• Journal of Applied Biological Chemistry
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• v.64 no.1
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• pp.49-55
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• 2021

The diet plays a fundamental role in the formation of the gut microbiota, determining the interrelationship between the gut microbiota and the host. The current study investigated the effect of Chlorella vulgaris on the gut microbiota by using simulated in vitro digestion and colonic fermentation. Bioaccessibility was measured after in vitro digestion, and SCFAs and microbial profiling were analyzed after colonic fermentation. The bioaccessibility of C. vulgaris was 0.24 g/g. The three major SCFAs (acetate, propionate, and butyrate) increased significantly when compared to the control group. In microbial profiling analysis, microorganisms such as Faecalibacterium, Dialister, Megasphaera, Dorea, Odoribacter, Roseburia, Bifidobacterium, Butyricmonas, and Veillonella were high in C. vulgaris group. Among them, Faecalibacterium, Dialister, Megasphaera, Roseburia, and Veillonella were thought to be closely associated with the increased level of SCFAs. Finally, it can be expected to help improve gut microbiota and health through ingestion of C. vulgaris. However, further studies are vital to confirm the changes in the gut microbiota in in vivo, when C. vulgaris is ingested.

• Journal of Microbiology and Biotechnology
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• v.33 no.9
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• pp.1162-1169
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• 2023

16S rRNA short amplicon sequencing-based microbiota profiling has been thought of and suggested as a feasible method to assess food safety. However, even if a comprehensive microbial information can be obtained by microbiota profiling, it would not be necessarily sufficient for all circumstances. To prove this, the feasibility of the most widely used V3-V4 amplicon sequencing method for food safety assessment was examined here. We designed a pathogen (Vibrio parahaemolyticus) contamination and/or V. parahaemolyticus-specific phage treatment model of raw oysters under improper storage temperature and monitored their microbial structure changes. The samples stored at refrigerator temperature (negative control, NC) and those that were stored at room temperature without any treatment (no treatment, NT) were included as control groups. The profiling results revealed that no statistical difference exists between the NT group and the pathogen spiked- and/or phage treated-groups even when the bacterial composition was compared at the possible lowest-rank taxa, family/genus level. In the beta-diversity analysis, all the samples except the NC group formed one distinct cluster. Notably, the samples with pathogen and/or phage addition did not form each cluster even though the enumerated number of V. parahaemolyticus in those samples were extremely different. These discrepant results indicate that the feasibility of 16S rRNA short amplicon sequencing should not be overgeneralized in microbiological safety assessment of food samples, such as raw oyster.

• Journal of Korean Dental Science
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• v.16 no.1
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• pp.35-46
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• 2023

Purpose: Culture-based methods for microbiological diagnosis and antibiotic susceptibility tests have limitations in the management of orofacial infections. We aimed to profile pus microbiota and identify antibiotic resistance genes (ARGs) using a culture-independent approach. Materials and Methods: Genomic DNA samples extracted from the pus specimens of two patients with orofacial abscesses were subjected to shotgun sequencing on the NovaSeq system. Taxonomic profiling and prediction of ARGs were performed directly from the metagenomic raw reads. Result: Taxonomic profiling revealed obligate anaerobic polymicrobial communities associated with infections of odontogenic origins: the microbial community of Patient 1 consisted of one predominant species (Prevotella oris 74.6%) with 27 minor species, while the sample from Patient 2 contained 3 abundant species (Porphyromonas endodontalis 33.0%; P. oris 31.6%; and Prevotella koreensis 13.4%) with five minor species. A total of 150 and 136 putative ARGs were predicted in the metagenome of each pus sample. The coverage of most predicted ARGs was less than 10%, and only the CfxA2 gene identified in Patient 1 was covered 100%. ARG analysis of the seven assembled genome/metagenome datasets of P. oris revealed that strain C735 carried the CfxA2 gene. Conclusion: A metagenomics-based approach is useful to profile predominantly anaerobic polymicrobial communities but needs further verification for reliable ARG detection.

• Nutrition Research and Practice
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• v.17 no.5
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• pp.883-898
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• 2023

BACKGROUND/OBJECTIVES: Probiotics have been suggested as potent modulators of age-related disorders in immunological functions, yet little is known about sex-dependent effects of probiotic supplements. Therefore, we aimed to investigate sex-dependent effects of probiotics on profiles of the gut microbiota and peripheral immune cells in healthy older adults. SUBJECTS/METHODS: In a randomized, double-blind, placebo-controlled, multicenter trial, healthy elderly individuals ≥ 65 yrs old were administered probiotic capsules (or placebo) for 12 wk. Gut microbiota was analyzed using 16S rRNA gene sequencing and bioinformatic analyses. Peripheral immune cells were profiled using flow cytometry for lymphocytes (natural killer, B, CD4⁺ T, and CD8⁺ T cells), dendritic cells, monocytes, and their subpopulations. RESULTS: Compared with placebo, phylum Firmicutes was significantly reduced in the probiotic group in women, but not in men. At the genus level, sex-specific responses included reductions in the relative abundances of pro-inflammatory gut microbes, including Catabacter and unclassified_Coriobacteriales, and Burkholderia and unclassified Enterobacteriaceae, in men and women, respectively. Peripheral immune cell profiling analysis revealed that in men, probiotics significantly reduced the proportions of dendritic cells and CD14⁺ CD16^- monocytes; however, these effects were not observed in women. In contrast, the proportion of total CD4⁺ T cells was significantly reduced in women in the probiotic group. Additionally, serum lipopolysaccharide-binding protein levels showed a decreasing tendency that were positively associated with changes in gut bacteria, including Catabacter (ρ = 0.678, P < 0.05) and Burkholderia (ρ = 0.673, P < 0.05) in men and women, respectively. CONCLUSIONS: These results suggest that probiotic supplementation may reduce the incidence of inflammation-related diseases by regulating the profiles of the gut microbiota and peripheral immune cells in healthy elders in a sex-specific manner.

• Journal of Animal Science and Technology
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• v.62 no.2
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• pp.239-246
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• 2020

Microorganism residing in the gut has been known to have important roles in the animal body. Microbes and host microenvironment are highly related with host's health including energy metabolism and immune system. Moreover, it reported that gut microbiome is correlated with diseases like obesity in human and dogs. There have been many studies to identify and characterize microbes and their genes in human body. However, there was little information of microbiome in companion animals. Here, we investigated microbiota communities in feaces from twenty - four Beagles (aged 2 years old) and analyzed the taxonomy profile using metagenomics to study the difference among gut microbiome based on body condition score (BCS). gDNA was isolated from feaces, sequenced and clustered. Taxonomy profiling was performed based on the NCBI database. BCS was evaluated once a week according to the description provided by World Small Animal Veterinary Association. Firmicutes phylum was the most abundant followed by Bacteroidetes, Fusobacteria, Proteobacteria and Actinobacteria. That main microbiota in gut were differently distributed based on the BCS. Fusobacteria has been known to be associated with colon cancer in human. Interestingly, Fusobacteria was in the third level from the top in healthy dog's gut microbiome. In addition, Fusobacteria was especially higher in overweight dogs which had 6 scales of BCS. Species Fusobacterium perfoetens was also more abundant when dogs were in BCS 6. It implied that F. perfoetens would be positively related with overweight in dogs. These finding would contribute to further studies of gut microbiome and their functions to improve dog's diets and health condition.

• Journal of Microbiology and Biotechnology
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• v.28 no.8
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• pp.1247-1259
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• 2018

Raspberries are polyphenol-rich fruits with the potential to reduce the severity of the clinical signs associated with obesity, a phenomenon that may be related to changes in the gut microbiota. The aim of this study was to investigate the effect of raspberry supplementation on the fecal microbiota using an in vivo model of obesity. Obese diabetic db/db mice were used in this study and assigned to two experimental groups (with and without raspberry supplementation). Fecal samples were collected at the end of the supplementation period (8 weeks) and used for bacterial 16S rRNA gene profiling using a MiSeq instrument (Illumina). QIIME 1.8 was used to analyze the 16S data. Raspberry supplementation was associated with an increased abundance of Lachnospiraceae (p = 0.009), a very important group for gut health, and decreased abundances of Lactobacillus, Odoribacter, and the fiber degrader S24-7 family as well as unknown groups of Bacteroidales and Enterobacteriaceae (p < 0.05). These changes were enough to clearly differentiate bacterial communities accordingly to treatment, based on the analysis of UniFrac distance metrics. However, a predictive approach of functional profiles showed no difference between the treatment groups. Fecal metabolomic analysis provided critical information regarding the raspberry-supplemented group, whose relatively higher phytosterol concentrations may be relevant for the host health, considering the proven health benefits of these phytochemicals. Further studies are needed to investigate whether the observed differences in microbial communities (e.g., Lachnospiraceae) or metabolites relate to clinically significant differences that can prompt the use of raspberry extracts to help patients with obesity.

• Journal of Periodontal and Implant Science
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• v.53 no.1
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• pp.69-84
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• 2023

Purpose: The objective of this study was to analyze the microbial profile of individuals with peri-implantitis (PI) compared to those of periodontally healthy (PH) subjects and periodontitis (PT) subjects using Illumina sequencing. Methods: Buccal, supragingival, and subgingival plaque samples were collected from 109 subjects (PH: 30, PT: 49, and PI: 30). The V3-V4 region of 16S rRNA was sequenced and analyzed to profile the plaque microbiota. Results: Microbial community diversity in the PI group was higher than in the other groups, and the 3 groups showed significantly separated clusters in the buccal samples. The PI group showed different patterns of relative abundance from those in the PH and PT groups depending on the sampling site at both genus and phylum levels. In all samples, some bacterial species presented considerably higher relative abundances in the PI group than in the PH and PT groups, including Anaerotignum lactatifermentans, Bacteroides vulgatus, Faecalibacterium prausnitzii, Olsenella uli, Parasutterella excrementihominis, Prevotella buccae, Pseudoramibacter alactolyticus, Treponema parvum, and Slackia exigua. Network analysis identified that several well-known periodontal pathogens and newly recognized bacteria were closely correlated with each other. Conclusions: The composition of the microbiota was considerably different in PI subjects compared to PH and PT subjects, and these results could shed light on the mechanisms involved in the development of PI.

• The Korean Journal of Physiology and Pharmacology
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• v.28 no.2
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• pp.153-164
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• 2024

This study aimed to identify metabolic biomarkers and investigate changes in intestinal microbiota in the feces of healthy participants following administration of Lactococcus lactis GEN-001. GEN-001 is a single-strain L. lactis strain isolated from the gut of a healthy human volunteer. The study was conducted as a parallel, randomized, phase 1, open design trial. Twenty healthy Korean males were divided into five groups according to the GEN-001 dosage and dietary control. Groups A, B, C, and D1 received 1, 3, 6, and 9 GEN-001 capsules (1 × 10¹¹ colony forming units), respectively, without dietary adjustment, whereas group D2 received 9 GEN-001 capsules with dietary adjustment. All groups received a single dose. Fecal samples were collected 2 days before GEN-001 administration to 7 days after for untargeted metabolomics and gut microbial metagenomic analyses; blood samples were collected simultaneously for immunogenicity analysis. Levels of phenylalanine, tyrosine, cholic acid, deoxycholic acid, and tryptophan were significantly increased at 5-6 days after GEN-001 administration when compared with predose levels. Compared with predose, the relative abundance (%) of Parabacteroides and Alistipes significantly decreased, whereas that of Lactobacillus and Lactococcus increased; Lactobacillus and tryptophan levels were negatively correlated. A single administration of GEN-001 shifted the gut microbiota in healthy volunteers to a more balanced state as evidenced by an increased abundance of beneficial bacteria, including Lactobacillus, and higher levels of the metabolites that have immunogenic properties.

• Journal of Life Science
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• v.29 no.9
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• pp.986-995
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• 2019

Intestinal microbiota play a key role in maintaining the host's health, and variety and richness of this microbiota is directly influenced and modulated by the host's diet. Kimchi is a fermented food rich in dietary fibers and lactic acid bacteria (LAB). To investigate the effect of fermented kimchi on the host's response and the composition of intestinal microbiota, 45 male Sprague-Dawley rats six weeks old were divided into three experimental groups that received either a basal diet (CON) or a basal diet supplemented with fermented kimchi (FK) or chitosan-added fermented kimchi (CFK) for four weeks. Body weights and feed intakes were measured weekly, and the intestinal contents were collected aseptically and were used for 16S rRNA gene profiling via pyrosequencing. As compared to the control, FK and CFK groups showed less body weight gain, feed efficiency, and blood triglyceride concentration. The diversity of intestinal microbiota was increased in both FK and CFK as compared to the control. At the phylum level, obesity-associated Firmicutes decreased, while leanness-associated Bacteroidetes increased. At the genus-level, the genera that consist of LAB, leanness-associated bacteria, and butyric acid-producing bacteria increased in FK and CFK as compared to the control. The overall results suggest that the consumption of fermented kimchi can reduce obesity and promote the host's health through mechanisms involving the modulation of intestinal microbiota.

• Biomedical Science Letters
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• v.22 no.4
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• pp.150-159
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• 2016

Knowledge of the distribution and biodiversity of environmental bacteria and the ecosystem that influences them is crucial for predicting an ecosystem. However, bacterial culture methods can only analyze approximately 0.1% of the existing microorganisms, those that are readily cultured under laboratory conditions. By contrast, next-generation sequencing (NGS) has generally been known to obtain more diverse profiling of bacterial composition. We compared the bacterial communities using both a culture-dependent (MALDI-TOF) and culture-independent (NGS) methods. Environmental specimens were obtained from both freshwater and seawater. Water samples were also analyzed by both pyrosequencing and MiSeq sequencing, in order to select one NGS platform which could analyze comparatively more diverse microbiota. Bacterial distribution analyzed with MALDI-TOF showed no difference between the microbiota of freshwater and seawater, whereas the results analyzed with NGS distinguished between the two. The diversity indexes of MiSeq sequencing were higher than for Pyrosequencing. This indicated that MiSeq sequencing is capable of analyzing a comparatively wider diversity of bacteria. The genus of Flavobacterium and Planktophila were identified as being unique to freshwater, whereas EU801223 and OM43 were found in the seawater. Difference between the bacterial composition of the freshwater and seawater environments was identified by MiSeq sequencing analysis.