ampicillin and cephalothin, non-hemolytic activity, and moderate inhibition of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 6538 were demonstrated by B. pseudocatenulatum JCLA3; it can survive 100% in simulated saliva, can tolerate primary and secondary glyco- or tauro-conjugated bile salts but not in a mix of bile; the strain did not survive at pH 1.5–5. The cbh gene coding to choloylglycine hydrolase was identified in its genome, which could be related to the ability to deconjugate secondary bile salts. Intact cells showed twice as much antioxidant activity than debris. B. pseudocatenulatum JCLA3 showed 49% of adhesion to Caco-2 cells. The genome and biochemical analysis help to elucidate further possible biotechnological applications of B. pseudocatenulatum JCLA3.

An In Vitro Colonic Fermentation Study of the Effects of Human Milk Oligosaccharides on Gut Microbiota and Short-Chain Fatty Acid Production in Infants Aged 0–6 Months

“…However, it has been suggested that B. dentium possesses the ability to remove terminal fucose from HMOs [ 48 ]. Researchers found a smaller number of glycosyl hydrolase genes in the genomes of Bifidobacterium angulatum JCM 7096(T) and Bifidobacterium pseudocatenulatum JCLA3 [ 49 , 50 ]. The B. thermophilum genome contains a β-galactosidase gene, a finding that hints at its potential to degrade HMOs since β-galactosidase can participate in their metabolism; however, the exact mechanism remains uncharted [ 50 ].…”

Bifidobacterium longum LBUX23 Isolated from Feces of a Newborn; Potential Probiotic Properties and Genomic Characterization

“…A comparison of constitutive genes in different strains of B. longum strains was made: tlyC , cbh , glnE , pNPOx , ahpC , trxA , trxB [ 11 , 17 , 18 ]. The MLSA approach has been used to generate a robust and highly discriminatory supertree to infer phylogeny in the genus Bifidobacterium .…”

“…The MLSA approach has been used to generate a robust and highly discriminatory supertree to infer phylogeny in the genus Bifidobacterium . MLSA was performed according to González–Vázquez et al, 2022 [ 18 ].…”

“…Assembling was carried out by IMR using SMRT analysis software v12.0. Data processing, plot construction, and genome annotation were performed according to González–Vázquez et al, 2022 [ 18 ].…”

“…Samples were collected at regular intervals of 2 h from time zero to 8 h. The bacterial concentration was determined by the plate count method [ 19 ]. The pH of the supernatant was measured according to González–Vázquez et al, 2022 [ 18 ]. All experiments were completed in triplicate.…”