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] [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
|
Wang YL, Ikuma K, Brown AMV, Deonarine A. Global survey of hgcA-carrying genomes in marine and freshwater sediments: Insights into mercury methylation processes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 352:124117. [PMID: 38714231 DOI: 10.1016/j.envpol.2024.124117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/11/2024] [Accepted: 05/05/2024] [Indexed: 05/09/2024]
Abstract
Mercury (Hg) methylation is a microbially mediated process that produces methylmercury (MeHg), a bioaccumulative neurotoxin. A highly conserved gene pair, hgcAB, is required for Hg methylation, which provides a basis for identifying Hg methylators and evaluating their genomic composition. In this study, we conducted a large-scale omics analysis in which 281 metagenomic freshwater and marine sediment samples from 46 geographic locations across the globe were queried. Specific objectives were to examine the prevalence of Hg methylators, to identify horizontal gene transfer (HGT) events involving hgcAB within Hg methylator communities, and to identify associations between hgcAB and microbial biochemical functions/genes. Hg methylators from the phyla Desulfobacterota and Bacteroidota were dominant in both freshwater and marine sediments while Firmicutes and methanogens belonging to Euryarchaeota were identified only in freshwater sediments. Novel Hg methylators were found in the Phycisphaerae and Planctomycetia classes within the phylum Planctomycetota, including potential hgcA-carrying anammox metagenome-assembled genomes (MAGs) from Candidatus Brocadiia. HGT of hgcA and hgcB were identified in both freshwater and marine methylator communities. Spearman's correlation analysis of methylator genomes suggested that in addition to sulfide, thiosulfate, sulfite, and ammonia may be important parameters for Hg methylation processes in sediments. Overall, our results indicated that the biochemical drivers of Hg methylation vary between marine and freshwater sites, lending insight into the influence of environmental perturbances, such as a changing climate, on Hg methylation processes.
Collapse
Affiliation(s)
- Yong-Li Wang
- Department of Civil, Environmental & Construction Engineering, Texas Tech University, Lubbock, TX, United States
| | - Kaoru Ikuma
- Department of Civil, Construction and Environmental Engineering, Iowa State University, Ames, IA, United States
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Amrika Deonarine
- Department of Civil, Environmental & Construction Engineering, Texas Tech University, Lubbock, TX, United States.
| |
Collapse
|
3
|
Ayayee PA, Wong RY. Zebrafish ( Danio rerio) behavioral phenotypes not underscored by different gut microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596447. [PMID: 38853862 PMCID: PMC11160693 DOI: 10.1101/2024.05.29.596447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Different animal behavioral phenotypes maintained and selectively bred over multiple generations may be underscored by dissimilar gut microbial community compositions or not have any significant dissimilarity in community composition. Operating within the microbiota-gut-brain axis framework, we anticipated differences in gut microbiome profiles between zebrafish (Danio rerio) selectively bred to display the bold and shy personality types. This would highlight gut microbe-mediated effects on host behavior. To this end, we amplified and sequenced a fragment of the 16S rRNA gene from the guts of bold and shy zebrafish individuals (n=10) via Miseq. We uncovered no significant difference in within-group microbial diversity nor between-group microbial community composition of the two behavioral phenotypes. Interestingly, though not statistically different, we determined that the gut microbial community of the bold phenotype was dominated by Burkholderiaceae, Micropepsaceae, and Propionibacteriaceae. In contrast, the shy phenotype was dominated by Beijerinckaceae, Pirelullacaeae, Rhizobiales_Incertis_Sedis, and Rubinishaeraceae. The absence of any significant difference in gut microbiota profiles between the two phenotypes would suggest that in this species, there might exist a stable "core" gut microbiome, regardless of behavioral phenotypes, and or possibly, a limited role for the gut microbiota in modulating this selected-for host behavior. This is the first study to characterize the gut microbial community of distinct innate behavioral phenotypes of the zebrafish (that are not considered dysbiotic states) and not rely on antibiotic or probiotic treatments to induce changes in behavior. Such studies are crucial to our understanding of the modulating impacts of the gut microbiome on normative animal behavior.
Collapse
Affiliation(s)
- Paul A Ayayee
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Ryan Y Wong
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| |
Collapse
|
4
|
Zakharevich NV, Morozov MD, Kanaeva VA, Filippov MS, Zyubko TI, Ivanov AB, Ulyantsev VI, Klimina KM, Olekhnovich EI. Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapy. Life Sci Alliance 2024; 7:e202302480. [PMID: 38448159 PMCID: PMC10917649 DOI: 10.26508/lsa.202302480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 03/08/2024] Open
Abstract
Immunotherapy has proven to be a boon for patients battling metastatic melanoma, significantly improving their clinical condition and overall quality of life. A compelling link between the composition of the gut microbiome and the efficacy of immunotherapy has been established in both animal models and human patients. However, the precise biological mechanisms by which gut microbes influence treatment outcomes remain poorly understood. Using a robust dataset of 680 fecal metagenomes from melanoma patients, a detailed catalog of metagenome-assembled genomes (MAGs) was constructed to explore the compositional and functional properties of the gut microbiome. Our study uncovered significant findings that deepen the understanding of the intricate relationship between gut microbes and the efficacy of melanoma immunotherapy. In particular, we discovered the specific metagenomic profile of patients with favorable treatment outcomes, characterized by a prevalence of MAGs with increased overall metabolic potential and proficiency in polysaccharide utilization, along with those responsible for cobalamin and amino acid production. Furthermore, our investigation of the biosynthetic pathways of short-chain fatty acids, known for their immunomodulatory role, revealed a differential abundance of these pathways among the specific MAGs. Among others, the cobalamin-dependent Wood-Ljungdahl pathway of acetate synthesis was directly associated with responsiveness to melanoma immunotherapy.
Collapse
Affiliation(s)
- Natalia V Zakharevich
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
| | - Maxim D Morozov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
| | - Vera A Kanaeva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
- Moscow Institute of Physics and Technology, Moscow, Russian
| | - Mikhail S Filippov
- https://ror.org/04btxg914 Bioinformatics Institute, Saint Petersburg, Russian
| | - Tatyana I Zyubko
- https://ror.org/04btxg914 Bioinformatics Institute, Saint Petersburg, Russian
| | - Artem B Ivanov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
- ITMO University, Saint Petersburg, Russian
| | | | - Ksenia M Klimina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
| | - Evgenii I Olekhnovich
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian
| |
Collapse
|
5
|
Chang HW, Lee EM, Wang Y, Zhou C, Pruss KM, Henrissat S, Chen RY, Kao C, Hibberd MC, Lynn HM, Webber DM, Crane M, Cheng J, Rodionov DA, Arzamasov AA, Castillo JJ, Couture G, Chen Y, Balcazo NP, Lebrilla CB, Terrapon N, Henrissat B, Ilkayeva O, Muehlbauer MJ, Newgard CB, Mostafa I, Das S, Mahfuz M, Osterman AL, Barratt MJ, Ahmed T, Gordon JI. Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition. Nat Microbiol 2024; 9:922-937. [PMID: 38503977 PMCID: PMC10994852 DOI: 10.1038/s41564-024-01628-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/31/2024] [Indexed: 03/21/2024]
Abstract
Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, improved weight gain in malnourished Bangladeshi children compared to a more calorically dense standard nutritional intervention. Metagenome-assembled genomes from study participants revealed a correlation between ponderal growth and expression of MDCF-2 glycan utilization pathways by Prevotella copri strains. To test this correlation, here we use gnotobiotic mice colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains, with or without P. copri isolates closely matching the metagenome-assembled genomes. Combining gut metagenomics and metatranscriptomics with host single-nucleus RNA sequencing and gut metabolomic analyses, we identify a key role of P. copri in metabolizing MDCF-2 glycans and uncover its interactions with other microbes including Bifidobacterium infantis. P. copri-containing consortia mediated weight gain and modulated energy metabolism within intestinal epithelial cells. Our results reveal structure-function relationships between MDCF-2 and members of the gut microbiota of malnourished children with potential implications for future therapies.
Collapse
Affiliation(s)
- Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Evan M Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Kali M Pruss
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Clara Kao
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hannah M Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel M Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marie Crane
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Chemistry, University of California, Davis, CA, USA
| | - Nikita P Balcazo
- Department of Chemistry, University of California, Davis, CA, USA
| | | | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Michael J Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
6
|
Koch F, Reyer H, Görs S, Hansen C, Wimmers K, Kuhla B. Heat stress and feeding effects on the mucosa-associated and digesta microbiome and their relationship to plasma and digesta fluid metabolites in the jejunum of dairy cows. J Dairy Sci 2024:S0022-0302(24)00520-4. [PMID: 38431250 DOI: 10.3168/jds.2023-24242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/25/2024] [Indexed: 03/05/2024]
Abstract
The intestinal microbiota plays a pivotal role in digestive processes and maintains gut health and intestinal homeostasis. These functions may be compromised by increased environmental heat which in turn reduces feed intake and gut integrity, while activating the intestinal immune system. It remains unknown whether high ambient temperatures, causing heat stress (HS) to dairy cows, disturb the eubiosis of the microbial community and if so, to which extent the reduction in feed intake and the impairment of circulating and intestinal metabolites account for the alterations of the jejunal microbiota. To address these questions, jejunal digesta, mucosa, and plasma samples from cows exposed to heat stress (HS: 28°C, temperature-humidity-index (THI) = 76, n = 10), control conditions (CON: 16°C, THI = 60, n = 10), or pair-feeding (PF: 16°C, THI = 60, n = 10) for 7 d were collected. Digesta fluids were examined for pH, acetate, nonesterified fatty acids (NEFA), glucose, and lactate, while plasma samples were analyzed for glucose, lactate, β-hydroxybutyrate (BHB), triglycerides, NEFA, creatinine and urea. The microbiota of digesta and mucosa samples were analyzed by 16S rRNA sequencing. The α diversity was higher in mucosa than digesta, but not affected by high ambient temperatures. However, the mucosa-associated microbiota appears more responsive to ambient heat than the digesta microbiome. The adaptive responses under HS conditions comprised an increased mucosal abundance of Bifidobacteriaceae, Succinivibrionaceae UCG-001, Clostridia and Lactobacillus. In the digesta, HS has exerted effects on microbial abundance of Colidextribacter and Lachnospiraceae UCG-008. Several correlations between plasma or intestinal metabolites and microbiota were elucidated, including Methanobacteriaceae correlating positively with plasma BHB and digesta glucose concentrations. Moreover, the reduction in feed intake during HS had non-negligible effects on microbial diversity and the abundance of certain taxa, underpinning the importance of nutrient supply on maintaining intestinal homeostasis.
Collapse
Affiliation(s)
- Franziska Koch
- Institute for Farm Animal Biology (FBN), Institute of Nutritional Physiology "Oskar Kellner," Dummerstorf, Germany
| | - Henry Reyer
- Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
| | - Solvig Görs
- Institute for Farm Animal Biology (FBN), Institute of Nutritional Physiology "Oskar Kellner," Dummerstorf, Germany
| | - Christiane Hansen
- State Research Institute for Agriculture and Fisheries, Institute for Animal Production, Dummerstorf, Germany
| | - Klaus Wimmers
- Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
| | - Björn Kuhla
- Institute for Farm Animal Biology (FBN), Institute of Nutritional Physiology "Oskar Kellner," Dummerstorf, Germany.
| |
Collapse
|
7
|
Price CE, Valls RA, Ramsey AR, Loeven NA, Jones JT, Barrack KE, Schwartzman JD, Royce DB, Cramer RA, Madan JC, Ross BD, Bliska J, O'Toole GA. Intestinal Bacteroides modulates inflammation, systemic cytokines, and microbial ecology via propionate in a mouse model of cystic fibrosis. mBio 2024; 15:e0314423. [PMID: 38179971 PMCID: PMC10865972 DOI: 10.1128/mbio.03144-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024] Open
Abstract
Persons with cystic fibrosis (CF), starting in early life, show intestinal microbiome dysbiosis characterized in part by a decreased relative abundance of the genus Bacteroides. Bacteroides is a major producer of the intestinal short chain fatty acid propionate. We demonstrate here that cystic fibrosis transmembrane conductance regulator-defective (CFTR-/-) Caco-2 intestinal epithelial cells are responsive to the anti-inflammatory effects of propionate. Furthermore, Bacteroides isolates inhibit the IL-1β-induced inflammatory response of CFTR-/- Caco-2 intestinal epithelial cells and do so in a propionate-dependent manner. The introduction of Bacteroides-supplemented stool from infants with cystic fibrosis into the gut of CftrF508del mice results in higher propionate in the stool as well as the reduction in several systemic pro-inflammatory cytokines. Bacteroides supplementation also reduced the fecal relative abundance of Escherichia coli, indicating a potential interaction between these two microbes, consistent with previous clinical studies. For a Bacteroides propionate mutant in the mouse model, pro-inflammatory cytokine KC is higher in the airway and serum compared with the wild-type (WT) strain, with no significant difference in the absolute abundance of these two strains. Taken together, our data indicate the potential multiple roles of Bacteroides-derived propionate in the modulation of systemic and airway inflammation and mediating the intestinal ecology of infants and children with CF. The roles of Bacteroides and the propionate it produces may help explain the observed gut-lung axis in CF and could guide the development of probiotics to mitigate systemic and airway inflammation for persons with CF.IMPORTANCEThe composition of the gut microbiome in persons with CF is correlated with lung health outcomes, a phenomenon referred to as the gut-lung axis. Here, we demonstrate that the intestinal microbe Bacteroides decreases inflammation through the production of the short-chain fatty acid propionate. Supplementing the levels of Bacteroides in an animal model of CF is associated with reduced systemic inflammation and reduction in the relative abundance of the opportunistically pathogenic group Escherichia/Shigella in the gut. Taken together, these data demonstrate a key role for Bacteroides and microbially produced propionate in modulating inflammation, gut microbial ecology, and the gut-lung axis in cystic fibrosis. These data support the role of Bacteroides as a potential probiotic in CF.
Collapse
Affiliation(s)
- Courtney E. Price
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Rebecca A. Valls
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Alexis R. Ramsey
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Nicole A. Loeven
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Jane T. Jones
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Kaitlyn E. Barrack
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | | | - Darlene B. Royce
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Robert A. Cramer
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Juliette C. Madan
- Department of Psychiatry, Geisel School of Medicine at Dartmouth, Hanove, USA
| | - Benjamin D. Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - James Bliska
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - George A. O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| |
Collapse
|
8
|
Xu L, Tang Z, Herrera-Balandrano DD, Qiu Z, Li B, Yang Y, Huang W. In vitro fermentation characteristics of blueberry anthocyanins and their impacts on gut microbiota from obese human. Food Res Int 2024; 176:113761. [PMID: 38163698 DOI: 10.1016/j.foodres.2023.113761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/06/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024]
Abstract
It has been demonstrated that the gut microbiota may play an important intermediary role in anthocyanins' beneficial impacts on obesity. However, the microbe-related anti-obesity mechanism of blueberry anthocyanins remains unclear. In this study, the interactions between blueberry anthocyanin extracts (BAE) and gut microbiota from obese humans were explored using an in vitro fermentation model. Due to hydrolysis and metabolism by the microbiota, the contents of blueberry anthocyanins are reduced during fermentation. It was demonstrated that both aglycones and glycosides affected the degradation rate. The microbial composition evaluation revealed that BAE could alleviate obesity by promoting the colonization of probiotics such as Lachnospiraceae_UCG-004 and Bacteroides, as well as inhibiting the proliferation of harmful bacteria including Escherichia-Shigella, Clostridium_sensu_stricto_1, and Klebsiella. Blueberry anthocyanin extracts facilitate the production of short-chain fatty acids (SCFAs), which is beneficial for obesity control. The relationship between blueberry anthocyanins, gut microbiota, and SCFAs was further investigated. Overall, this data provides new insights into the positive interaction between blueberry anthocyanins and gut microbiota in obese humans.
Collapse
Affiliation(s)
- Lujing Xu
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China.
| | - Zhaocheng Tang
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China.
| | | | - Zeyu Qiu
- Provincial Key Laboratory of Agrobiology and Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China.
| | - Bin Li
- College of Food Science, Shenyang Agricultural University, Liaoning 110866, PR China.
| | - Yiyun Yang
- Zhejiang Lanmei Technology Co., Ltd, Zhuji 311899, PR China.
| | - Wuyang Huang
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China.
| |
Collapse
|
9
|
Ahmad AF, Caparrós-Martin JA, Gray N, Lodge S, Wist J, Lee S, O'Gara F, Dwivedi G, Ward NC. Gut microbiota and metabolomics profiles in patients with chronic stable angina and acute coronary syndrome. Physiol Genomics 2024; 56:48-64. [PMID: 37811721 DOI: 10.1152/physiolgenomics.00072.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death worldwide. The gut microbiota and its associated metabolites may be involved in the development and progression of CVD, although the mechanisms and impact on clinical outcomes are not fully understood. This study investigated the gut microbiome profile and associated metabolites in patients with chronic stable angina (CSA) and acute coronary syndrome (ACS) compared with healthy controls. Bacterial alpha diversity in stool from patients with ACS or CSA was comparable to healthy controls at both baseline and follow-up visits. Differential abundance analysis identified operational taxonomic units (OTUs) assigned to commensal taxa differentiating patients with ACS from healthy controls at both baseline and follow-up. Patients with CSA and ACS had significantly higher levels of trimethylamine N-oxide compared with healthy controls (CSA: 0.032 ± 0.023 mmol/L, P < 0.01 vs. healthy, and ACS: 0.032 ± 0.023 mmol/L, P = 0.02 vs. healthy, respectively). Patients with ACS had reduced levels of propionate and butyrate (119 ± 4 vs. 139 ± 5.1 µM, P = 0.001, and 14 ± 4.3 vs. 23.5 ± 8.1 µM, P < 0.001, respectively), as well as elevated serum sCD14 (2245 ± 75.1 vs. 1834 ± 45.8 ng/mL, P < 0.0001) and sCD163 levels (457.3 ± 31.8 vs. 326.8 ± 20.7 ng/mL, P = 0.001), compared with healthy controls at baseline. Furthermore, a modified small molecule metabolomic and lipidomic signature was observed in patients with CSA and ACS compared with healthy controls. These findings provide evidence of a link between gut microbiome composition and gut bacterial metabolites with CVD. Future time course studies in patients to observe temporal changes and subsequent associations with gut microbiome composition are required to provide insight into how these are affected by transient changes following an acute coronary event.NEW & NOTEWORTHY The study found discriminative microorganisms differentiating patients with acute coronary syndrome (ACS) from healthy controls. In addition, reduced levels of certain bacterial metabolites and elevated sCD14 and sCD163 were observed in patients with ACS compared with healthy controls. Furthermore, modified small molecule metabolomic and lipidomic signatures were found in both patient groups. Although it is not known whether these differences in profiles are associated with disease development and/or progression, the findings provide exciting options for potential new disease-related mechanism(s) and associated therapeutic target(s).
Collapse
Affiliation(s)
- Adilah F Ahmad
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Jose A Caparrós-Martin
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Nicola Gray
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia
| | - Samantha Lodge
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia
| | - Julien Wist
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia
| | - Silvia Lee
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine, Perth, Western Australia, Australia
| | - Fergal O'Gara
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, Western Australia, Australia
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Girish Dwivedi
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
- Department of Cardiology, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Natalie C Ward
- Dobney Hypertension Centre, Medical School, The University of Western Australia, Perth, Western Australia, Australia
| |
Collapse
|
10
|
Chang HW, Lee EM, Wang Y, Zhou C, Pruss KM, Henrissat S, Chen RY, Kao C, Hibberd MC, Lynn HM, Webber DM, Crane M, Cheng J, Rodionov DA, Arzamasov AA, Castillo JJ, Couture G, Chen Y, Balcazo NP, Lebrilla CB, Terrapon N, Henrissat B, Ilkayeva O, Muehlbauer MJ, Newgard CB, Mostafa I, Das S, Mahfuz M, Osterman AL, Barratt MJ, Ahmed T, Gordon JI. Prevotella copri-related effects of a therapeutic food for malnutrition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553030. [PMID: 37645712 PMCID: PMC10461977 DOI: 10.1101/2023.08.11.553030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Preclinical and clinical studies are providing evidence that the healthy growth of infants and children reflects, in part, healthy development of their gut microbiomes1-5. This process of microbial community assembly and functional maturation is perturbed in children with acute malnutrition. Gnotobiotic animals, colonized with microbial communities from children with severe and moderate acute malnutrition, have been used to develop microbiome-directed complementary food (MDCF) formulations for repairing the microbiomes of these children during the weaning period5. Bangladeshi children with moderate acute malnutrition (MAM) participating in a previously reported 3-month-long randomized controlled clinical study of one such formulation, MDCF-2, exhibited significantly improved weight gain compared to a commonly used nutritional intervention despite the lower caloric density of the MDCF6. Characterizing the 'metagenome assembled genomes' (MAGs) of bacterial strains present in the microbiomes of study participants revealed a significant correlation between accelerated ponderal growth and the expression by two Prevotella copri MAGs of metabolic pathways involved in processing of MDCF-2 glycans1. To provide a direct test of these relationships, we have now performed 'reverse translation' experiments using a gnotobiotic mouse model of mother-to-offspring microbiome transmission. Mice were colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains cultured from Bangladeshi infants/children in the study population, with or without P. copri isolates resembling the MAGs. By combining analyses of microbial community assembly, gene expression and processing of glycan constituents of MDCF-2 with single nucleus RNA-Seq and mass spectrometric analyses of the intestine, we establish a principal role for P. copri in mediating metabolism of MDCF-2 glycans, characterize its interactions with other consortium members including Bifidobacterium longum subsp. infantis, and demonstrate the effects of P. copri-containing consortia in mediating weight gain and modulating the activities of metabolic pathways involved in lipid, amino acid, carbohydrate plus other facets of energy metabolism within epithelial cells positioned at different locations in intestinal crypts and villi. Together, the results provide insights into structure/function relationships between MDCF-2 and members of the gut communities of malnourished children; they also have implications for developing future prebiotic, probiotic and/or synbiotic therapeutics for microbiome restoration in children with already manifest malnutrition, or who are at risk for this pervasive health challenge.
Collapse
Affiliation(s)
- Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Evan M. Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Kali M. Pruss
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Robert Y. Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Clara Kao
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Matthew C. Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Hannah M. Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Daniel M. Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Marie Crane
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Juan J. Castillo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Nikita P. Balcazo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | | | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710 USA
| | - Michael J. Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
| | - Christopher B. Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710 USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710 USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Michael J. Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| |
Collapse
|
11
|
Zhang C, Sui Y, Liu S, Yang M. Molecular mechanisms of metabolic disease-associated hepatic inflammation in non-alcoholic fatty liver disease and non-alcoholic steatohepatitis. EXPLORATION OF DIGESTIVE DISEASES 2023:246-275. [DOI: https:/doi.org/10.37349/edd.2023.00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/05/2023] [Indexed: 11/27/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the leading chronic liver disease worldwide, with a progressive form of non-alcoholic steatohepatitis (NASH). It may progress to advanced liver diseases, including liver fibrosis, cirrhosis, and hepatocellular carcinoma. NAFLD/NASH is a comorbidity of many metabolic disorders such as obesity, insulin resistance, type 2 diabetes, cardiovascular disease, and chronic kidney disease. These metabolic diseases are often accompanied by systemic or extrahepatic inflammation, which plays an important role in the pathogenesis and treatment of NAFLD or NASH. Metabolites, such as short-chain fatty acids, impact the function, inflammation, and death of hepatocytes, the primary parenchymal cells in the liver tissue. Cholangiocytes, the epithelial cells that line the bile ducts, can differentiate into proliferative hepatocytes in chronic liver injury. In addition, hepatic non-parenchymal cells, including liver sinusoidal endothelial cells, hepatic stellate cells, and innate and adaptive immune cells, are involved in liver inflammation. Proteins such as fibroblast growth factors, acetyl-coenzyme A carboxylases, and nuclear factor erythroid 2-related factor 2 are involved in liver metabolism and inflammation, which are potential targets for NASH treatment. This review focuses on the effects of metabolic disease-induced extrahepatic inflammation, liver inflammation, and the cellular and molecular mechanisms of liver metabolism on the development and progression of NAFLD and NASH, as well as the associated treatments.
Collapse
Affiliation(s)
- Chunye Zhang
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Yuxiang Sui
- School of Life Science, Shanxi Normal University, Linfen 041004, Shanxi Province, China
| | - Shuai Liu
- The First Affiliated Hospital, Zhejiang University, Hangzhou 310006, Zhejiang Province, China
| | - Ming Yang
- Department of Surgery, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
12
|
Jin S, Chen X, Yang J, Ding J. Lactate dehydrogenase D is a general dehydrogenase for D-2-hydroxyacids and is associated with D-lactic acidosis. Nat Commun 2023; 14:6638. [PMID: 37863926 PMCID: PMC10589216 DOI: 10.1038/s41467-023-42456-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
Mammalian lactate dehydrogenase D (LDHD) catalyzes the oxidation of D-lactate to pyruvate. LDHD mutations identified in patients with D-lactic acidosis lead to deficient LDHD activity. Here, we perform a systematic biochemical study of mouse LDHD (mLDHD) and determine the crystal structures of mLDHD in FAD-bound form and in complexes with FAD, Mn2+ and a series of substrates or products. We demonstrate that mLDHD is an Mn2+-dependent general dehydrogenase which exhibits catalytic activity for D-lactate and other D-2-hydroxyacids containing hydrophobic moieties, but no activity for their L-isomers or D-2-hydroxyacids containing hydrophilic moieties. The substrate-binding site contains a positively charged pocket to bind the common glycolate moiety and a hydrophobic pocket with some elasticity to bind the varied hydrophobic moieties of substrates. The structural and biochemical data together reveal the molecular basis for the substrate specificity and catalytic mechanism of LDHD, and the functional roles of mutations in the pathogenesis of D-lactic acidosis.
Collapse
Affiliation(s)
- Shan Jin
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Xingchen Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Jun Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
| |
Collapse
|
13
|
Hwang IC, Vasquez R, Song JH, Engstrand L, Valeriano VD, Kang DK. Alterations in the gut microbiome and its metabolites are associated with the immune response to mucosal immunization with Lactiplantibacillus plantarum-displaying recombinant SARS-CoV-2 spike epitopes in mice. Front Cell Infect Microbiol 2023; 13:1242681. [PMID: 37705931 PMCID: PMC10495993 DOI: 10.3389/fcimb.2023.1242681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/11/2023] [Indexed: 09/15/2023] Open
Abstract
Lactic acid bacteria (LAB) expressing foreign antigens have great potential as mucosal vaccines. Our previous study reported that recombinant Lactiplantibacillus plantarum SK156 displaying SARS-CoV-2 spike S1 epitopes elicited humoral and cell-mediated immune responses in mice. Here, we further examined the effect of the LAB-based mucosal vaccine on gut microbiome composition and function, and gut microbiota-derived metabolites. Forty-nine (49) female BALB/c mice were orally administered L. plantarum SK156-displaying SARS-CoV-2 spike S1 epitopes thrice (at 14-day intervals). Mucosal immunization considerably altered the gut microbiome of mice by enriching the abundance of beneficial gut bacteria, such as Muribaculaceae, Mucispirillum, Ruminococcaceae, Alistipes, Roseburia, and Clostridia vadinBB60. Moreover, the predicted function of the gut microbiome showed increased metabolic pathways for amino acids, energy, carbohydrates, cofactors, and vitamins. The fecal concentration of short-chain fatty acids, especially butyrate, was also altered by mucosal immunization. Notably, alterations in gut microbiome composition, function, and butyrate levels were positively associated with the immune response to the vaccine. Our results suggest that the gut microbiome and its metabolites may have influenced the immunogenicity of the LAB-based SARS-CoV-2 vaccine.
Collapse
Affiliation(s)
- In-Chan Hwang
- Department of Animal Biotechnology, Dankook University, Cheonan, Republic of Korea
| | - Robie Vasquez
- Department of Animal Biotechnology, Dankook University, Cheonan, Republic of Korea
| | - Ji Hoon Song
- Department of Animal Biotechnology, Dankook University, Cheonan, Republic of Korea
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Valerie Diane Valeriano
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Dae-Kyung Kang
- Department of Animal Biotechnology, Dankook University, Cheonan, Republic of Korea
| |
Collapse
|
14
|
Peterson CT, Iablokov SN, Rodionov DA, Peterson SN. Personalized Response of Parkinson's Disease Gut Microbiota to Nootropic Medicinal Herbs In Vitro: A Proof of Concept. Microorganisms 2023; 11:1979. [PMID: 37630539 PMCID: PMC10457923 DOI: 10.3390/microorganisms11081979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disease characterized by the loss of dopaminergic neurons. Although the etiology of PD remains elusive, it has been hypothesized that initial dysregulation may occur in the gastrointestinal tract and may be accompanied by gut barrier defects. A strong clinical interest in developing therapeutics exists, including for the treatment of gut microbiota and physiology. We previously reported the impact of healthy fecal microbiota anaerobic cultures supplemented with nootropic herbs. Here, we evaluated the effect of nootropic Ayurvedic herbs on fecal microbiota derived from subjects with PD in vitro using 16S rRNA sequencing. The microbiota underwent substantial change in response to each treatment, comparable in magnitude to that observed from healthy subjects. However, the fecal samples derived from each participant displayed unique changes, consistent with a personalized response. We used genome-wide metabolic reconstruction to predict the community's metabolic potential to produce products relevant to PD pathology, including SCFAs, vitamins and amino acid degradation products. These results suggest the potential value of conducting in vitro cultivation and analyses of PD stool samples as a means of prescreening patients to select the medicinal herbs for which that individual is most likely to respond and derive benefit.
Collapse
Affiliation(s)
- Christine Tara Peterson
- Center of Excellence for Research and Training in Integrative Health, Department of Family Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92023, USA
| | | | - Dmitry A. Rodionov
- Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA;
| | - Scott N. Peterson
- Tumor Microenvironment and Cancer Immunology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA;
| |
Collapse
|
15
|
Dedon LR, Hilliard MA, Rani A, Daza-Merchan ZT, Story G, Briere CE, Sela DA. Fucosylated Human Milk Oligosaccharides Drive Structure-Specific Syntrophy between Bifidobacterium infantis and Eubacterium hallii within a Modeled Infant Gut Microbiome. Mol Nutr Food Res 2023; 67:e2200851. [PMID: 36938958 PMCID: PMC11010582 DOI: 10.1002/mnfr.202200851] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/23/2023] [Indexed: 03/21/2023]
Abstract
SCOPE Fucosylated human milk oligosaccharides (fHMOs) are metabolized by Bifidobacterium infantis and promote syntrophic interactions between microbiota that colonize the infant gut. The role of fHMO structure on syntrophic interactions and net microbiome function is not yet fully understood. METHODS AND RESULTS Metabolite production and microbial populations are tracked during mono- and co-culture fermentations of 2'fucosyllactose (2'FL) and difucosyllactose (DFL) by two B. infantis strains and Eubacterium hallii. This is also conducted in an in vitro modeled microbiome supplemented by B. infantis and/or E. hallii. Metabolites are quantified by high performance liquid chromatography. Total B. infantis and E. hallii populations are quantified through qRT-PCR and community composition through 16S amplicon sequencing. Differential metabolism of 2'FL and DFL by B. infantis strains gives rise to strain- and fHMO structure-specific syntrophy with E. hallii. Within the modeled microbial community, fHMO structure does not strongly alter metabolite production in aggregate, potentially due to functional redundancy within the modeled community. In contrast, community composition is dependent on fHMO structure. CONCLUSION Whereas short chain fatty acid production is not significantly altered by the specific fHMO structure introduced to the modeled community, specific fHMO structure influences the composition of the gut microbiome.
Collapse
Affiliation(s)
- Liv R. Dedon
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
| | - Margaret A. Hilliard
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA United States
| | - Asha Rani
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
| | | | - Galaxie Story
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
| | - Carrie-Ellen Briere
- Elaine Marieb College of Nursing, University of Massachusetts Amherst, Amherst, MA, United States
| | - David A. Sela
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
- Department of Nutrition, University of Massachusetts Amherst, Amherst, MA, United States
- Department of Microbiology and Physiological Systems and Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, United States
| |
Collapse
|
16
|
Peterson CT, Pérez-Santiago J, Iablokov SN, Rodionov DA, Peterson SN. Alteration of Community Metabolism by Prebiotics and Medicinal Herbs. Microorganisms 2023; 11:868. [PMID: 37110291 PMCID: PMC10141170 DOI: 10.3390/microorganisms11040868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023] Open
Abstract
Several studies have examined the impact of prebiotics on gut microbiota and associated changes in host physiology. Here, we used the in vitro cultivation of human fecal samples stimulated with a series of chemically related prebiotics and medicinal herbs commonly used in Ayurvedic medicine, followed by 16S rRNA sequencing. We applied a genome-wide metabolic reconstruction of enumerated communities to compare and contrast the structural and functional impact of prebiotics and medicinal herbs. In doings so, we examined the relationships between discrete variations in sugar composition and sugar linkages associated with each prebiotic to drive changes in microbiota composition. The restructuring of microbial communities with glycan substrates alters community metabolism and its potential impact on host physiology. We analyzed sugar fermentation pathways and products predicted to be formed and prebiotic-induced changes in vitamin and amino acid biosynthesis and degradation. These results highlight the utility of combining a genome-wide metabolic reconstruction methodology with 16S rRNA sequence-based community profiles to provide insights pertaining to community metabolism. This process also provides a rational means for prioritizing in vivo analysis of prebiotics and medicinal herbs in vivo to test hypotheses related to therapeutic potential in specific diseases of interest.
Collapse
Affiliation(s)
- Christine Tara Peterson
- Center of Excellence for Research and Training in Integrative Health, Department of Family Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Josué Pérez-Santiago
- Division of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00927, USA
- School of Dental Medicine, Office of Research, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00921, USA
| | | | - Dmitry A. Rodionov
- Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Scott N. Peterson
- Tumor Microenvironment and Cancer Immunology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| |
Collapse
|
17
|
Asai T, Yoshikawa S, Ikeda Y, Taniguchi K, Sawamura H, Tsuji A, Matsuda S. Encouraging Tactics with Genetically Modified Probiotics to Improve Immunity for the Prevention of Immune-Related Diseases including Cardio-Metabolic Disorders. Biomolecules 2022; 13:biom13010010. [PMID: 36671395 PMCID: PMC9855998 DOI: 10.3390/biom13010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
The PI3K/AKT/mTOR signaling pathway may play crucial roles in the pathogenesis of obesity and diabetes mellitus, as well as metabolic syndromes, which could also be risk factors for cardio-metabolic disorders. Consistently, it has been shown that beneficial effects may be convoyed by the modulation of the PI3K/AKT/mTOR pathway against the development of these diseases. Importantly, the PI3K/AKT/mTOR signaling pathway can be modulated by probiotics. Probiotics have a variety of beneficial properties, with the potential of treating specific diseases such as immune-related diseases, which are valuable to human health. In addition, an increasing body of work in the literature emphasized the contribution of genetically modified probiotics. There now seems to be a turning point in the research of probiotics. A better understanding of the interactions between microbiota, lifestyle, and host factors such as genetics and/or epigenetics might lead to a novel therapeutic approach with probiotics for these diseases. This study might provide a theoretical reference for the development of genetically modified probiotics in health products and/or in functional foods for the treatment of cardio-metabolic disorders.
Collapse
|