1
|
Kok CR, Rose DJ, Cui J, Whisenhunt L, Hutkins R. Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses. BMC Microbiol 2024; 24:183. [PMID: 38796418 PMCID: PMC11127362 DOI: 10.1186/s12866-024-03344-y] [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: 10/15/2023] [Accepted: 05/21/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders. RESULTS Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial. CONCLUSIONS Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders.
Collapse
Affiliation(s)
- Car Reen Kok
- Complex Biosystems, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Devin J Rose
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Food Science and Technology, University of Nebraska, 268 Food Innovation Center, Lincoln, NE, 68588, USA
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Lisa Whisenhunt
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Robert Hutkins
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Department of Food Science and Technology, University of Nebraska, 268 Food Innovation Center, Lincoln, NE, 68588, USA.
- Department of Food Science and Technology, University of Nebraska, 258 Food Innovation Center, Lincoln, NE, 68588-6205, USA.
| |
Collapse
|
2
|
Zhang X, Wang J, Zhang T, Li S, Liu J, Li M, Lu J, Zhang M, Chen H. Updated Progress on Polysaccharides with Anti-Diabetic Effects through the Regulation of Gut Microbiota: Sources, Mechanisms, and Structure-Activity Relationships. Pharmaceuticals (Basel) 2024; 17:456. [PMID: 38675416 PMCID: PMC11053653 DOI: 10.3390/ph17040456] [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: 02/26/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
Diabetes mellitus (DM) is a common chronic metabolic disease worldwide. The disturbance of the gut microbiota has a complex influence on the development of DM. Polysaccharides are one type of the most important natural components with anti-diabetic effects. Gut microbiota can participate in the fermentation of polysaccharides, and through this, polysaccharides regulate the gut microbiota and improve DM. This review begins by a summary of the sources, anti-diabetic effects and the gut microbiota regulation functions of natural polysaccharides. Then, the mechanisms of polysaccharides in regulating the gut microbiota to exert anti-diabetic effects and the structure-activity relationship are summarized. It is found that polysaccharides from plants, fungi, and marine organisms show great hypoglycemic activities and the gut microbiota regulation functions. The mechanisms mainly include repairing the gut burrier, reshaping gut microbiota composition, changing the metabolites, regulating anti-inflammatory activity and immune function, and regulating the signal pathways. Structural characteristics of polysaccharides, such as monosaccharide composition, molecular weight, and type of glycosidic linkage, show great influence on the anti-diabetic activity of polysaccharides. This review provides a reference for the exploration and development of the anti-diabetic effects of polysaccharides.
Collapse
Affiliation(s)
- Xiaoyu Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Jia Wang
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Tingting Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Shuqin Li
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Junyu Liu
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Mingyue Li
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Jingyang Lu
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| | - Min Zhang
- China-Russia Agricultural Processing Joint Laboratory, Tianjin Agricultural University, Tianjin 300384, China;
- State Key Laboratory of Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Haixia Chen
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; (X.Z.); (J.W.); (T.Z.); (S.L.); (J.L.); (M.L.); (J.L.)
| |
Collapse
|
3
|
Basak S, Hridayanka KSN, Duttaroy AK. Bioactives and their roles in bone metabolism of osteoarthritis: evidence and mechanisms on gut-bone axis. Front Immunol 2024; 14:1323233. [PMID: 38235147 PMCID: PMC10792057 DOI: 10.3389/fimmu.2023.1323233] [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: 10/17/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Bioactives significantly modify and maintain human health. Available data suggest that Bioactives might play a beneficial role in chronic inflammatory diseases. Although promised, defining their mechanisms and opting to weigh their benefits and limitations is imperative. Detailed mechanisms by which critical Bioactives, including probiotics and prebiotics such as dietary lipids (DHA, EPA, alpha LA), vitamin D, polysaccharides (fructooligosaccharide), polyphenols (curcumin, resveratrol, and capsaicin) potentially modulate inflammation and bone metabolism is limited. Certain dietary bioactive significantly impact the gut microbiota, immune system, and pain response via the gut-immune-bone axis. This narrative review highlights a recent update on mechanistic evidence that bioactive is demonstrated demonstrated to reduce osteoarthritis pathophysiology.
Collapse
Affiliation(s)
- Sanjay Basak
- Molecular Biology Division, National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, India
| | - Kota Sri Naga Hridayanka
- Molecular Biology Division, National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, India
| | - Asim K. Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| |
Collapse
|
4
|
Widjaja F, Rietjens IMCM. From-Toilet-to-Freezer: A Review on Requirements for an Automatic Protocol to Collect and Store Human Fecal Samples for Research Purposes. Biomedicines 2023; 11:2658. [PMID: 37893032 PMCID: PMC10603957 DOI: 10.3390/biomedicines11102658] [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: 09/04/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
The composition, viability and metabolic functionality of intestinal microbiota play an important role in human health and disease. Studies on intestinal microbiota are often based on fecal samples, because these can be sampled in a non-invasive way, although procedures for sampling, processing and storage vary. This review presents factors to consider when developing an automated protocol for sampling, processing and storing fecal samples: donor inclusion criteria, urine-feces separation in smart toilets, homogenization, aliquoting, usage or type of buffer to dissolve and store fecal material, temperature and time for processing and storage and quality control. The lack of standardization and low-throughput of state-of-the-art fecal collection procedures promote a more automated protocol. Based on this review, an automated protocol is proposed. Fecal samples should be collected and immediately processed under anaerobic conditions at either room temperature (RT) for a maximum of 4 h or at 4 °C for no more than 24 h. Upon homogenization, preferably in the absence of added solvent to allow addition of a buffer of choice at a later stage, aliquots obtained should be stored at either -20 °C for up to a few months or -80 °C for a longer period-up to 2 years. Protocols for quality control should characterize microbial composition and viability as well as metabolic functionality.
Collapse
Affiliation(s)
- Frances Widjaja
- Division of Toxicology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
| | | |
Collapse
|
5
|
Ayakdaş G, Ağagündüz D. Microbiota-accessible carbohydrates (MACs) as novel gut microbiome modulators in noncommunicable diseases. Heliyon 2023; 9:e19888. [PMID: 37809641 PMCID: PMC10559293 DOI: 10.1016/j.heliyon.2023.e19888] [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: 05/16/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
The gut microbiota has a significant role in human health and is affected by many factors. Diet and dietary components have profound impacts on the composition of the gut microbiome and largely contribute to the change in bacterial flora. A high-fiber diet increased dietary fiber (DF) fermentation and the production of short-chain fatty acids (SCFAs), which increased the number of microorganisms. Microbiota-accessible carbohydrates (MACs), a subgroup of fermentable carbohydrates such as DF, are defined as indigestible carbohydrates metabolized by microbes. These carbohydrates are important components to sustain the microbial environment of the complicated digestive tract and avoid intestinal dysbiosis. Each MAC has a unique property and can therefore be used as a sensitive output microbiota modulator to support host homeostasis and modulate health. In addition to the overall health-developing effects, MACs are thought to have a promising effect on the prevention of non-communicable diseases (NCDs), which are major health problems worldwide. The aim of the manuscript was to describe microbiota-accessible carbohydrates and summarize their effects on gut modulation and NCDs.
Collapse
Affiliation(s)
- Gamze Ayakdaş
- Department of Nutrition and Dietetics, Acıbadem University, Kerem Aydınlar Campus, Ataşehir, İstanbul, 34755, Turkey
| | - Duygu Ağagündüz
- Department of Nutrition and Dietetics, Gazi University, Emek, Ankara, 06490, Turkey
| |
Collapse
|
6
|
Gaike AH, Kalamkar SD, Gajjar V, Divate U, Karandikar-Iyer S, Goel P, Shouche YS, Ghaskadbi SS. Effect of long-term oral glutathione supplementation on gut microbiome of type 2 diabetic individuals. FEMS Microbiol Lett 2023; 370:fnad116. [PMID: 37935462 DOI: 10.1093/femsle/fnad116] [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: 07/06/2023] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
The aim of this study was to check the effect of long-term oral glutathione (GSH) supplementation on alteration in gut microbiome of Indian diabetic individuals. Early morning fresh stool sample of diabetic individuals recruited in a randomized clinical trial wherein they were given 500 mg GSH supplementation orally once a day for a period of 6 months was collected and gut microbiome was analysed using high throughput 16S rRNA metagenomic sequencing. Long-term GSH supplementation as reported in our earlier work showed significant increase in body stores of GSH and stabilized decreased glycated haemoglobin (HbA1c). Analysis of gut microbiome revealed that abundance of phylum Proteobacteria significantly decreased (P < 0.05) in individuals with GSH supplementation after 6 months compared to those without it. Beneficial dominant genera such as Megasphaera, Bacteroides, and Megamonas were found to be significantly enriched (P < 0.05), while pathogenic Escherichia/Shigella was found to be depleted (P < 0.05) after supplementation. Data clearly demonstrate that GSH supplementation along with antidiabetic treatment helps restore the gut microbiome by enriching beneficial bacteria of healthy gut and reducing significantly the load of pathogenic bacteria of diabetic gut.
Collapse
Affiliation(s)
- Akshay H Gaike
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
- National Centre for Cell Science, Pune 411007, India
| | - Saurabh D Kalamkar
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
| | | | | | | | - Pranay Goel
- Biology Division, Indian Institute of Science Education and Research, Pune 411008, India
| | - Yogesh S Shouche
- National Centre for Cell Science, Pune 411007, India
- SKAN Research Trust, Bengaluru 560034, India
| | - Saroj S Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
| |
Collapse
|
7
|
Ye S, Shah BR, Li J, Liang H, Zhan F, Geng F, Li B. A critical review on interplay between dietary fibers and gut microbiota. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.04.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
8
|
Onyango SO, Juma J, De Paepe K, Van de Wiele T. Oral and Gut Microbial Carbohydrate-Active Enzymes Landscape in Health and Disease. Front Microbiol 2021; 12:653448. [PMID: 34956106 PMCID: PMC8702856 DOI: 10.3389/fmicb.2021.653448] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
Inter-individual variability in the microbial gene complement encoding for carbohydrate-active enzymes (CAZymes) can profoundly regulate how the host interacts with diverse carbohydrate sources thereby influencing host health. CAZy-typing, characterizing the microbiota-associated CAZyme-coding genes within a host individual, can be a useful tool to predict carbohydrate pools that the host can metabolize, or identify which CAZyme families are underrepresented requiring supplementation via microbiota transplantation or probiotics. CAZy-typing, moreover, provides a novel framework to search for disease biomarkers. As a proof of concept, we used publicly available metagenomes (935) representing 310 type strain bacterial genomes to establish the link between disease status and CAZymes in the oral and gut microbial ecosystem. The abundance and distribution of 220 recovered CAZyme families in saliva and stool samples from patients with colorectal cancer, rheumatoid arthritis, and type 1 diabetes were compared with healthy subjects. Based on the multivariate discriminant analysis, the disease phenotype did not alter the CAZyme profile suggesting a functional conservation in carbohydrate metabolism in a disease state. When disease and healthy CAZyme profiles were contrasted in differential analysis, CAZyme markers that were underrepresented in type 1 diabetes (15), colorectal cancer (12), and rheumatoid arthritis (5) were identified. Of interest, are the glycosyltransferase which can catalyze the synthesis of glycoconjugates including lipopolysaccharides with the potential to trigger inflammation, a common feature in many diseases. Our analysis has also confirmed the expansive carbohydrate metabolism in the gut as evidenced by the overrepresentation of CAZyme families in the gut compared to the oral site. Nevertheless, each site exhibited specific CAZyme markers. Taken together, our analysis provides an insight into the CAZyme landscape in health and disease and has demonstrated the diversity in carbohydrate metabolism in host-microbiota which can be a sound basis for optimizing the selection of pre, pro, and syn-biotic candidate products.
Collapse
Affiliation(s)
- Stanley O Onyango
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - John Juma
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Kim De Paepe
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| |
Collapse
|
9
|
An In Vitro Pilot Fermentation Study on the Impact of Chlorella pyrenoidosa on Gut Microbiome Composition and Metabolites in Healthy and Coeliac Subjects. Molecules 2021; 26:molecules26082330. [PMID: 33923841 PMCID: PMC8072933 DOI: 10.3390/molecules26082330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 11/25/2022] Open
Abstract
The response of a coeliac and a healthy gut microbiota to the green algae Chlorella pyrenoidosa was evaluated using an in vitro continuous, pH controlled, gut model system, which simulated the human colon. The effect of C. pyrenoidosa on the microbial structure was determined by 16S rRNA gene sequencing and inferred metagenomics, whereas the metabolic activitywas determined by1H-nuclear magnetic resonancespectroscopic analysis. The addition of C. pyrenoidosa significantly increased the abundance of the genera Prevotella, Ruminococcus and Faecalibacterium in the healthy donor, while an increase in Faecalibacterium, Bifidobacterium and Megasphaera and a decrease in Enterobacteriaceae were observed in the coeliac donor. C. pyrenoidosa also altered several microbial pathways including those involved in short-chain fatty acid (SCFA) production. At the metabolic level, a significant increase from baseline was seen in butyrate and propionate (p < 0.0001) in the healthy donor, especially in vessels 2 and 3. While acetate was significantly higher in the healthy donor at baseline in vessel 3 (p < 0.001) compared to the coeliac donor, this was markedly decreased after in vitro fermentation with C. pyrenoidosa. This is the first in vitro fermentation study of C. pyrenoidosa and human gut microbiota, however, further in vivo studies are needed to prove its efficacy.
Collapse
|
10
|
Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS, Hazelhurst S. Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition. BMC Microbiol 2020; 20:330. [PMID: 33129264 PMCID: PMC7603784 DOI: 10.1186/s12866-020-02017-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most communities in the very diverse African continent. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To characterize the microbiome of African adults living in more mainstream lifestyle settings and investigate associations between the microbiome and obesity, we conducted a pilot study, designed collaboratively with community leaders, in two South African cohorts representative of urban and transitioning rural populations. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. RESULTS We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, we find that geographical location was more important for sample clustering than lean/obese status and observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in Bushbuckridge. Also, Prevotella, despite its generally high prevalence in the cohorts, showed an association with obesity. In comparisons with benchmarked datasets representative of non-Western populations, relatively higher abundance values were observed in our dataset for Barnesiella (log2fold change (FC) = 4.5), Alistipes (log2FC = 3.9), Bacteroides (log2FC = 4.2), Parabacteroides (log2FC = 3.1) and Treponema (log2FC = 1.6), with the exception of Prevotella (log2FC = - 4.7). CONCLUSIONS Altogether, this work identifies putative microbial features associated with host health in a historically understudied community undergoing an epidemiological transition. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research.
Collapse
Affiliation(s)
- O. H. Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F. B. Tamburini
- Department of Genetics, Stanford University, Stanford, CA USA
| | - V. Sahibdeen
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - R. Brewster
- School of Medicine, Stanford University, Stanford, CA USA
| | - F. X. Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- INDEPTH Network, East Legon, Accra, Ghana
| | - K. Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- INDEPTH Network, East Legon, Accra, Ghana
| | - S. A. Norris
- SAMRC Developmental Pathways for Health Research Unit, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Development and Health, University of Southampton, Southampton, UK
| | - S. M. Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- INDEPTH Network, East Legon, Accra, Ghana
| | - R. Twine
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. N. Wade
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - R. G. Wagner
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- INDEPTH Network, East Legon, Accra, Ghana
| | - Z. Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. S. Bhatt
- Department of Genetics, Stanford University, Stanford, CA USA
- School of Medicine, Stanford University, Stanford, CA USA
- Department of Medicine (Hematology), Stanford University, Stanford, CA USA
| | - S. Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
11
|
Fang Q, Hu J, Nie Q, Nie S. Effects of polysaccharides on glycometabolism based on gut microbiota alteration. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.08.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
12
|
Cabral DJ, Penumutchu S, Reinhart EM, Zhang C, Korry BJ, Wurster JI, Nilson R, Guang A, Sano WH, Rowan-Nash AD, Li H, Belenky P. Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome. Cell Metab 2019; 30:800-823.e7. [PMID: 31523007 PMCID: PMC6948150 DOI: 10.1016/j.cmet.2019.08.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/24/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Although antibiotics disturb the structure of the gut microbiota, factors that modulate these perturbations are poorly understood. Bacterial metabolism is an important regulator of susceptibility in vitro and likely plays a large role within the host. We applied a metagenomic and metatranscriptomic approach to link antibiotic-induced taxonomic and transcriptional responses within the murine microbiome. We found that antibiotics significantly alter the expression of key metabolic pathways at the whole-community and single-species levels. Notably, Bacteroides thetaiotaomicron, which blooms in response to amoxicillin, upregulated polysaccharide utilization. In vitro, we found that the sensitivity of this bacterium to amoxicillin was elevated by glucose and reduced by polysaccharides. Accordingly, we observed that dietary composition affected the abundance and expansion of B. thetaiotaomicron, as well as the extent of microbiome disruption with amoxicillin. Our work indicates that the metabolic environment of the microbiome plays a role in the response of this community to antibiotics.
Collapse
Affiliation(s)
- Damien J Cabral
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Elizabeth M Reinhart
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Rachael Nilson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - August Guang
- Center for Computation & Visualization, Brown University, Brown University, Providence, RI 02906, USA; Center for Computational Biology of Human Disease, Brown University, Providence, RI 02906, USA
| | - William H Sano
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA.
| |
Collapse
|
13
|
Singhal M, Turturice BA, Manzella CR, Ranjan R, Metwally AA, Theorell J, Huang Y, Alrefai WA, Dudeja PK, Finn PW, Perkins DL, Gill RK. Serotonin Transporter Deficiency is Associated with Dysbiosis and Changes in Metabolic Function of the Mouse Intestinal Microbiome. Sci Rep 2019; 9:2138. [PMID: 30765765 PMCID: PMC6375953 DOI: 10.1038/s41598-019-38489-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/19/2018] [Indexed: 02/07/2023] Open
Abstract
Serotonin transporter (SERT) plays a critical role in regulating extracellular availability of serotonin (5-HT) in the gut and brain. Mice with deletion of SERT develop metabolic syndrome as they age. Changes in the gut microbiota are being increasingly implicated in Metabolic Syndrome and Diabetes. To investigate the relationship between the gut microbiome and SERT, this study assessed the fecal and cecal microbiome profile of 11 to 12 week-old SERT+/+ and SERT-/- mice. Microbial DNA was isolated, processed for metagenomics shotgun sequencing, and taxonomic and functional profiles were assessed. 34 differentially abundant bacterial species were identified between SERT+/+ and SERT-/-. SERT-/- mice displayed higher abundances of Bacilli species including genera Lactobacillus, Streptococcus, Enterococcus, and Listeria. Furthermore, SERT-/- mice exhibited significantly lower abundances of Bifidobacterium species and Akkermansia muciniphilia. Bacterial community structure was altered in SERT-/- mice. Differential abundance of bacteria was correlated with changes in host gene expression. Bifidobacterium and Bacilli species exhibited significant associations with host genes involved in lipid metabolism pathways. Our results show that SERT deletion is associated with dysbiosis similar to that observed in obesity. This study contributes to the understanding as to how changes in gut microbiota are associated with metabolic phenotype seen in SERT deficiency.
Collapse
Affiliation(s)
- Megha Singhal
- Division of Gastroenterology & Hepatology, University of Illinois at Chicago, Chicago, USA
| | - Benjamin A Turturice
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, USA
- Department of Microbiology & Immunology, University of Illinois at Chicago, Chicago, USA
| | - Christopher R Manzella
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, USA
| | - Ravi Ranjan
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, USA
| | - Ahmed A Metwally
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | - Juliana Theorell
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, USA
| | - Yue Huang
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, USA
| | - Waddah A Alrefai
- Division of Gastroenterology & Hepatology, University of Illinois at Chicago, Chicago, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Pradeep K Dudeja
- Division of Gastroenterology & Hepatology, University of Illinois at Chicago, Chicago, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Patricia W Finn
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, USA
| | - David L Perkins
- Division of Nephrology, University of Illinois at Chicago, Chicago, USA
- Department of Surgery, University of Illinois at Chicago, Chicago, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | - Ravinder K Gill
- Division of Gastroenterology & Hepatology, University of Illinois at Chicago, Chicago, USA.
| |
Collapse
|
14
|
Zhang Q, Xiao X, Zheng J, Li M, Yu M, Ping F, Wang T, Wang X. Influence of Maternal Inulin-Type Prebiotic Intervention on Glucose Metabolism and Gut Microbiota in the Offspring of C57BL Mice. Front Endocrinol (Lausanne) 2019; 10:675. [PMID: 31632351 PMCID: PMC6779716 DOI: 10.3389/fendo.2019.00675] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/17/2019] [Indexed: 01/14/2023] Open
Abstract
Scope: Maternal obesity leads to glucose intolerance in the offspring. Changes in the gut microbiota are being increasingly implicated in the pathogenesis of diabetes. We hypothesized that inulin intervention during gestation and lactation improves glucose metabolism disorders in mouse offspring from high-fat diet (HD)-fed dams. Procedures: Female C57BL mice were fed a control diet or HD for 4 weeks before mating. After mating, pregnant mice were randomly divided into three groups through gestation and lactation: control diet (CD) group, HD group, and HD treated with inulin (HD-inulin) group. At weaning, glucose metabolic status was assessed. Gut microbial DNA from offspring cecal contents was isolated and processed for metagenomic shotgun sequencing, and taxonomic and functional profiling were performed. Results: Offspring from dams in the HD-inulin groups demonstrated reduced fasting blood glucose, decreased blood glucose area under the curve during the oral glucose tolerance test, and reduced fasting serum insulin and HOMA-IR compared to offspring from dams in the HD group. Nineteen differentially abundant bacterial species were identified between the HD-inulin and HD groups. The HD-inulin group displayed significantly greater abundances of Bacteroides_acidifaciens, Eubacterium_sp_CAG_786, Clostridium_sp_CAG_343, and Bifidobacterium_breve species and lower abundances of Oscillibacter_sp_1_3, Ruminococcus_gnavus_CAG_126, and Bacteroides_massiliensis species. Differentially abundant bacterial species among the three groups were involved in 38 metabolic pathways, including several glucose and lipid metabolism pathways. Conclusion: Our results show that early inulin intervention in HD-fed mouse dams moderates offspring glucose metabolism and gut dysbiosis.
Collapse
|
15
|
Cenci U, Sibbald SJ, Curtis BA, Kamikawa R, Eme L, Moog D, Henrissat B, Maréchal E, Chabi M, Djemiel C, Roger AJ, Kim E, Archibald JM. Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids. BMC Biol 2018; 16:137. [PMID: 30482201 PMCID: PMC6260743 DOI: 10.1186/s12915-018-0593-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/12/2018] [Indexed: 11/21/2022] Open
Abstract
Background The evolution of photosynthesis has been a major driver in eukaryotic diversification. Eukaryotes have acquired plastids (chloroplasts) either directly via the engulfment and integration of a photosynthetic cyanobacterium (primary endosymbiosis) or indirectly by engulfing a photosynthetic eukaryote (secondary or tertiary endosymbiosis). The timing and frequency of secondary endosymbiosis during eukaryotic evolution is currently unclear but may be resolved in part by studying cryptomonads, a group of single-celled eukaryotes comprised of both photosynthetic and non-photosynthetic species. While cryptomonads such as Guillardia theta harbor a red algal-derived plastid of secondary endosymbiotic origin, members of the sister group Goniomonadea lack plastids. Here, we present the genome of Goniomonas avonlea—the first for any goniomonad—to address whether Goniomonadea are ancestrally non-photosynthetic or whether they lost a plastid secondarily. Results We sequenced the nuclear and mitochondrial genomes of Goniomonas avonlea and carried out a comparative analysis of Go. avonlea, Gu. theta, and other cryptomonads. The Go. avonlea genome assembly is ~ 92 Mbp in size, with 33,470 predicted protein-coding genes. Interestingly, some metabolic pathways (e.g., fatty acid biosynthesis) predicted to occur in the plastid and periplastidal compartment of Gu. theta appear to operate in the cytoplasm of Go. avonlea, suggesting that metabolic redundancies were generated during the course of secondary plastid integration. Other cytosolic pathways found in Go. avonlea are not found in Gu. theta, suggesting secondary loss in Gu. theta and other plastid-bearing cryptomonads. Phylogenetic analyses revealed no evidence for algal endosymbiont-derived genes in the Go. avonlea genome. Phylogenomic analyses point to a specific relationship between Cryptista (to which cryptomonads belong) and Archaeplastida. Conclusion We found no convincing genomic or phylogenomic evidence that Go. avonlea evolved from a secondary red algal plastid-bearing ancestor, consistent with goniomonads being ancestrally non-photosynthetic eukaryotes. The Go. avonlea genome sheds light on the physiology of heterotrophic cryptomonads and serves as an important reference point for studying the metabolic “rewiring” that took place during secondary plastid integration in the ancestor of modern-day Cryptophyceae. Electronic supplementary material The online version of this article (10.1186/s12915-018-0593-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ugo Cenci
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Shannon J Sibbald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Bruce A Curtis
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.,Present address: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Daniel Moog
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.,Present address: Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France.,INRA, USC 1408 AFMB, 13288, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRA, Université Grenoble Alpes, Institut de Biosciences et Biotechnologies de Grenoble, CEA-Grenoble, 17 rue des Martyrs, 38000, Grenoble, France
| | - Malika Chabi
- Present address: UMR 8576 - Unité de glycobiologie structurale et fonctionnelle, Université Lille 1, 59650, Villeneuve d'Ascq, France
| | - Christophe Djemiel
- Present address: UMR 8576 - Unité de glycobiologie structurale et fonctionnelle, Université Lille 1, 59650, Villeneuve d'Ascq, France
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.,Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Toronto, Ontario, Canada
| | - Eunsoo Kim
- Division of Invertebrate Zoology & Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79 Street, New York, NY, 10024, USA
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada. .,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada. .,Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Toronto, Ontario, Canada.
| |
Collapse
|
16
|
Causal Relationship between Diet-Induced Gut Microbiota Changes and Diabetes: A Novel Strategy to Transplant Faecalibacterium prausnitzii in Preventing Diabetes. Int J Mol Sci 2018; 19:ijms19123720. [PMID: 30467295 PMCID: PMC6320976 DOI: 10.3390/ijms19123720] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/18/2018] [Accepted: 11/20/2018] [Indexed: 02/06/2023] Open
Abstract
The incidence of metabolic disorders, including diabetes, has elevated exponentially during the last decades and enhanced the risk of a variety of complications, such as diabetes and cardiovascular diseases. In the present review, we have highlighted the new insights on the complex relationships between diet-induced modulation of gut microbiota and metabolic disorders, including diabetes. Literature from various library databases and electronic searches (ScienceDirect, PubMed, and Google Scholar) were randomly collected. There exists a complex relationship between diet and gut microbiota, which alters the energy balance, health impacts, and autoimmunity, further causes inflammation and metabolic dysfunction, including diabetes. Faecalibacterium prausnitzii is a butyrate-producing bacterium, which plays a vital role in diabetes. Transplantation of F. prausnitzii has been used as an intervention strategy to treat dysbiosis of the gut’s microbial community that is linked to the inflammation, which precedes autoimmune disease and diabetes. The review focuses on literature that highlights the benefits of the microbiota especially, the abundant of F. prausnitzii in protecting the gut microbiota pattern and its therapeutic potential against inflammation and diabetes.
Collapse
|