Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics

Sharma, Vikas; Mobeen, Fauzul; Prakash, Tulika

doi:10.3390/genes9100477

Cited by 18 publications

(10 citation statements)

References 139 publications

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“…Some highly conserved functional categories, such as translation, ribosomal structure and biogenesis (J, 12.71%), general function prediction only (R, 12.35%), function unknown (S, 10.45%), and amino acid transport and metabolism (E, 7.4%), were enriched among the core-genome of Lacticaseibacillus strains (Supplementary Figure 3). Translation functions are important for maintaining physiological parameters during changes to which gut microorganisms are exposed, suggesting their adaptive and survival roles (Sharma et al, 2018). Similar to our study, genomic analysis of Bifidobacterium showed high conservation of "Translation, ribosomal structure, and biogenesis (J)" class in the core-genome, demonstrating the importance of information storage for these bacteria to adapt and survive in the gut (Sharma et al, 2018).…”

Section: Comparative Genomic Analysis Of Lacticaseibacillus Strainssupporting

confidence: 82%

“…Translation functions are important for maintaining physiological parameters during changes to which gut microorganisms are exposed, suggesting their adaptive and survival roles (Sharma et al, 2018). Similar to our study, genomic analysis of Bifidobacterium showed high conservation of "Translation, ribosomal structure, and biogenesis (J)" class in the core-genome, demonstrating the importance of information storage for these bacteria to adapt and survive in the gut (Sharma et al, 2018). In addition, for the accessory-genome and unique-genome, we observed enrichment of genes in the COG category "Carbohydrate transport and metabolism (G, 17.73-17.52%)."…”

Section: Comparative Genomic Analysis Of Lacticaseibacillus Strainsmentioning

confidence: 99%

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Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8

et al. 2022

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Lacticaseibacillus casei, Lacticaseibacillus chiayiensis, and Lacticaseibacillus zeae are very closely related Lacticaseibacillus species. L. casei has long been proposed as a probiotic, whereas studies on functional characterization for L. chiayiensis and L. zeae are some compared to L. casei. In this study, L. casei FBL6, L. chiayiensis FBL7, and L. zeae FBL8 were isolated from raw milk, and their probiotic properties were investigated. Genomic analysis demonstrated the role of L. chiayiensis and L. zeae as probiotic candidates. The three strains were tolerant to acid and bile salt, with inhibitory action against pathogenic bacterial strains and capacity of antioxidants. Complete genome sequences of the three strains were analyzed to highlight the probiotic properties at the genetic level, which results in the discovery of genes corresponding to phenotypic characterization. Moreover, genes known to confer probiotic characteristics were identified, including genes related to biosynthesis, defense machinery, adhesion, and stress adaptation. The comparative genomic analysis with other available genomes revealed 256, 214, and 32 unique genes for FBL6, FBL7, and FBL8, respectively. These genomes contained individual genes encoding proteins that are putatively involved in carbohydrate transport and metabolism, prokaryotic immune system for antiviral defense, and physiological control processes. In particular, L. casei FBL6 had a bacteriocin gene cluster that was not present in other genomes of L. casei, resulting in this strain may exhibit a wide range of antimicrobial activity compared to other L. casei strains. Our data can help us understand the probiotic functionalities of the three strains and suggest that L. chiayiensis and L. zeae species, which are closely related to L. casei, can also be considered as novel potential probiotic candidate strains.

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Section: Comparative Genomic Analysis Of Lacticaseibacillus Strainssupporting

confidence: 82%

Section: Comparative Genomic Analysis Of Lacticaseibacillus Strainsmentioning

confidence: 99%

Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8

et al. 2022

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“…The few studies that have considered the association between bifidobacteria diversity and their hosts and environments have found contradictory results. Some studies observe no relationship between hosts and the type of genes bifidobacteria carry [21,22], while others do [23][24][25].…”

Section: Introductionmentioning

confidence: 99%

Evolutionary relationships among bifidobacteria and their hosts and environments

Rodriguez

Martiny

2020

BMC Genomics

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Background: The assembly of animal microbiomes is influenced by multiple environmental factors and host genetics, although the relative importance of these factors remains unclear. Bifidobacteria (genus Bifidobacterium, phylum Actinobacteria) are common first colonizers of gut microbiomes in humans and inhabit other mammals, social insects, food, and sewages. In humans, the presence of bifidobacteria in the gut has been correlated with health-promoting benefits. Here, we compared the genome sequences of a subset of the over 400 Bifidobacterium strains publicly available to investigate the adaptation of bifidobacteria diversity. We tested 1) whether bifidobacteria show a phylogenetic signal with their isolation sources (hosts and environments) and 2) whether key traits encoded by the bifidobacteria genomes depend on the host or environment from which they were isolated. We analyzed Bifidobacterium genomes available in the PATRIC and NCBI repositories and identified the hosts and/or environment from which they were isolated. A multilocus phylogenetic analysis was conducted to compare the genetic relatedness the strains harbored by different hosts and environments. Furthermore, we examined differences in genomic traits and genes related to amino acid biosynthesis and degradation of carbohydrates. Results: We found that bifidobacteria diversity appears to have evolved with their hosts as strains isolated from the same host were non-randomly associated with their phylogenetic relatedness. Moreover, bifidobacteria isolated from different sources displayed differences in genomic traits such as genome size and accessory gene composition and on particular traits related to amino acid production and degradation of carbohydrates. In contrast, when analyzing diversity within human-derived bifidobacteria, we observed no phylogenetic signal or differences on specific traits (amino acid biosynthesis genes and CAZymes). Conclusions: Overall, our study shows that bifidobacteria diversity is strongly adapted to specific hosts and environments and that several genomic traits were associated with their isolation sources. However, this signal is not observed in human-derived strains alone. Looking into the genomic signatures of bifidobacteria strains in different environments can give insights into how this bacterial group adapts to their environment and what types of traits are important for these adaptations.

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“…This is possibly due to the exogenous protective effects accelerating the survival rate of the probiotic cells within the host gastrointestinal tract [79][80]78]. The metabolic substrates of the human milk oligosaccharides enhance the Bi dobacterial probiotic adhesions and colonisations to the host intestinal mucosa, especially during the host's early life [79][80][81]. In particular, members of the Bi dobacterium are among the key bacterial compontents (i.e., B. longum, B. dum, and B. breve species) of the infant intestines.…”

Section: Discussionmentioning

confidence: 99%

Identifying ligand-binding specificity of the oligopeptide receptor OppA from Bifidobacterium longum KACC91563 by Structure-based molecular modeling

Chai¹,

Kim²,

Ham³

et al. 2020

Preprint

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Background: The OppA receptor as a ATP-binding cassette (ABC) transporter plays key roles in protecting host organism and transport nutrients across the intestine by the oligopeptide transporter from symbiotic bacteria directs maturation of the host immune system. Among lactic acid bacteria, Bifidobacterium longum KACC91563, isolated from fecal samples of healthy Korean neonates, has the capability to alleviate food allergy effects. The extracellular OppA receptor from gram-positive Bifidobacterium longum KACC91563 translocate nutrients-peptides from the outside environment of intestinal tract to the inside of the symbiotic cell, as a peptide importer. Hence, it was attempting to explicate the relationship between the substrate’s specificity from the OppA importer and the probiotic effects of B. logum KACC91563 in the host intestine. The probiotic effects of B. logum KACC91563 were attributed to the enhancement of the epithelial barrier by several different strain sepcific ways to prevent the strong adhesion of pathogens. The specialized structure-function relationship from the OppA importer could provide the abstract of substrate specificity into unique immunological properties of that the host organism.Results: In the study, we characterized the extracellular OppA importer from B. longum KACC91563 of intestinal microbiome by various protein structure-based modelings in silico. Structural characterization by conserved 5 patches and 4 functional motifs from specific trace residues of the OppA importer. The hydrate surface of the binding site had been decipted by specific trace residues of the OppA that trace residues of Thr58, Lys185, Trp443, and Tyr447, which were characterized in highly exposed hydrophobic binding pocket by its aggregation prones. Therefore, the spatial aggregation propensity in the binding site of the extracellular OppA importer plays a vital role in the specific interaction determinant for peptide binding. In addition, alanine mutation energy values allowed for the virtual determination of the relationships between the energy effects of the peptide binding site mutation on the transporter structural stability, the peptide binding affinity, and the transporter-related peptide substrate selectivity from OppA importer. In particular, distinctive seven pharmacophoric features comprised of two H-bonding donor(P1), three H-bonding acceptor(P8), and two hydrophobic points (P5 and P8) matched the the OppA receptor-peptide ligand interactions within their binding pocket structure. There are distinct interactions to fix the positions of the N(P1) and C(P8) termini of the complex of OppA-peptide from B. longum KACC91563 such as side chain-specific interactions with the OppA, compared to that of the Lactococcus latis (L. lactics) OppA.Conclusions: The specialized structure-function relationship from the OppA import could provide the abstract of substrate specificity into unique immunological properties of the host organism by stucutre-based molecular modeling. In the current study, we attempted explication of the relationship between the substrate’s specificity from the OppA importer and the probiotic effects of B. longum KACC91563 in the host intestine based on the structure-function perspectives of the OppA importer. Moreover, functional characterization of solute-binding proteins (such as 15 cell wall proteins and 20 extracellular proteins) on the B. longum KACC91563 genome will lead to insight of key switch for substate’s metabolism into reprogramming immune responses in the host intestine.

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Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics

Cited by 18 publications

References 139 publications

Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8

Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8

Evolutionary relationships among bifidobacteria and their hosts and environments

Identifying ligand-binding specificity of the oligopeptide receptor OppA from Bifidobacterium longum KACC91563 by Structure-based molecular modeling

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