1
|
Sheng Y, Wang J, Gao Y, Peng Y, Li X, Huang W, Zhou H, Liu R, Zhang W. Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries. Comput Struct Biotechnol J 2024; 23:87-95. [PMID: 38116074 PMCID: PMC10730331 DOI: 10.1016/j.csbj.2023.11.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
Despite extensive research on the gut microbiome of healthy individuals from a single country, there are still a limited number of population-level comparative studies. Moreover, the sequencing approach used in most related studies involves 16 S ribosomal RNA (rRNA) sequencing with a limited resolution, which cannot provide detailed functional profiles. In the present study, we applied a combined analysis approach to analyze whole metagenomic shotgun sequencing data from 2035 healthy adult samples from six countries across four continents. Analysis of core species revealed that 13 species were present in more than 90 % of all investigated individuals, the majority of which produced short-chain fatty acids (SCFA)-producing bacteria. Our analysis revealed consistently significant differences in gut microbial species and pathways between Western and non-Western countries, such as Escherichia coli and the relation of MetaCyc pathways to the TCA cycle. Specific changes in microbial species and pathways are potentially related to lifestyle and diet. Furthermore, we identified several noteworthy microbial species and pathways that exhibit distinct characteristics specific to China. Interestingly, we observed that China (CHN) was more similar to the United States (USA) and United Kingdom (GBR) in terms of the taxonomic and functional composition of the gut microbiome than India (IND) and Madagascar (MDG), which were more similar to the China (CHN) diet. The current study identified consistent microbial features associated with population and geography, which will inspire further clinical translations that consider paying attention to differences in microbiota backgrounds and confounding factors.
Collapse
Affiliation(s)
- Yanghao Sheng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jue Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yongchao Gao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Yilei Peng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Xiong Li
- Center for Clinical Precision Pharmacy, School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Center for Clinical Precision Pharmacy, School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
- The First Affifiliated Hospital of Shantou University Medical College, Shantou, China
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education, Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, China
| |
Collapse
|
2
|
Han H, Lee HJ, Kim KS, Chung J, Na HS. Comparison of the performance of MiSeq and NovaSeq in oral microbiome study. J Oral Microbiol 2024; 16:2344293. [PMID: 38645704 PMCID: PMC11028001 DOI: 10.1080/20002297.2024.2344293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/15/2024] [Indexed: 04/23/2024] Open
Abstract
Objective Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is most commonly used to analyze the microbiome due to its relatively long read length. Illumina also introduced the 250 × 2 chip for NovaSeq. The purpose of this study was to compare the performance of MiSeq and NovaSeq in the context of oral microbiome study. Methods Total read count, read quality score, relative bacterial abundance, community diversity, and correlation between two platforms were analyzed. Phylogenetic trees were analyzed for Streptococcus and periodontopathogens. Results NovaSeq produced significantly more read counts and assigned more operational taxonomic units (OTUs) compared to MiSeq. Community diversity was similar between MiSeq and NovaSeq. NovaSeq were able to detect more unique OTUs compared to MiSeq. When phylogenetic trees were constructed for Streptococcus and periodontopathogens, both platforms detected OTUs for most of the clades. Conclusion Taken together, while both MiSeq and NovaSeq platforms effectively characterize the oral microbiome, NovaSeq outperformed MiSeq in terms of read counts and detection of unique OTUs, highlighting its potential as a valuable tool for large scale oral microbiome studies.
Collapse
Affiliation(s)
- Hyejung Han
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Keun-Suh Kim
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Jin Chung
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
| | - Hee Sam Na
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
| |
Collapse
|
3
|
Seo B, Jeon K, Kim WK, Jang YJ, Cha KH, Ko G. Strain-Specific Anti-Inflammatory Effects of Faecalibacterium prausnitzii Strain KBL1027 in Koreans. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10213-7. [PMID: 38411865 DOI: 10.1007/s12602-024-10213-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2024] [Indexed: 02/28/2024]
Abstract
Faecalibacterium prausnitzii is one of the most dominant commensal bacteria in the human gut, and certain anti-inflammatory functions have been attributed to a single microbial anti-inflammatory molecule (MAM). Simultaneously, substantial diversity among F. prausnitzii strains is acknowledged, emphasizing the need for strain-level functional studies aimed at developing innovative probiotics. Here, two distinct F. prausnitzii strains, KBL1026 and KBL1027, were isolated from Korean donors, exhibiting notable differences in the relative abundance of F. prausnitzii. Both strains were identified as the core Faecalibacterium amplicon sequence variant (ASV) within the healthy Korean cohort, and their MAM sequences showed a high similarity of 98.6%. However, when a single strain was introduced to mice with dextran sulfate sodium (DSS)-induced colitis, KBL1027 showed the most significant ameliorative effects, including alleviation of colonic inflammation and restoration of gut microbial dysbiosis. Moreover, the supernatant from KBL1027 elevated the secretion of IL-10 cytokine more than that of KBL1026 in mouse bone marrow-derived macrophage (BMDM) cells, suggesting that the strain-specific, anti-inflammatory efficacy of KBL1027 might involve effector compounds other than MAM. Through analysis of the Faecalibacterium pan-genome and comparative genomics, strain-specific functions related to extracellular polysaccharide biosynthesis were identified in KBL1027, which could contribute to the observed morphological disparities. Collectively, our findings highlight the strain-specific, anti-inflammatory functions of F. prausnitzii, even within the same core ASV, emphasizing the influence of their human origin.
Collapse
Affiliation(s)
- Boram Seo
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- Personalized Diet Research Group, Food Functionality Research Division, Korea Food Research Institute, Jeollabuk-do, Republic of Korea
| | - Kyungchan Jeon
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Woon-Ki Kim
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - You Jin Jang
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Kwang Hyun Cha
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea.
- N-Bio, Seoul National University, Seoul, Republic of Korea.
- Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea.
- KoBioLabs Inc., Seoul, Republic of Korea.
| |
Collapse
|
4
|
Abstract
As the proportion of older people in the world's population steadily increases, there is an urgent need to identify ways to support healthy aging. The gut microbiome has been proposed to be involved in aging-related diseases and has become an attractive target for improving health in older people. Herein, we cover the relationship between the gut microbiome and chronological age in adults, and then, we discuss the gut microbiome features associated with frailty, as a hallmark of unhealthy aging in older people. Furthermore, we describe the effects of microbiome-targeted interventions, such as dietary patterns and consumption of probiotics, prebiotics, and synbiotics, on modulating the gut microbiome composition and further promoting healthy aging. Further studies are needed to explore the underlying mechanisms of gut microbiome-induced aging complications and to develop personalized microbiome-based strategies for reducing the severity of frailty or preventing the onset of frailty in older adults.
Collapse
Affiliation(s)
- Mi Young Lim
- Personalized Diet Research Group, Korea Food Research Institute, Jeollabuk-do, Republic of Korea
| | - Young-Do Nam
- Personalized Diet Research Group, Korea Food Research Institute, Jeollabuk-do, Republic of Korea
| |
Collapse
|
5
|
Kong T, Fan X, Tran NT. Changes in Hemolymph Microbiota of Chinese Mitten Crab ( Eriocheir sinensis) in Response to Aeromonas hydrophila or Staphylococcus aureus Infection. Animals (Basel) 2023; 13:3058. [PMID: 37835665 PMCID: PMC10571569 DOI: 10.3390/ani13193058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
The Chinese mitten crab (Eriocheir sinensis) has significant economic potential in both the Chinese domestic and global markets. The hemolymph microbiota is known to play a critical role in regulating physiological and biochemical functions in crustaceans. However, the study of the hemolymph microbiota of E. sinensis in response to infections has not been undertaken. In this study, changes in the composition and function of the hemolymph microbiota in E. sinensis infected with either Staphylococcus aureus (Sa) or Aeromonas hydrophila (Ah) were investigated using 16S rRNA sequencing, with a phosphate buffer saline (PBS) injection serving as the control. Results showed that the dominant hemolymph microbiota of E. sinensis were Proteobacteria, Bacteroidota, and Firmicutes. The relative abundance of the phyla Firmicutes, Bdellovibrionota, and Myxococcota was significantly reduced in both Sa and Ah groups compared to the PBS group. At the genus level, compared to the PBS group, a significant increase in the abundance of Flavobacterium and Aeromonas was found in both Ah and Sa groups. The analysis of the functional profile showed that pathways related to 'cell growth and death', 'metabolism of terpenoids and polyketides', 'cancers', 'lipid metabolism', 'neurodegenerative diseases', 'metabolism of other amino acids', 'xenobiotics biodegradation and metabolism', and 'circulatory system and endocrine system' were predominant in the Ah group. Meanwhile, pathways related to 'metabolism or genetic information progressing', such as 'translation', 'metabolic diseases', and 'cellular processes and signaling', were enriched in the Sa group. This study revealed the effects of pathogens (S. aureus or A. hydrophila) on the maintenance of the hemolymph microbiota in E. sinensis. It shed light on the mechanisms employed by the hemolymph microbiota of E. sinensis under pathogen stimulation.
Collapse
Affiliation(s)
- Tongtong Kong
- School of Life Sciences, Qufu Normal University, Qufu 273165, China; (T.K.)
| | - Xinyue Fan
- School of Life Sciences, Qufu Normal University, Qufu 273165, China; (T.K.)
| | - Ngoc Tuan Tran
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou 515063, China
- Institute of Marine Sciences, Shantou University, Shantou 515063, China
| |
Collapse
|
6
|
Kim H, Kim J, Choi JW, Ahn KS, Park DI, Kim S. A streamlined pipeline based on HmmUFOtu for microbial community profiling using 16S rRNA amplicon sequencing. Genomics Inform 2023; 21:e40. [PMID: 37813636 PMCID: PMC10584646 DOI: 10.5808/gi.23044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 06/25/2023] [Indexed: 10/11/2023] Open
Abstract
Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We present a streamlined pipeline that integrates FastP for read trimming, HmmUFOtu for operational taxonomic units (OTU) clustering, Vsearch for chimera checking, and Kraken2 for taxonomic assignment. To assess the pipeline's performance, we reprocessed two published stool datasets of normal Korean populations: one with 890 and the other with 1,462 independent samples. In the first dataset, HmmUFOtu retained 93.2% of over 104 million read pairs after quality trimming, discarding chimeric or unclassifiable reads, while DADA2, a commonly used ASV method, retained only 44.6% of the reads. Nonetheless, both methods yielded qualitatively similar β-diversity plots. For the second dataset, HmmUFOtu retained 89.2% of read pairs, while DADA2 retained a mere 18.4% of the reads. HmmUFOtu, being a closed-reference clustering method, facilitates merging separately processed datasets, with shared OTUs between the two datasets exhibiting a correlation coefficient of 0.92 in total abundance (log scale). While the first two dimensions of the β-diversity plot exhibited a cohesive mixture of the two datasets, the third dimension revealed the presence of a batch effect. Our comparative evaluation of ASV and OTU methods within this streamlined pipeline provides valuable insights into their performance when processing large-scale microbial 16S rRNA amplicon sequencing data. The strengths of HmmUFOtu and its potential for dataset merging are highlighted.
Collapse
Affiliation(s)
- Hyeonwoo Kim
- Department of Bioinformatics, Soongsil University, Seoul 06978, Korea
| | - Jiwon Kim
- Department of Bioinformatics, Soongsil University, Seoul 06978, Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
- Functional Genome Institute, PDXen Biosystems, Co., Daejeon 34027, Korea
| | - Kwang-Sung Ahn
- Functional Genome Institute, PDXen Biosystems, Co., Daejeon 34027, Korea
| | - Dong-Il Park
- Division of Gastroenterology, Department of Internal Medicine and Inflammatory Bowel Disease Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea
| | - Sangsoo Kim
- Department of Bioinformatics, Soongsil University, Seoul 06978, Korea
| |
Collapse
|
7
|
Yin P, Zhang C, Du T, Yi S, Yu L, Tian F, Chen W, Zhai Q. Meta-analysis reveals different functional characteristics of human gut Bifidobacteria associated with habitual diet. Food Res Int 2023; 170:112981. [PMID: 37316017 DOI: 10.1016/j.foodres.2023.112981] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 05/03/2023] [Accepted: 05/13/2023] [Indexed: 06/16/2023]
Abstract
Dietary habits contribute to the composition and function of the gut microbiota. Different dietary structures, including vegan, vegetarian, and omnivorous diets, affect intestinal Bifidobacteria; however, the relationship between Bifidobacterial function and host metabolism in subjects with different dietary patterns is unclear. Here, we analyzed five metagenomics studies and six 16S sequencing studies, including 206 vegetarians (VG), 249 omnivores (O), and 270 vegans (V), through an unbiased theme-level meta-analysis framework and discovered that diet significantly affects the composition and functionality of intestinal Bifidobacteria. The relative abundance of Bifidobacterium pseudocatenulatum was significantly higher in V than in O and Bifidobacterium longum, Bifidobacterium adolescentis, and B. pseudocatenulatum differed significantly in carbohydrate transport and metabolism in subjects with different diet types. Diets high in fiber were associated with B. longum with increased capacity for carbohydrate catabolism and genes encoding GH29 and GH43_27 were significantly enriched in V. Bifidobacterium adolescentis and B. pseudocatenulatum, associated with O, had a higher prevalence of the genes related to carbohydrate transport and metabolism, which showed the enrichment of GH26 and GH27 families. The same Bifidobacterium species has different functions in subjects with different diet types, resulting in different physiological significance. The diversification and functionalities of Bifidobacterial species in the gut microbiome can be influenced by the host diet and this aspect should be considered when studying host-microbe associations.
Collapse
Affiliation(s)
- Pingping Yin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ting Du
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Shanrong Yi
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
8
|
Lim MY, Kim JH, Nam YD. Oral microbiome correlates with selected clinical biomarkers in individuals with no significant systemic disease. Front Cell Infect Microbiol 2023; 13:1114014. [PMID: 37065205 PMCID: PMC10102430 DOI: 10.3389/fcimb.2023.1114014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
The oral microbiome is an important component of the microbiome in the human body. Although the association of the oral microbiome with various diseases, including periodontitis and cancer, has been reported, information on how the oral microbiome is related to health-related indicators in healthy populations is still insufficient. In this study, we examined the associations of the oral microbiome with 15 metabolic and 19 complete blood count (CBC)-based markers in 692 healthy Korean individuals. The richness of the oral microbiome was associated with four CBC markers and one metabolic marker. Compositional variation in the oral microbiome was significantly explained by four markers: fasting glucose, fasting insulin, white blood cell count, and total leukocyte count. Furthermore, we found that these biomarkers were associated with the relative abundances of numerous microbial genera, such as Treponema, TG5, and Tannerella. By identifying the relationship between the oral microbiome and clinical biomarkers in a healthy population, our study presents a direction for future studies on oral microbiome-based diagnosis and interventions.
Collapse
Affiliation(s)
- Mi Young Lim
- Personalized Diet Research Group, Korea Food Research Institute, Jeollabuk-do, Republic of Korea
| | - Jung-Ha Kim
- Department of Family Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Young-Do Nam
- Personalized Diet Research Group, Korea Food Research Institute, Jeollabuk-do, Republic of Korea
- *Correspondence: Young-Do Nam,
| |
Collapse
|
9
|
Shin JH, Lee Y, Song EJ, Lee D, Jang SY, Byeon HR, Hong MG, Lee SN, Kim HJ, Seo JG, Jun DW, Nam YD. Faecalibacterium prausnitzii prevents hepatic damage in a mouse model of NASH induced by a high-fructose high-fat diet. Front Microbiol 2023; 14:1123547. [PMID: 37007480 PMCID: PMC10060964 DOI: 10.3389/fmicb.2023.1123547] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
IntroductionNonalcoholic steatohepatitis (NASH) is an advanced nonalcoholic fatty liver disease characterized by chronic inflammation and fibrosis. A dysbiosis of the gut microbiota has been associated with the pathophysiology of NASH, and probiotics have proven helpful in its treatment and prevention. Although both traditional and next-generation probiotics have the potential to alleviate various diseases, studies that observe the therapeutic effect of next-generation probiotics on NASH are lacking. Therefore, we investigated whether a next-generation probiotic candidate, Faecalibacterium prausnitzii, contributed to the mitigation of NASH.MethodsIn this study, we conducted 16S rRNA sequencing analyses in patients with NASH and healthy controls. To test F. prausnitzii could alleviate NASH symptoms, we isolated four F. prausnitzii strains (EB-FPDK3, EB-FPDK9, EB-FPDK11, and EB-FPYYK1) from fecal samples collected from four healthy individuals. Mice were maintained on a high-fructose high-fat diet for 16 weeks to induce a NASH model and received oral administration of the bacterial strains. Changes in characteristic NASH phenotypes were assessed via oral glucose tolerance tests, biochemical assays, and histological analyses.Results16S rRNA sequencing analyses confirmed that the relative abundance of F. prausnitzii reduced significantly in patients with NASH compared to healthy controls (p < 0.05). In the NASH mice, F. prausnitzii supplementation improved glucose homeostasis, prevented hepatic lipid accumulation, curbed liver damage and fibrosis, restored damaged gut barrier functions, and alleviated hepatic steatosis and liver inflammation. Furthermore, real-time PCR assays documented that the four F. prausnitzii strains regulated the expression of genes related to hepatic steatosis in these mice.DiscussionOur study, therefore, confirms that the administration of F. prausnitzii bacteria can alleviate NASH symptoms. We propose that F. prausnitzii has the potential to contribute to the next-generation probiotic treatment of NASH.
Collapse
Affiliation(s)
- Ji-Hee Shin
- Research Group of Personalized Diet, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Yoonmi Lee
- R&D Center, Enterobiome Inc., Goyang-si, Republic of Korea
| | - Eun-Ji Song
- Research Group of Personalized Diet, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Dokyung Lee
- R&D Center, Enterobiome Inc., Goyang-si, Republic of Korea
| | - Seo-Yul Jang
- R&D Center, Enterobiome Inc., Goyang-si, Republic of Korea
| | - Hye Rim Byeon
- R&D Center, Enterobiome Inc., Goyang-si, Republic of Korea
| | - Moon-Gi Hong
- R&D Center, Enterobiome Inc., Goyang-si, Republic of Korea
| | - Sang-Nam Lee
- R&D Center, Enterobiome Inc., Goyang-si, Republic of Korea
| | - Hyun-Jin Kim
- Division of Applied Life Science (BK21 Four), Institute of Agriculture and Life Science, Gyeongsang National University, Jinju-si, Republic of Korea
| | - Jae-Gu Seo
- R&D Center, Enterobiome Inc., Goyang-si, Republic of Korea
- *Correspondence: Jae-Gu Seo,
| | - Dae Won Jun
- Department of Internal Medicine, Hanyang University, College of Medicine, Seoul, Republic of Korea
- Dae Won Jun,
| | - Young-Do Nam
- Research Group of Personalized Diet, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, Republic of Korea
- Young-Do Nam,
| |
Collapse
|
10
|
Jang HH, Noh H, Kim G, Cho SY, Kim HJ, Choe JS, Kim J, Scalbert A, Gunter MJ, Kwon O, Kim H. Differences in dietary patterns related to metabolic health by gut microbial enterotypes of Korean adults. Front Nutr 2023; 9:1045397. [PMID: 36687725 PMCID: PMC9853283 DOI: 10.3389/fnut.2022.1045397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/13/2022] [Indexed: 01/07/2023] Open
Abstract
Diet has a profound impact on the progression of metabolic syndrome (MetS) into various diseases. The gut microbiota could modulate the effect of diet on metabolic health. We examined whether dietary patterns related to MetS differed according to gut microbial enterotypes among 348 Korean adults aged 18-60 years recruited between 2018∼2021 in a cross-sectional study. The enterotype of each participant was identified based on 16S rRNA gut microbiota data. The main dietary pattern predicting MetS (MetS-DP) of each enterotype was derived using reduced-rank regression (RRR) models. In the RRR models, 27 food group intakes assessed by a semi-quantitative food frequency questionnaire and MetS prediction markers including triglyceride to high-density lipoprotein cholesterol (TG/HDL) ratio and homeostatic model assessment for insulin resistance (HOMA-IR) were used as predictor and response variables, respectively. The MetS-DP extracted in Bacteroides enterotype (B-type) was characterized by high consumption of refined white rice and low consumption of eggs, vegetables, and mushrooms. The MetS-DP derived among Prevotella enterotype (P-type) was characterized by a high intake of sugary food and low intakes of bread, fermented legumes, and fermented vegetables. The MetS-DP of B-type was positively associated with metabolic unhealthy status (OR T3 vs. T1 = 3.5; 95% CI = 1.5-8.2), comparing the highest tertile to the lowest tertile. Although it was not significantly associated with overall metabolic unhealthy status, the MetS-DP of P-type was positively associated with hyperglycemia risk (OR T3 vs. T1 = 6.2; 95% CI = 1.6-24.3). These results suggest that MetS-DP may differ according to the gut microbial enterotype of each individual. If such associations are found to be causal, personalized nutrition guidelines based on the enterotypes could be recommended to prevent MetS.
Collapse
Affiliation(s)
- Hwan-Hee Jang
- National Institute of Agricultural Sciences, Rural Development Administration (NAS-RDA), Wanju, Jeollabuk-do, Republic of Korea
| | - Hwayoung Noh
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
- Department of Cancer Prevention and Environment, Léon Bérard Cancer Center, L’Institut National de la Santé et de la Recherche Médicale (INSERM) U1296, Lyon, France
| | - Gichang Kim
- National Institute of Agricultural Sciences, Rural Development Administration (NAS-RDA), Wanju, Jeollabuk-do, Republic of Korea
| | - Su-Yeon Cho
- National Institute of Agricultural Sciences, Rural Development Administration (NAS-RDA), Wanju, Jeollabuk-do, Republic of Korea
| | - Hyeon-Jeong Kim
- National Institute of Agricultural Sciences, Rural Development Administration (NAS-RDA), Wanju, Jeollabuk-do, Republic of Korea
| | - Jeong-Sook Choe
- National Institute of Agricultural Sciences, Rural Development Administration (NAS-RDA), Wanju, Jeollabuk-do, Republic of Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Republic of Korea
| | - Augustin Scalbert
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Marc J. Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Oran Kwon
- Graduate Program in System Health Science and Engineering, Department of Nutritional Science and Food Management, Ewha Womans University, Seoul, Republic of Korea
| | - Hyesook Kim
- Graduate Program in System Health Science and Engineering, Department of Nutritional Science and Food Management, Ewha Womans University, Seoul, Republic of Korea
| |
Collapse
|
11
|
Oh S, Lee J, Chun S, Choi JE, Kim MN, Chon YE, Ha Y, Hwang SG, Choi SW, Hong KW. Interaction between the PNPLA3 Gene and Nutritional Factors on NAFLD Development: The Korean Genome and Epidemiology Study. Nutrients 2022; 15:nu15010152. [PMID: 36615809 PMCID: PMC9824262 DOI: 10.3390/nu15010152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Genetic and nutritional factors contribute to the development of non-alcoholic fatty liver disease (NAFLD); however, gene-diet interactions in NAFLD development are poorly understood. In this case-control study, a large dataset from the Korean Genome and Epidemiology Study cohort (n = 72,299) comprising genomic data, medical records, social history, and dietary data was used. We investigated the interactions between the PNPLA3 rs738409 genotype and nutritional factors and their possible effect on the risk of NAFLD development in 2950 patients with NAFLD and 12,907 controls. In the PNPLA3 risk allele group, high protein, fat, sodium, phosphorus, niacin, and vitamin B6 intakes were associated with a decreased risk of NAFLD. In the non-risk allele group, only high fat intake was associated with a decreased risk of NAFLD. Among these nutrients, high sodium intake had a significant protective interaction with the PNPLA3 genotype against NAFLD (p = 0.002). Among salty foods, only kimchi had a significant protective effect against the PNPLA3 genotype (p = 0.012). Thus, the PNPLA3 genotype is differentially associated with nutritional factors. In particular, it interacts with kimchi, a fermented vegetable dish. Therefore, fermented vegetables may serve as a tailored therapeutic food for people with the PNPLA3 risk allele.
Collapse
Affiliation(s)
- Sooyeon Oh
- Chaum Life Center, CHA University School of Medicine, Seoul 06062, Republic of Korea
| | - Jooho Lee
- Department of Gastroenterology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam 13496, Republic of Korea
- Correspondence: (J.L.); (K.-W.H.); Tel.: +82-31-780-1811 (J.L.); +82-10-3922-7089 (K.-W.H.); Fax: +82-31-780-1812 (J.L.); +82-31-888-9440 (K.-W.H.)
| | - Sukyung Chun
- Department of Gastroenterology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam 13496, Republic of Korea
| | - Ja-Eun Choi
- Healthcare R&D Division, Theragen Bio Co., Ltd., Suwon 16229, Republic of Korea
| | - Mi Na Kim
- Department of Gastroenterology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam 13496, Republic of Korea
| | - Young Eun Chon
- Department of Gastroenterology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam 13496, Republic of Korea
| | - Yeonjung Ha
- Department of Gastroenterology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam 13496, Republic of Korea
| | - Seong-Gyu Hwang
- Department of Gastroenterology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam 13496, Republic of Korea
| | - Sang-Woon Choi
- Chaum Life Center, CHA University School of Medicine, Seoul 06062, Republic of Korea
| | - Kyung-Won Hong
- Healthcare R&D Division, Theragen Bio Co., Ltd., Suwon 16229, Republic of Korea
- Correspondence: (J.L.); (K.-W.H.); Tel.: +82-31-780-1811 (J.L.); +82-10-3922-7089 (K.-W.H.); Fax: +82-31-780-1812 (J.L.); +82-31-888-9440 (K.-W.H.)
| |
Collapse
|
12
|
Lee Y, Byeon HR, Jang SY, Hong MG, Kim D, Lee D, Shin JH, Kim Y, Kang SG, Seo JG. Oral administration of Faecalibacterium prausnitzii and Akkermansia muciniphila strains from humans improves atopic dermatitis symptoms in DNCB induced NC/Nga mice. Sci Rep 2022; 12:7324. [PMID: 35513696 PMCID: PMC9072367 DOI: 10.1038/s41598-022-11048-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/11/2022] [Indexed: 12/27/2022] Open
Abstract
Atopic dermatitis (AD) is a common inflammatory skin disease, and its pathogenesis is closely associated with microbial homeostasis in the gut, namely the gut-skin axis. Particularly, recent metagenomics studies revealed that the abundance of two major bacterial species in the gut, Faecalibacterium prausnitzii and Akkermansia muciniphila, may play a critical role in the pathogenesis of AD, but the effect of these species in AD has not yet been elucidated. To evaluate the potential beneficial effect of F. prausnitzii or A. muciniphila in AD, we conducted an animal model study where F. prausnitzii EB-FPDK11 or A. muciniphila EB-AMDK19, isolated from humans, was orally administered to 2,5-dinitrochlorobenzene (DNCB)-induced AD models using NC/Nga mice at a daily dose of 108 CFUs/mouse for six weeks. As a result, the administration of each strain of F. prausnitzii and A. muciniphila improved AD-related markers, such as dermatitis score, scratching behavior, and serum immunoglobulin E level. Also, the F. prausnitzii and A. muciniphila treatments decreased the level of thymic stromal lymphopoietin (TSLP), triggering the production of T helper (Th) 2 cytokines, and improved the imbalance between the Th1 and Th2 immune responses induced by DNCB. Meanwhile, the oral administration of the bacteria enhanced the production of filaggrin in the skin and ZO-1 in the gut barrier, leading to the recovery of functions. Taken together, our findings suggest that F. prausnitzii EB-FPDK11 and A. muciniphila EB-AMDK19 have a therapeutic potential in AD, which should be verified in humans.
Collapse
Affiliation(s)
- Yoonmi Lee
- R&D Center, Enterobiome Inc., 814 Siksa-dong, Ilsandong-gu, Goyang-si, 10326, Korea
| | - Hye Rim Byeon
- R&D Center, Enterobiome Inc., 814 Siksa-dong, Ilsandong-gu, Goyang-si, 10326, Korea
| | - Seo-Yul Jang
- R&D Center, Enterobiome Inc., 814 Siksa-dong, Ilsandong-gu, Goyang-si, 10326, Korea
| | - Moon-Gi Hong
- R&D Center, Enterobiome Inc., 814 Siksa-dong, Ilsandong-gu, Goyang-si, 10326, Korea
| | - Dohak Kim
- R&D Center, Enterobiome Inc., 814 Siksa-dong, Ilsandong-gu, Goyang-si, 10326, Korea
| | - Dokyung Lee
- R&D Center, Enterobiome Inc., 814 Siksa-dong, Ilsandong-gu, Goyang-si, 10326, Korea
| | - Joo-Hyun Shin
- R&D Center, Enterobiome Inc., 814 Siksa-dong, Ilsandong-gu, Goyang-si, 10326, Korea
| | - Yesol Kim
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Korea
| | - Seung-Goo Kang
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Korea
| | - Jae-Gu Seo
- R&D Center, Enterobiome Inc., 814 Siksa-dong, Ilsandong-gu, Goyang-si, 10326, Korea.
| |
Collapse
|
13
|
Yeo LF, Lee SC, Palanisamy UD, Khalid BAK, Ayub Q, Lim SY, Lim YAL, Phipps ME. The Oral, Gut Microbiota and Cardiometabolic Health of Indigenous Orang Asli Communities. Front Cell Infect Microbiol 2022; 12:812345. [PMID: 35531342 PMCID: PMC9074829 DOI: 10.3389/fcimb.2022.812345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
The Orang Asli (OA) of Malaysia have been relatively understudied where little is known about their oral and gut microbiomes. As human health is closely intertwined with the human microbiome, this study first assessed the cardiometabolic health in four OA communities ranging from urban, rural to semi-nomadic hunter-gatherers. The urban Temuan suffered from poorer cardiometabolic health while rural OA communities were undergoing epidemiological transition. The oral microbiota of the OA were characterised by sequencing the V4 region of the 16S rRNA gene. The OA oral microbiota were unexpectedly homogenous, with comparably low alpha diversity across all four communities. The rural Jehai and Temiar PP oral microbiota were enriched for uncharacterised bacteria, exhibiting potential for discoveries. This finding also highlights the importance of including under-represented populations in large cohort studies. The Temuan oral microbiota were also elevated in opportunistic pathogens such as Corynebacterium, Prevotella, and Mogibacterium, suggesting possible oral dysbiosis in these urban settlers. The semi-nomadic Jehai gut microbiota had the highest alpha diversity, while urban Temuan exhibited the lowest. Rural OA gut microbiota were distinct from urban-like microbiota and were elevated in bacteria genera such as Prevotella 2, Prevotella 9, Lachnospiraceae ND3007, and Solobacterium. Urban Temuan microbiota were enriched in Odoribacter, Blautia, Parabacetroides, Bacteroides and Ruminococcacecae UCG-013. This study brings to light the current health trend of these indigenous people who have minimal access to healthcare and lays the groundwork for future, in-depth studies in these populations.
Collapse
Affiliation(s)
- Li-Fang Yeo
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
- *Correspondence: Maude Elvira Phipps, ; Li-Fang Yeo,
| | - Soo Ching Lee
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Uma Devi Palanisamy
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - BAK. Khalid
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Qasim Ayub
- Tropical Medicine and Biology Multidisciplinary Platform, School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
- Monash University Malaysia Genomics Facility, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Shu Yong Lim
- Monash University Malaysia Genomics Facility, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Yvonne AL. Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Maude Elvira Phipps
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
- *Correspondence: Maude Elvira Phipps, ; Li-Fang Yeo,
| |
Collapse
|
14
|
Imdad S, Lim W, Kim JH, Kang C. Intertwined Relationship of Mitochondrial Metabolism, Gut Microbiome and Exercise Potential. Int J Mol Sci 2022; 23:ijms23052679. [PMID: 35269818 PMCID: PMC8910986 DOI: 10.3390/ijms23052679] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 02/04/2023] Open
Abstract
The microbiome has emerged as a key player contributing significantly to the human physiology over the past decades. The potential microbial niche is largely unexplored in the context of exercise enhancing capacity and the related mitochondrial functions. Physical exercise can influence the gut microbiota composition and diversity, whereas a sedentary lifestyle in association with dysbiosis can lead to reduced well-being and diseases. Here, we have elucidated the importance of diverse microbiota, which is associated with an individual's fitness, and moreover, its connection with the organelle, the mitochondria, which is the hub of energy production, signaling, and cellular homeostasis. Microbial by-products, such as short-chain fatty acids, are produced during regular exercise that can enhance the mitochondrial capacity. Therefore, exercise can be employed as a therapeutic intervention to circumvent or subside various metabolic and mitochondria-related diseases. Alternatively, the microbiome-mitochondria axis can be targeted to enhance exercise performance. This review furthers our understanding about the influence of microbiome on the functional capacity of the mitochondria and exercise performance, and the interplay between them.
Collapse
Affiliation(s)
- Saba Imdad
- Molecular Metabolism in Health & Disease, Exercise Physiology Laboratory, Sport Science Research Institute, Inha University, Incheon 22212, Korea;
- Department of Biomedical Laboratory Science, College of Health Science, Cheongju University, Cheongju 28503, Korea
| | - Wonchung Lim
- Department of Sports Medicine, College of Health Science, Cheongju University, Cheongju 28503, Korea;
| | - Jin-Hee Kim
- Department of Biomedical Laboratory Science, College of Health Science, Cheongju University, Cheongju 28503, Korea
- Correspondence: (J.-H.K.); (C.K.)
| | - Chounghun Kang
- Molecular Metabolism in Health & Disease, Exercise Physiology Laboratory, Sport Science Research Institute, Inha University, Incheon 22212, Korea;
- Department of Physical Education, College of Education, Inha University, Incheon 22212, Korea
- Correspondence: (J.-H.K.); (C.K.)
| |
Collapse
|