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De Sales-Millán A, Reyes-Ferreira P, Aguirre-Garrido JF, Corral-Guillé I, Barrientos-Ríos R, Velázquez-Aragón JA. Comprehensive Analysis of Gut Microbiota Composition and Functional Metabolism in Children with Autism Spectrum Disorder and Neurotypical Children: Implications for Sex-Based Differences and Metabolic Dysregulation. Int J Mol Sci 2024; 25:6701. [PMID: 38928411 PMCID: PMC11203636 DOI: 10.3390/ijms25126701] [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: 04/29/2024] [Revised: 05/31/2024] [Accepted: 06/02/2024] [Indexed: 06/28/2024] Open
Abstract
This study aimed to investigate the gut microbiota composition in children with autism spectrum disorder (ASD) compared to neurotypical (NT) children, with a focus on identifying potential differences in gut bacteria between these groups. The microbiota was analyzed through the massive sequencing of region V3-V4 of the 16S RNA gene, utilizing DNA extracted from stool samples of participants. Our findings revealed no significant differences in the dominant bacterial phyla (Firmicutes, Bacteroidota, Actinobacteria, Proteobacteria, Verrucomicrobiota) between the ASD and NT groups. However, at the genus level, notable disparities were observed in the abundance of Blautia, Prevotella, Clostridium XI, and Clostridium XVIII, all of which have been previously associated with ASD. Furthermore, a sex-based analysis unveiled additional discrepancies in gut microbiota composition. Specifically, three genera (Megamonas, Oscilibacter, Acidaminococcus) exhibited variations between male and female groups in both ASD and NT cohorts. Particularly noteworthy was the exclusive presence of Megamonas in females with ASD. Analysis of predicted metabolic pathways suggested an enrichment of pathways related to amine and polyamine degradation, as well as amino acid degradation in the ASD group. Conversely, pathways implicated in carbohydrate biosynthesis, degradation, and fermentation were found to be underrepresented. Despite the limitations of our study, including a relatively small sample size (30 ASD and 31 NT children) and the utilization of predicted metabolic pathways derived from 16S RNA gene analysis rather than metagenome sequencing, our findings contribute to the growing body of evidence suggesting a potential association between gut microbiota composition and ASD. Future research endeavors should focus on validating these findings with larger sample sizes and exploring the functional significance of these microbial differences in ASD. Additionally, there is a critical need for further investigations to elucidate sex differences in gut microbiota composition and their potential implications for ASD pathology and treatment.
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Affiliation(s)
- Amapola De Sales-Millán
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Ciudad de México 09340, Mexico;
| | - Paulina Reyes-Ferreira
- Departamento de Salud Mental, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico;
| | - José Félix Aguirre-Garrido
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana-Lerma, Lerma 52006, Estado de Mexico, Mexico;
| | - Ismene Corral-Guillé
- Centro de Investigación del Neurodesarrollo, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico;
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Park Y, Ahn JB, Kim DH, Park IS, Son M, Kim JH, Ma HW, Kim SW, Cheon JH. Integrated Analysis of Microbiome and Metabolome Reveals Disease-Specific Profiles in Inflammatory Bowel Diseases and Intestinal Behçet's Disease. Int J Mol Sci 2024; 25:6697. [PMID: 38928402 PMCID: PMC11203907 DOI: 10.3390/ijms25126697] [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: 05/14/2024] [Revised: 06/09/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
The gut microbial and metabolic characteristics of intestinal Behçet's disease (BD), a condition sharing many clinical similarities with ulcerative colitis (UC) and Crohn's disease (CD), are largely unexplored. This study investigated the gut microbial and metabolic characteristics of intestinal BD as well as potential biomarkers, comparing them with those in UC, CD, and healthy controls. Colon tissue and stool samples from 100 patients (35 UC, 30 CD, and 35 intestinal BD) and 41 healthy volunteers were analyzed using 16S ribosomal RNA sequencing to assess microbial diversity, taxonomic composition, and functional profiling. Plasma metabolomic analyses were performed using gas chromatography and ultra-performance liquid chromatography-mass spectrometry. Results indicated reduced microbial diversity in CD but not in intestinal BD, with intestinal BD showing fewer changes compared to controls yet distinct taxonomic features from UC, CD, and controls. Common alterations across all diseases included a reduction in beneficial bacteria producing short-chain fatty acids. Intestinal BD-specific changes featured a decreased abundance of Bacteroides fragilis. Metabolomic profiles in intestinal BD were similar to those in CD but distinct from those in UC, displaying significant changes in energy metabolism and genetic information processing. This integrative analysis revealed both shared and unique profiles in intestinal BD compared with UC, CD, and controls, advancing our understanding of the distinctive features of these diseases.
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Affiliation(s)
- Yehyun Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Department of Internal Medicine, Ewha Womans University Seoul Hospital, Seoul 03760, Republic of Korea
| | - Jae Bum Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
| | - Da Hye Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
| | - I Seul Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Mijeong Son
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ji Hyung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyun Woo Ma
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Seung Won Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jae Hee Cheon
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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Amaral AR, Risolia LW, Rentas MF, Marchi PH, Balieiro JCDC, Vendramini THA, Brunetto MA. Translating Human and Animal Model Studies to Dogs' and Cats' Veterinary Care: Beta-Glucans Application for Skin Disease, Osteoarthritis, and Inflammatory Bowel Disease Management. Microorganisms 2024; 12:1071. [PMID: 38930453 PMCID: PMC11205328 DOI: 10.3390/microorganisms12061071] [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: 05/09/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
The inclusion of beta-glucans in dog and cat food is associated with numerous beneficial effects on the health of these animals. In this regard, there is an effort to elucidate the potential of this nutraceutical in chronic patients. Since there is a lack of a review on the topic, this review article aims to compile and discuss the evidence found to date. Atopic dermatitis, inflammatory bowel disease, and osteoarthritis are diseases of significant clinical relevance in dogs and cats. In general, the pathophysiology of these chronic conditions is related to immune-mediated and inflammatory mechanisms. Therefore, the immunomodulation and anti-inflammatory effects of beta-glucans are highlighted throughout this review. The available information seems to indicate that the studies on beta-glucans' impact on allergic processes in dogs indicate a reduction in clinical signs in atopic dermatitis cases. Additionally, while beta-glucans show promise as a safe supplement, particularly for osteoarthritis, further clinical trials are imperative, especially in uncontrolled environments. Beta-glucans emerge as a potential nutraceutical offering immune benefits for inflammatory bowel disease patients, although extensive research is required to define its optimal origin, molecular weight, dosage, and specific applications across animals suffering from this disease.
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Affiliation(s)
- Andressa Rodrigues Amaral
- Veterinary Nutrology Service, Veterinary Teaching Hospital, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo 05508-270, Brazil;
| | - Larissa Wünsche Risolia
- Pet Nutrology Research Center (CEPEN-PET), Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Pirassununga 13635-000, Brazil; (L.W.R.); (M.F.R.); (P.H.M.); (J.C.d.C.B.)
| | - Mariana Fragoso Rentas
- Pet Nutrology Research Center (CEPEN-PET), Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Pirassununga 13635-000, Brazil; (L.W.R.); (M.F.R.); (P.H.M.); (J.C.d.C.B.)
| | - Pedro Henrique Marchi
- Pet Nutrology Research Center (CEPEN-PET), Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Pirassununga 13635-000, Brazil; (L.W.R.); (M.F.R.); (P.H.M.); (J.C.d.C.B.)
| | - Júlio Cesar de Carvalho Balieiro
- Pet Nutrology Research Center (CEPEN-PET), Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Pirassununga 13635-000, Brazil; (L.W.R.); (M.F.R.); (P.H.M.); (J.C.d.C.B.)
| | - Thiago Henrique Annibale Vendramini
- Veterinary Nutrology Service, Veterinary Teaching Hospital, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo 05508-270, Brazil;
- Pet Nutrology Research Center (CEPEN-PET), Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Pirassununga 13635-000, Brazil; (L.W.R.); (M.F.R.); (P.H.M.); (J.C.d.C.B.)
| | - Marcio Antonio Brunetto
- Veterinary Nutrology Service, Veterinary Teaching Hospital, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo 05508-270, Brazil;
- Pet Nutrology Research Center (CEPEN-PET), Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Pirassununga 13635-000, Brazil; (L.W.R.); (M.F.R.); (P.H.M.); (J.C.d.C.B.)
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Odriozola A, González A, Odriozola I, Álvarez-Herms J, Corbi F. Microbiome-based precision nutrition: Prebiotics, probiotics and postbiotics. ADVANCES IN GENETICS 2024; 111:237-310. [PMID: 38908901 DOI: 10.1016/bs.adgen.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Microorganisms have been used in nutrition and medicine for thousands of years worldwide, long before humanity knew of their existence. It is now known that the gut microbiota plays a key role in regulating inflammatory, metabolic, immune and neurobiological processes. This text discusses the importance of microbiota-based precision nutrition in gut permeability, as well as the main advances and current limitations of traditional probiotics, new-generation probiotics, psychobiotic probiotics with an effect on emotional health, probiotic foods, prebiotics, and postbiotics such as short-chain fatty acids, neurotransmitters and vitamins. The aim is to provide a theoretical context built on current scientific evidence for the practical application of microbiota-based precision nutrition in specific health fields and in improving health, quality of life and physiological performance.
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Affiliation(s)
- Adrián Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Adriana González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Iñaki Odriozola
- Health Department of Basque Government, Donostia-San Sebastián, Spain
| | - Jesús Álvarez-Herms
- Phymo® Lab, Physiology, and Molecular Laboratory, Collado Hermoso, Segovia, Spain
| | - Francesc Corbi
- Institut Nacional d'Educació Física de Catalunya (INEFC), Centre de Lleida, Universitat de Lleida (UdL), Lleida, Spain
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Luangphiphat W, Prombutara P, Muangsillapasart V, Sukitpunyaroj D, Eeckhout E, Taweechotipatr M. Exploring of gut microbiota features in dyslipidemia and chronic coronary syndrome patients undergoing coronary angiography. Front Microbiol 2024; 15:1384146. [PMID: 38646625 PMCID: PMC11026706 DOI: 10.3389/fmicb.2024.1384146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Chronic coronary syndrome (CCS) has a high mortality rate, and dyslipidemia is a major risk factor. Atherosclerosis, a cause of CCS, is influenced by gut microbiota dysbiosis and its metabolites. The objective of this study was to study the diversity and composition of gut microbiota and related clinical parameters among CCS patients undergoing coronary angiography and dyslipidemia patients in comparison to healthy volunteers in Thailand. CCS patients had more risk factors and higher inflammatory markers, high-sensitivity C-reactive protein (hs-CRP) than others. The alpha diversity was lower in dyslipidemia and CCS patients than in the healthy group. A significant difference in the composition of gut microbiota was observed among the three groups. The relative abundance of Proteobacteria, Fusobacteria, Enterobacteriaceae, Prevotella, and Streptococcus was significantly increased while Roseburia, Ruminococcus, and Faecalibacterium were lower in CCS patients. In CCS patients, Lachnospiraceae, Peptostreptococcaceae, and Pediococcus were positively correlated with hs-CRP. In dyslipidemia patients, Megasphaera was strongly positively correlated with triglyceride (TG) level and negatively correlated with high-density lipoprotein cholesterol (HDL-C). The modification of gut microbiota was associated with changes in clinical parameters involved in the development of coronary artery disease (CAD) in CCS patients.
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Affiliation(s)
- Wongsakorn Luangphiphat
- Innovative Anatomy Program, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand
- Division of Cardiology, Department of Medicine, Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Pinidphon Prombutara
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Mod Gut Co., Ltd., Bangkok, Thailand
| | - Viroj Muangsillapasart
- Division of Cardiology, Department of Medicine, Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Damrong Sukitpunyaroj
- Division of Cardiology, Department of Medicine, Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Eric Eeckhout
- Service of Cardiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Malai Taweechotipatr
- Center of Excellence in Probiotics, Srinakharinwirot University, Bangkok, Thailand
- Department of Microbiology, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand
- Clinical Research Center, Faculty of Medicine, Srinakharinwirot University, Ongkharak, Thailand
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Wang Z, Peters BA, Yu B, Grove ML, Wang T, Xue X, Thyagarajan B, Daviglus ML, Boerwinkle E, Hu G, Mossavar-Rahmani Y, Isasi CR, Knight R, Burk RD, Kaplan RC, Qi Q. Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes. Circ Res 2024; 134:842-854. [PMID: 38547246 PMCID: PMC10987058 DOI: 10.1161/circresaha.123.323634] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/14/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Consistent evidence suggests diabetes-protective effects of dietary fiber intake. However, the underlying mechanisms, particularly the role of gut microbiota and host circulating metabolites, are not fully understood. We aimed to investigate gut microbiota and circulating metabolites associated with dietary fiber intake and their relationships with type 2 diabetes (T2D). METHODS This study included up to 11 394 participants from the HCHS/SOL (Hispanic Community Health Study/Study of Latinos). Diet was assessed with two 24-hour dietary recalls at baseline. We examined associations of dietary fiber intake with gut microbiome measured by shotgun metagenomics (350 species/85 genera and 1958 enzymes; n=2992 at visit 2), serum metabolome measured by untargeted metabolomics (624 metabolites; n=6198 at baseline), and associations between fiber-related gut bacteria and metabolites (n=804 at visit 2). We examined prospective associations of serum microbial-associated metabolites (n=3579 at baseline) with incident T2D over 6 years. RESULTS We identified multiple bacterial genera, species, and related enzymes associated with fiber intake. Several bacteria (eg, Butyrivibrio, Faecalibacterium) and enzymes involved in fiber degradation (eg, xylanase EC3.2.1.156) were positively associated with fiber intake, inversely associated with prevalent T2D, and favorably associated with T2D-related metabolic traits. We identified 159 metabolites associated with fiber intake, 47 of which were associated with incident T2D. We identified 18 of these 47 metabolites associated with the identified fiber-related bacteria, including several microbial metabolites (eg, indolepropionate and 3-phenylpropionate) inversely associated with the risk of T2D. Both Butyrivibrio and Faecalibacterium were associated with these favorable metabolites. The associations of fiber-related bacteria, especially Faecalibacterium and Butyrivibrio, with T2D were attenuated after further adjustment for these microbial metabolites. CONCLUSIONS Among United States Hispanics/Latinos, dietary fiber intake was associated with favorable profiles of gut microbiota and circulating metabolites for T2D. These findings advance our understanding of the role of gut microbiota and microbial metabolites in the relationship between diet and T2D.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology and Population Health (Z.W., B.A.P., T.W., X.X., Y.M.-R., C.R.I., R.D.B., R.C.K., Q.Q.), Albert Einstein College of Medicine, Bronx, NY
| | - Brandilyn A Peters
- Department of Epidemiology and Population Health (Z.W., B.A.P., T.W., X.X., Y.M.-R., C.R.I., R.D.B., R.C.K., Q.Q.), Albert Einstein College of Medicine, Bronx, NY
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston (B.Y., M.L.G., E.B.)
| | - Megan L Grove
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston (B.Y., M.L.G., E.B.)
| | - Tao Wang
- Department of Epidemiology and Population Health (Z.W., B.A.P., T.W., X.X., Y.M.-R., C.R.I., R.D.B., R.C.K., Q.Q.), Albert Einstein College of Medicine, Bronx, NY
| | - Xiaonan Xue
- Department of Epidemiology and Population Health (Z.W., B.A.P., T.W., X.X., Y.M.-R., C.R.I., R.D.B., R.C.K., Q.Q.), Albert Einstein College of Medicine, Bronx, NY
| | - Bharat Thyagarajan
- Division of Molecular Pathology and Genomics, University of Minnesota, Minneapolis, MN (B.T.)
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago College of Medicine, Chicago, IL (M.L.D.)
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston (B.Y., M.L.G., E.B.)
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX (E.B.)
| | - Gang Hu
- Chronic Disease Epidemiology Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA (G.H.)
| | - Yasmin Mossavar-Rahmani
- Department of Epidemiology and Population Health (Z.W., B.A.P., T.W., X.X., Y.M.-R., C.R.I., R.D.B., R.C.K., Q.Q.), Albert Einstein College of Medicine, Bronx, NY
| | - Carmen R Isasi
- Department of Epidemiology and Population Health (Z.W., B.A.P., T.W., X.X., Y.M.-R., C.R.I., R.D.B., R.C.K., Q.Q.), Albert Einstein College of Medicine, Bronx, NY
| | - Rob Knight
- Center for Microbiome Innovation (R.K.), University of California, San Diego, La Jolla
- Department of Pediatrics (R.K.), University of California, San Diego, La Jolla
| | - Robert D Burk
- Department of Epidemiology and Population Health (Z.W., B.A.P., T.W., X.X., Y.M.-R., C.R.I., R.D.B., R.C.K., Q.Q.), Albert Einstein College of Medicine, Bronx, NY
- Department of Pediatrics (R.D.B.), Albert Einstein College of Medicine, Bronx, NY
- Department of Obstetrics and Gynecology and Women's Health (R.D.B.), Albert Einstein College of Medicine, Bronx, NY
- Department of Microbiology and Immunology (R.D.B.), Albert Einstein College of Medicine, Bronx, NY
| | - Robert C Kaplan
- Department of Epidemiology and Population Health (Z.W., B.A.P., T.W., X.X., Y.M.-R., C.R.I., R.D.B., R.C.K., Q.Q.), Albert Einstein College of Medicine, Bronx, NY
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA (R.C.K.)
| | - Qibin Qi
- Department of Epidemiology and Population Health (Z.W., B.A.P., T.W., X.X., Y.M.-R., C.R.I., R.D.B., R.C.K., Q.Q.), Albert Einstein College of Medicine, Bronx, NY
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA (Q.Q.)
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Kibria MK, Ali MA, Yaseen M, Khan IA, Bhat MA, Islam MA, Mahumud RA, Mollah MNH. Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications. Pharmaceuticals (Basel) 2024; 17:432. [PMID: 38675393 PMCID: PMC11053588 DOI: 10.3390/ph17040432] [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: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
SARS-CoV-2 infections, commonly referred to as COVID-19, remain a critical risk to both human life and global economies. Particularly, COVID-19 patients with weak immunity may suffer from different complications due to the bacterial co-infections/super-infections/secondary infections. Therefore, different variants of alternative antibacterial therapeutic agents are required to inhibit those infection-causing drug-resistant pathogenic bacteria. This study attempted to explore these bacterial pathogens and their inhibitors by using integrated statistical and bioinformatics approaches. By analyzing bacterial 16S rRNA sequence profiles, at first, we detected five bacterial genera and taxa (Bacteroides, Parabacteroides, Prevotella Clostridium, Atopobium, and Peptostreptococcus) based on differentially abundant bacteria between SARS-CoV-2 infection and control samples that are significantly enriched in 23 metabolic pathways. A total of 183 bacterial genes were found in the enriched pathways. Then, the top-ranked 10 bacterial genes (accB, ftsB, glyQ, hldD, lpxC, lptD, mlaA, ppsA, ppc, and tamB) were selected as the pathogenic bacterial key genes (bKGs) by their protein-protein interaction (PPI) network analysis. Then, we detected bKG-guided top-ranked eight drug molecules (Bemcentinib, Ledipasvir, Velpatasvir, Tirilazad, Acetyldigitoxin, Entreatinib, Digitoxin, and Elbasvir) by molecular docking. Finally, the binding stability of the top-ranked three drug molecules (Bemcentinib, Ledipasvir, and Velpatasvir) against three receptors (hldD, mlaA, and lptD) was investigated by computing their binding free energies with molecular dynamic (MD) simulation-based MM-PBSA techniques, respectively, and was found to be stable. Therefore, the findings of this study could be useful resources for developing a proper treatment plan against bacterial co-/super-/secondary-infection in SARS-CoV-2 infections.
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Affiliation(s)
- Md. Kaderi Kibria
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Statistics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Chemistry, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Imran Ahmad Khan
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11421, Saudi Arabia;
| | - Md. Ariful Islam
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
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Jackson R, Yao T, Bulut N, Cantu-Jungles TM, Hamaker BR. Protein combined with certain dietary fibers increases butyrate production in gut microbiota fermentation. Food Funct 2024; 15:3186-3198. [PMID: 38441170 DOI: 10.1039/d3fo04187e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The modern diet delivers nearly equal amounts of carbohydrates and protein into the colon representing an important protein increase compared to past higher fiber diets. At the same time, plant-based protein foods have become increasingly popular, and these sources of protein are generally less digestible than animal protein sources. As a result, a significant amount of protein is expected to reach the colon and be available for fermentation by gut microbiota. While studies on diet-microbiota interventions have mainly focused on carbohydrate fermentation, limited attention has been given to the role of protein or protein-fiber mixtures as fermentation substrates for the colonic microbiota. In this study, we aimed to investigate: (1) how changing the ratio of protein to fiber substrates affects the types and quantities of gut microbial metabolites and bacteria; and (2) how the specific fermentation characteristics of different types of fiber might influence the utilization of protein by gut microbes to produce beneficial short chain fatty acids. Our results revealed that protein fermentation in the gut plays a crucial role in shaping the overall composition of microbiota communities and their metabolic outputs. Surprisingly, butyrate production was maintained or increased when fiber and protein were combined, and even when pure protein samples were used as substrates. These findings suggest that indigestible protein in fiber-rich substrates may promote the production of microbial butyrate perhaps including the later stages of fermentation in the large intestine.
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Affiliation(s)
- Rachel Jackson
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA.
| | - Tianming Yao
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA.
| | - Nuseybe Bulut
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA.
| | - Thaisa M Cantu-Jungles
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA.
| | - Bruce R Hamaker
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA.
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9
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Choy WH, Adler A, Morgan-Lang C, Gough EK, Hallam SJ, Manges AR, Chew BH, Penniston K, Miller A, Lange D. Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease. Urolithiasis 2024; 52:38. [PMID: 38413462 DOI: 10.1007/s00240-024-01534-x] [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: 10/17/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Intestinal microbiome dysbiosis is a known risk factor for recurrent kidney stone disease (KSD) with prior data suggesting a role for dysfunctional metabolic pathways other than those directly utilizing oxalate. To identify alternative mechanisms, the current study analyzed differences in the metabolic potential of intestinal microbiomes of patients (n = 17) and live-in controls (n = 17) and determined their relevance to increased risk for KSD using shotgun metagenomic sequencing. We found no differences in the abundance of genes associated with known oxalate degradation pathways, supporting the notion that dysfunction in other metabolic pathways plays a role in KSD. Further analysis showed decreased abundance of key enzymes involved in butyrate biosynthesis in patient intestinal microbiomes. Furthermore, de novo construction of microbial genomes showed that the majority of genes significantly enriched in non-stone formers are affiliated with Faecalibacterium prausnitzii, a major butyrate producer. Specifically pertaining to butyrate metabolism, the majority of abundant genes mapped back to F. prausnitzii, Alistipes spp., and Akkermansia muciniphila. No differences were observed in ascorbate or glyoxylate metabolic pathways. Collectively, these data suggest that impaired bacterial-associated butyrate metabolism may be an oxalate-independent mechanism that contributes to an increased risk for recurrent KSD. This indicates that the role of the intestinal microbiome in recurrent KSD is multi-factorial, which is representative of the highly intertwined metabolic nature of this complex environment. Future bacteria-based treatments must not be restricted to targeting only oxalate metabolism.
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Affiliation(s)
- Wai Ho Choy
- Department of Urologic Sciences, The Stone Centre at VGH, University of British Columbia, Jack Bell Research Centre, Rm. 550-3, 2660 Oak Street, Vancouver, BC, V6J 1G7, Canada
| | - Ava Adler
- Departments of Urology and Immunology, Cleveland Clinic, Cleveland, OH, USA
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Ethan K Gough
- Johns Hopkins Bloomberg School of Public Health US, Baltimore, USA
| | - Steven J Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
| | - Amee R Manges
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
- BC Centre for Disease Control, Vancouver, BC, Canada
| | - Ben H Chew
- Department of Urologic Sciences, The Stone Centre at VGH, University of British Columbia, Jack Bell Research Centre, Rm. 550-3, 2660 Oak Street, Vancouver, BC, V6J 1G7, Canada
| | - Kristina Penniston
- Department of Urology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Aaron Miller
- Departments of Urology and Immunology, Cleveland Clinic, Cleveland, OH, USA
| | - Dirk Lange
- Department of Urologic Sciences, The Stone Centre at VGH, University of British Columbia, Jack Bell Research Centre, Rm. 550-3, 2660 Oak Street, Vancouver, BC, V6J 1G7, Canada.
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10
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D'Hooghe SMTJ, Bosch G, Sun M, Cools A, Hendriks WH, Becker AAMJ, Janssens GPJ. How important is food structure when cats eat mice? Br J Nutr 2024; 131:369-383. [PMID: 37694489 DOI: 10.1017/s0007114523002039] [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] [Indexed: 09/12/2023]
Abstract
Feeding whole prey to felids has shown to benefit their gastrointestinal health. Whether this effect is caused by the chemical or physical nature of whole prey is unknown. Fifteen domestic cats, as a model for strict carnivores, were either fed minced mice (MM) or whole mice (WM), to determine the effect of food structure on digestibility, mean urinary excretion time (MUET) of 15N, intestinal microbial activity and fermentation products. Faeces samples were collected after feeding all cats a commercially available extruded diet (EXT) for 10 d before feeding for 19 d the MM and WM diets with faeces and urine collected from day 11 to 15. Samples for microbiota composition and determination of MUET were obtained from day 16 to 19. The physical structure of the mice diet (minced or not) did not affect large intestinal fermentation as total SCFA and branched-chain fatty acid (BCFA), and most biogenic amine (BA) concentrations were not different (P > 0·10). When changing from EXT to the mice diets, the microbial community composition shifted from a carbolytic (Prevotellaceae) to proteolytic (Fusobacteriaceae) profile and led to a reduced faecal acetic to propionic acid ratio, SCFA, total BCFA (P < 0·001), NH3 (P = 0·04), total BA (P < 0·001) and para-cresol (P = 0·08). The results of this study indicate that food structure within a whole-prey diet is less important than the overall diet type, with major shifts in microbiome and decrease in potentially harmful fermentation products when diet changes from extruded to mice. This urges for careful consideration of the consequences of prey-based diets for gut health in cats.
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Affiliation(s)
- Sylvie M-T J D'Hooghe
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Guido Bosch
- Animal Nutrition Group, Wageningen University & Research, PO Box 338, 6700 AH Wageningen, The Netherlands
| | - Mengmeng Sun
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - An Cools
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Wouter H Hendriks
- Animal Nutrition Group, Wageningen University & Research, PO Box 338, 6700 AH Wageningen, The Netherlands
| | - Anne A M J Becker
- Department of Biomedical sciences, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre, Saint Kitts and Nevis
| | - Geert P J Janssens
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
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11
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Imdad S, So B, Jang J, Park J, Lee SJ, Kim JH, Kang C. Temporal variations in the gut microbial diversity in response to high-fat diet and exercise. Sci Rep 2024; 14:3282. [PMID: 38332014 PMCID: PMC10853223 DOI: 10.1038/s41598-024-52852-4] [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: 05/16/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024] Open
Abstract
High-fat diet-induced obesity is a pandemic caused by an inactive lifestyle and increased consumption of Western diets and is a major risk factor for diabetes and cardiovascular diseases. In contrast, exercise can positively influence gut microbial diversity and is linked to a decreased inflammatory state. To understand the gut microbial variations associated with exercise and high-fat diet over time, we conducted a longitudinal study to examine the effect of covariates on gut microbial diversity and composition. Young mice were divided into four groups: Chow-diet (CHD), high-fat diet (HFD), high-fat diet + exercise (HFX), and exercise only (EXE) and underwent experimental intervention for 12 weeks. Fecal samples at week 0 and 12 were collected for DNA extraction, followed by 16S library preparation and sequencing. Data were analyzed using QIIME 2, R and MicrobiomeAnalyst. The Bacteroidetes-to-Firmicutes ratio decreased fivefold in the HFD and HFX groups compared to that in the CHD and EXE groups and increased in the EXE group over time. Alpha diversity was significantly increased in the EXE group longitudinally (p < 0.02), whereas diversity (Shannon, Faith's PD, and Fisher) and richness (ACE) was significantly reduced in the HFD (p < 0.005) and HFX (p < 0.03) groups over time. Beta diversity, based on the Jaccard, Bray-Curtis, and unweighted UniFrac distance metrics, was significant among the groups. Prevotella, Paraprevotella, Candidatus arthromitus, Lactobacillus salivarius, L. reuteri, Roseburia, Bacteroides uniformis, Sutterella, and Corynebacterium were differentially abundant in the chow-diet groups (CHD and EXE). Exercise significantly reduced the proportion of taxa characteristic of a high-fat diet, including Butyricimonas, Ruminococcus gnavus, and Mucispirillum schaedleri. Diet, age, and exercise significantly contributed to explaining the bacterial community structure and diversity in the gut microbiota. Modulating the gut microbiota and maintaining its stability can lead to targeted microbiome therapies to manage chronic and recurrent diseases and infections.
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Affiliation(s)
- Saba Imdad
- Molecular Metabolism in Health and Disease, Exercise Physiology Laboratory, Sport Science Research Institute, Inha University, Incheon, 22212, South Korea
- Department of Biomedical Laboratory Science, College of Health Science, Cheongju University, Cheongju, 28503, South Korea
| | - Byunghun So
- Molecular Metabolism in Health and Disease, Exercise Physiology Laboratory, Sport Science Research Institute, Inha University, Incheon, 22212, South Korea
| | - Junho Jang
- Molecular Metabolism in Health and Disease, Exercise Physiology Laboratory, Sport Science Research Institute, Inha University, Incheon, 22212, South Korea
| | - Jinhan Park
- Molecular Metabolism in Health and Disease, Exercise Physiology Laboratory, Sport Science Research Institute, Inha University, Incheon, 22212, South Korea
| | - Sam-Jun Lee
- Department of Sport Rehabilitation, College of Health, Welfare, and Education, Tong Myong University, Busan, 48520, South Korea
| | - Jin-Hee Kim
- Department of Biomedical Laboratory Science, College of Health Science, Cheongju University, Cheongju, 28503, South Korea.
| | - Chounghun Kang
- Molecular Metabolism in Health and Disease, Exercise Physiology Laboratory, Sport Science Research Institute, Inha University, Incheon, 22212, South Korea.
- Department of Physical Education, College of Education, Inha University, Incheon, 22212, South Korea.
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12
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Zhao S, Lau R, Zhong Y, Chen MH. Lactate cross-feeding between Bifidobacterium species and Megasphaera indica contributes to butyrate formation in the human colonic environment. Appl Environ Microbiol 2024; 90:e0101923. [PMID: 38126785 PMCID: PMC10807433 DOI: 10.1128/aem.01019-23] [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: 06/19/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Butyrate, a physiologically active molecule, can be synthesized through metabolic interactions among colonic microorganisms. Previously, in a fermenting trial of human fecal microbiota, we observed that the butyrogenic effect positively correlated with the increasing Bifidobacterium population and an unidentified Megasphaera species. Therefore, we hypothesized that a cross-feeding phenomenon exists between Bifidobacterium and Megasphaera, where Megasphaera is the butyrate producer, and its growth relies on the metabolites generated by Bifidobacterium. To validate this hypothesis, three bacterial species (B. longum, B. pseudocatenulatum, and M. indica) were isolated from fecal cultures fermenting hydrolyzed xylan; pairwise cocultures were conducted between the Bifidobacterium and M. indica isolates; the microbial interactions were determined based on bacterial genome information, cell growth, substrate consumption, metabolite quantification, and metatranscriptomics. The results indicated that two Bifidobacterium isolates contained distinct gene clusters for xylan utilization and expressed varying substrate preferences. In contrast, M. indica alone scarcely grew on the xylose-based substrates. The growth of M. indica was significantly elevated by coculturing it with bifidobacteria, while the two Bifidobacterium species responded differently in the kinetics of cell growth and substrate consumption. Coculturing led to the depletion of lactate and increased the formation of butyrate. An RNA-seq analysis further revealed the upregulation of M. indica genes involved in the lactate utilization and butyrate formation pathways. We concluded that lactate generated by Bifidobacterium through catabolizing xylose fueled the growth of M. indica and triggered the synthesis of butyrate. Our findings demonstrated a novel cross-feeding mechanism to generate butyrate in the human colon.IMPORTANCEButyrate is an important short-chain fatty acid that is produced in the human colon through microbial fermentation. Although many butyrate-producing bacteria exhibit a limited capacity to degrade nondigestible food materials, butyrate can be formed through cross-feeding microbial metabolites, such as acetate or lactate. Previously, the literature has explicated the butyrate-forming links between Bifidobacterium and Faecalibacterium prausnitzii and between Bifidobacterium and Eubacterium rectale. In this study, we provided an alternative butyrate synthetic pathway through the interaction between Bifidobacterium and Megasphaera indica. M. indica is a species named in 2014 and is indigenous to the human intestinal tract. Scientific studies explaining the function of M. indica in the human colon are still limited. Our results show that M. indica proliferated based on the lactate generated by bifidobacteria and produced butyrate as its end metabolic product. The pathways identified here may contribute to understanding butyrate formation in the gut microbiota.
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Affiliation(s)
- Sainan Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Raymond Lau
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Yang Zhong
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Department of Clinical Translational Research, Singapore General Hospital, Singapore, Singapore
| | - Ming-Hsu Chen
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
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13
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Pi XE, Fu H, Yang XX, Yu ZC, Teng WL, Zhang Y, Ye XW, Quan HH, Lu LZ, Liu W. Bacterial, short-chain fatty acid and gas profiles of partially hydrolyzed guar gum in vitro fermentation by human fecal microbiota. Food Chem 2024; 430:137006. [PMID: 37541036 DOI: 10.1016/j.foodchem.2023.137006] [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: 12/01/2022] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/06/2023]
Abstract
Carbohydrates with different structures have metabolic differences in the human body, as well as individual differences. The present study aimed to investigate the effects of bacterial, short-chain fatty acids (SCFAs) and gas profiles of partially hydrolyzed guar gum (PHGG) on the fecal microbiota of 41 Chinese individuals by simulated fermentation in vitro. Results showed that PHGG stimulated the growth of Bifidobacterium and Faecalibacterium, inhibited the growth of Escherichia-Shigella, Klebsiella, and Dorea, and induced the production of fermentation gases (CO2, and H2) and SCFAs (acetic acid, butyric acid). Furthermore, Bifidobacterium was significantly increased in the young female and the old male-originated samples, while Klebsiella was significantly decreased in the old female ones after PHGG intervention, and there were also certain differences in gases and SCFAs among different population samples. These findings indicate that PHGG can modulate gut microbiota and metabolism well, whereas its use varies in different populations.
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Affiliation(s)
- Xiong-E Pi
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China.
| | - Hao Fu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China
| | - Xiao-Xia Yang
- College of Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zai-Chun Yu
- College of Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei-Lin Teng
- Department of Infectious Disease Control and Prevention, HangZhou Center for Disease Control and Prevention, Hangzhou 310006, China
| | - Yinjun Zhang
- College of Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Xue-Wei Ye
- Shulan International Medical College, Department of Basic Medical Sciences, Zhejiang Shuren University, Hangzhou 310015, China.
| | - Hui Hui Quan
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China.
| | - Li-Zhi Lu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China.
| | - Wei Liu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China.
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14
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Nie S, Wang A, Chen X, Gong Y, Yuan Y. Microbial-Related Metabolites May Be Involved in Eight Major Biological Processes and Represent Potential Diagnostic Markers in Gastric Cancer. Cancers (Basel) 2023; 15:5271. [PMID: 37958446 PMCID: PMC10649575 DOI: 10.3390/cancers15215271] [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: 09/09/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Metabolites associated with microbes regulate human immunity, inhibit bacterial colonization, and promote pathogenicity. Integrating microbe and metabolome research in GC provides a direction for understanding the microbe-associated pathophysiological process of metabolic changes and disease occurrence. The present study included 30 GC patients with 30 cancerous tissues and paired non-cancerous tissues (NCs) as controls. LC-MS/MS metabolomics and 16S rRNA sequencing were performed to obtain the metabolic and microbial characteristics. Integrated analysis of the microbes and metabolomes was conducted to explore the coexistence relationship between the microbial and metabolic characteristics of GC and to identify microbial-related metabolite diagnostic markers. The metabolic analysis showed that the overall metabolite distribution differed between the GC tissues and the NC tissues: 25 metabolites were enriched in the NC tissues and 42 metabolites were enriched in the GC tissues. The α and β microbial diversities were higher in the GC tissues than in the NC tissues, with 11 differential phyla and 52 differential genera. In the correlation and coexistence integrated analysis, 66 differential metabolites were correlated and coexisted, with specific differential microbes. The microbes in the GC tissue likely regulated eight metabolic pathways. In the efficacy evaluation of the microbial-related differential metabolites in the diagnosis of GC, 12 differential metabolites (area under the curve [AUC] >0.9) exerted relatively high diagnostic efficiency, and the combined diagnostic efficacy of 5 to 6 microbial-related differential metabolites was higher than the diagnostic efficacy of a single feature. Therefore, microbial diversity and metabolite distribution differed between the GC tissues and the NC tissues. Microbial-related metabolites may be involved in eight major metabolism-based biological processes in GC and represent potential diagnostic markers.
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Affiliation(s)
- Siru Nie
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Ang Wang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Xiaohui Chen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yuehua Gong
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
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15
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Janetos TM, Zakaria N, Goldstein DA. The Microbiome and Uveitis: A Narrative Review. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1638-1647. [PMID: 37024044 DOI: 10.1016/j.ajpath.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/11/2023] [Accepted: 03/22/2023] [Indexed: 04/07/2023]
Abstract
The human intestinal microbiome is composed of hundreds of species and has recently been recognized as an important source of immune homeostasis. While dysbiosis, an altered microbiome from the normal core microbiome, has been associated with both intestinal and extraintestinal autoimmune disorders, including uveitis, causality has been difficult to establish. There are four proposed mechanisms of how the gut microbiome may influence the development of uveitis: molecular mimicry, imbalance of regulatory and effector T cells, increased intestinal permeability, and loss of intestinal metabolites. This review summarizes current literature on both animal and human studies that establish the link between dysbiosis and the development of uveitis, as well as provides evidence for the above mechanisms. Current studies provide valuable mechanistic insights as well as identify potential therapeutic targets. However, study limitations and the wide variability in the intestinal microbiome among populations and diseases make a specific targeted therapy difficult to establish. Further longitudinal clinical studies are required to identify any potential therapeutic that targets the intestinal microbiome.
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Affiliation(s)
- Timothy M Janetos
- Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Nancy Zakaria
- Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Department of Ophthalmology, Faculty of Medicine, Alexandria University, Alexandria, Arab Republic of Egypt
| | - Debra A Goldstein
- Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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16
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Li M, Liu M, Wang X, Wei H, Jin S, Liu X. Comparison of intestinal microbes and metabolites in active VKH versus acute anterior uveitis associated with ankylosing spondylitis. Br J Ophthalmol 2023:bjo-2023-324125. [PMID: 37821210 DOI: 10.1136/bjo-2023-324125] [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: 06/22/2023] [Accepted: 09/02/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND It has been reported that the gut microbiome is involved in the pathogenesis of uveitis, but the specific pathogenic microbes and metabolites in different types of uveitis are still unclear. METHODS Microbiome and metabolites were detected using 16S ribosomal DNA and LC‒MS/MS (liquid chromatography tandem mass spectrometry) in 45 individuals, including 16 patients with Vogt Koyanagi Harada (VKH), 11 patients with acute anterior uveitis (AAU) and 18 healthy controls. RESULT The diversity of intestinal microbes among the VKH, AAU and control groups was not significantly different. Thirteen specific microbes and 38 metabolites were detected in the VKH group, and 7 metabolites (vanillin, erythro-isoleucine, pyrimidine, 1-aminocyclopropanecarboxylic acid, beta-tocopherol, (-)-gallocatechin and N1-methyl-4-pyridone-3-carboxamide) significantly changed only in patients with VKH, which mainly acted on nicotinamide and nicotinamide metabolism and biotin metabolism (p<0.05). Compared with the VKH group, the AAU group had milder intestinal changes. Only 11 specific microbes and 29 metabolites changed in the AAU group, while these metabolites were not specific (p<0.05). These metabolites mainly acted on arachidonic acid metabolism. In addition, three microbes and two metabolites had the same changes in the VKH and AAU groups (p<0.05). Multiple correlations were found between gut microbes and metabolites in the VKH and AAU groups. Six microbes (Pediococcus, Pseudomonas, Rhodococcus, Photobacterium, Gardnerella and Lawsonia) and two metabolites (pyrimidine and gallocatechin) as biomarkers could effectively distinguish patients with VKH from patients with AAU and healthy individuals, with AUC (area under the curve) values greater than 82%. Four microbes (Lentilactobacillus, Lachnospiraceae_UCG-010, Cetobacterium, Liquorilactobacillus) could distinguish patients with AAU from patients with VKH and healthy controls with AUC>76%. CONCLUSION Significant differences in intestinal microbes and metabolites suggest their different roles in the pathogenesis of uveitis entities. Changes in the metabolism of certain B vitamins may be involved in the pathogenesis of VKH.
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Affiliation(s)
- Mengyao Li
- Ophthalmologic Center of the Second Hospital, Jilin University, Changchun, China
| | - Mingzhu Liu
- Ophthalmologic Center of the Second Hospital, Jilin University, Changchun, China
| | - Xia Wang
- Ophthalmologic Center of the Second Hospital, Jilin University, Changchun, China
| | - Haihui Wei
- Ophthalmologic Center of the Second Hospital, Jilin University, Changchun, China
| | - Siyan Jin
- Ophthalmologic Center of the Second Hospital, Jilin University, Changchun, China
| | - Xiaoli Liu
- Ophthalmologic Center of the Second Hospital, Jilin University, Changchun, China
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17
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Mandal RK, Schmidt NW. Mechanistic insights into the interaction between the host gut microbiome and malaria. PLoS Pathog 2023; 19:e1011665. [PMID: 37824458 PMCID: PMC10569623 DOI: 10.1371/journal.ppat.1011665] [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] [Indexed: 10/14/2023] Open
Abstract
Malaria is a devastating infectious disease and significant global health burden caused by the bite of a Plasmodium-infected female Anopheles mosquito. Gut microbiota was recently discovered as a risk factor of severe malaria. This review entails the recent advances on the impact of gut microbiota composition on malaria severity and consequence of malaria infection on gut microbiota in mammalian hosts. Additionally, this review provides mechanistic insight into interactions that might occur between gut microbiota and host immunity which in turn can modulate malaria severity. Finally, approaches to modulate gut microbiota composition are discussed. We anticipate this review will facilitate novel hypotheses to move the malaria-gut microbiome field forward.
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Affiliation(s)
- Rabindra K. Mandal
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indiana, United States of America
| | - Nathan W. Schmidt
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indiana, United States of America
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18
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Xiong W, Devkota L, Flanagan BM, Gu Z, Zhang B, Dhital S. Plant cell wall composition modulates the gut microbiota and metabolites in in-vitro fermentation. Carbohydr Polym 2023; 316:121074. [PMID: 37321749 DOI: 10.1016/j.carbpol.2023.121074] [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: 03/05/2023] [Revised: 05/19/2023] [Accepted: 05/28/2023] [Indexed: 06/17/2023]
Abstract
This research investigated the effect of different types of plant cell wall fibres, including cereal (i.e., barley, sorghum, and rice), legume (i.e., pea, faba bean, and mung bean), and tuber (potato, sweet potato, and yam) cell wall fibres on in vitro faecal fermentation profiles and gut microbiota composition. The cell wall composition, specifically the content of lignin and pectin, was found to have a significant influence on the gut microbiota and fermentation outcomes. Compared with type I cell walls (legume and tuber) which have high pectin content, the type II cell walls (cereal) which are high in lignin but low in pectin had a lower fermentation rates and less short-chain fatty acid production. The redundancy analysis showed samples with similar fibre composition and fermentation profiles clustered together, and the principal coordinate analysis revealed separation among different types of cell walls and closer proximity among the same cell wall types. These findings emphasize the importance of cell wall composition in shaping the microbial community during fermentation and contribute to a better understanding of the relationship between plant cell walls and gut health. This research has practical implications for the development of functional foods and dietary interventions.
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Affiliation(s)
- Weiyan Xiong
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Lavaraj Devkota
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Bernadine M Flanagan
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Zhipeng Gu
- Sino-Singapore International Research Institute, Guangzhou 510555, China; School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Bin Zhang
- Sino-Singapore International Research Institute, Guangzhou 510555, China; School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Sushil Dhital
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia.
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19
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Nawab S, Bao Q, Ji LH, Luo Q, Fu X, Fan S, Deng Z, Ma W. The Pathogenicity of Fusobacterium nucleatum Modulated by Dietary Fibers-A Possible Missing Link between the Dietary Composition and the Risk of Colorectal Cancer. Microorganisms 2023; 11:2004. [PMID: 37630564 PMCID: PMC10458976 DOI: 10.3390/microorganisms11082004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/20/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
The dietary composition has been approved to be strongly associated with the risk of colorectal cancer (CRC), one of the most serious malignancies worldwide, through regulating the gut microbiota structure, thereby influencing the homeostasis of colonic epithelial cells by producing carcinogens, i.e., ammonia or antitumor metabolites, like butyrate. Though butyrate-producing Fusobacterium nucleatum has been considered a potential tumor driver associated with chemotherapy resistance and poor prognosis in CRC, it was more frequently identified in the gut microbiota of healthy individuals rather than CRC tumor tissues. First, within the concentration range tested, the fermentation broth of F. nucleatum exhibited no significant effects on Caco-2 and NCM460 cells viability except for a notable up-regulation of the expression of TLR4 (30.70%, p < 0.0001) and Myc (47.67%, p = 0.021) and genes encoding proinflammatory cytokines including IL1B (197.57%, p < 0.0001), IL6 (1704.51%, p < 0.0001), and IL8 (897.05%, p < 0.0001) in Caco-2 cells exclusively. Although no marked effects of polydextrose or fibersol-2 on the growth of F. nucleatum, Caco-2 and NCM460 cells were observed, once culture media supplemented with polydextrose or fibersol-2, the corresponding fermentation broths of F. nucleatum significantly inhibited the growth of Caco-2 cells up to 48.90% (p = 0.0003, 72 h, 10%) and 52.96% (p = 0.0002, 72 h, 10%), respectively in a dose-dependent manner. These two kinds of fibers considerably promoted butyrate production of F. nucleatum up to 205.67% (p < 0.0001, 6% polydextrose at 24 h) and 153.46% (p = 0.0002, 6% fibersol-2 at 12 h), which explained why and how the fermentation broths of F. nucleatum cultured with fibers suppressing the growth of Caco-2 cells. Above findings indicated that dietary fiber determined F. nucleatum to be a carcinogenic or antitumor bacterium, and F. nucleatum played an important role in the association between the dietary composition, primarily the content of dietary fibers, and the risk of CRC.
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Affiliation(s)
- Sadia Nawab
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qelger Bao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lin-Hua Ji
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Qian Luo
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiang Fu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shuxuan Fan
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wei Ma
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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20
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Vandoni G, D'Amico F, Fabbrini M, Mariani L, Sieri S, Casirati A, Di Guardo L, Del Vecchio M, Anichini A, Mortarini R, Sgambelluri F, Celano G, Serale N, De Angelis M, Brigidi P, Gavazzi C, Turroni S. Gut Microbiota, Metabolome, and Body Composition Signatures of Response to Therapy in Patients with Advanced Melanoma. Int J Mol Sci 2023; 24:11611. [PMID: 37511376 PMCID: PMC10380337 DOI: 10.3390/ijms241411611] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Despite the recent breakthroughs in targeted and immunotherapy for melanoma, the overall survival rate remains low. In recent years, considerable attention has been paid to the gut microbiota and other modifiable patient factors (e.g., diet and body composition), though their role in influencing therapeutic responses has yet to be defined. Here, we characterized a cohort of 31 patients with unresectable IIIC-IV-stage cutaneous melanoma prior to initiation of targeted or first-line immunotherapy via the following methods: (i) fecal microbiome and metabolome via 16S rRNA amplicon sequencing and gas chromatography/mass spectrometry, respectively, and (ii) anthropometry, body composition, nutritional status, physical activity, biochemical parameters, and immunoprofiling. According to our data, patients subsequently classified as responders were obese (i.e., with high body mass index and high levels of total, visceral, subcutaneous, and intramuscular adipose tissue), non-sarcopenic, and enriched in certain fecal taxa (e.g., Phascolarctobacterium) and metabolites (e.g., anethole), which were potentially endowed with immunostimulatory and oncoprotective activities. On the other hand, non-response was associated with increased proportions of Streptococcus, Actinomyces, Veillonella, Dorea, Fusobacterium, higher neutrophil levels (and a higher neutrophil-to-lymphocyte ratio), and higher fecal levels of butyric acid and its esters, which also correlated with decreased survival. This exploratory study provides an integrated list of potential early prognostic biomarkers that could improve the clinical management of patients with advanced melanoma, in particular by guiding the design of adjuvant therapeutic strategies to improve treatment response and support long-term health improvement.
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Affiliation(s)
- Giulia Vandoni
- Clinical Nutrition Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Federica D'Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Luigi Mariani
- Data Science Unit, Fondazione IRCCS Istituito Nazionale dei Tumori, 20133 Milan, Italy
| | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Amanda Casirati
- Clinical Nutrition and Dietetics Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Lorenza Di Guardo
- Melanoma Medical Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Michele Del Vecchio
- Melanoma Medical Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Andrea Anichini
- Human Tumors Immunobiology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Roberta Mortarini
- Human Tumors Immunobiology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Francesco Sgambelluri
- Human Tumors Immunobiology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Giuseppe Celano
- Department of Soil, Plant and Food Science (DiSSPA), University of Bari Aldo Moro, 70126 Bari, Italy
| | - Nadia Serale
- Department of Soil, Plant and Food Science (DiSSPA), University of Bari Aldo Moro, 70126 Bari, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Science (DiSSPA), University of Bari Aldo Moro, 70126 Bari, Italy
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Cecilia Gavazzi
- Clinical Nutrition Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
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21
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Bazeli J, Banikazemi Z, Hamblin MR, Sharafati Chaleshtori R. Could probiotics protect against human toxicity caused by polystyrene nanoplastics and microplastics? Front Nutr 2023; 10:1186724. [PMID: 37492595 PMCID: PMC10363603 DOI: 10.3389/fnut.2023.1186724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/23/2023] [Indexed: 07/27/2023] Open
Abstract
Nanoplastics (NPs) and microplastics (MPs) made of polystyrene (PS) can be toxic to humans, especially by ingestion of plastic particles. These substances are often introduced into the gastrointestinal tract, where they can cause several adverse effects, including disturbances in intestinal flora, mutagenicity, cytotoxicity, reproductive toxicity, neurotoxicity, and exacerbated oxidative stress. Although there are widespread reports of the protective effects of probiotics on the harm caused by chemical contaminants, limited information is available on how these organisms may protect against PS toxicity in either humans or animals. The protective effects of probiotics can be seen in organs, such as the gastrointestinal tract, reproductive tract, and even the brain. It has been shown that both MPs and NPs could induce microbial dysbiosis in the gut, nose and lungs, and probiotic bacteria could be considered for both prevention and treatment. Furthermore, the improvement in gut dysbiosis and intestinal leakage after probiotics consumption may reduce inflammatory biomarkers and avoid unnecessary activation of the immune system. Herein, we show probiotics may overcome the toxicity of polystyrene nanoplastics and microplastics in humans, although some studies are required before any clinical recommendations can be made.
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Affiliation(s)
- Javad Bazeli
- Department of Medical Emergencies, School of Nursing, Social Development and Health Promotion Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Zarrin Banikazemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Michael R. Hamblin
- Laser Research Centre, University of Johannesburg, Doornfontein, South Africa
| | - Reza Sharafati Chaleshtori
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Social Determinants of Health (SDH) Research Center, Kashan University of Medical Sciences, Kashan, Iran
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22
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Negrut RL, Cote A, Maghiar AM. Exploring the Potential of Oral Microbiome Biomarkers for Colorectal Cancer Diagnosis and Prognosis: A Systematic Review. Microorganisms 2023; 11:1586. [PMID: 37375087 DOI: 10.3390/microorganisms11061586] [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: 05/23/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
There is growing evidence indicating that the oral microbiota, specifically certain periodontopathogens such as Fusobacterium nucleatum, may play a role in the development of colorectal cancer and that it could potentially be used as a biomarker for diagnosing colorectal cancer (CRC). The question beneath this systematic review is whether the development or progression of colorectal cancer can be attributed to the presence of certain oral bacteria, which could be used for discovering non-invasive biomarkers for CRC. This review aims to give an overview of the actual status of published studies regarding the oral pathogens related to colorectal cancer and assess the effectiveness of the oral microbiome derived biomarkers. A systematic literature search was performed using four databases, Web of Science, Scopus, PubMed, and Science Direct, on the 3rd and 4th of March 2023. The studies that did not have matching inclusion/exclusion criteria were winnowed out. A total of fourteen studies were included. The risk of bias was performed by using QUADAS-2. After assessing the studies, the general conclusion is that oral microbiota-based biomarkers can become a promising non-invasive tool for detecting CRC, but further research is needed in order to determine the mechanisms of oral dysbiosis in colorectal carcinogenesis.
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Affiliation(s)
- Roxana Loriana Negrut
- Department Medicine, Doctoral School of Biomedical Sciences, Faculty of Medicine and Pharmacy, University of Oradea, 410087 Oradea, Romania
- County Clinical Emergency Hospital Bihor, 410087 Oradea, Romania
| | - Adrian Cote
- Department of Surgical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | - Adrian Marius Maghiar
- Department Medicine, Doctoral School of Biomedical Sciences, Faculty of Medicine and Pharmacy, University of Oradea, 410087 Oradea, Romania
- Department of Surgical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
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23
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Zhang W, Mackay CR, Gershwin ME. Immunomodulatory Effects of Microbiota-Derived Short-Chain Fatty Acids in Autoimmune Liver Diseases. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1629-1639. [PMID: 37186939 PMCID: PMC10188201 DOI: 10.4049/jimmunol.2300016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/01/2023] [Indexed: 05/17/2023]
Abstract
Nonpathogenic commensal microbiota and their metabolites and components are essential to maintain a tolerogenic environment and promote beneficial health effects. The metabolic environment critically impacts the outcome of immune responses and likely impacts autoimmune and allergic responses. Short-chain fatty acids (SCFAs) are the main metabolites produced by microbial fermentation in the gut. Given the high concentration of SCFAs in the gut and portal vein and their broad immune regulatory functions, SCFAs significantly influence immune tolerance and gut-liver immunity. Alterations of SCFA-producing bacteria and SCFAs have been identified in a multitude of inflammatory diseases. These data have particular significance in primary biliary cholangitis, primary sclerosing cholangitis, and autoimmune hepatitis because of the close proximity of the liver to the gut. In this focused review, we provide an update on the immunologic consequences of SCFA-producing microbiota and in particular on three dominant SCFAs in autoimmune liver diseases.
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Affiliation(s)
- Weici Zhang
- Division of Rheumatology, Allergy, and Clinical Immunology, School of Medicine, University of California Davis, CA, USA
| | - Charles R. Mackay
- Department of Microbiology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Australia
| | - M. Eric Gershwin
- Division of Rheumatology, Allergy, and Clinical Immunology, School of Medicine, University of California Davis, CA, USA
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24
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Li X, Yi Y, Wu T, Chen N, Gu X, Xiang L, Jiang Z, Li J, Jin H. Integrated microbiome and metabolome analysis reveals the interaction between intestinal flora and serum metabolites as potential biomarkers in hepatocellular carcinoma patients. Front Cell Infect Microbiol 2023; 13:1170748. [PMID: 37260707 PMCID: PMC10227431 DOI: 10.3389/fcimb.2023.1170748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/02/2023] [Indexed: 06/02/2023] Open
Abstract
Globally, liver cancer poses a serious threat to human health and quality of life. Despite numerous studies on the microbial composition of the gut in hepatocellular carcinoma (HCC), little is known about the interactions of the gut microbiota and metabolites and their role in HCC. This study examined the composition of the gut microbiota and serum metabolic profiles in 68 patients with HCC, 33 patients with liver cirrhosis (LC), and 34 healthy individuals (NC) using a combination of metagenome sequencing and liquid chromatography-mass spectrometry (LC-MS). The composition of the serum metabolites and the structure of the intestinal microbiota were found to be significantly altered in HCC patients compared to non-HCC patients. LEfSe and metabolic pathway enrichment analysis were used to identify two key species (Odoribacter splanchnicus and Ruminococcus bicirculans) and five key metabolites (ouabain, taurochenodeoxycholic acid, glycochenodeoxycholate, theophylline, and xanthine) associated with HCC, which then were combined to create panels for HCC diagnosis. The study discovered that the diagnostic performance of the metabolome was superior to that of the microbiome, and a panel comprised of key species and key metabolites outperformed alpha-fetoprotein (AFP) in terms of diagnostic value. Spearman's rank correlation test was used to determine the relationship between the intestinal flora and serum metabolites and their impact on hepatocarcinogenesis and progression. A random forest model was used to assess the diagnostic performance of the different histologies alone and in combination. In summary, this study describes the characteristics of HCC patients' intestinal flora and serum metabolism, demonstrates that HCC is caused by the interaction of intestinal flora and serum metabolites, and suggests that two key species and five key metabolites may be potential markers for the diagnosis of HCC.
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Affiliation(s)
- Xiaoyue Li
- Department of Infectious Diseases, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Hepatobiliary Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yongxiang Yi
- Department of Infectious Diseases, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Hepatobiliary Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Nanjing, China
| | - Tongxin Wu
- Department of Infectious Diseases, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Nan Chen
- Department of Infectious Diseases, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xinyu Gu
- Department of Hepatobiliary Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Liangliang Xiang
- Department of Hepatobiliary Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhaodi Jiang
- Department of Hepatobiliary Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Junwei Li
- Department of Infectious Diseases, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Heiying Jin
- Department of Colorectal Surgery, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
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25
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Fusco W, Lorenzo MB, Cintoni M, Porcari S, Rinninella E, Kaitsas F, Lener E, Mele MC, Gasbarrini A, Collado MC, Cammarota G, Ianiro G. Short-Chain Fatty-Acid-Producing Bacteria: Key Components of the Human Gut Microbiota. Nutrients 2023; 15:2211. [PMID: 37432351 DOI: 10.3390/nu15092211] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 07/12/2023] Open
Abstract
Short-chain fatty acids (SCFAs) play a key role in health and disease, as they regulate gut homeostasis and their deficiency is involved in the pathogenesis of several disorders, including inflammatory bowel diseases, colorectal cancer, and cardiometabolic disorders. SCFAs are metabolites of specific bacterial taxa of the human gut microbiota, and their production is influenced by specific foods or food supplements, mainly prebiotics, by the direct fostering of these taxa. This Review provides an overview of SCFAs' roles and functions, and of SCFA-producing bacteria, from their microbiological characteristics and taxonomy to the biochemical process that lead to the release of SCFAs. Moreover, we will describe the potential therapeutic approaches to boost the levels of SCFAs in the human gut and treat different related diseases.
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Affiliation(s)
- William Fusco
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Manuel Bernabeu Lorenzo
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), 46022 Valencia, Spain
| | - Marco Cintoni
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
| | - Serena Porcari
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Emanuele Rinninella
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
| | - Francesco Kaitsas
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Elena Lener
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Maria Cristina Mele
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
| | - Antonio Gasbarrini
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), 46022 Valencia, Spain
| | - Giovanni Cammarota
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Gianluca Ianiro
- Department of Medical and Surgical Sciences, Digestive Disease Center, Universitary Policlinic Agostino Gemelli Foundation IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
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26
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Nuzum ND, Szymlek-Gay EA, Loke S, Dawson SL, Teo WP, Hendy AM, Loughman A, Macpherson H. Differences in the gut microbiome across typical ageing and in Parkinson's disease. Neuropharmacology 2023; 235:109566. [PMID: 37150399 DOI: 10.1016/j.neuropharm.2023.109566] [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: 12/22/2022] [Revised: 04/21/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023]
Abstract
The microbiota-gut-brain axis' role in Parkinson's disease (PD) pathophysiology, and how this differs from typical ageing, is poorly understood. Presently, gut-bacterial diversity, taxonomic abundance and metabolic bacterial pathways were compared across healthy young (n = 22, 18-35 years), healthy older (n = 33, 50-80 years), and PD groups (n = 18, 50-80 years) using shotgun sequencing and compositional data analysis. Associations between the gut-microbiome and PD symptoms, and between lifestyle factors (fibre intake, physical activity, and sleep) and the gut-microbiome were conducted. Alpha-diversity did not differ between PD participants and older adults, whilst beta-diversity differed between these groups. Lower abundance of Butyricimonas synergistica, a butyrate-producer, was associated with worse PD non-motor symptoms in the PD group. Regarding typical ageing, Bifidobacterium bifidum, was greater in the younger compared to older group, with no difference between the older and PD group. Abundance of metabolic pathways related to butyrate production did not differ among the groups, while 100 other metabolic pathways differed among the three groups. Sleep efficiency was positively associated with Roseburia inulinivorans in the older group. These results highlight the relevance of gut-microbiota to PD and that reduced butyrate-production may be involved with PD pathophysiology. Future studies should account for lifestyle factors when investigating gut-microbiomes across ageing and in PD.
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Affiliation(s)
- Nathan D Nuzum
- Deakin University, Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Sciences, Geelong, Australia.
| | - Ewa A Szymlek-Gay
- Deakin University, Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Sciences, Geelong, Australia
| | - Stella Loke
- Deakin University, School of Life and Environmental Sciences, Australia
| | - Samantha L Dawson
- Deakin University, Food & Mood Centre, IMPACT Strategic Research Centre, School of Medicine, Geelong, Australia
| | - Wei-Peng Teo
- Physical Education and Sports Science Academic Group, National Institute of Education, Nanyang Technological University, Singapore
| | - Ashlee M Hendy
- Deakin University, Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Sciences, Geelong, Australia
| | - Amy Loughman
- Deakin University, Food & Mood Centre, IMPACT Strategic Research Centre, School of Medicine, Geelong, Australia
| | - Helen Macpherson
- Deakin University, Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Sciences, Geelong, Australia
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27
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Tian P, Yang W, Guo X, Wang T, Tan S, Sun R, Xiao R, Wang Y, Jiao D, Xu Y, Wei Y, Wu Z, Li C, Gao L, Ma C, Liang X. Early life gut microbiota sustains liver-resident natural killer cells maturation via the butyrate-IL-18 axis. Nat Commun 2023; 14:1710. [PMID: 36973277 PMCID: PMC10043027 DOI: 10.1038/s41467-023-37419-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Liver-resident natural killer cells, a unique lymphocyte subset in liver, develop locally and play multifaceted immunological roles. However, the mechanisms for the maintenance of liver-resident natural killer cell homeostasis remain unclear. Here we show that early-life antibiotic treatment blunt functional maturation of liver-resident natural killer cells even at adulthood, which is dependent on the durative microbiota dysbiosis. Mechanistically, early-life antibiotic treatment significantly decreases butyrate level in liver, and subsequently led to defective liver-resident natural killer cell maturation in a cell-extrinsic manner. Specifically, loss of butyrate impairs IL-18 production in Kupffer cells and hepatocytes through acting on the receptor GPR109A. Disrupted IL-18/IL-18R signaling in turn suppresses the mitochondrial activity and the functional maturation of liver-resident natural killer cells. Strikingly, dietary supplementation of experimentally or clinically used Clostridium butyricum restores the impaired liver-resident natural killer cell maturation and function induced by early-life antibiotic treatment. Our findings collectively unmask a regulatory network of gut-liver axis, highlighting the importance of the early-life microbiota in the development of tissue-resident immune cells.
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Affiliation(s)
- Panpan Tian
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
| | - Wenwen Yang
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
| | - Xiaowei Guo
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
| | - Tixiao Wang
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
| | - Siyu Tan
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
| | - Renhui Sun
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
| | - Rong Xiao
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
| | - Yuzhen Wang
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
| | - Deyan Jiao
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
| | - Yachen Xu
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
| | - Yanfei Wei
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
| | - Zhuanchang Wu
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, 250012, Shandong, China
| | - Chunyang Li
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Histology and Embryology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Lifen Gao
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, 250012, Shandong, China
| | - Chunhong Ma
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China.
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, 250012, Shandong, China.
| | - Xiaohong Liang
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, 250012, Shandong, China.
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, 250012, Shandong, China.
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28
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Siptroth J, Moskalenko O, Krumbiegel C, Ackermann J, Koch I, Pospisil H. Variation of butyrate production in the gut microbiome in type 2 diabetes patients. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2023:10.1007/s10123-023-00324-6. [PMID: 36780038 PMCID: PMC10397123 DOI: 10.1007/s10123-023-00324-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 02/14/2023]
Abstract
BACKGROUND Diabetes mellitus type 2 is a common disease that poses a challenge to the healthcare system. The disease is very often diagnosed late. A better understanding of the relationship between the gut microbiome and type 2 diabetes can support early detection and form an approach for therapies. Microbiome analysis offers a potential opportunity to find markers for this disease. Next-generation sequencing methods can be used to identify the bacteria present in the stool sample and to generate a microbiome profile through an analysis pipeline. Statistical analysis, e.g., using Student's t-test, allows the identification of significant differences. The investigations are not only focused on single bacteria, but on the determination of a comprehensive profile. Also, the consideration of the functional microbiome is included in the analyses. The dataset is not from a clinical survey, but very extensive. RESULTS By examining 946 microbiome profiles of diabetes mellitus type 2 sufferers (272) and healthy control persons (674), a large number of significant genera (25) are revealed. It is possible to identify a large profile for type 2 diabetes disease. Furthermore, it is shown that the diversity of bacteria per taxonomic level in the group of persons with diabetes mellitus type 2 is significantly reduced compared to a healthy control group. In addition, six pathways are determined to be significant for type 2 diabetes describing the fermentation to butyrate. These parameters tend to have high potential for disease detection. CONCLUSIONS With this investigation of the gut microbiome of persons with diabetes type 2 disease, we present significant bacteria and pathways characteristic of this disease.
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Affiliation(s)
- Julienne Siptroth
- High Performance Computing in Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany.
| | - Olga Moskalenko
- BIOMES NGS GmbH, Schwartzkopffstraße 1, 15745, Wildau, Germany
| | | | - Jörg Ackermann
- Department of Molecular Bioinformatics, Institute of Computer Science, Goethe University Frankfurt, 60325, Frankfurt am Main, Germany
| | - Ina Koch
- Department of Molecular Bioinformatics, Institute of Computer Science, Goethe University Frankfurt, 60325, Frankfurt am Main, Germany
| | - Heike Pospisil
- High Performance Computing in Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany
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Bai X, Lan J, He S, Bu T, Zhang J, Wang L, Jin X, Mao Y, Guan W, Zhang L, Lu M, Piao H, Jo I, Quan C, Nam KH, Xu Y. Structural and Biochemical Analyses of the Butanol Dehydrogenase from Fusobacterium nucleatum. Int J Mol Sci 2023; 24:ijms24032994. [PMID: 36769315 PMCID: PMC9917632 DOI: 10.3390/ijms24032994] [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: 12/21/2022] [Revised: 01/19/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Butanol dehydrogenase (BDH) plays a significant role in the biosynthesis of butanol in bacteria by catalyzing butanal conversion to butanol at the expense of the NAD(P)H cofactor. BDH is an attractive enzyme for industrial application in butanol production; however, its molecular function remains largely uncharacterized. In this study, we found that Fusobacterium nucleatum YqdH (FnYqdH) converts aldehyde into alcohol by utilizing NAD(P)H, with broad substrate specificity toward aldehydes but not alcohols. An in vitro metal ion substitution experiment showed that FnYqdH has higher enzyme activity in the presence of Co2+. Crystal structures of FnYqdH, in its apo and complexed forms (with NAD and Co2+), were determined at 1.98 and 2.72 Å resolution, respectively. The crystal structure of apo- and cofactor-binding states of FnYqdH showed an open conformation between the nucleotide binding and catalytic domain. Key residues involved in the catalytic and cofactor-binding sites of FnYqdH were identified by mutagenesis and microscale thermophoresis assays. The structural conformation and preferred optimal metal ion of FnYqdH differed from that of TmBDH (homolog protein of FnYqdH). Overall, we proposed an alternative model for putative proton relay in FnYqdH, thereby providing better insight into the molecular function of BDH.
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Affiliation(s)
- Xue Bai
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Jing Lan
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Shanru He
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Tingting Bu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Jie Zhang
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Lulu Wang
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
| | - Xiaoling Jin
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Yuanchao Mao
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Wanting Guan
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Liying Zhang
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Ming Lu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuel, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hailong Piao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Inseong Jo
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Chunshan Quan
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Ki Hyun Nam
- Department of Life Science, Pohang University of Science and Technology, Pohang 35398, Republic of Korea
- POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 35398, Republic of Korea
- Correspondence: (K.H.N.); (Y.X.)
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Correspondence: (K.H.N.); (Y.X.)
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Hodgkinson K, El Abbar F, Dobranowski P, Manoogian J, Butcher J, Figeys D, Mack D, Stintzi A. Butyrate's role in human health and the current progress towards its clinical application to treat gastrointestinal disease. Clin Nutr 2023; 42:61-75. [PMID: 36502573 DOI: 10.1016/j.clnu.2022.10.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/17/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022]
Abstract
Butyrate is a key energy source for colonocytes and is produced by the gut microbiota through fermentation of dietary fiber. Butyrate is a histone deacetylase inhibitor and also signals through three G-protein coupled receptors. It is clear that butyrate has an important role in gastrointestinal health and that butyrate levels can impact both host and microbial functions that are intimately coupled with each other. Maintaining optimal butyrate levels improves gastrointestinal health in animal models by supporting colonocyte function, decreasing inflammation, maintaining the gut barrier, and promoting a healthy microbiome. Butyrate has also shown protective actions in the context of intestinal diseases such as inflammatory bowel disease, graft-versus-host disease of the gastrointestinal tract, and colon cancer, whereas lower levels of butyrate and/or the microbes which are responsible for producing this metabolite are associated with disease and poorer health outcomes. However, clinical efforts to increase butyrate levels in humans and reverse these negative outcomes have generated mixed results. This article discusses our current understanding of the molecular mechanisms of butyrate action with a focus on the gastrointestinal system, the links between host and microbial factors, and the efforts that are currently underway to apply the knowledge gained from the bench to bedside.
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Affiliation(s)
- Kendra Hodgkinson
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Faiha El Abbar
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Peter Dobranowski
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Juliana Manoogian
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - James Butcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; School of Pharmaceutical Sciences, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - David Mack
- Department of Paediatrics, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8L1, Canada; Children's Hospital of Eastern Ontario Inflammatory Bowel Disease Centre and Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
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31
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Gut Microbiota of the Asian-Indian Type 2 Diabetes Phenotype: How Different It Is from the Rest of the World? J Indian Inst Sci 2023. [DOI: 10.1007/s41745-022-00351-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Mahalak KK, Firrman J, Narrowe AB, Hu W, Jones SM, Bittinger K, Moustafa AM, Liu L. Fructooligosaccharides (FOS) differentially modifies the in vitro gut microbiota in an age-dependent manner. Front Nutr 2023; 9:1058910. [PMID: 36712525 PMCID: PMC9879625 DOI: 10.3389/fnut.2022.1058910] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction Fructooligosaccharides (FOS) are well-known carbohydrates that promote healthy gut microbiota and have been previously demonstrated to enhance levels of Bifidobacterium and Lactobacillus. Its bifidogenic properties are associated with positive health outcomes such as reduced obesity and anti-inflammatory properties, and, therefore, is in use as a prebiotic supplement to support healthy gut microbiota. However, the gut microbiota changes with age, which may lead to differential responses to treatments with prebiotics and other dietary supplements. Methods To address this concern, we implemented a 24-h in vitro culturing method to determine whether FOS treatment in three different adult age groups would have a differential effect. The age groups of interest ranged from 25 to 70 years and were split into young adults, adults, and older adults for the purposes of this analysis. Metagenomics and short-chain fatty acid analysis were performed to determine changes in the structure and function of the microbial communities. Results These analyses found that FOS created a bifidogenic response in all age groups, increased overall SCFA levels, decreased alpha diversity, and shifted the communities to be more similar in beta diversity metrics. However, the age groups differed in which taxa were most prevalent or most affected by FOS treatment. Discussion Overall, the results of this study demonstrate the positive effects of FOS on the gut microbiome, and importantly, how age may play a role in the effectiveness of this prebiotic.
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Affiliation(s)
- Karley K. Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States,*Correspondence: Karley K. Mahalak,
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Weiming Hu
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Steven M. Jones
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Ahmed M. Moustafa
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
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Chi Y, Wu Z, Du C, Zhang M, Wang X, Xie A, Wang P, Li R. Regulatory effects mediated by ulvan oligosaccharide and its zinc complex on lipid metabolism in high-fat diet-fed mice. Carbohydr Polym 2023; 300:120249. [DOI: 10.1016/j.carbpol.2022.120249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
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Gut Microbiota Eubacterium callanderi Exerts Anti-Colorectal Cancer Activity. Microbiol Spectr 2022; 10:e0253122. [PMID: 36448791 PMCID: PMC9769849 DOI: 10.1128/spectrum.02531-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The gut microbiota (GM) is associated with colorectal cancer (CRC) development. However, studies demonstrating the role of GM in CRC are limited to metagenomic analyses. These studies lack direct evidence proving that the candidate strains are involved in CRC, and isolated probiotics for bacteriotherapy. Therefore, to identify novel GM with anti-CRC activity, we previously isolated gut bacteria from the feces of healthy individuals, screened the isolated GM's anti-CRC activity, and discovered that cell-free supernatants of GM isolates demonstrated antiproliferative activity against CRC cells. Here, our study identified one of them as Eubacterium callanderi and chose it for further study because the genus Eubacterium has been suggested to contribute to various aspects of gut health; however, the functions are unknown. First, we confirmed that E. callanderi cell-free supernatant (EcCFS) exerted antiproliferative activity-by inducing apoptosis and cell cycle arrest-that was dose-dependent and specific to cancer cell lines. Next, we discovered that EcCFS active molecules were heat stable and protease insensitive. High-performance liquid chromatography analysis revealed that EcCFS contained high butyrate concentrations possessing anticancer activity. Additionally, gas chromatography-mass spectrometry analysis of the aqueous phase of ethyl acetate-extracted EcCFS and an antiproliferation assay of the aqueous phase and 4-aminobutanoic acid (GABA) suggested that GABA is a possible anti-CRC agent. Finally, in the CT26 allograft mouse model, E. callanderi oral administration and EcCFS peri-tumoral injection inhibited tumor growth in vivo. Therefore, our study reveals that E. callanderi has an anti-CRC effect and suggests that it may be a potential candidate for developing probiotics to control CRC. IMPORTANCE The gut microbiota has been reported to be involved in colorectal cancer, as suggested by metagenomic analysis. However, metagenomic analysis has limitations, such as bias in the analysis and the absence of bacterial resources for follow-up studies. Therefore, we attempted to discover gut microorganisms that are related to colorectal cancer using the culturomics method. In this study, we discovered that Eubacterium callanderi possesses anti-colorectal cancer activity in vitro and in vivo, suggesting that E. callanderi could be used in bacteriotherapy for colorectal cancer treatment.
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35
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Yousuf S, Liu H, Yingshu Z, Zahid D, Ghayas H, Li M, Ding Y, Li W. Ginsenoside Rg1 modulates intestinal microbiota and supports re-generation of immune cells in dexamethasone-treated mice. Acta Microbiol Immunol Hung 2022; 69:259-269. [PMID: 36342667 DOI: 10.1556/030.2022.01881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022]
Abstract
Ginsenoside Rg1 is one of the major ginsenosides found in roots of Panax ginseng and Panax notoginseng. Ginsenoside Rg1 is known to possess various biological activities including immunity enhancement activity. However, it is not clear whether the regulation of immune function by Rg1 is related to the intestinal microbiota. In the present study, the immuno-modulatory and gut microbiota-reshaping effects of ginsenoside Rg1 were evaluated. Ginsenoside Rg1 acts as an immune-enhancing agent to increase spleen index and the number of T, B and dendritic cells in dexamethasone (Dex)-treated mice. Ginsenoside Rg1 also increased the production of sIgA and regulated the expression of interleukin 2 (IL-2), IL-4, IL-10 and IFN-γ. Meanwhile, Rg1 administration regulated the structure of intestinal microbiota. The relative abundance of mouse intestinal microbial groups, such as Alistipes, Ruminococcaceae, Lachnospiraceae, and Roseburia were increased by Rg1 administration, whereas a decrease in the potential pathogens like Helicobacteraceae, Dubosiella, Mycoplasma, Alloprevotella, Allobaculum was observed. Moreover, Rg1 metabolites of Lachnospiraceae bacterium enhanced the proliferation of CD4+ T cells and T regulatory (Treg) cells. Ginsenoside Rg1 improved the inflammatory condition of the colonic tissue and repaired the destructed mucosal barrier. This study suggested that Rg1 strengthens immunity with regulating the homeostasis of intestinal microbiota in mice.
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Affiliation(s)
- Sabiha Yousuf
- College of Basic Medical Sciences, Dalian Medical University, 9-Western Section, Lvshun South Road, Dalian, Liaoning, 116044, China
| | - He Liu
- College of Basic Medical Sciences, Dalian Medical University, 9-Western Section, Lvshun South Road, Dalian, Liaoning, 116044, China
| | - Zhang Yingshu
- College of Basic Medical Sciences, Dalian Medical University, 9-Western Section, Lvshun South Road, Dalian, Liaoning, 116044, China
| | - Danish Zahid
- College of Basic Medical Sciences, Dalian Medical University, 9-Western Section, Lvshun South Road, Dalian, Liaoning, 116044, China
| | - Hassan Ghayas
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, 116044, China
| | - Ming Li
- College of Basic Medical Sciences, Dalian Medical University, 9-Western Section, Lvshun South Road, Dalian, Liaoning, 116044, China
| | - Yan Ding
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, 116034, China
| | - Wenzhe Li
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, 515041, China
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Hu Q, Liu B, Fan Y, Zheng Y, Wen F, Yu U, Wang W. Multi-omics association analysis reveals interactions between the oropharyngeal microbiome and the metabolome in pediatric patients with influenza A virus pneumonia. Front Cell Infect Microbiol 2022; 12:1011254. [PMID: 36389138 PMCID: PMC9651038 DOI: 10.3389/fcimb.2022.1011254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/03/2022] [Indexed: 11/30/2022] Open
Abstract
Children are at high risk for influenza A virus (IAV) infections, which can develop into severe illnesses. However, little is known about interactions between the microbiome and respiratory tract metabolites and their impact on the development of IAV pneumonia in children. Using a combination of liquid chromatography tandem mass spectrometry (LC-MS/MS) and 16S rRNA gene sequencing, we analyzed the composition and metabolic profile of the oropharyngeal microbiota in 49 pediatric patients with IAV pneumonia and 42 age-matched healthy children. The results indicate that compared to healthy children, children with IAV pneumonia exhibited significant changes in the oropharyngeal macrobiotic structure (p = 0.001), and significantly lower microbial abundance and diversity (p < 0.05). These changes came with significant disturbances in the levels of oropharyngeal metabolites. Intergroup differences were observed in 204 metabolites mapped to 36 metabolic pathways. Significantly higher levels of sphingolipid (sphinganine and phytosphingosine) and propanoate (propionic acid and succinic acid) metabolism were observed in patients with IAV pneumonia than in healthy controls. Using Spearman’s rank-correlation analysis, correlations between IAV pneumonia-associated discriminatory microbial genera and metabolites were evaluated. The results indicate significant correlations and consistency in variation trends between Streptococcus and three sphingolipid metabolites (phytosphingosine, sphinganine, and sphingosine). Besides these three sphingolipid metabolites, the sphinganine-to-sphingosine ratio and the joint analysis of the three metabolites indicated remarkable diagnostic efficacy in children with IAV pneumonia. This study confirmed significant changes in the characteristics and metabolic profile of the oropharyngeal microbiome in pediatric patients with IAV pneumonia, with high synergy between the two factors. Oropharyngeal sphingolipid metabolites may serve as potential diagnostic biomarkers of IAV pneumonia in children.
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Affiliation(s)
- Qian Hu
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Baiming Liu
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Yanqun Fan
- Department of Trans-omics Research, Biotree Metabolomics Technology Research Center, Shanghai, China
| | - Yuejie Zheng
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Feiqiu Wen
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Uet Yu
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
- *Correspondence: Wenjian Wang, ; Uet Yu,
| | - Wenjian Wang
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
- *Correspondence: Wenjian Wang, ; Uet Yu,
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Herrera G, Arboleda JC, Pérez-Jaramillo JE, Patarroyo MA, Ramírez JD, Muñoz M. Microbial Interdomain Interactions Delineate the Disruptive Intestinal Homeostasis in Clostridioides difficile Infection. Microbiol Spectr 2022; 10:e0050222. [PMID: 36154277 PMCID: PMC9602525 DOI: 10.1128/spectrum.00502-22] [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: 02/08/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile infection (CDI) creates an imbalance in the intestinal microbiota due to the interaction of the components making up this ecosystem, but little is known about the impact of this disease on other microbial members. This work has thus been aimed at evaluating the taxonomic composition, potential gene-associated functions, virulence factors, and antimicrobial resistance profiles of gut microbiomes. A total of 48 DNA samples obtained from patients with health care facility-acquired (HCFO) and community-onset (CO) diarrhea were distributed in the following four groups according to CDI status: HCFO/+ (n = 13), HCFO/- (n = 8), CO/+ (n = 13), and CO/- (n = 14). These samples were subjected to shotgun metagenomics sequencing. Although the CDI groups' microbiota had microbiome alterations, the greatest imbalance was observed in the in the HCFO+/- groups, with an increase in common pathogens and phage populations, as well as a decrease in beneficial microorganisms that leads to a negative impact on some intestinal homeostasis-related metabolic processes. A reduction in the relative abundance of butyrate metabolism-associated genes was also detected in the HCFO groups (P < 0.01), with an increase in some virulence factors and antibiotic-resistance markers. A set of 51 differentially abundant species in the groups with potential association to CDI enabled its characterization, leading to their spatial separation by onset. Strong correlations between phages and some archaeal and bacterial phyla were identified. This highlighted the need to study the microbiota's various components since their imbalance is multifactorial, with some pathogens contributing to a greater or lesser extent because of their interaction with the ecosystem they inhabit. IMPORTANCE Clostridioides difficile infection represents a serious public health problem in different countries due to its high morbi-mortality and the high costs it represents for health care systems. Studies have shown the impact of this infection on intestinal microbiome homeostasis, mainly on bacterial populations. Our research provides evidence of the impact of CDI at both the compositional (bacteria, archaea, and viruses), and functional levels, allowing us to understand that the alterations of the microbiota occur systemically and are caused by multiple perturbations generated by different members of the microbiota as well as by some pathogens that take advantage of the imbalance to proliferate. Likewise, the 51 differentially abundant species in the study groups with potential association to CDI found in this study could help us envisage future treatments against this and other inflammatory diseases, improving future therapeutic options for patients.
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Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan Camilo Arboleda
- Unidad de Bioprospección and Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
- Semillero de Investigación en Bioinformática-GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Juan E. Pérez-Jaramillo
- Semillero de Investigación en Bioinformática-GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- Health Sciences Division, Universidad Santo Tomás, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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Bucheli JEV, Todorov SD, Holzapfel WH. Role of gastrointestinal microbial populations, a terra incognita of the human body in the management of intestinal bowel disease and metabolic disorders. Benef Microbes 2022; 13:295-318. [PMID: 35866598 DOI: 10.3920/bm2022.0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intestinal bowel disease (IBD) is a chronic immune-mediated clinical condition that affects the gastrointestinal tract and is mediated by an inflammatory response. Although it has been extensively studied, the multifactorial aetiology of this disorder makes it difficult to fully understand all the involved mechanisms in its development and therefore its treatment. In recent years, the fundamental role played by the human microbiota in the pathogenesis of IBD has been emphasised. Microbial imbalances in the gut bacterial communities and a lower species diversity in patients suffering from inflammatory gastrointestinal disorders compared to healthy individuals have been reported as principal factors in the development of IBD. These served to support scientific arguments for the use of probiotic microorganisms in alternative approaches for the prevention and treatment of IBD. In a homeostatic environment, the presence of bacteria (including probiotics) on the intestinal epithelial surface activates a cascade of processes by which immune responses inhibited and thereby commensal organisms maintained. At the same time these processes may support activities against specific pathogenic bacteria. In dysbiosis, these underlying mechanisms will serve to provoke a proinflammatory response, that, in combination with the use of antibiotics and the genetic predisposition of the host, will culminate in the development of IBD. In this review, we summarised the main causes of IBD, the physiological mechanisms involved and the related bacterial groups most frequently associated with these processes. The intention was to enable a better understanding of the interaction between the intestinal microbiota and the host, and to suggest possibilities by which this knowledge can be useful for the development of new therapeutic treatments.
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Affiliation(s)
- J E Vazquez Bucheli
- Human Effective Microbes, Department of Advanced Convergence, Handong Global University, Pohang, Gyeongbuk 37554, Republic of Korea
| | - S D Todorov
- ProBacLab, Department of Advanced Convergence, Handong Global University, Pohang, Gyeongbuk 37554, Republic of Korea
| | - W H Holzapfel
- Human Effective Microbes, Department of Advanced Convergence, Handong Global University, Pohang, Gyeongbuk 37554, Republic of Korea
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Wang XH, Xu DQ, Chen YY, Yue SJ, Fu RJ, Huang L, Tang YP. Traditional Chinese Medicine: A promising strategy to regulate inflammation, intestinal disorders and impaired immune function due to sepsis. Front Pharmacol 2022; 13:952938. [PMID: 36188532 PMCID: PMC9523403 DOI: 10.3389/fphar.2022.952938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Sepsis is described as a dysregulation of the immune response to infection, which leads to life-threatening organ dysfunction. The interaction between intestinal microbiota and sepsis can’t be ignored. Furthermore, the intestinal microbiota may regulate the progress of sepsis and attenuate organ damage. Thus, maintaining or restoring microbiota may be a new way to treat sepsis. Traditional Chinese medicine (TCM) assumes a significant part in the treatment of sepsis through multi-component, multi-pathway, and multi-targeting abilities. Moreover, TCM can prevent the progress of sepsis and improve the prognosis of patients with sepsis by improving the imbalance of intestinal microbiota, improving immunity and reducing the damage to the intestinal barrier. This paper expounds the interaction between intestinal microbiota and sepsis, then reviews the current research on the treatment of sepsis with TCM, to provide a theoretical basis for its clinical application.
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Ko YJ, Kim S, Pan CH, Park K. Identification of Functional Microbial Modules Through Network-Based Analysis of Meta-Microbial Features Using Matrix Factorization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:2851-2862. [PMID: 34329170 DOI: 10.1109/tcbb.2021.3100893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As the microbiome is composed of a variety of microbial interactions, it is imperative in microbiome research to identify a microbial sub-community that collectively conducts a specific function. However, current methodologies have been highly limited to analyzing conditional abundance changes of individual microorganisms without considering group-wise collective microbial features. To overcome this limitation, we developed a network-based method using nonnegative matrix factorization (NMF) to identify functional meta-microbial features (MMFs) that, as a group, better discriminate specific environmental conditions of samples using microbiome data. As proof of concept, large-scale human microbiome data collected from different body sites were used to identify body site-specific MMFs by applying NMF. The statistical test for MMFs led us to identify highly discriminative MMFs on sample classes, called synergistic MMFs (SYMMFs). Finally, we constructed a SYMMF-based microbial interaction network (SYMMF-net) by integrating all of the SYMMF information. Network analysis revealed core microbial modules closely related to critical sample properties. Similar results were also found when the method was applied to various disease-associated microbiome data. The developed method interprets high-dimensional microbiome data by identifying functional microbial modules on sample properties and intuitively representing their systematic relationships via a microbial network.
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Burakova I, Smirnova Y, Gryaznova M, Syromyatnikov M, Chizhkov P, Popov E, Popov V. The Effect of Short-Term Consumption of Lactic Acid Bacteria on the Gut Microbiota in Obese People. Nutrients 2022; 14:nu14163384. [PMID: 36014890 PMCID: PMC9415828 DOI: 10.3390/nu14163384] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 02/07/2023] Open
Abstract
Obesity is a problem of modern health care that causes the occurrence of many concomitant diseases: arterial hypertension, diabetes mellitus, non-alcoholic fatty liver disease, and cardiovascular diseases. New strategies for the treatment and prevention of obesity are being developed that are based on using probiotics for modulation of the gut microbiota. Our study aimed to evaluate the bacterial composition of the gut of obese patients before and after two weeks of lactic acid bacteria (Lactobacillus acidophilus, Lactiplantibacillus plantarum, Limosilactobacillus fermentum, and Lactobacillus delbrueckii) intake. The results obtained showed an increase in the number of members of the phylum Actinobacteriota in the group taking nutritional supplements, while the number of phylum Bacteroidota decreased in comparison with the control group. There has also been an increase in potentially beneficial groups: Bifidobacterium, Blautia, Eubacterium, Anaerostipes, Lactococcus, Lachnospiraceae ND3007, Streptococcus, Escherichia-Shigella, and Lachnoclostridium. Along with this, a decrease in the genera was demonstrated: Faecalibacterium, Pseudobutyrivibrio, Subdoligranulum, Faecalibacterium, Clostridium sensu stricto 1 and 2, Catenibacterium, Megasphaera, Phascolarctobacterium, and the Oscillospiraceae NK4A214 group, which contribute to the development of various metabolic disorders. Modulation of the gut microbiota by lactic acid bacteria may be one of the ways to treat obesity.
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Affiliation(s)
- Inna Burakova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Yuliya Smirnova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Mariya Gryaznova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Mikhail Syromyatnikov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
- Correspondence: ; Tel.: +7-473-220-0876
| | - Pavel Chizhkov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Evgeny Popov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Vasily Popov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
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Imai T, Inoue R, Nishida A, Yokota Y, Morishima S, Kawahara M, Kusada H, Tamaki H, Andoh A. Features of the gut prokaryotic virome of Japanese patients with Crohn's disease. J Gastroenterol 2022; 57:559-570. [PMID: 35689701 DOI: 10.1007/s00535-022-01882-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/16/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND/AIMS The gut virome is mainly composed of bacteriophages and influences gut homeostasis and pathogenic conditions. In this study, we analyzed the gut prokaryotic virome in Japanese patients with Crohn's disease (CD). MATERIALS/METHODS We collected 19 fecal samples from CD patients and 16 samples from healthy controls. The gut bacteriome was analyzed by 16S rRNA gene sequencing and the virome was profiled by shotgun metagenomic sequencing. RESULTS Despite no differences in richness and evenness, there was a significant difference in the overall structure of the gut virome between CD patients and controls (P = 0.013). CrAssphage and Staphylococcus virus, belonging to the order Caudovirales, were dominant in the gut virome of controls and CD patients. The abundance of crAssphage was significantly greater in CD patients than controls (P = 0.021). Lactococcus, Enterococcus and Lactobacillus phages were present only in CD patients, while Xanthomonas and Escherichia phages were unique to the controls. In the gut bacteriome of CD patients, richness and evenness were significantly lower, and a significant difference in the overall structure was observed between groups (P = 0.014). The gut bacteriome of CD patients was characterized by a decrease of the genera Faecalibacterium, Roseburia, and Ruminococcus and an increase of the family Enterobacteriaceae. There were more significant correlations between viruses and bacteria in CD patients than controls. CONCLUSIONS The gut virome of CD patients was distinct from that of healthy controls in a Japanese population. An altered gut virome may be one of the factors associated with the bacterial dysbiosis of CD.
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Affiliation(s)
- Takayuki Imai
- Department of Medicine, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Shiga, 520-2192, Japan
| | - Ryo Inoue
- Department of Applied Biological Science, Faculty of Agriculture, Setsunan University, Hirakata, Osaka, 573-0101, Japan
| | - Atsushi Nishida
- Department of Medicine, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Shiga, 520-2192, Japan
| | - Yoshihiro Yokota
- Department of Medicine, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Shiga, 520-2192, Japan
| | - So Morishima
- Department of Applied Biological Science, Faculty of Agriculture, Setsunan University, Hirakata, Osaka, 573-0101, Japan
| | - Masahiro Kawahara
- Department of Medicine, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Shiga, 520-2192, Japan
| | - Hiroyuki Kusada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
| | - Akira Andoh
- Department of Medicine, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Shiga, 520-2192, Japan.
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Ye L, Wang JY, Liu XF, Guan Q, Dou NX, Li J, Zhang Q, Gao YM, Wang M, Li JS, Zhou B. Nematicidal activity of volatile organic compounds produced by Bacillus altitudinis AMCC 1040 against Meloidogyne incognita. Arch Microbiol 2022; 204:521. [PMID: 35879581 DOI: 10.1007/s00203-022-03024-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022]
Abstract
The application of nematicidal microorganisms and their virulence factors provides more opportunities to control root-knot nematodes. Bacillus altitudinis AMCC 1040, previously isolated from suppressive soils, showed significant nematicidal activity, and in this study, nematicidal substances produced by Bacillus altitudinis AMCC 1040 were investigated. The results of the basic properties of active substances showed that these compounds have good thermal stability and passage, are resistant to acidic environment and sensitive to alkaline conditions. Further analysis showed that it is a volatile component. Using HS-SPME-GC/MS, the volatile compounds produced by Bacillus altitudinis AMCC 1040 were identified and grouped into four major categories: ethers, alcohols, ketone, and organic acids, comprising a total of eight molecules. Six of them possess nematicidal activities, including 2,3-butanedione, acetic acid, 2-isopropoxy ethylamine, 3-methylbutyric acid, 2-methylbutyric acid and octanoic acid. Our results further our understanding of the effects of Bacillus altitudinis and its nematicidal metabolites on the management of Meloidogyne incognita and may help in finding less toxic nematicides to control root knot nematodes.
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Affiliation(s)
- Lin Ye
- Agriculture College, Ningxia University, Yinchuan, Ning'xia, China
| | - Jian-Yu Wang
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an , 271018, China
| | - Xiao-Fang Liu
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an , 271018, China
| | - Qi Guan
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an , 271018, China
| | - Nong-Xiao Dou
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an , 271018, China
| | - Jian Li
- College of Food and Bioengineering, Jimei University, Xiamen, 361021, China.
| | - Qian Zhang
- Shandong Institute of Pomology, Tai'an, 271018, China
| | - Yan-Ming Gao
- Agriculture College, Ningxia University, Yinchuan, Ning'xia, China
| | - Min Wang
- Shandong Wanhao Fertilizer Co., LTD, Jinan, 25000, China
| | - Jian-She Li
- Agriculture College, Ningxia University, Yinchuan, Ning'xia, China.
| | - Bo Zhou
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an , 271018, China. .,National Engineering Research Center for Efficient Utilization of Soil and Fertilizer, Tai'an, 271018, China.
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Abstract
Fusobacterium nucleatum is a common constituent of the oral microbiota in both periodontal health and disease. Previously, we discovered ornithine cross-feeding between F. nucleatum and Streptococcus gordonii, where S. gordonii secretes ornithine via an arginine-ornithine antiporter (ArcD), which in turn supports the growth and biofilm development of F. nucleatum; however, broader metabolic aspects of F. nucleatum within polymicrobial communities and their impact on periodontal pathogenesis have not been addressed. Here, we show that when cocultured with S. gordonii, F. nucleatum increased amino acid availability to enhance the production of butyrate and putrescine, a polyamine produced by ornithine decarboxylation. Coculture with Veillonella parvula, another common inhabitant of the oral microbiota, also increased lysine availability, promoting cadaverine production by F. nucleatum. We confirmed that ArcD-dependent S. gordonii-excreted ornithine induces synergistic putrescine production, and mass spectrometry imaging revealed that this metabolic capability creates a putrescine-rich microenvironment on the surface of F. nucleatum biofilms. We further demonstrated that polyamines caused significant changes in the biofilm phenotype of a periodontal pathogen, Porphyromonas gingivalis, with putrescine accelerating the biofilm life cycle of maturation and dispersal. This phenomenon was also observed with putrescine derived from S. gordonii-F. nucleatum coculture. Lastly, analysis of plaque samples revealed cooccurrence of P. gingivalis with genetic modules for putrescine production by S. gordonii and F. nucleatum. Overall, our results highlight the ability of F. nucleatum to induce synergistic polyamine production within multispecies consortia and provide insight into how the trophic web in oral biofilm ecosystems can eventually shape disease-associated communities. IMPORTANCE Periodontitis is caused by a pathogenic shift in subgingival biofilm ecosystems, which is accompanied by alterations in microbiome composition and function, including changes in the metabolic activity of the biofilm, which comprises multiple commensals and pathogens. While Fusobacterium nucleatum is a common constituent of the supra- and subgingival biofilms, its metabolic integration within polymicrobial communities and the impact on periodontal pathogenesis are poorly understood. Here, we report that amino acids supplied by other commensal bacteria induce polyamine production by F. nucleatum, creating polyamine-rich microenvironments. Polyamines reportedly have diverse functions in bacterial physiology and possible involvement in periodontal pathogenesis. We show that the F. nucleatum-integrated trophic network yielding putrescine from arginine through ornithine accelerates the biofilm life cycle of Porphyromonas gingivalis, a periodontal pathogen, from the planktonic state through biofilm formation to dispersal. This work provides insight into how cooperative metabolism within oral biofilms can tip the balance toward periodontitis.
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Lactobacillus salivarius UCC118™ Dampens Inflammation and Promotes Microbiota Recovery to Provide Therapeutic Benefit in a DSS-Induced Colitis Model. Microorganisms 2022; 10:microorganisms10071383. [PMID: 35889102 PMCID: PMC9324116 DOI: 10.3390/microorganisms10071383] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
The use of probiotics such as Lactobacillus and Bifidobacterium spp. as a therapeutic against inflammatory bowel disease (IBD) is of significant interest. Lactobacillus salivarus strain UCC118TM is a commensal that has been shown to possess probiotic properties in vitro and anti-infective properties in vivo. However, the usefulness of UCC118 TM as a therapeutic against colitis remains unclear. This study investigates the probiotic potential of Lactobacillus salivarius, UCC118™ in a mouse model of colitis. DSS-induced colitis was coupled with pre-treatment or post-treatment with UCC118TM by daily oral gavage. In the pre-treatment model of colitis, UCC118TM reduced the severity of the disease in the early stages. Improvement in disease severity was coupled with an upregulation of tissue IL-10 levels and increased expression of macrophage M2 markers. This anti-inflammatory activity of UCC118TM was further confirmed in vitro, using a model of LPS-treated bone marrow-derived macrophages. Taken together, these results suggest that UCC118TM may promote the resolution of inflammation. This was supported in a mouse model of established DSS-induced colitis whereby UCC118TM treatment accelerated recovery, as evidenced by weight, stool, histological markers and the recovery of microbiome-associated dysbiosis with an increased abundance of beneficial commensal species. These results demonstrate the potential of Lactobacillus salivarius UCC118TM as a probiotic-based therapeutic strategy to promote health through the upregulation of anti-inflammatory IL-10 and protect against dysbiosis during IBD.
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Sharp C, Foster KR. Host control and the evolution of cooperation in host microbiomes. Nat Commun 2022; 13:3567. [PMID: 35732630 PMCID: PMC9218092 DOI: 10.1038/s41467-022-30971-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/27/2022] [Indexed: 12/14/2022] Open
Abstract
Humans, and many other species, are host to diverse symbionts. It is often suggested that the mutual benefits of host-microbe relationships can alone explain cooperative evolution. Here, we evaluate this hypothesis with evolutionary modelling. Our model predicts that mutual benefits are insufficient to drive cooperation in systems like the human microbiome, because of competition between symbionts. However, cooperation can emerge if hosts can exert control over symbionts, so long as there are constraints that limit symbiont counter evolution. We test our model with genomic data of two bacterial traits monitored by animal immune systems. In both cases, bacteria have evolved as predicted under host control, tending to lose flagella and maintain butyrate production when host-associated. Moreover, an analysis of bacteria that retain flagella supports the evolution of host control, via toll-like receptor 5, which limits symbiont counter evolution. Our work puts host control mechanisms, including the immune system, at the centre of microbiome evolution.
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Affiliation(s)
- Connor Sharp
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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Benito-Vaquerizo S, Parera Olm I, de Vroet T, Schaap PJ, Sousa DZ, Martins Dos Santos VAP, Suarez-Diez M. Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. Microb Cell Fact 2022; 21:116. [PMID: 35710409 PMCID: PMC9205015 DOI: 10.1186/s12934-022-01841-1] [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: 04/12/2022] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial production of propionate from diluted streams of ethanol (e.g., deriving from syngas fermentation) is a sustainable alternative to the petrochemical production route. Yet, few ethanol-fermenting propionigenic bacteria are known, and understanding of their metabolism is limited. Anaerotignum neopropionicum is a propionate-producing bacterium that uses the acrylate pathway to ferment ethanol and CO2 to propionate and acetate. In this work, we used computational and experimental methods to study the metabolism of A. neopropionicum and, in particular, the pathway for conversion of ethanol into propionate. RESULTS Our work describes iANEO_SB607, the first genome-scale metabolic model (GEM) of A. neopropionicum. The model was built combining the use of automatic tools with an extensive manual curation process, and it was validated with experimental data from this and published studies. The model predicted growth of A. neopropionicum on ethanol, lactate, sugars and amino acids, matching observed phenotypes. In addition, the model was used to implement a dynamic flux balance analysis (dFBA) approach that accurately predicted the fermentation profile of A. neopropionicum during batch growth on ethanol. A systematic analysis of the metabolism of A. neopropionicum combined with model simulations shed light into the mechanism of ethanol fermentation via the acrylate pathway, and revealed the presence of the electron-transferring complexes NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) and acryloyl-CoA reductase-EtfAB, identified for the first time in this bacterium. CONCLUSIONS The realisation of the GEM iANEO_SB607 is a stepping stone towards the understanding of the metabolism of the propionate-producer A. neopropionicum. With it, we have gained insight into the functioning of the acrylate pathway and energetic aspects of the cell, with focus on the fermentation of ethanol. Overall, this study provides a basis to further exploit the potential of propionigenic bacteria as microbial cell factories.
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Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Thijs de Vroet
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.,Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Vening Meinesz building C, Princetonlaan 6, Utrecht, 3584 CB, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.,Bioprocess Engineering, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.
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48
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Wang Y, Dong Q, Hu S, Zou H, Wu T, Shi J, Zhang H, Sheng Y, Sun W, Kong X, Chen L. Decoding microbial genomes to understand their functional roles in human complex diseases. IMETA 2022; 1:e14. [PMID: 38868571 PMCID: PMC10989872 DOI: 10.1002/imt2.14] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/20/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2024]
Abstract
Complex diseases such as cardiovascular disease (CVD), obesity, inflammatory bowel disease (IBD), kidney disease, type 2 diabetes (T2D), and cancer have become a major burden to public health and affect more than 20% of the population worldwide. The etiology of complex diseases is not yet clear, but they are traditionally thought to be caused by genetics and environmental factors (e.g., dietary habits), and by their interactions. Besides this, increasing pieces of evidence now highlight that the intestinal microbiota may contribute substantially to the health and disease of the human host via their metabolic molecules. Therefore, decoding the microbial genomes has been an important strategy to shed light on their functional potential. In this review, we summarize the roles of the gut microbiome in complex diseases from its functional perspective. We further introduce artificial tools in decoding microbial genomes to profile their functionalities. Finally, state-of-the-art techniques have been highlighted which may contribute to a mechanistic understanding of the gut microbiome in human complex diseases and promote the development of the gut microbiome-based personalized medicine.
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Affiliation(s)
- Yifeng Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Quanbin Dong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Shixian Hu
- Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat‐Sen UniversitySun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Huayiyang Zou
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
| | - Tingting Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
| | - Jing Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
| | - Haifeng Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Yanhui Sheng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Xiangqing Kong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Lianmin Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
- Department of Genetics, University Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
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49
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Bellés A, Aguirre-Ramírez D, Abad I, Parras-Moltó M, Sánchez L, Grasa L. Lactoferrin modulates gut microbiota and Toll-like receptors (TLRs) in mice with dysbiosis induced by antibiotics. Food Funct 2022; 13:5854-5869. [PMID: 35545893 DOI: 10.1039/d2fo00287f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background: Antibiotic administration can result in gut microbiota and immune system alterations that impact health. Bovine lactoferrin is a milk protein with anticancer, anti-inflammatory, antimicrobial and immune modulatory activities. The aim was to study the ability of native and iron-saturated lactoferrin to reverse the effects of clindamycin on gut microbiota and intestinal Toll-like receptor (TLR) expression in a murine model. Methods: Male C57BL/6 mice were treated with vehicle, clindamycin (Clin), native bovine lactoferrin (nLf), nLf + clindamycin (nLf_Clin), iron-saturated bovine lactoferrin (sLf) and sLf + clindamycin (sLf_Clin). Fecal samples of each group were collected, and bacterial DNA was extracted. Sequencing of 16s rRNA V4 hypervariable gene regions was conducted to assess the microbial composition. mRNA expression levels of TLRs (1-9) were determined in mouse colon by qPCR. Pearson's correlation test was carried out between bacteria showing differences in abundance among samples and TLR2, TLR8 and TLR9. Results: Beta-diversity analysis showed that the microbial community of the vehicle was different from the communities of Clin, nLf_Clin and sLf_Clin. At the family level, Bacteroidaceae, Prevotellaceae and Rikenellaceae decreased in the Clin group, and treatment with nLf or sLf reverted these effects. Clin reduced the expression of TLR2, TLR8 and TLR9 and sLf reverted the decrease in the expression of these receptors. Finally, TLR8 was positively correlated with Rikenellaceae abundance. Conclusion: In a situation of intestinal dysbiosis induced by clindamycin, lactoferrin restores the normal levels of some anti-inflammatory bacteria and TLRs and, therefore, could be a good ingredient to be added to functional foods.
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Affiliation(s)
- Andrea Bellés
- Universidad de Zaragoza, Facultad de Veterinaria, Departamento de Farmacología, Fisiología y Medicina Legal y Forense, Zaragoza, Spain. .,Instituto Agroalimentario de Aragón IA2 (UNIZAR-CITA), Zaragoza, Spain
| | - Diego Aguirre-Ramírez
- Universidad de Zaragoza, Facultad de Veterinaria, Departamento de Farmacología, Fisiología y Medicina Legal y Forense, Zaragoza, Spain.
| | - Inés Abad
- Instituto Agroalimentario de Aragón IA2 (UNIZAR-CITA), Zaragoza, Spain.,Universidad de Zaragoza, Facultad de Veterinaria, Departamento de Producción Animal y Tecnología de los Alimentos, Zaragoza, Spain
| | - Marcos Parras-Moltó
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden.,Igenomix Foundation/INCLIVA Biomedical Research Institute, Spain.,Department of Science, Universidad Internacional de Valencia-VIU, Valencia, Spain
| | - Lourdes Sánchez
- Instituto Agroalimentario de Aragón IA2 (UNIZAR-CITA), Zaragoza, Spain.,Universidad de Zaragoza, Facultad de Veterinaria, Departamento de Producción Animal y Tecnología de los Alimentos, Zaragoza, Spain
| | - Laura Grasa
- Universidad de Zaragoza, Facultad de Veterinaria, Departamento de Farmacología, Fisiología y Medicina Legal y Forense, Zaragoza, Spain. .,Instituto Agroalimentario de Aragón IA2 (UNIZAR-CITA), Zaragoza, Spain.,Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain
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50
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Naveed M, Makhdoom SI, Abbas G, Safdari M, Farhadi A, Habtemariam S, Shabbir MA, Jabeen K, Asif MF, Tehreem S. The Virulent Hypothetical Proteins: The Potential Drug Target Involved in Bacterial Pathogenesis. Mini Rev Med Chem 2022; 22:2608-2623. [DOI: 10.2174/1389557522666220413102107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/01/2021] [Accepted: 01/21/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
Hypothetical proteins (HPs) are non-predicted sequences that are identified only by open reading frames in sequenced genomes but their protein products remain uncharacterized by any experimental means. The genome of every species consists of HPs that are involved in various cellular processes and signaling pathways. Annotation of HPs is important as they play a key role in disease mechanisms, drug designing, vaccine production, antibiotic production, and host adaptation. In the case of bacteria, 25-50% of the genome comprises of HPs, which are involved in metabolic pathways and pathogenesis. The characterization of bacterial HPs helps to identify virulent proteins that are involved in pathogenesis. This can be done using in-silico studies, which provide sequence analogs, physiochemical properties, cellular or subcellular localization, structure and function validation, and protein-protein interactions. The most diverse types of virulent proteins are exotoxins, endotoxins, and adherent virulent factors that are encoded by virulent genes present on the chromosomal DNA of the bacteria. This review evaluates virulent HPs of pathogenic bacteria, such as Staphylococcus aureus, Chlamydia trachomatis, Fusobacterium nucleatum, and Yersinia pestis. The potential of these HPs as a drug target in bacteria-caused infectious diseases along with the mode of action and treatment approaches have been discussed.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Pakistan
| | - Syeda Izma Makhdoom
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Pakistan
| | - Ghulam Abbas
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mohammadreza Safdari
- Department of Orthopedic Surgery, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Amin Farhadi
- Kavian Institute of Higher Education, Mashhad, Iran
| | - Solomon Habtemariam
- Pharmacognosy Research Laboratories & Herbal Analysis Services UK, University of Greenwich, Medway Campus-Science, Grenville Building (G102/G107), Central Avenue, Chatham-Maritime, Kent, ME4 4TB, UK
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Pakistan
| | - Khizra Jabeen
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Pakistan
| | - Muhammad Farrukh Asif
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Pakistan
| | - Sana Tehreem
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, Hubei, China
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