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Soni J, Pandey R. Single cell genomics based insights into the impact of cell-type specific microbial internalization on disease severity. Front Immunol 2024; 15:1401320. [PMID: 38835769 PMCID: PMC11148356 DOI: 10.3389/fimmu.2024.1401320] [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: 03/15/2024] [Accepted: 04/19/2024] [Indexed: 06/06/2024] Open
Abstract
Host-microbe interactions are complex and ever-changing, especially during infections, which can significantly impact human physiology in both health and disease by influencing metabolic and immune functions. Infections caused by pathogens such as bacteria, viruses, fungi, and parasites are the leading cause of global mortality. Microbes have evolved various immune evasion strategies to survive within their hosts, which presents a multifaceted challenge for detection. Intracellular microbes, in particular, target specific cell types for survival and replication and are influenced by factors such as functional roles, nutrient availability, immune evasion, and replication opportunities. Identifying intracellular microbes can be difficult because of the limitations of traditional culture-based methods. However, advancements in integrated host microbiome single-cell genomics and transcriptomics provide a promising basis for personalized treatment strategies. Understanding host-microbiota interactions at the cellular level may elucidate disease mechanisms and microbial pathogenesis, leading to targeted therapies. This article focuses on how intracellular microbes reside in specific cell types, modulating functions through persistence strategies to evade host immunity and prolong colonization. An improved understanding of the persistent intracellular microbe-induced differential disease outcomes can enhance diagnostics, therapeutics, and preventive measures.
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Affiliation(s)
- Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst PathogEn (INGEN-HOPE) Laboratory, Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst PathogEn (INGEN-HOPE) Laboratory, Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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2
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Liu Q, Wang Z, Sun S, Nemes J, Brenner LA, Hoisington A, Skotak M, LaValle CR, Ge Y, Carr W, Haghighi F. Association of Blast Exposure in Military Breaching with Intestinal Permeability Blood Biomarkers Associated with Leaky Gut. Int J Mol Sci 2024; 25:3549. [PMID: 38542520 PMCID: PMC10971443 DOI: 10.3390/ijms25063549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Injuries and subclinical effects from exposure to blasts are of significant concern in military operational settings, including tactical training, and are associated with self-reported concussion-like symptomology and physiological changes such as increased intestinal permeability (IP), which was investigated in this study. Time-series gene expression and IP biomarker data were generated from "breachers" exposed to controlled, low-level explosive blast during training. Samples from 30 male participants at pre-, post-, and follow-up blast exposure the next day were assayed via RNA-seq and ELISA. A battery of symptom data was also collected at each of these time points that acutely showed elevated symptom reporting related to headache, concentration, dizziness, and taking longer to think, dissipating ~16 h following blast exposure. Evidence for bacterial translocation into circulation following blast exposure was detected by significant stepwise increase in microbial diversity (measured via alpha-diversity p = 0.049). Alterations in levels of IP protein biomarkers (i.e., Zonulin, LBP, Claudin-3, I-FABP) assessed in a subset of these participants (n = 23) further evidenced blast exposure associates with IP. The observed symptom profile was consistent with mild traumatic brain injury and was further associated with changes in bacterial translocation and intestinal permeability, suggesting that IP may be linked to a decrease in cognitive functioning. These preliminary findings show for the first time within real-world military operational settings that exposures to blast can contribute to IP.
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Affiliation(s)
- Qingkun Liu
- James J. Peters VA Medical Center, Bronx, NY 10468, USA; (Q.L.); (Z.W.); (S.S.)
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Zhaoyu Wang
- James J. Peters VA Medical Center, Bronx, NY 10468, USA; (Q.L.); (Z.W.); (S.S.)
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Shengnan Sun
- James J. Peters VA Medical Center, Bronx, NY 10468, USA; (Q.L.); (Z.W.); (S.S.)
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Jeffrey Nemes
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA (C.R.L.); (W.C.)
| | - Lisa A. Brenner
- Rocky Mountain Mental Illness, Research, Education and Clinical Care, Department of Veterans Affairs, Aurora, CO 80045, USA; (L.A.B.); (A.H.)
- Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA
| | - Andrew Hoisington
- Rocky Mountain Mental Illness, Research, Education and Clinical Care, Department of Veterans Affairs, Aurora, CO 80045, USA; (L.A.B.); (A.H.)
- Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA
- Department of Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson Air Force Base, OH 45433, USA
| | - Maciej Skotak
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA (C.R.L.); (W.C.)
| | - Christina R. LaValle
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA (C.R.L.); (W.C.)
| | - Yongchao Ge
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Walter Carr
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA (C.R.L.); (W.C.)
| | - Fatemeh Haghighi
- James J. Peters VA Medical Center, Bronx, NY 10468, USA; (Q.L.); (Z.W.); (S.S.)
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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3
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Nikitina D, Lukosevicius R, Tilinde D, Muskieta T, Hov JR, Melum E, Klovins J, Org E, Kiudelis G, Kupcinskas J, Skieceviciene J. Cell-Free Microbial DNA Analysis: Effects of Blood Plasma and Serum Quantity, Biobanking Protocols, and Isolation Kits. Biopreserv Biobank 2024. [PMID: 38416864 DOI: 10.1089/bio.2023.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024] Open
Abstract
Recent studies highlight the presence of bacterial sequences in the human blood, suggesting potential clinical significance for circulating microbial signatures. These sequences could presumably serve in the diagnosis, prediction, or monitoring of various health conditions. Ensuring the similarity of samples before bacterial analysis is crucial, especially when combining samples from different biobanks prepared under varying conditions (such as different DNA extraction kits, centrifugation conditions, blood collection tubes, etc.). In this study, we aimed to analyze the impact of different sample collection and nucleic acid extraction criteria (blood collection tube, centrifugation, input volume, and DNA extraction kit) on circulating bacterial composition. Blood samples from four healthy individuals were collected into three different sample collection tubes: K2EDTA plasma tube, sodium citrate plasma tube, and gel tube for blood serum. Tubes were centrifugated at standard and double centrifugation conditions. DNA extraction was performed using 100, 200, and 500 μL plasma/serum input volumes. DNA extraction was performed using three different isolation kits: Norgen plasma/serum cell-free circulating DNA purification micro kit, Applied Biosystems MagMAX cell-free DNA isolation kit, and Qiagen QIAamp MinElute cell-free circulating DNA mini kit. All samples were subjected to 16S rRNA V1-V2 library preparation and sequencing. In total, 216 DNA and 18 water control samples were included in the study. According to PERMANOVA, PCoA, Mann-Whitney, and FDR tests the effect of the DNA extraction kit on the microbiota composition was the greatest, whereas the type of blood collection tube, centrifugation type, and sample input volume for the extraction had minor effects. Samples extracted with the Norgen DNA extraction kit were enriched with Gram-negative bacteria, whereas samples extracted with the Qiagen and MagMAX kits were enriched with Gram-positive bacteria. Bacterial profiles of samples prepared with the Qiagen and MagMAX DNA extraction kits were more similar, whereas samples prepared with the Norgen DNA extraction kit were significantly different from other groups.
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Affiliation(s)
- Darja Nikitina
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rokas Lukosevicius
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Deimante Tilinde
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Tomas Muskieta
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Johannes Roksund Hov
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
| | - Espen Melum
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, Hybrid Technology Hub Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Janis Klovins
- Latvian Biomedical Research and Study Center, Riga, Latvia
| | - Elin Org
- Institute of Genomics, Estonian Genome Centre, University of Tartu, Tartu, Estonia
| | - Gediminas Kiudelis
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
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Noor Eddin A, Alfuwais M, Noor Eddin R, Alkattan K, Yaqinuddin A. Gut-Modulating Agents and Amyotrophic Lateral Sclerosis: Current Evidence and Future Perspectives. Nutrients 2024; 16:590. [PMID: 38474719 DOI: 10.3390/nu16050590] [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: 01/21/2024] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a highly fatal neurodegenerative disorder characterized by the progressive wasting and paralysis of voluntary muscle. Despite extensive research, the etiology of ALS remains elusive, and effective treatment options are limited. However, recent evidence implicates gut dysbiosis and gut-brain axis (GBA) dysfunction in ALS pathogenesis. Alterations to the composition and diversity of microbial communities within the gut flora have been consistently observed in ALS patients. These changes are often correlated with disease progression and patient outcome, suggesting that GBA modulation may have therapeutic potential. Indeed, targeting the gut microbiota has been shown to be neuroprotective in several animal models, alleviating motor symptoms and mitigating disease progression. However, the translation of these findings to human patients is challenging due to the complexity of ALS pathology and the varying diversity of gut microbiota. This review comprehensively summarizes the current literature on ALS-related gut dysbiosis, focusing on the implications of GBA dysfunction. It delineates three main mechanisms by which dysbiosis contributes to ALS pathology: compromised intestinal barrier integrity, metabolic dysfunction, and immune dysregulation. It also examines preclinical evidence on the therapeutic potential of gut-microbiota-modulating agents (categorized as prebiotics, probiotics, and postbiotics) in ALS.
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Affiliation(s)
- Ahmed Noor Eddin
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Mohammed Alfuwais
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Reena Noor Eddin
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Ahmed Yaqinuddin
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
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5
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Wang P, Zhang S, Qi C, Wang C, Zhu Z, Shi L, Cheng L, Zhang X. Blood microbial analyses reveal long-term effects of SARS-CoV-2 infection on patients who recovered from COVID-19. Comput Biol Med 2024; 168:107721. [PMID: 38016374 DOI: 10.1016/j.compbiomed.2023.107721] [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: 09/23/2023] [Revised: 10/17/2023] [Accepted: 11/15/2023] [Indexed: 11/30/2023]
Abstract
OBJECTIVE Few symptoms persist for a long time after patients recover from COVID-19, called "long COVID". We explored the potential microbial risk factors for COVID-19 for a deeper understanding and assistance in the follow-up treatment of these sequelae. METHODS Microbiome re-annotation was performed using whole blood RNA-Seq data collected from recovered COVID-19 patients and healthy controls at multiple time points. Subsequently, a series of downstream analyses were conducted to reveal the microbial characteristics of patients who recovered from SARS-CoV-2 infection. RESULTS The blood microbiome at 12 weeks post-infection was most evidently disturbed, including an increasing ratio of Bacillota/Bacteroidota and a higher microbial alpha diversity. In addition, a group of pathogenic microbes at 12 weeks post-infection were identified, including Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, which were positively associated with host genes involved in immune regulatory and olfactory transduction pathways. Several microbes, such as Streptococcus pneumoniae were associated with infiltrating immune cells, such as M2 macrophages. CONCLUSION This study provides insights into the relationship between the blood microbiome and COVID-19 sequelae. Several pathogenic microbes were enriched in recovered COVID-19 patients and thus affected host genes participating in the immune and olfactory transduction pathways, which play critical roles in COVID-19 sequelae.
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Affiliation(s)
- Ping Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Changlu Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Chao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Zijun Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Lei Shi
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China.
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China; NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China.
| | - Xue Zhang
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China; McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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6
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Liu Z, Liu J, Geng J, Wu E, Zhu J, Cong B, Wu R, Sun H. Metatranscriptomic characterization of six types of forensic samples and its potential application to body fluid/tissue identification: A pilot study. Forensic Sci Int Genet 2024; 68:102978. [PMID: 37995518 DOI: 10.1016/j.fsigen.2023.102978] [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: 06/02/2023] [Revised: 10/21/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Microorganisms are potential markers for identifying body fluids (venous and menstrual blood, semen, saliva, and vaginal secretion) and skin tissue in forensic genetics. Existing published studies have mainly focused on investigating microbial DNA by 16 S rRNA gene sequencing or metagenome shotgun sequencing. We rarely find microbial RNA level investigations on common forensic body fluid/tissue. Therefore, the use of metatranscriptomics to characterize common forensic body fluids/tissue has not been explored in detail, and the potential application of metatranscriptomics in forensic science remains unknown. Here, we performed 30 metatranscriptome analyses on six types of common forensic sample from healthy volunteers by massively parallel sequencing. After quality control and host RNA filtering, a total of 345,300 unigenes were assembled from clean reads. Four kingdoms, 137 phyla, 267 classes, 488 orders, 985 families, 2052 genera, and 4690 species were annotated across all samples. Alpha- and beta-diversity and differential analysis were also performed. As a result, the saliva and skin groups demonstrated high alpha diversity (Simpson index), while the venous blood group exhibited the lowest diversity despite a high Chao1 index. Specifically, we discussed potential microorganism contamination and the "core microbiome," which may be of special interest to forensic researchers. In addition, we implemented and evaluated artificial neural network (ANN), random forest (RF), and support vector machine (SVM) models for forensic body fluid/tissue identification (BFID) using genus- and species-level metatranscriptome profiles. The ANN and RF prediction models discriminated six forensic body fluids/tissue, demonstrating that the microbial RNA-based method could be applied to BFID. Unlike metagenomic research, metatranscriptomic analysis can provide information about active microbial communities; thus, it may have greater potential to become a powerful tool in forensic science for microbial-based individual identification. This study represents the first attempt to explore the application potential of metatranscriptome profiles in forensic science. Our findings help deepen our understanding of the microorganism community structure at the RNA level and are beneficial for other forensic applications of metatranscriptomics.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Enlin Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jianzhang Zhu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510080, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China.
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Ling Z, Cheng Y, Liu X, Yan X, Wu L, Shao L, Gao J, Lei W, Song Q, Zhao L, Jin G. Altered oral microbiota and immune dysfunction in Chinese elderly patients with schizophrenia: a cross-sectional study. Transl Psychiatry 2023; 13:383. [PMID: 38071192 PMCID: PMC10710460 DOI: 10.1038/s41398-023-02682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Schizophrenia (SZ) is a complex psychiatric neurodevelopmental disorder with uncertain etiology and pathogenesis. Increasing evidence has recognized the key role of the gut microbiota in SZ. However, few studies have investigated the potential link between oral microbiota and SZ. We studied the tongue coating microbiota and inflammatory profiles of 118 elderly SZ patients and 97 age-matched healthy controls using Illumina MiSeq sequencing and multiplex immunoassays, respectively. Reduced α-diversity, along with a significant difference in β-diversity, were observed in patients with SZ. We have identified SZ-associated oral dysbiosis, characterized by increased Streptococcus and Fusobacterium, as well as decreased Prevotella and Veillonella. These differential genera could potentially serve as biomarkers for SZ, either alone or in combination. Additionally, an elevated Streptococcus/Prevotella ratio could indicate oral dysbiosis. These differential genera formed two distinct clusters: Streptococcus-dominated and Prevotella-dominated, which exhibited different correlations with the altered immunological profiles. Furthermore, we also observed disruptions in the inferred microbiota functions in SZ-associated microbiota, particularly in lipid and amino acid metabolism. Our study provides novel insights into the characteristics of tongue coating microbiota and its associations with immunological disturbances in elderly SZ patients, which offer new targets for the diagnosis and treatment of SZ in the elderly.
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Affiliation(s)
- Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, Zhejiang, China.
- Jinan Microecological Biomedicine Shandong Laboratory, 250000, Jinan, Shandong, China.
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, 250000, Jinan, Shandong, China
| | - Xia Liu
- Department of Intensive Care Unit, the First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, Zhejiang, China
| | - Xiumei Yan
- Department of Laboratory Medicine, Lishui Second People's Hospital, 323000, Lishui, Zhejiang, China
| | - Lingbin Wu
- Department of Laboratory Medicine, Lishui Second People's Hospital, 323000, Lishui, Zhejiang, China
| | - Li Shao
- School of Clinical Medicine, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, The Affiliated Hospital of Hangzhou Normal University, 310015, Hangzhou, Zhejiang, China
| | - Jie Gao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, Zhejiang, China
| | - Wenhui Lei
- Jinan Microecological Biomedicine Shandong Laboratory, 250000, Jinan, Shandong, China
- School of Basic Medicine, Shandong First Medical University, 250000, Jinan, Shandong, China
| | - Qinghai Song
- Department of Psychiatry, Lishui Second People's Hospital, 323000, Lishui, Zhejiang, China
| | - Longyou Zhao
- Department of Laboratory Medicine, Lishui Second People's Hospital, 323000, Lishui, Zhejiang, China.
| | - Guolin Jin
- Department of Psychiatry, Lishui Second People's Hospital, 323000, Lishui, Zhejiang, China.
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Rust C, Malan-Muller S, van den Heuvel LL, Tonge D, Seedat S, Pretorius E, Hemmings SMJ. Platelets bridging the gap between gut dysbiosis and neuroinflammation in stress-linked disorders: A narrative review. J Neuroimmunol 2023; 382:578155. [PMID: 37523892 DOI: 10.1016/j.jneuroim.2023.578155] [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: 03/20/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/02/2023]
Abstract
In this narrative review, we examine the association between gut dysbiosis, neuroinflammation, and stress-linked disorders, including depression, anxiety, and post-traumatic stress disorder (PTSD), and investigate whether tryptophan (TRP) metabolism and platelets play a role in this association. The mechanisms underlying the aetiology of stress-linked disorders are complex and not yet completely understood. However, a potential link between chronic inflammation and these disorders may potentially be found in TRP metabolism and platelets. By critically analysing existing literature on platelets, the gut microbiome, and stress-linked disorders, we hope to elicit the role of platelets in mediating the effects on serotonin (5-HT) levels and neuroinflammation. We have included studies specifically investigating platelets and TRP metabolism in relation to inflammation, neuroinflammation and neuropsychiatric disorders. Alteration in microbial composition due to stress could contribute to increased intestinal permeability, facilitating the translocation of microbial products, and triggering the release of pro-inflammatory cytokines. This causes platelets to become hyperactive and secrete 5-HT into the plasma. Increased levels of pro-inflammatory cytokines may also lead to increased permeability of the blood-brain barrier (BBB), allowing inflammatory mediators entry into the brain, affecting the balance of TRP metabolism products, such as 5-HT, kynurenic acid (KYNA), and quinolinic acid (QUIN). These alterations may contribute to neuroinflammation and possible neurological damage. Furthermore, platelets can cross the compromised BBB and interact with astrocytes and neurons, leading to the secretion of 5-HT and pro-inflammatory factors, exacerbating inflammatory conditions in the brain. The mechanisms underlying neuroinflammation resulting from peripheral inflammation are still unclear, but the connection between the brain and gut through the bloodstream could be significant. Identifying peripheral biomarkers and mechanisms in the plasma that reflect neuroinflammation may be important. This review serves as a foundation for further research on the association between the gut microbiome, blood microbiome, and neuropsychiatric disorders. The integration of these findings with protein and metabolite markers in the blood may expand our understanding of the subject.
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Affiliation(s)
- Carlien Rust
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa.
| | - Stefanie Malan-Muller
- Department of Pharmacology and Toxicology, Faculty of Medicine, Universidad Complutense de Madrid (UCM), Madrid, Spain; Biomedical Network Research Center of Mental Health (CIBERSAM), Institute of Health Carlos III, Madrid, Spain; Neurochemistry Research Institute UCM, Hospital 12 de Octubre Research Institute (Imas12), Madrid, Spain
| | - Leigh L van den Heuvel
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa
| | - Daniel Tonge
- School of Life Sciences, Faculty of Natural Sciences, Keele University, ST5 5BG Newcastle, England, UK
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa
| | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa; Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology Biosciences Building, University of Liverpool, Liverpool, United Kingdom.
| | - Sian M J Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa
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Nohesara S, Abdolmaleky HM, Thiagalingam S. Epigenetic Aberrations in Major Psychiatric Diseases Related to Diet and Gut Microbiome Alterations. Genes (Basel) 2023; 14:1506. [PMID: 37510410 PMCID: PMC10379841 DOI: 10.3390/genes14071506] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Nutrition and metabolism modify epigenetic signatures like histone acetylation and DNA methylation. Histone acetylation and DNA methylation in the central nervous system (CNS) can be altered by bioactive nutrients and gut microbiome via the gut-brain axis, which in turn modulate neuronal activity and behavior. Notably, the gut microbiome, with more than 1000 bacterial species, collectively contains almost three million functional genes whose products interact with millions of human epigenetic marks and 30,000 genes in a dynamic manner. However, genetic makeup shapes gut microbiome composition, food/nutrient metabolism, and epigenetic landscape, as well. Here, we first discuss the effect of changes in the microbial structure and composition in shaping specific epigenetic alterations in the brain and their role in the onset and progression of major mental disorders. Afterward, potential interactions among maternal diet/environmental factors, nutrition, and gastrointestinal microbiome, and their roles in accelerating or delaying the onset of severe mental illnesses via epigenetic changes will be discussed. We also provide an overview of the association between the gut microbiome, oxidative stress, and inflammation through epigenetic mechanisms. Finally, we present some underlying mechanisms involved in mediating the influence of the gut microbiome and probiotics on mental health via epigenetic modifications.
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Affiliation(s)
- Shabnam Nohesara
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02218, USA; (S.N.); (S.T.)
| | - Hamid Mostafavi Abdolmaleky
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02218, USA; (S.N.); (S.T.)
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boson, MA 02215, USA
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02218, USA; (S.N.); (S.T.)
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA 02218, USA
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10
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Amdanee N, Shao M, Hu X, Fang X, Zhou C, Chen J, Ridwan Chattun M, Wen L, Pan X, Zhang X, Xu Y. Serum Metabolic Profile in Schizophrenia Patients With Antipsychotic-Induced Constipation and Its relationship With Gut Microbiome. Schizophr Bull 2023; 49:646-658. [PMID: 36723169 PMCID: PMC10154739 DOI: 10.1093/schbul/sbac202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND AND HYPOTHESIS Antipsychotics (APs), the cornerstone of schizophrenia treatment, confer a relatively high risk of constipation. However, the mechanisms underpinning AP-induced constipation are poorly understood. Thus, we hypothesized that (1) schizophrenia patients with AP-induced constipation have distinct metabolic patterns; (2) there is more than one mechanism at play in producing this adverse drug effect; and (3) AP-associated changes in the gut microbiome are related to the altered metabolic profiles. STUDY DESIGN Eighty-eight schizophrenia patients, including 44 with constipation (C) and 44 matched patients without constipation (NC), were enrolled in this study. Constipation was diagnosed by Rome IV criteria for constipation and colonic transit time using radiopaque markers (ROMs) while severity was evaluated with the Bristol Stool Form Scale (BSS) and Constipation Assessment Scale (CAS). Fasting blood samples were drawn from all participants and were subjected to non-targeted liquid chromatography-mass spectrometry (LC-MS) metabolomic analysis. STUDY RESULTS Eleven metabolites were significantly altered in AP-induced constipation which primarily disturbed sphingolipid metabolism, choline metabolism, and sphingolipid signaling pathway (P value < .05, FDR < 0.05). In the C group, changes in the gut bacteria showed a certain degree of correlation with 2 of the significantly altered serum metabolites and were associated with alterations in choline metabolism. CONCLUSIONS Our findings indicated that there were disturbances in distinct metabolic pathways that were associated with AP-induced constipation. In addition, this study presents evidence of a link between alterations in the gut microbiome and host metabolism which provides additional mechanistic insights on AP-induced constipation.
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Affiliation(s)
- Nousayhah Amdanee
- Department of Geriatric Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Miaomiao Shao
- Department of Geriatric Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
- Department of Psychiatry, The Second People’s Hospital of Jiangning District, Nanjing, Jiangsu, China
| | - Xiuxiu Hu
- Department of Geriatric Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
- Department of Psychiatry, The Second People’s Hospital of Jiangning District, Nanjing, Jiangsu, China
| | - Xinyu Fang
- Department of Geriatric Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Chao Zhou
- Department of Geriatric Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Jiu Chen
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Mohammad Ridwan Chattun
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Lu Wen
- Department of Psychiatry, The Second People’s Hospital of Jiangning District, Nanjing, Jiangsu, China
| | - Xinming Pan
- Department of Psychiatry, The Second People’s Hospital of Jiangning District, Nanjing, Jiangsu, China
| | - Xiangrong Zhang
- Department of Geriatric Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
- The Affiliated Xuzhou Oriental Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yue Xu
- Department of Geriatric Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
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11
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Ullah Goraya M, Li R, Gu L, Deng H, Wang G. Blood Stream Microbiota Dysbiosis Establishing New Research Standards in Cardio-Metabolic Diseases, A Meta-Analysis Study. Microorganisms 2023; 11:microorganisms11030777. [PMID: 36985350 PMCID: PMC10052040 DOI: 10.3390/microorganisms11030777] [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: 02/16/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023] Open
Abstract
AIMS Scientists have recently discovered a link between the circulating microbiome and homeostasis, as well as the pathogenesis of a number of metabolic diseases. It has been demonstrated that low-grade chronic inflammation is one of the primary mechanisms that has long been implicated in the risk of cardio-metabolic disease (CMDs) and its progression. Currently, the dysbiosis of circulating bacteria is considered as a key regulator for chronic inflammation in CMDs, which is why we have conducted this systemic review focused on circulating bacterial dysbiosis. METHODS A systemic review of clinical and research-based studies was conducted via PubMed, Scopus, Medline, and Web of Science. Literature was considered for risk of bias and patterns of intervention effects. A randomized effect model was used to evaluate the dysbiosis of circulating microbiota and clinical outcomes. We conducted a meta-analysis considering the circulating bacteria in both healthy people and people with cardio-metabolic disorders, in reports published mainly from 2008 to 2022, according to the PRISMA guidelines. RESULTS We searched 627 studies and, after completing the risk of bias and selection, 31 studies comprising of 11,132 human samples were considered. This meta-analysis found that dysbiosis of phyla Proteobacteria, Firmicutes, and Bacteroidetes was associated with metabolic diseases. CONCLUSIONS In most instances, metabolic diseases are linked to higher diversity and elevated bacterial DNA levels. Bacteroides abundance was higher in healthy people than with metabolic disorders. However, more rigorous studies are required to determine the role of bacterial dysbiosis in cardio-metabolic diseases. Understanding the relationship between dysbiosis and cardio-metabolic diseases, we can use the bacteria as therapeutics for the reversal of dysbiosis and targets for therapeutics use in cardio-metabolic diseases. In the future, circulating bacterial signatures can be used as biomarkers for the early detection of metabolic diseases.
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Affiliation(s)
| | - Rui Li
- Correspondence: (R.L.); (G.W.)
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12
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Liu Y, Li H, Ren P, Che Y, Zhou J, Wang W, Yang Y, Guan L. Polysaccharide from Flammulina velutipes residues protects mice from Pb poisoning by activating Akt/GSK3β/Nrf-2/HO-1 signaling pathway and modulating gut microbiota. Int J Biol Macromol 2023; 230:123154. [PMID: 36610568 DOI: 10.1016/j.ijbiomac.2023.123154] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/10/2022] [Accepted: 01/02/2023] [Indexed: 01/06/2023]
Abstract
Lead (Pb) can cause damages to the brain, liver, kidney, endocrine and other systems. Flammulina velutipes residues polysaccharide (FVRP) has been reported to exhibit anti-heavy metal toxicity on yeast, but its regulating mechanism is unclear. Therefore, the protective effect and the underlying mechanism of FVRP on Pb-intoxicated mice were investigated. The results showed that FVRP could reduce liver and kidney function indexes, serum inflammatory factor levels, and increase antioxidant enzyme activity of Pb-poisoned mice. FVRP also exhibited a protective effect on histopathological damages in organs of Pb-intoxicated mice. Furthermore, FVRP attenuated Pb-induced kidney injury by inhibiting apoptosis via activating the Akt/GSK3β/Nrf-2/HO-1 signaling pathway. In addition, based on 16 s rRNA and ITS-2 sequencing data, FVRP regulated the imbalance of gut microbiota to alleviate the damage of Pb-poisoned mice by increasing the abundance of beneficial microbiota (Lachnospiraceae, Lactobacillaceae, Saccharomyces and Mycosphaerella) and decreasing the abundance of harmful microbiota (Muribaculaceae and Pleosporaceae). In conclusion, FVRP inhibited kidney injury in Pb-poisoned mice by inhibiting apoptosis via activating Akt/GSK3β/Nrf-2/HO-1 signaling pathway, and regulating gut fungi and gut bacteria. This study not only revealed the role of gut fungi in Pb-toxicity, but also laid a theoretical foundation for FVRP as a natural drug against Pb-toxicity.
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Affiliation(s)
- Yingying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Hailong Li
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Ping Ren
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yange Che
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Jiaming Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Wanting Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yiting Yang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Lili Guan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China; Engineering Research Center of Bioreactor and Pharmaceutical Development, Ministry of Education, Jilin Agricultural University, Changchun 130118, China.
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13
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Li H, Liu Y, Zhou J, Liu S, Liu Y, Yang Y, Wang W, Che Y, Inam M, Guan L. The protective mechanism of a novel polysaccharide from Lactobacillus-fermented Nostoc commune Vauch. on attenuating cadmium-induced kidney injury in mice. Int J Biol Macromol 2023; 226:1444-1454. [PMID: 36442563 DOI: 10.1016/j.ijbiomac.2022.11.256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
A novel polysaccharide (NCVP-F) from Lactobacillus-fermented Nostoc commune Vauch. was obtained to investigate its underlying mechanism in cadmium-induced kidney injury. Results indicated that in comparison with NCVP, NCVP-F with lower molecular weight of 365.369 kDa, exhibited higher mole percentage of Man and Glc-UA, whereas slightly lower mole percentage of other monosaccharides. NCVP-F is a α-pyran polysaccharide similar to NCVP. Meanwhile, NCVP-F can more effectively alleviate hepatorenal injury (ALT, AST, TG, BUN and SCr) and kidney tissue lesions in Cd-injured mice model by increasing antioxidant enzyme activity (SOD, GSH and GSH-Px), inhibiting cytokines levels (IL-6, IL-1β, TNF-α and IL-18). In addition, NCVP-F effectively inhibited apoptosis proteins (Bax, cytochrome c, a-caspase-9 and a-caspase-3) and enhanced anti-apoptotic protein (Bcl-2) probably via activating PI3K/AKT/mTOR pathway in the Cd-injury kidney. Furthermore, 16S rRNA sequencing results indicated that NCVP-F better enriched Lachnospiraceae, reduced Muribaculaceae, Alloprevotella and Blautia to regulate Cd-induced gut microbiota disorders, which was probably down-regulated 7 pathways including apoptosis and lipopolysaccharide biosynthesis, and up-regulated 63 pathways, such as carbohydrate metabolism and lipid metabolism. This study suggested that applying functional NCVP-F prepared by biotransformation with low molecular weight might be more beneficial.
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Affiliation(s)
- Hailong Li
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yingying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Jiaming Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Su Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yue Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yiting Yang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Wanting Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yange Che
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Muhammad Inam
- Department of Animal Sciences, Shaheed Benazir Bhutto University Sheringal, Dir Upper, Pakistan
| | - Lili Guan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China; Engineering Research Center of Bioreactor and Pharmaceutical Development, Ministry of Education, Jilin Agricultural University, Changchun 130118, China.
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14
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Khan I, Khan I, Usman M, Xiao Wei Z, Ping X, Khan S, Khan F, Jianye Z, Zhiqiang L, Lizhe A. Circulating microbiota and metabolites: Insights into cardiovascular diseases. J Clin Lab Anal 2022; 36:e24779. [DOI: 10.1002/jcla.24779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/10/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022] Open
Affiliation(s)
- Ikram Khan
- Department of Microbiology, School of Life Sciences Lanzhou University Lanzhou Gansu China
- School of Stomatology Northwest Minzu University Lanzhou Gansu China
| | - Imran Khan
- Department of Microbiology Khyber Medical University Peshawar Peshawar Khyber Pakhtunkhwa Pakistan
| | - Muhammad Usman
- State Key Laboratory of Grassland Agro‐ecosystem, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Ruler Affairs, Collegeof Pastoral Agriculture Sciences and Technology Lanzhou University Lanzhou Gansu China
| | - Zhang Xiao Wei
- Department of Cardiology Lanzhou University Second Hospital Lanzhou Gansu China
| | - Xie Ping
- Department of Cardiology Gansu Provincial Hospital Lanzhou China
| | - Sarmir Khan
- Department of Reproductive Medicine, Academy of Medical Sciences The First Affiliated Hospital of Zheng University Zhengzhou Henan China
| | - Feroz Khan
- Department of Zoology, Wildlife, and Fisheries PirMehr Ali Shah Arid Agriculture University Rawalpindi Pakistan
| | - Zhou Jianye
- School of Stomatology Northwest Minzu University Lanzhou Gansu China
| | - Li Zhiqiang
- School of Stomatology Northwest Minzu University Lanzhou Gansu China
| | - An Lizhe
- Department of Microbiology, School of Life Sciences Lanzhou University Lanzhou Gansu China
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15
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Khan I, Khan I, Usman M, Jianye Z, Wei ZX, Ping X, Zhiqiang L, Lizhe A. Analysis of the blood bacterial composition of patients with acute coronary syndrome and chronic coronary syndrome. Front Cell Infect Microbiol 2022; 12:943808. [PMID: 36268223 PMCID: PMC9577097 DOI: 10.3389/fcimb.2022.943808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
Emerging evidence revealed that the blood microbiota plays a role in several non-communicable diseases, including cardiovascular disease. However, the role of circulating microbes in atherosclerosis remains understudied. To test this hypothesis, we performed this study to investigate the microbial profile in the blood of Chines atherosclerosis volunteers. A total of seventy Acute Coronary Syndrome patients, seventy Chronic Coronary Syndrome patients, and seventy healthy individuals were examined using high-throughput Illumina Novaseq targeting the V3-V4 regions of the 16S rRNA gene. The relationship between atherosclerosis and blood microbiome, clinical variables, and their functional pathways were also investigated. Our study observed significantly higher alpha diversity indices (Chao1, p = 0.001, and Shannon, p = 0.004) in the acute coronary syndrome group compared with chronic coronary syndrome and healthy group, although a significantly lower alpha diversity was observed in the chronic coronary syndrome compared to acute coronary syndrome and healthy group. Beta diversity based on principal coordinate analysis demonstrated a major separation among the three groups. In addition, using linear discriminant analysis, a significant distinct taxon such as Actinobacteria _ phylum, and Staphylococcus_ genus in the healthy group; Firmicutes_ phylum, and Lactobacillus_ genus in the chronic coronary syndrome group, and Proteobacteria and Acidobacteriota _ phyla in acute coronary syndrome group were observed among three groups. Clusters of Orthologous Genes grouped and Kyoto Encyclopedia of Genes and Genomes pathways suggested a significant variation among all groups (p < 0.05). The blood microbiota analysis provides potential biomarkers for the detection of coronary syndromes in this population.
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Affiliation(s)
- Ikram Khan
- Department of Microbiology, School of Life Sciences, Lanzhou University, Lanzhou, China
- School of Stomatology, Northwest Minzu University, Lanzhou, China
| | - Imran Khan
- Department of Microbiology, Khyber Medical University Peshawar, Peshawar, Pakistan
| | - Muhammad Usman
- State Key Laboratory of Grassland Agro-ecosystem, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Ruler Affairs, College of Pastoral Agriculture Sciences and Technology, Lanzhou University, Lanzhou, China
| | - Zhou Jianye
- School of Stomatology, Northwest Minzu University, Lanzhou, China
| | - Zhang Xiao Wei
- Department of Cardiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Xie Ping
- Department of Cardiology, Gansu Provincial Hospital, Lanzhou, China
| | - Li Zhiqiang
- School of Stomatology, Northwest Minzu University, Lanzhou, China
- *Correspondence: Li Zhiqiang, ; An Lizhe,
| | - An Lizhe
- Department of Microbiology, School of Life Sciences, Lanzhou University, Lanzhou, China
- *Correspondence: Li Zhiqiang, ; An Lizhe,
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16
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The potential role of ischaemia-reperfusion injury in chronic, relapsing diseases such as rheumatoid arthritis, Long COVID, and ME/CFS: evidence, mechanisms, and therapeutic implications. Biochem J 2022; 479:1653-1708. [PMID: 36043493 PMCID: PMC9484810 DOI: 10.1042/bcj20220154] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Ischaemia–reperfusion (I–R) injury, initiated via bursts of reactive oxygen species produced during the reoxygenation phase following hypoxia, is well known in a variety of acute circumstances. We argue here that I–R injury also underpins elements of the pathology of a variety of chronic, inflammatory diseases, including rheumatoid arthritis, ME/CFS and, our chief focus and most proximally, Long COVID. Ischaemia may be initiated via fibrin amyloid microclot blockage of capillaries, for instance as exercise is started; reperfusion is a necessary corollary when it finishes. We rehearse the mechanistic evidence for these occurrences here, in terms of their manifestation as oxidative stress, hyperinflammation, mast cell activation, the production of marker metabolites and related activities. Such microclot-based phenomena can explain both the breathlessness/fatigue and the post-exertional malaise that may be observed in these conditions, as well as many other observables. The recognition of these processes implies, mechanistically, that therapeutic benefit is potentially to be had from antioxidants, from anti-inflammatories, from iron chelators, and via suitable, safe fibrinolytics, and/or anti-clotting agents. We review the considerable existing evidence that is consistent with this, and with the biochemical mechanisms involved.
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17
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Goraya MU, Li R, Mannan A, Gu L, Deng H, Wang G. Human circulating bacteria and dysbiosis in non-infectious diseases. Front Cell Infect Microbiol 2022; 12:932702. [PMID: 36093202 PMCID: PMC9448904 DOI: 10.3389/fcimb.2022.932702] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/01/2022] [Indexed: 02/05/2023] Open
Abstract
Blood microorganisms were once thought to indicate infection. Blood in healthy people appears to be devoid of growing bacteria; nonetheless, intracellular dormant forms of bacteria have been reported previously. With breakthroughs in sequencing and bioinformatics, the presence of bacterial DNA in healthy human blood initiated the controversy of human blood microbiota (HBM). Recently, bacteria-specific DNA and culturable bacteria were found in healthy human blood. Researchers wanted to study the phenomena of a "healthy blood microbiota" by providing a thorough description of bacterially produced nucleic acids using many complementing molecular and traditional microbiological approaches. Because blood is a relatively limited and particular environment, culturability and plate count issues can be overcome using enhanced cultured procedures. However, more evidence is required to confirm that healthy human blood contains normal microbiota. Cavities, mouth and intestinal microbiota, trauma, surgery, and animal/insect bites can introduce bacteria into human blood. All these factors strengthen the concept of transient blood bacteria too. The presence of blood bacteria may be caused by temporary immunological clearance and absorption by dendritic or M cells. This review provides an extensive and comprehensive analysis that suggests that healthy blood bacteria may not be typical microbiota but transient circulatory microorganisms. In this study, we look at how contaminants (Escherichia, Shigella, Pseudomonads, etc.) from the skin, laboratory environments, and reagents can affect the interpretation of blood-derived microbial information and the relationship between the circulating bacteria and non-communicable diseases. Circulating transient bacteria may play a role in the pathogenesis of non-infectious diseases such as diabetes and CVD. Contamination-free hematological studies can aid in understanding the disease mechanisms, therapy, and biomarkers.
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Affiliation(s)
- Mohsan Ullah Goraya
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Rui Li
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Abdul Mannan
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
| | - Liming Gu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Huixiong Deng
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Gefei Wang
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
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18
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Prasad R, Patton MJ, Floyd JL, Fortmann S, DuPont M, Harbour A, Wright J, Lamendella R, Stevens BR, Oudit GY, Grant MB. Plasma Microbiome in COVID-19 Subjects: An Indicator of Gut Barrier Defects and Dysbiosis. Int J Mol Sci 2022; 23:9141. [PMID: 36012406 PMCID: PMC9409329 DOI: 10.3390/ijms23169141] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/16/2022] Open
Abstract
The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) complications. We aimed to investigate whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n = 146) and healthy individuals (n = 47) were collected during hospitalization and routine visits. Plasma microbiome was analyzed using 16S rRNA sequencing and gut permeability markers including fatty acid binding protein 2 (FABP2), peptidoglycan (PGN), and lipopolysaccharide (LPS) in both patient cohorts. Plasma samples of both cohorts contained predominately Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria. COVID-19 subjects exhibit significant dysbiosis (p = 0.001) of the plasma microbiome with increased abundance of Actinobacteria spp. (p = 0.0332), decreased abundance of Bacteroides spp. (p = 0.0003), and an increased Firmicutes:Bacteroidetes ratio (p = 0.0003) compared to healthy subjects. The concentration of the plasma gut permeability marker FABP2 (p = 0.0013) and the gut microbial antigens PGN (p < 0.0001) and LPS (p = 0.0049) were significantly elevated in COVID-19 patients compared to healthy subjects. These findings support the notion that the intestine may represent a source for bacteremia and contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.
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Affiliation(s)
- Ram Prasad
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Michael John Patton
- Hugh Kaul Precision Medicine Institute, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jason Levi. Floyd
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Seth Fortmann
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Mariana DuPont
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Angela Harbour
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | | | | | - Bruce R. Stevens
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32611, USA
| | - Gavin Y. Oudit
- Division of Cardiology, Department of Medicine, University of Alberta, Mazankowski Alberta Heart Institute, Edmonton, AB T6G 2B7, Canada
| | - Maria B. Grant
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
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19
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Human Blood Bacteriome: Eubiotic and Dysbiotic States in Health and Diseases. Cells 2022; 11:cells11132015. [PMID: 35805098 PMCID: PMC9265464 DOI: 10.3390/cells11132015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/07/2022] [Accepted: 06/21/2022] [Indexed: 01/27/2023] Open
Abstract
The human gut microbiome is acknowledged as being associated with homeostasis and the pathogenesis of several diseases. Conventional culture techniques are limited in that they cannot culture the commensals; however, next-generation sequencing has facilitated the discovery of the diverse and delicate microbial relationship in body sites and blood. Increasing evidence regarding the blood microbiome has revolutionized the concept of sterility and germ theory in circulation. Among the types of microbial communities in the blood, bacteriomes associated with many health conditions have been thoroughly investigated. Blood bacterial profiles in healthy subjects are identified as the eubiotic blood bacteriome, whereas the dysbiotic blood bacteriome represents the change in bacterial characteristics in subjects with diseases showing deviations from the eubiotic profiles. The blood bacterial characteristics in each study are heterogeneous; thus, the association between eubiotic and dysbiotic blood bacteriomes and health and disease is still debatable. Thereby, this review aims to summarize and discuss the evidence concerning eubiotic and dysbiotic blood bacteriomes characterized by next-generation sequencing in human studies. Knowledge pertaining to the blood bacteriome will transform the concepts around health and disease in humans, facilitating clinical implementation in the near future.
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Lessons to Learn from the Gut Microbiota: A Focus on Amyotrophic Lateral Sclerosis. Genes (Basel) 2022; 13:genes13050865. [PMID: 35627250 PMCID: PMC9140531 DOI: 10.3390/genes13050865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 02/04/2023] Open
Abstract
The gut microbiota is able to modulate the development and homeostasis of the central nervous system (CNS) through the immune, circulatory, and neuronal systems. In turn, the CNS influences the gut microbiota through stress responses and at the level of the endocrine system. This bidirectional communication forms the “gut microbiota–brain axis” and has been postulated to play a role in the etiopathology of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Numerous studies in animal models of ALS and in patients have highlighted the close communication between the immune system and the gut microbiota and, therefore, it is possible that alterations in the gut microbiota may have a direct impact on neuronal function and survival in ALS patients. Consequently, if the gut dysbiosis does indeed play a role in ALS-related neurodegeneration, nutritional immunomodulatory interventions based on probiotics, prebiotics, and/or postbiotics could emerge as innovative therapeutic strategies. This review aimed to shed light on the impact of the gut microbiota in ALS disease and on the use of potential nutritional interventions based on different types of biotics to ameliorate ALS symptoms.
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Bacterial DNA Detection in the Blood of Healthy Subjects. IRANIAN BIOMEDICAL JOURNAL 2022; 26:230-9. [PMID: 35280042 PMCID: PMC9440687 DOI: 10.52547/ibj.26.3.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background: The presence of microbiome in the blood samples of healthy individuals has been addressed. However, no information can be found on the healthy human blood microbiome of Iranian subjects. The current study is thus aimed to investigate the existence of bacteria or bacterial DNA in healthy individuals. Methods: Blood samples of healthy subjects were incubated in BHI broth at 37 °C for 72 h. The 16S rRNA PCR and sequencing were performed to analyze bacterial isolates. The 16S rRNA PCR was directly carried out on DNA samples extracted from the blood of healthy individuals. NGS was conducted on blood samples with culture-positive results. Results: Fifty blood samples were tested, and six samples were positive by culture as confirmed by Gram staining and microscopy. The obtained 16S rRNA sequences of cultured bacterial isolates revealed the presence of Bacilli and Staphylococcus species by clustering in the GeneBank database (≥97% identity). The 16S rRNA gene sequencing results of one non-cultured blood specimen showed the presence of Burkholderia. NGS results illustrated the presence of Romboutsia, Lactobacillus, Streptococcus, Bacteroides, and Staphylococcus in the blood samples of positive cultures. Conclusion: The dormant blood microbiome of healthy individuals may give the idea that the steady transfer of bacteria into the blood does not necessarily lead to sepsis. However, the origins and identities of blood-associated bacterial rDNA sequences need more evaluation in the healthy population.
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Chakaroun R, Massier L, Musat N, Kovacs P. New Paradigms for Familiar Diseases: Lessons Learned on Circulatory Bacterial Signatures in Cardiometabolic Diseases. Exp Clin Endocrinol Diabetes 2022; 130:313-326. [PMID: 35320847 DOI: 10.1055/a-1756-4509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Despite the strongly accumulating evidence for microbial signatures in metabolic tissues, including the blood, suggesting a novel paradigm for metabolic disease development, the notion of a core blood bacterial signature in health and disease remains a contentious concept. Recent studies clearly demonstrate that under a strict contamination-free environment, methods such as 16 S rRNA gene sequencing, fluorescence in-situ hybridization, transmission electron microscopy, and several more, allied with advanced bioinformatics tools, allow unambiguous detection and quantification of bacteria and bacterial DNA in human tissues. Bacterial load and compositional changes in the blood have been reported for numerous disease states, suggesting that bacteria and their components may partially induce systemic inflammation in cardiometabolic disease. This concept has been so far primarily based on measurements of surrogate parameters. It is now highly desirable to translate the current knowledge into diagnostic, prognostic, and therapeutic approaches.This review addresses the potential clinical relevance of a blood bacterial signature pertinent to cardiometabolic diseases and outcomes and new avenues for translational approaches. It discusses pitfalls related to research in low bacterial biomass while proposing mitigation strategies for future research and application approaches.
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Affiliation(s)
- Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.,Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, Gothenburg, Sweden
| | - Lucas Massier
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.,Department of Medicine (H7), Karolinska Institutet, Stockholm, Sweden
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.,Deutsches Zentrum für Diabetesforschung eV, Neuherberg, Germany
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Dash S, Syed YA, Khan MR. Understanding the Role of the Gut Microbiome in Brain Development and Its Association With Neurodevelopmental Psychiatric Disorders. Front Cell Dev Biol 2022; 10:880544. [PMID: 35493075 PMCID: PMC9048050 DOI: 10.3389/fcell.2022.880544] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome has a tremendous influence on human physiology, including the nervous system. During fetal development, the initial colonization of the microbiome coincides with the development of the nervous system in a timely, coordinated manner. Emerging studies suggest an active involvement of the microbiome and its metabolic by-products in regulating early brain development. However, any disruption during this early developmental process can negatively impact brain functionality, leading to a range of neurodevelopment and neuropsychiatric disorders (NPD). In this review, we summarize recent evidence as to how the gut microbiome can influence the process of early human brain development and its association with major neurodevelopmental psychiatric disorders such as autism spectrum disorders, attention-deficit hyperactivity disorder, and schizophrenia. Further, we discuss how gut microbiome alterations can also play a role in inducing drug resistance in the affected individuals. We propose a model that establishes a direct link of microbiome dysbiosis with the exacerbated inflammatory state, leading to functional brain deficits associated with NPD. Based on the existing research, we discuss a framework whereby early diet intervention can boost mental wellness in the affected subjects and call for further research for a better understanding of mechanisms that govern the gut-brain axis may lead to novel approaches to the study of the pathophysiology and treatment of neuropsychiatric disorders.
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Affiliation(s)
- Somarani Dash
- Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Yasir Ahmed Syed
- School of Biosciences and Neuroscience and Mental Health Research Institute, Cardiff University, Hadyn Ellis Building, Cardiff, United Kingdom
| | - Mojibur R. Khan
- Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, India
- *Correspondence: Mojibur R. Khan,
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Karagiannis TT, Monti S, Sebastiani P. Cell Type Diversity Statistic: An Entropy-Based Metric to Compare Overall Cell Type Composition Across Samples. Front Genet 2022; 13:855076. [PMID: 35464841 PMCID: PMC9023789 DOI: 10.3389/fgene.2022.855076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/18/2022] [Indexed: 12/31/2022] Open
Abstract
Changes of cell type composition across samples can carry biological significance and provide insight into disease and other conditions. Single cell transcriptomics has made it possible to study cell type composition at a fine resolution. Most single cell studies investigate compositional changes between samples for each cell type independently, not accounting for the fixed number of cells per sample in sequencing data. Here, we provide a metric of the distribution of cell type proportions in a sample that can be used to compare the overall distribution of cell types across multiple samples and biological conditions. This is the first method to measure overall cell type composition at the single cell level. We use the method to assess compositional changes in peripheral blood mononuclear cells (PBMCs) related to aging and extreme old age using multiple single cell datasets from individuals of four age groups across the human lifespan.
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Affiliation(s)
- Tanya T Karagiannis
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, United States
- Bioinformatics Program, Boston University, Boston, MA, United States
- *Correspondence: Tanya T Karagiannis,
| | - Stefano Monti
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, United States
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, United States
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - Paola Sebastiani
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, United States
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25
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Bonnechère B, Amin N, van Duijn C. The Role of Gut Microbiota in Neuropsychiatric Diseases – Creation of An Atlas-Based on Quantified Evidence. Front Cell Infect Microbiol 2022; 12:831666. [PMID: 35360098 PMCID: PMC8964285 DOI: 10.3389/fcimb.2022.831666] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/21/2022] [Indexed: 01/15/2023] Open
Abstract
There is a growing body of evidence highlighting the significant role of gut microbiota in various pathologies. We performed a systematic review to review the different microbiota involved in neuropsychiatric diseases. 50 studies (23 studies for autism spectrum disorders, 18 for major depression, and 9 for schizophrenia), representing 2,137 patients and 2,844 controls. Concerning the microbiota, the genera Prevotella, Clostridium, Bacteroides, Bifidobacterium, Ruminococcus, Megamonas, and Faecalbacterium were the ones detected with the most frequent variation of their relatives abundance. We also assess the overlap between the different pathologies. This study provides new insights into the complex relationship between the brain and the gut and the implications in neuropsychiatric pathologies. The identification of unique signatures in neuropsychiatric diseases suggests new possibilities in targeted anti or probiotic treatment.
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Affiliation(s)
- Bruno Bonnechère
- REVAL Rehabilitation Research Center, Faculty of Rehabilitation Sciences, Hasselt University, Diepenbeek, Belgium
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Najaf Amin
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Cornelia van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- *Correspondence: Cornelia van Duijn,
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A Bioinformatics Approach to Mine the Microbial Proteomic Profile of COVID-19 Mass Spectrometry Data. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2010010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mass spectrometry (MS) is one of the key technologies used in proteomics. The majority of studies carried out using proteomics have focused on identifying proteins in biological samples such as human plasma to pin down prognostic or diagnostic biomarkers associated with particular conditions or diseases. This study aims to quantify microbial (viral and bacterial) proteins in healthy human plasma. MS data of healthy human plasma were searched against the complete proteomes of all available viruses and bacteria. With this baseline established, the same strategy was applied to characterize the metaproteomic profile of different SARS-CoV-2 disease stages in the plasma of patients. Two SARS-CoV-2 proteins were detected with a high confidence and could serve as the early markers of SARS-CoV-2 infection. The complete bacterial and viral protein content in SARS-CoV-2 samples was compared for the different disease stages. The number of viral proteins was found to increase significantly with the progression of the infection, at the expense of bacterial proteins. This strategy can be extended to aid in the development of early diagnostic tests for other infectious diseases based on the presence of microbial biomarkers in human plasma samples.
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Martin S, Foulon A, El Hage W, Dufour-Rainfray D, Denis F. Is There a Link between Oropharyngeal Microbiome and Schizophrenia? A Narrative Review. Int J Mol Sci 2022; 23:ijms23020846. [PMID: 35055031 PMCID: PMC8775665 DOI: 10.3390/ijms23020846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 11/16/2022] Open
Abstract
The study aimed to examine the impact of the oropharyngeal microbiome in the pathophysiology of schizophrenia and to clarify whether there might be a bidirectional link between the oral microbiota and the brain in a context of dysbiosis-related neuroinflammation. We selected nine articles including three systemic reviews with several articles from the same research team. Different themes emerged, which we grouped into 5 distinct parts concerning the oropharyngeal phageome, the oropharyngeal microbiome, the salivary microbiome and periodontal disease potentially associated with schizophrenia, and the impact of drugs on the microbiome and schizophrenia. We pointed out the presence of phageoma in patients suffering from schizophrenia and that periodontal disease reinforces the role of inflammation in the pathophysiology of schizophrenia. Moreover, saliva could be an interesting substrate to characterize the different stages of schizophrenia. However, the few studies we have on the subject are limited in scope, and some of them are the work of a single team. At this stage of knowledge, it is difficult to conclude on the existence of a bidirectional link between the brain and the oral microbiome. Future studies on the subject will clarify these questions that for the moment remain unresolved.
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Affiliation(s)
- Stanislas Martin
- Department of Psychiatry, Centre Hospitalier Universitaire Tours, 37000 Tours, France;
| | - Audrey Foulon
- Faculty of Medicine, Université de Tours, 37000 Tours, France;
| | - Wissam El Hage
- U1253, iBrain, Inserm, CHU Tours, Université de Tours, 37000 Tours, France; (W.E.H.); (D.D.-R.)
| | - Diane Dufour-Rainfray
- U1253, iBrain, Inserm, CHU Tours, Université de Tours, 37000 Tours, France; (W.E.H.); (D.D.-R.)
- Service de Médecine Nucléaire In Vitro, Centre Hospitalier Universitaire Tours, 37044 Tours, France
| | - Frédéric Denis
- Department of Odontology, Centre Hospitalier Universitaire Tours, 37000 Tours, France
- Faculty of Dentistry, Nantes University, 44000 Nantes, France
- EA 75-05 Education, Ethics, Health, Faculty of Medicine, Université de Tours, 37000 Tours, France
- Correspondence: ; Tel.: +33-6-77-15-69-68
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Dehhaghi M, Panahi HKS, Kavyani B, Heng B, Tan V, Braidy N, Guillemin GJ. The Role of Kynurenine Pathway and NAD + Metabolism in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Aging Dis 2022; 13:698-711. [PMID: 35656104 PMCID: PMC9116917 DOI: 10.14336/ad.2021.0824] [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: 07/12/2021] [Accepted: 08/24/2021] [Indexed: 11/18/2022] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a serious, complex, and highly debilitating long-term illness. People with ME/CFS are typically unable to carry out their routine activities. Key hallmarks of the disease are neurological and gastrointestinal impairments accompanied by pervasive malaise that is exacerbated after physical and/or mental activity. Currently, there is no validated cure of biomarker signature for this illness. Impaired tryptophan (TRYP) metabolism is thought to play significant role in the pathobiology of ME/CFS. TRYP is an important precursor for serotonin and the essential pyridine nucleotide nicotinamide adenine dinucleotide (NAD+). TRYP has been associated with the development of some parts of the brain responsible for behavioural functions. The main catabolic route for TRYP is the kynurenine pathway (KP). The KP produces NAD+ and several neuroactive metabolites with neuroprotective (i.e., kynurenic acid (KYNA)) and neurotoxic (i.e., quinolinic acid (QUIN)) activities. Hyperactivation of the KP, whether compensatory or a driving mechanism of degeneration can limit the availability of NAD+ and exacerbate the symptoms of ME/CFS. This review discusses the potential association of altered KP metabolism in ME/CFS. The review also evaluates the role of the patient’s gut microbiota on TRYP availability and KP activation. We propose that strategies aimed at raising the levels of NAD+ (e.g., using nicotinamide mononucleotide and nicotinamide riboside) may be a promising intervention to overcome symptoms of fatigue and to improve the quality of life in patients with ME/CFS. Future clinical trials should further assess the potential benefits of NAD+ supplements for reducing some of the clinical features of ME/CFS.
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Affiliation(s)
- Mona Dehhaghi
- Neuroinflammation Group, Faculty of Medicine and Health Sciences, Macquarie University, NSW, Australia.
- PANDIS.org, Australia.
| | | | - Bahar Kavyani
- Neuroinflammation Group, Faculty of Medicine and Health Sciences, Macquarie University, NSW, Australia.
| | - Benjamin Heng
- Neuroinflammation Group, Faculty of Medicine and Health Sciences, Macquarie University, NSW, Australia.
- PANDIS.org, Australia.
| | - Vanessa Tan
- Neuroinflammation Group, Faculty of Medicine and Health Sciences, Macquarie University, NSW, Australia.
- PANDIS.org, Australia.
| | - Nady Braidy
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia.
| | - Gilles J. Guillemin
- Neuroinflammation Group, Faculty of Medicine and Health Sciences, Macquarie University, NSW, Australia.
- PANDIS.org, Australia.
- Correspondence should be addressed to: Dr. Gilles J. Guillemin, Neuroinflammation Group, Faculty of Medicine and Health Sciences, Macquarie University, NSW, Australia. .
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29
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Rosa rugosa polysaccharide attenuates alcoholic liver disease in mice through the gut-liver axis. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101385] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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30
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Identifying active rumen epithelial associated bacteria and archaea in beef cattle divergent in feed efficiency using total RNA-seq. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100064. [PMID: 34841354 PMCID: PMC8610342 DOI: 10.1016/j.crmicr.2021.100064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 01/08/2023] Open
Abstract
The most active archaea in the epimural community were different from that of the liquid and content-associated community, but the exact taxonomy requires further identification. Rumen epithelial attached methanogens may not contribute to differences in CH4 production and variations in feed efficiency. Families Campylobacteraceae and Neisseriaceae, which contain oxygen scavenging bacteria were significantly more active on the epithelium of efficient cattle.
To date, the role of ruminal epithelial attached microbiota in cattle feed efficiency is undefined. In this study, we aimed to characterize transcriptionally active bacteria and archaea attached to the rumen epithelial wall and to determine whether they differ in cattle with varied feed efficiency. RNA-sequencing was performed to obtain the rumen epithelial transcriptomes from 9 of the most efficient (low RFI) and 9 of the most inefficient (high RFI) animals. The bacteria and archaea 16S rRNA transcripts were identified using an in-house developed pipeline, enriched from filtered reads that did not map to the bovine genome. Archaea from unclassified genera belonging to the Euryarchaeota phylum showed the most activity on the rumen epithelium of low RFI (81.3 ± 1.9%) and high RFI (76.4 ± 3.0%) steers. Bacteria from the Succinivibrionaceae family showed the greatest activity of bacteria on the low RFI (28.7 ± 9.0%) and high RFI (33.9± 8.8%) epithelium. Of the bacterial families, Campylobacteraceae and Neisseriaceae had significantly greater activity on the low RFI epithelium (p < 0.05) and are known to play a role in oxygen scavenging. Greater activity of rumen epithelial attached oxygen scavenging bacteria may provide more optimal feed fermentation conditions, which contributes to high fermentation efficiency in the rumen.
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Yu D, Meng X, de Vos WM, Wu H, Fang X, Maiti AK. Implications of Gut Microbiota in Complex Human Diseases. Int J Mol Sci 2021; 22:12661. [PMID: 34884466 PMCID: PMC8657718 DOI: 10.3390/ijms222312661] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/30/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023] Open
Abstract
Humans, throughout the life cycle, from birth to death, are accompanied by the presence of gut microbes. Environmental factors, lifestyle, age and other factors can affect the balance of intestinal microbiota and their impact on human health. A large amount of data show that dietary, prebiotics, antibiotics can regulate various diseases through gut microbes. In this review, we focus on the role of gut microbes in the development of metabolic, gastrointestinal, neurological, immune diseases and, cancer. We also discuss the interaction between gut microbes and the host with respect to their beneficial and harmful effects, including their metabolites, microbial enzymes, small molecules and inflammatory molecules. More specifically, we evaluate the potential ability of gut microbes to cure diseases through Fecal Microbial Transplantation (FMT), which is expected to become a new type of clinical strategy for the treatment of various diseases.
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Affiliation(s)
- Dahai Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China; (X.M.); (X.F.)
| | - Xin Meng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China; (X.M.); (X.F.)
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands;
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Hao Wu
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA;
| | - Xuexun Fang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China; (X.M.); (X.F.)
| | - Amit K. Maiti
- Department of Genetics and Genomics, Mydnavar, 2645 Somerset Boulevard, Troy, MI 48084, USA
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Salivary microbiome profiling reveals a dysbiotic schizophrenia-associated microbiota. NPJ SCHIZOPHRENIA 2021; 7:51. [PMID: 34711862 PMCID: PMC8553823 DOI: 10.1038/s41537-021-00180-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/01/2021] [Indexed: 01/01/2023]
Abstract
Schizophrenia is a debilitating mental disorder and often has a prodromal period, referred to as clinical high risk (CHR) for psychosis, prior to the first episode. The etiology and pathogenesis of schizophrenia remain unclear. Despite the human gut microbiome being associated with schizophrenia, the role of the oral microbiome, which is a vital player in the mouth-body connection, is not well understood. To address this, we performed 16S rRNA gene sequencing to investigate the salivary microbiome in 85 patients with drug-naïve first-episode schizophrenia (FES), 43 individuals at CHR, and 80 healthy controls (HCs). The salivary microbiome of FES patients was characterized by higher α-diversity and lower β-diversity heterogeneity than those of CHR subjects and HCs. Proteobacteria, the predominant phylum, was depleted, while Firmicutes and the Firmicutes/Proteobacteria ratio was enriched, in a stepwise manner from HC to CHR to FES. H2S-producing bacteria exhibited disease-stage-specific enrichment and could be potential diagnostic biomarkers for FES and CHR. Certain salivary microbiota exhibited disease-specific correlation patterns with symptomatic severities, peripheral pro-inflammatory cytokines, thioredoxin, and S100B in FES. Furthermore, the metabolic functions from inferred metagenomes of the salivary microbiome were disrupted in FES, especially amino acid metabolism, carbohydrate metabolism, and xenobiotic degradation. This study has established a link between salivary microbiome alterations and disease initiation and provided the hypothesis of how the oral microbiota could influence schizophrenia.
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Alagiakrishnan K, Halverson T. Microbial Therapeutics in Neurocognitive and Psychiatric Disorders. J Clin Med Res 2021; 13:439-459. [PMID: 34691318 PMCID: PMC8510649 DOI: 10.14740/jocmr4575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/28/2021] [Indexed: 12/12/2022] Open
Abstract
Microbial therapeutics, which include gut biotics and fecal transplantation, are interventions designed to improve the gut microbiome. Gut biotics can be considered as the administration of direct microbial populations. The delivery of this can be done through live microbial flora, certain food like fiber, microbial products (metabolites and elements) obtained through the fermentation of food products, or as genetically engineered substances, that may have therapeutic benefit on different health disorders. Dietary intervention and pharmacological supplements with gut biotics aim at correcting disruption of the gut microbiota by repopulating with beneficial microorganism leading to decrease in gut permeability, inflammation, and alteration in metabolic activities, through a variety of mechanisms of action. Our understanding of the pharmacokinetics of microbial therapeutics has improved with in vitro models, sampling techniques in the gut, and tools for the reliable identification of gut biotics. Evidence from human studies points out that prebiotics, probiotics and synbiotics have the potential for treating and preventing mental health disorders, whereas with paraprobiotics, proteobiotics and postbiotics, the research is limited at this point. Some animal studies point out that gut biotics can be used with conventional treatments for a synergistic effect on mental health disorders. If future research shows that there is a possibility of synergistic effect of psychotropic medications with gut biotics, then a gut biotic or nutritional prescription can be given along with psychotropics. Even though the overall safety of gut biotics seems to be good, caution is needed to watch for any known and unknown side effects as well as the need for risk benefit analysis with certain vulnerable populations. Future research is needed before wide spread use of natural and genetically engineered gut biotics. Regulatory framework for gut biotics needs to be optimized. Holistic understanding of gut dysbiosis, along with life style factors, by health care providers is necessary for the better management of these conditions. In conclusion, microbial therapeutics are a new psychotherapeutic approach which offer some hope in certain conditions like dementia and depression. Future of microbial therapeutics will be driven by well-done randomized controlled trials and longitudinal research, as well as by replication studies in human subjects.
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Affiliation(s)
- Kannayiram Alagiakrishnan
- Division of Geriatric Medicine, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Tyler Halverson
- Division of Psychiatry, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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Morrow JD, Castaldi PJ, Chase RP, Yun JH, Lee S, Liu YY, Hersh CP. Peripheral blood microbial signatures in current and former smokers. Sci Rep 2021; 11:19875. [PMID: 34615932 PMCID: PMC8494912 DOI: 10.1038/s41598-021-99238-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/15/2021] [Indexed: 12/13/2022] Open
Abstract
The human microbiome has a role in the development of multiple diseases. Individual microbiome profiles are highly personalized, though many species are shared. Understanding the relationship between the human microbiome and disease may inform future individualized treatments. We hypothesize the blood microbiome signature may be a surrogate for some lung microbial characteristics. We sought associations between the blood microbiome signature and lung-relevant host factors. Based on reads not mapped to the human genome, we detected microbial nucleic acids through secondary use of peripheral blood RNA-sequencing from 2,590 current and former smokers with and without chronic obstructive pulmonary disease (COPD) from the COPDGene study. We used the Genome Analysis Toolkit (GATK) microbial pipeline PathSeq to infer microbial profiles. We tested associations between the inferred profiles and lung disease relevant phenotypes and examined links to host gene expression pathways. We replicated our analyses using a second independent set of blood RNA-seq data from 1,065 COPDGene study subjects and performed a meta-analysis across the two studies. The four phyla with highest abundance across all subjects were Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. In our meta-analysis, we observed associations (q-value < 0.05) between Acinetobacter, Serratia, Streptococcus and Bacillus inferred abundances and Modified Medical Research Council (mMRC) dyspnea score. Current smoking status was associated (q < 0.05) with Acinetobacter, Serratia and Cutibacterium abundance. All 12 taxa investigated were associated with at least one white blood cell distribution variable. Abundance for nine of the 12 taxa was associated with sex, and seven of the 12 taxa were associated with race. Host-microbiome interaction analysis revealed clustering of genera associated with mMRC dyspnea score and smoking status, through shared links to several host pathways. This study is the first to identify a bacterial microbiome signature in the peripheral blood of current and former smokers. Understanding the relationships between systemic microbial signatures and lung-related phenotypes may inform novel interventions and aid understanding of the systemic effects of smoking.
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Affiliation(s)
- Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Jeong H Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Sool Lee
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
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35
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Alagiakrishnan K, Halverson T. Holistic perspective of the role of gut microbes in diabetes mellitus and its management. World J Diabetes 2021; 12:1463-1478. [PMID: 34630900 PMCID: PMC8472496 DOI: 10.4239/wjd.v12.i9.1463] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/24/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota (GM) plays a role in the development and progression of type 1 and type 2 diabetes mellitus (DM) and its complications. Gut dysbiosis contributes to the pathogenesis of DM. The GM has been shown to influence the efficacy of different antidiabetic medications. Intake of gut biotics, like prebiotics, probiotics and synbiotics, can improve the glucose control as well as the metabolic profile associated with DM. There is some preliminary evidence that it might even help with the cardiovascular, ophthalmic, nervous, and renal complications of DM and even contribute to the prevention of DM. More large-scale research studies are needed before wide spread use of gut biotics in clinical practice as an adjuvant therapy to the current management of DM.
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Affiliation(s)
| | - Tyler Halverson
- Department of Medicine, University of Alberta, Edmonton T6G 2G3, Alberta, Canada
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36
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Dawidowski B, Górniak A, Podwalski P, Lebiecka Z, Misiak B, Samochowiec J. The Role of Cytokines in the Pathogenesis of Schizophrenia. J Clin Med 2021; 10:jcm10173849. [PMID: 34501305 PMCID: PMC8432006 DOI: 10.3390/jcm10173849] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Schizophrenia is a chronic mental illness of unknown etiology. A growing and compelling body of evidence implicates immunologic dysfunction as the key element in its pathomechanism. Cytokines, whose altered levels have been increasingly reported in various patient populations, are the major mediators involved in the coordination of the immune system. The available literature reports both elevated levels of proinflammatory as well as reduced levels of anti-inflammatory cytokines, and their effects on clinical status and neuroimaging changes. There is evidence of at least a partial genetic basis for the association between cytokine alterations and schizophrenia. Two other factors implicated in its development include early childhood trauma and disturbances in the gut microbiome. Moreover, its various subtypes, characterized by individual symptom severity and course, such as deficit schizophrenia, seem to differ in terms of changes in peripheral cytokine levels. While the use of a systematic review methodology could be difficult due to the breadth and diversity of the issues covered in this review, the applied narrative approach allows for a more holistic presentation. The aim of this narrative review was to present up-to-date evidence on cytokine dysregulation in schizophrenia, its effect on the psychopathological presentation, and links with antipsychotic medication. We also attempted to summarize its postulated underpinnings, including early childhood trauma and gut microbiome disturbances, and propose trait and state markers of schizophrenia.
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Affiliation(s)
- Bartosz Dawidowski
- Department of Psychiatry, Pomeranian Medical University, 71-460 Szczecin, Poland; (B.D.); (A.G.); (J.S.)
| | - Adrianna Górniak
- Department of Psychiatry, Pomeranian Medical University, 71-460 Szczecin, Poland; (B.D.); (A.G.); (J.S.)
| | - Piotr Podwalski
- Department of Psychiatry, Pomeranian Medical University, 71-460 Szczecin, Poland; (B.D.); (A.G.); (J.S.)
- Correspondence: ; Tel.: +48-510-091-466
| | - Zofia Lebiecka
- Department of Health Psychology, Pomeranian Medical University, 71-210 Szczecin, Poland;
| | - Błażej Misiak
- Department of Psychiatry, Division of Consultation Psychiatry and Neuroscience, Medical University, 50-367 Wroclaw, Poland;
| | - Jerzy Samochowiec
- Department of Psychiatry, Pomeranian Medical University, 71-460 Szczecin, Poland; (B.D.); (A.G.); (J.S.)
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37
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Klein-Petersen AW, Köhler-Forsberg O, Benros ME. Infections, antibiotic treatment and the Microbiome in relation to schizophrenia. Schizophr Res 2021; 234:71-77. [PMID: 31859119 DOI: 10.1016/j.schres.2019.11.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022]
Abstract
Schizophrenia is a heterogeneous disorder with several potential pathophysiological mechanisms, including immune activation. Infections have been identified as a significant contributing risk factor for schizophrenia; this association is reviewed together with the potential impact of antibiotic treatment and alterations of the intestinal microbiota. Both infections and the treatment with antibiotics may alter the composition of the gut microbiota, causing dysbiosis, which in animal studies has been associated with alterations of behavior. Of the few studies that have been conducted on humans, some have suggested alterations in the microbial composition of individuals with schizophrenia compared to healthy controls, albeit with conflicting results. Recently, increased attention has emerged regarding potential adverse effects from antibiotics, as a number of these have been associated with an increased risk of psychotic episodes. Particularly, the fluoroquinolones have been associated with neurotoxic adverse events. The association between schizophrenia and infections, antibiotic treatment and dysbiosis, may be an epiphenomenon, which could be explained by other confounding factors. However, these associations could be causal and could therefore be important risk factors in a subgroup of patients. Large-scale well-matched longitudinal studies are needed with measurements of immune markers from multiple biological samples, ranging from material close to the brain, as cerebrospinal fluid and brain-scans targeting neuroinflammation, to analysis of blood and intestinal microbiota. This would help to obtain more definite results on the association between infections, immune components and microbiota alterations in relation to schizophrenia.
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Affiliation(s)
| | - Ole Köhler-Forsberg
- Mental Health Centre Copenhagen, Copenhagen University Hospital, Denmark; Psychosis Research Unit, Aarhus University Hospital - Psychiatry, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Michael E Benros
- Mental Health Centre Copenhagen, Copenhagen University Hospital, Denmark.
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38
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D'Aquila P, Giacconi R, Malavolta M, Piacenza F, Bürkle A, Villanueva MM, Dollé MET, Jansen E, Grune T, Gonos ES, Franceschi C, Capri M, Grubeck-Loebenstein B, Sikora E, Toussaint O, Debacq-Chainiaux F, Hervonen A, Hurme M, Slagboom PE, Schön C, Bernhardt J, Breusing N, Passarino G, Provinciali M, Bellizzi D. Microbiome in Blood Samples From the General Population Recruited in the MARK-AGE Project: A Pilot Study. Front Microbiol 2021; 12:707515. [PMID: 34381434 PMCID: PMC8350766 DOI: 10.3389/fmicb.2021.707515] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/29/2021] [Indexed: 01/12/2023] Open
Abstract
The presence of circulating microbiome in blood has been reported in both physiological and pathological conditions, although its origins, identities and function remain to be elucidated. This study aimed to investigate the presence of blood microbiome by quantitative real-time PCRs targeting the 16S rRNA gene. To our knowledge, this is the first study in which the circulating microbiome has been analyzed in such a large sample of individuals since the study was carried out on 1285 Randomly recruited Age-Stratified Individuals from the General population (RASIG). The samples came from several different European countries recruited within the EU Project MARK-AGE in which a series of clinical biochemical parameters were determined. The results obtained reveal an association between microbial DNA copy number and geographic origin. By contrast, no gender and age-related difference emerged, thus demonstrating the role of the environment in influencing the above levels independent of age and gender at least until the age of 75. In addition, a significant positive association was found with Free Fatty Acids (FFA) levels, leukocyte count, insulin, and glucose levels. Since these factors play an essential role in both health and disease conditions, their association with the extent of the blood microbiome leads us to consider the blood microbiome as a potential biomarker of human health.
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Affiliation(s)
- Patrizia D'Aquila
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, Rende, Italy
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, IRCCS (Scientific Institute for Research, Hospitalization and Healthcare) INRCA National Institute on Health and Science on Ageing, Ancona, Italy
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, IRCCS (Scientific Institute for Research, Hospitalization and Healthcare) INRCA National Institute on Health and Science on Ageing, Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, IRCCS (Scientific Institute for Research, Hospitalization and Healthcare) INRCA National Institute on Health and Science on Ageing, Ancona, Italy
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - María Moreno Villanueva
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Sport Science, Human Performance Research Centre, University of Konstanz, Konstanz, Germany
| | - Martijn E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Eugène Jansen
- Centre for Health Protection, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany.,NutriAct-Competence Cluster Nutrition Research Berlin-Potsdam, Nuthetal, Germany
| | - Efstathios S Gonos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Athens, Greece
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Interdepartmental Center, Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | | | - Ewa Sikora
- Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Olivier Toussaint
- Research Unit of Cellular Biology (URBC) Namur Research Institute for Life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Florence Debacq-Chainiaux
- Research Unit of Cellular Biology (URBC) Namur Research Institute for Life Sciences (Narilis), University of Namur, Namur, Belgium
| | | | - Mikko Hurme
- Medical School, University of Tampere, Tampere, Finland
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Centre, Leiden, Netherlands
| | | | | | - Nicolle Breusing
- Department of Applied Nutritional Science/Dietetics, Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, Rende, Italy
| | - Mauro Provinciali
- Advanced Technology Center for Aging Research, IRCCS (Scientific Institute for Research, Hospitalization and Healthcare) INRCA National Institute on Health and Science on Ageing, Ancona, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, Rende, Italy
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39
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Panaiotov S, Hodzhev Y, Tsafarova B, Tolchkov V, Kalfin R. Culturable and Non-Culturable Blood Microbiota of Healthy Individuals. Microorganisms 2021; 9:1464. [PMID: 34361900 PMCID: PMC8304615 DOI: 10.3390/microorganisms9071464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/23/2021] [Accepted: 07/06/2021] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing (NGS) and metagenomics revolutionized our capacity for analysis and identification of the microbial communities in complex samples. The existence of a blood microbiome in healthy individuals has been confirmed by sequencing, but some researchers suspect that this is a cell-free circulating DNA in blood, while others have had isolated a limited number of bacterial and fungal species by culture. It is not clear what part of the blood microbiota could be resuscitated and cultured. Here, we quantitatively measured the culturable part of blood microbiota of healthy individuals by testing a medium supplemented with a high concentration of vitamin K (1 mg/mL) and culturing at 43 °C for 24 h. We applied targeted sequencing of 16S rDNA and internal transcribed spacer (ITS) markers on cultured and non-cultured blood samples from 28 healthy individuals. Dominant bacterial phyla among non-cultured samples were Proteobacteria 92.97%, Firmicutes 2.18%, Actinobacteria 1.74% and Planctomycetes 1.55%, while among cultured samples Proteobacteria were 47.83%, Firmicutes 25.85%, Actinobacteria 16.42%, Bacteroidetes 3.48%, Cyanobacteria 2.74%, and Fusobacteria 1.53%. Fungi phyla Basidiomycota, Ascomycota, and unidentified fungi were 65.08%, 17.72%, and 17.2% respectively among non-cultured samples, while among cultured samples they were 58.08%, 21.72%, and 20.2% respectively. In cultured and non-cultured samples we identified 241 OTUs belonging to 40 bacterial orders comprising 66 families and 105 genera. Fungal biodiversity accounted for 272 OTUs distributed in 61 orders, 105 families, and 133 genera. Bacterial orders that remained non-cultured, compared to blood microbiota isolated from fresh blood collection, were Sphingomonadales, Rhizobiales, and Rhodospirillales. Species of orders Bacillales, Lactobacillales, and Corynebacteriales showed the best cultivability. Fungi orders Tremellales, Polyporales, and Filobasidiales were mostly unculturable. Species of fungi orders Pleosporales, Saccharomycetales, and Helotiales were among the culturable ones. In this study, we quantified the capacity of a specific medium applied for culturing of blood microbiota in healthy individuals. Other culturing conditions and media should be tested for optimization and better characterization of blood microbiota in healthy and diseased individuals.
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Affiliation(s)
- Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (Y.H.); (B.T.); (V.T.)
| | - Yordan Hodzhev
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (Y.H.); (B.T.); (V.T.)
| | - Borislava Tsafarova
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (Y.H.); (B.T.); (V.T.)
| | - Vladimir Tolchkov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (Y.H.); (B.T.); (V.T.)
| | - Reni Kalfin
- Institute of Neurobiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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40
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Proal AD, VanElzakker MB. Long COVID or Post-acute Sequelae of COVID-19 (PASC): An Overview of Biological Factors That May Contribute to Persistent Symptoms. Front Microbiol 2021; 12:698169. [PMID: 34248921 PMCID: PMC8260991 DOI: 10.3389/fmicb.2021.698169] [Citation(s) in RCA: 414] [Impact Index Per Article: 138.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/17/2021] [Indexed: 12/23/2022] Open
Abstract
The novel virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic of coronavirus disease 2019 (COVID-19). Across the globe, a subset of patients who sustain an acute SARS-CoV-2 infection are developing a wide range of persistent symptoms that do not resolve over the course of many months. These patients are being given the diagnosis Long COVID or Post-acute sequelae of COVID-19 (PASC). It is likely that individual patients with a PASC diagnosis have different underlying biological factors driving their symptoms, none of which are mutually exclusive. This paper details mechanisms by which RNA viruses beyond just SARS-CoV-2 have be connected to long-term health consequences. It also reviews literature on acute COVID-19 and other virus-initiated chronic syndromes such as post-Ebola syndrome or myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) to discuss different scenarios for PASC symptom development. Potential contributors to PASC symptoms include consequences from acute SARS-CoV-2 injury to one or multiple organs, persistent reservoirs of SARS-CoV-2 in certain tissues, re-activation of neurotrophic pathogens such as herpesviruses under conditions of COVID-19 immune dysregulation, SARS-CoV-2 interactions with host microbiome/virome communities, clotting/coagulation issues, dysfunctional brainstem/vagus nerve signaling, ongoing activity of primed immune cells, and autoimmunity due to molecular mimicry between pathogen and host proteins. The individualized nature of PASC symptoms suggests that different therapeutic approaches may be required to best manage care for specific patients with the diagnosis.
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Affiliation(s)
- Amy D. Proal
- PolyBio Research Foundation, Kenmore, WA, United States
| | - Michael B. VanElzakker
- PolyBio Research Foundation, Kenmore, WA, United States
- Division of Neurotherapeutics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
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41
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Chakaroun RM, Massier L, Heintz-Buschart A, Said N, Fallmann J, Crane A, Schütz T, Dietrich A, Blüher M, Stumvoll M, Musat N, Kovacs P. Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery. Genome Med 2021; 13:105. [PMID: 34158092 PMCID: PMC8218394 DOI: 10.1186/s13073-021-00919-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The microbiome has emerged as an environmental factor contributing to obesity and type 2 diabetes (T2D). Increasing evidence suggests links between circulating bacterial components (i.e., bacterial DNA), cardiometabolic disease, and blunted response to metabolic interventions. In this aspect, thorough next-generation sequencing-based and contaminant-aware approaches are lacking. To address this, we tested whether bacterial DNA could be amplified in the blood of subjects with obesity and high metabolic risk under strict experimental and analytical control and whether a putative bacterial signature is related to metabolic improvement after bariatric surgery. METHODS Subjects undergoing bariatric surgery were recruited into sex- and BMI-matched subgroups with (n = 24) or without T2D (n = 24). Bacterial DNA in the blood was quantified and prokaryotic 16S rRNA gene amplicons were sequenced. A contaminant-aware approach was applied to derive a compositional microbial signature from bacterial sequences in all subjects at baseline and at 3 and 12 months after surgery. We modeled associations between bacterial load and composition with host metabolic and anthropometric markers. We further tested whether compositional shifts were related to weight loss response and T2D remission. Lastly, bacteria were visualized in blood samples using catalyzed reporter deposition (CARD)-fluorescence in situ hybridization (FISH). RESULTS The contaminant-aware blood bacterial signature was associated with metabolic health. Based on bacterial phyla and genera detected in the blood samples, a metabolic syndrome classification index score was derived and shown to robustly classify subjects along their actual clinical group. T2D was characterized by decreased bacterial richness and loss of genera associated with improved metabolic health. Weight loss and metabolic improvement following bariatric surgery were associated with an early and stable increase of these genera in parallel with improvements in key cardiometabolic risk parameters. CARD-FISH allowed the detection of living bacteria in blood samples in obesity. CONCLUSIONS We show that the circulating bacterial signature reflects metabolic disease and its improvement after bariatric surgery. Our work provides contaminant-aware evidence for the presence of living bacteria in the blood and suggests a putative crosstalk between components of the blood and metabolism in metabolic health regulation.
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Affiliation(s)
- Rima M Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
| | - Lucas Massier
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Department of Medicine (H7), Karolinska Institutet, C2-94, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Heintz-Buschart
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Helmholtz Centre for Environmental Research GmbH - UFZ, Halle, Germany
| | - Nedal Said
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Joerg Fallmann
- Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Alyce Crane
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Tatjana Schütz
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Arne Dietrich
- Department of Visceral, Transplantation, Thoracic and Vascular Surgery, Section of Bariatric Surgery, Leipzig University Hospital, Leipzig, Germany
| | - Matthias Blüher
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Deutsches Zentrum für Diabetesforschung, Neuherberg, Germany
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42
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Patrono E, Svoboda J, Stuchlík A. Schizophrenia, the gut microbiota, and new opportunities from optogenetic manipulations of the gut-brain axis. Behav Brain Funct 2021; 17:7. [PMID: 34158061 PMCID: PMC8218443 DOI: 10.1186/s12993-021-00180-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/01/2021] [Indexed: 12/18/2022] Open
Abstract
Schizophrenia research arose in the twentieth century and is currently rapidly developing, focusing on many parallel research pathways and evaluating various concepts of disease etiology. Today, we have relatively good knowledge about the generation of positive and negative symptoms in patients with schizophrenia. However, the neural basis and pathophysiology of schizophrenia, especially cognitive symptoms, are still poorly understood. Finding new methods to uncover the physiological basis of the mental inabilities related to schizophrenia is an urgent task for modern neuroscience because of the lack of specific therapies for cognitive deficits in the disease. Researchers have begun investigating functional crosstalk between NMDARs and GABAergic neurons associated with schizophrenia at different resolutions. In another direction, the gut microbiota is getting increasing interest from neuroscientists. Recent findings have highlighted the role of a gut-brain axis, with the gut microbiota playing a crucial role in several psychopathologies, including schizophrenia and autism. There have also been investigations into potential therapies aimed at normalizing altered microbiota signaling to the enteric nervous system (ENS) and the central nervous system (CNS). Probiotics diets and fecal microbiota transplantation (FMT) are currently the most common therapies. Interestingly, in rodent models of binge feeding, optogenetic applications have been shown to affect gut colony sensitivity, thus increasing colonic transit. Here, we review recent findings on the gut microbiota–schizophrenia relationship using in vivo optogenetics. Moreover, we evaluate if manipulating actors in either the brain or the gut might improve potential treatment research. Such research and techniques will increase our knowledge of how the gut microbiota can manipulate GABA production, and therefore accompany changes in CNS GABAergic activity.
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Affiliation(s)
- Enrico Patrono
- Institute of Physiology of the Czech Academy of Sciences, Videnska, 1830, Prague, 142 20, Czech Republic.
| | - Jan Svoboda
- Institute of Physiology of the Czech Academy of Sciences, Videnska, 1830, Prague, 142 20, Czech Republic
| | - Aleš Stuchlík
- Institute of Physiology of the Czech Academy of Sciences, Videnska, 1830, Prague, 142 20, Czech Republic.
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43
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Shah NB, Nigwekar SU, Kalim S, Lelouvier B, Servant F, Dalal M, Krinsky S, Fasano A, Tolkoff-Rubin N, Allegretti AS. The Gut and Blood Microbiome in IgA Nephropathy and Healthy Controls. KIDNEY360 2021; 2:1261-1274. [PMID: 35369657 PMCID: PMC8676391 DOI: 10.34067/kid.0000132021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/08/2021] [Indexed: 02/04/2023]
Abstract
Background IgA nephropathy (IgAN) has been associated with gut dysbiosis, intestinal membrane disruption, and translocation of bacteria into blood. Our study aimed to understand the association of gut and blood microbiomes in patients with IgAN in relation to healthy controls. Methods We conducted a case-control study with 20 patients with progressive IgAN, matched with 20 healthy controls, and analyzed bacterial DNA quantitatively in blood using 16S PCR and qualitatively in blood and stool using 16S metagenomic sequencing. We conducted between-group comparisons as well as comparisons between the blood and gut microbiomes. Results Higher median 16S bacterial DNA in blood was found in the IgAN group compared with the healthy controls group (7410 versus 6030 16S rDNA copies/μl blood, P=0.04). α- and β-Diversity in both blood and stool was largely similar between the IgAN and healthy groups. In patients with IgAN, in comparison with healthy controls, we observed higher proportions of the class Coriobacteriia and species of the genera Legionella, Enhydrobacter, and Parabacteroides in blood, and species of the genera Bacteroides, Escherichia-Shigella, and some Ruminococcus in stool. Taxa distribution were markedly different between the blood and stool samples of each subject in both IgAN and healthy groups, without any significant correlation between corresponding gut and blood phyla. Conclusions Important bacterial taxonomic differences, quantitatively in blood and qualitatively in both blood and stool samples, that were detected between IgAN and healthy groups warrant further investigation into their roles in the pathogenesis of IgAN. Although gut bacterial translocation into blood may be one of the potential sources of the blood microbiome, marked taxonomic differences between gut and blood samples in each subject in both groups confirms that the blood microbiome does not directly reflect the gut microbiome. Further research is needed into other possible sites of origin and internal regulation of the blood microbiome.
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Affiliation(s)
- Neal B. Shah
- Division of Hospital Medicine, Department of Medicine, Johns Hopkins Bayview Medical Center, Baltimore, Maryland
| | - Sagar U. Nigwekar
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Sahir Kalim
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | | | - Monika Dalal
- Division of Hospital Medicine, Department of Medicine, Johns Hopkins Bayview Medical Center, Baltimore, Maryland
| | - Scott Krinsky
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Alessio Fasano
- Division of Pediatric Gastroenterology and Nutrition, Center for Celiac Research, Massachusetts General Hospital for Children, Boston, Massachusetts
| | - Nina Tolkoff-Rubin
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Andrew S. Allegretti
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
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44
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Le Masters T, Johnson S, Jeraldo PR, Greenwood-Quaintance KE, Cunningham SA, Abdel MP, Chia N, Patel R. Comparative Transcriptomic Analysis of Staphylococcus aureus Associated with Periprosthetic Joint Infection under in Vivo and in Vitro Conditions. J Mol Diagn 2021; 23:986-999. [PMID: 34098085 DOI: 10.1016/j.jmoldx.2021.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 02/25/2021] [Accepted: 05/06/2021] [Indexed: 11/15/2022] Open
Abstract
Transcriptomic analysis can provide insight as to how Staphylococcus aureus adapts to the environmental niche of periprosthetic joint infection (PJI), a challenging clinical infection. Here, in vivo RNA expression of eight S. aureus PJIs was compared with expression of the corresponding isolates in planktonic culture using a total RNA-sequencing approach. Expression varied among isolates, with a common trend showing increased expression of several ica-independent biofilm formation genes, including sdr, fnb, ebpS, and aaa; genes encoding enzymes and toxins, including coa, nuc, hlb, and hlgA/B/C; and genes facilitating acquisition of iron via the iron-binding molecule siderophore B (snb) and heme consumption protein (isd) pathways in PJI. Several antimicrobial resistance determinants were detected; although their presence correlated with phenotypic susceptibility of the associated isolates, no difference in expression between in vivo and in vitro conditions was identified.
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Affiliation(s)
- Thao Le Masters
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stephen Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Patricio R Jeraldo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Scott A Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota.
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45
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Xing Y, Yang X, Chen H, Zhu S, Xu J, Chen Y, Zeng J, Chen F, Johnson MR, Jiang H, Wang WJ. The effect of cell isolation methods on the human transcriptome profiling and microbial transcripts of peripheral blood. Mol Biol Rep 2021; 48:3059-3068. [PMID: 33929647 PMCID: PMC8085658 DOI: 10.1007/s11033-021-06382-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/24/2021] [Indexed: 11/25/2022]
Abstract
The expression of human and microbial genes serves as biomarkers for disease and health. Blood RNA is an important biological resource for precision medicine and translational medicine. However, few studies have assessed the human transcriptome profiles and microbial communities composition and diversity of peripheral blood from different cell isolation methods, which could affect the reproducibility of researches. We collected peripheral blood from three healthy donors and processed it immediately. We used RNA sequencing to investigate the effect of three leukocyte isolation methods including buffy coat (BC) extraction, red blood cell (RBC) lysis and peripheral blood mononuclear cell (PBMC) isolation with the comparison with whole blood (WB), through analyzing the sensitivity of gene detection, the whole transcriptome profiling and microbial composition and diversity. Our data showed that BC extraction with high globin mRNA mapping rate had similar transcriptome profiles with WB, while RBC lysis and PBMC isolation depleted RBCs effectively. With the efficient depletion of RBC and distinct compositions of leukocyte subsets, RNA-seq of RBC lysis and PBMC isolation uniquely detected genes from specific cell types, like granulocytes and NK cells. In addition, we observed that the microbial composition and diversity were more affected by individuals than isolation methods. Our results showed that blood cell isolations could largely influence the sensitivity of detection of human genes and transcriptome profile.
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Affiliation(s)
- Yanru Xing
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xi Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Haixiao Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Sujun Zhu
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Jinjin Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yuan Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Juan Zeng
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Mark Richard Johnson
- Academic Obstetric Department, Imperial College London, Chelsea & Westminster Hospital campus, London, UK
| | - Hui Jiang
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Guangdong Enterprise Key Laboratory of Human Disease Genomics, Shenzhen, China
| | - Wen-Jing Wang
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.
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46
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Peña-Cearra A, Belanche A, Gonzalez-Lopez M, Lavín JL, Pascual-Itoiz MÁ, Jiménez E, Rodríguez H, Aransay AM, Anguita J, Yáñez-Ruiz DR, Abecia L. Peripheral blood mononuclear cells (PBMC) microbiome is not affected by colon microbiota in healthy goats. Anim Microbiome 2021; 3:28. [PMID: 33853683 PMCID: PMC8048065 DOI: 10.1186/s42523-021-00091-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 03/30/2021] [Indexed: 12/15/2022] Open
Abstract
Background The knowledge about blood circulating microbiome and its functional relevance in healthy individuals remains limited. An assessment of changes in the circulating microbiome was performed by sequencing peripheral blood mononuclear cells (PBMC) bacterial DNA from goats supplemented or not in early life with rumen liquid transplantation. Results Most of the bacterial DNA associated to PBMC was identified predominantly as Proteobacteria (55%) followed by Firmicutes (24%), Bacteroidetes (11%) and Actinobacteria (8%). The predominant genera found in PBMC samples were Pseudomonas, Prevotella, Sphingomonas, Acinetobacter, Corynebacterium and Ruminococcus. Other genera such as Butyrivibrivio, Bifidobacterium, Dorea and Coprococcus were also present in lower proportions. Several species known as blood pathogens or others involved in gut homeostasis such as Faecalibacterium prausnitzii were also identified. However, the PBMC microbiome phylum composition differed from that in the colon of goats (P ≤ 0.001), where Firmicutes was the predominant phylum (83%). Although, rumen liquid administration in early-life altered bacterial community structure and increased Tlr5 expression (P = 0.020) in colon pointing to higher bacterial translocation, less than 8% of OTUs in colon were also observed in PBMCs. Conclusions Data suggest that in physiological conditions, PBMC microbiome differs from and is not affected by colon gut microbiota in small ruminants. Although, further studies with larger number of animals and covering other animal tissues are required, results point to a common circulating bacterial profile on mammals being phylum Proteobacteria, and genera Pseudomonas and Prevotella the most abundants. All suggest that PBMC microbiome in healthy ruminants could be implicated in homeostatic condition. This study expands our knowledge about PBMC microbiome contribution to health in farm animals. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00091-7.
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Affiliation(s)
- Ainize Peña-Cearra
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,Departamento de Inmunología, Microbiología y Parasitología, Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Apartado 699, 48080, Bilbao, Spain
| | | | - Monika Gonzalez-Lopez
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain
| | - José Luis Lavín
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,Present Address: NEIKER Instituto Vasco de Investigación y Desarrollo Agrario, Parque Tecnológico Bizkaia Ed. 812, 48160, Derio, Spain
| | | | | | - Héctor Rodríguez
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain
| | - Ana Mª Aransay
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,CIBERehd, ISCIII, Madrid, Spain
| | - Juan Anguita
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | | | - Leticia Abecia
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain. .,Departamento de Inmunología, Microbiología y Parasitología, Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Apartado 699, 48080, Bilbao, Spain.
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47
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Prasad R, Patton MJ, Floyd JL, Vieira CP, Fortmann S, DuPont M, Harbour A, Jeremy CS, Wright J, Lamendella R, Stevens BR, Grant MB. Plasma microbiome in COVID-19 subjects: an indicator of gut barrier defects and dysbiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33851159 DOI: 10.1101/2021.04.06.438634] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal ( GI ) symptoms. We asked whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n=30) and healthy control (n=16) were collected during hospitalization. Plasma microbiome was analyzed using 16S rRNA sequencing, metatranscriptomic analysis, and gut permeability markers including FABP-2, PGN and LPS in both patient cohorts. Almost 65% (9 out 14) COVID-19 patients showed abnormal presence of gut microbes in their bloodstream. Plasma samples contained predominately Proteobacteria, Firmicutes, and Actinobacteria . The abundance of gram-negative bacteria ( Acinetobacter, Nitrospirillum, Cupriavidus, Pseudomonas, Aquabacterium, Burkholderia, Caballeronia, Parabhurkholderia, Bravibacterium, and Sphingomonas ) was higher than the gram-positive bacteria ( Staphylococcus and Lactobacillus ) in COVID-19 subjects. The levels of plasma gut permeability markers FABP2 (1282±199.6 vs 838.1±91.33; p=0.0757), PGN (34.64±3.178 vs 17.53±2.12; p<0.0001), and LPS (405.5±48.37 vs 249.6±17.06; p=0.0049) were higher in COVID-19 patients compared to healthy subjects. These findings support that the intestine may represent a source for bacteremia and may contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.
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48
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Joura MI, Brunner A, Nemes-Nikodém É, Sárdy M, Ostorházi E. Interactions between immune system and the microbiome of skin, blood and gut in pathogenesis of rosacea. Acta Microbiol Immunol Hung 2021; 68:1-6. [PMID: 33522984 DOI: 10.1556/030.2021.01366] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022]
Abstract
The increasingly wide use of next-generation sequencing technologies has revolutionised our knowledge of microbial environments associated with human skin, gastrointestinal tract and blood. The collective set of microorganisms influences metabolic processes, affects immune responses, and so directly or indirectly modulates disease. Rosacea is a skin condition of abnormal inflammation and vascular dysfunction, and its progression is affected by Demodex mites on the skin surface. When looking into the effects influencing development of rosacea, it is not only the skin microbiome change that needs to be considered. Changes in the intestinal microbiome and their circulating metabolites, as well as changes in the blood microbiome also affect the progression of rosacea. Recent research has confirmed the increased presence of bacterial genera like Acidaminococcus and Megasphera in the intestinal microbiome and Rheinheimera and Sphingobium in the blood microbiome of rosacea patients. In this review we discuss our current knowledge of the interactions between the immune system and the skin, gut and blood microbiome, with particular attention to rosacea diagnostic opportunities.
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Affiliation(s)
- Marie Isolde Joura
- 1Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Alexandra Brunner
- 1Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Éva Nemes-Nikodém
- 2Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Miklós Sárdy
- 1Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Eszter Ostorházi
- 1Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, Hungary
- 3Department of Medical Microbiology, Semmelweis University, Budapest, Hungary
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49
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Emery DC, Cerajewska TL, Seong J, Davies M, Paterson A, Allen-Birt SJ, West NX. Comparison of Blood Bacterial Communities in Periodontal Health and Periodontal Disease. Front Cell Infect Microbiol 2021; 10:577485. [PMID: 33469518 PMCID: PMC7813997 DOI: 10.3389/fcimb.2020.577485] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/19/2020] [Indexed: 12/13/2022] Open
Abstract
The use of Next Generation Sequencing (NGS) techniques has generated a wide variety of blood microbiome data. Due to the large variation in bacterial DNA profiles between studies and the likely high concentrations of cell-free bacterial DNA in the blood, it is still not clear how such microbiome data relates to viable microbiota. For these reasons much remains to be understood about the true nature of any possible healthy blood microbiota and of bacteraemic events associated with disease. The gut, reproductive tracts, skin, and oral cavity are all likely sources of blood-borne bacteria. Oral bacteria, especially those associated with periodontal diseases, are also commonly associated with cardiovascular diseases such as infective endocarditis, and also have been linked to rheumatoid arthritis and Alzheimer’s disease. Periodontal treatment, dental probing, and toothbrushing have been shown to cause transient bacteraemia and oral bacteria from the phyla Firmicutes (e.g. Streptococci) and Bacteroidetes (e.g. Porphyromonas) are found in cardiovascular lesions (CVD). Many studies of blood bacterial DNA content however, find Proteobacteria DNA to be the dominant microbiome component, suggesting a gut origin. Most studies of this type use total DNA extracted from either whole blood or blood fractions, such as buffy coat. Here, using a method that purifies DNA from intact bacterial cells only, we examined blood donated by those with active, severe periodontitis and periodontally healthy controls and show that 43–52% of bacterial species in blood are classified as oral. Firmicutes, consisting largely of members of the Streptococcus mitis group and Staphylococcus epidermidis, were predominant at 63.5% of all bacterial sequences detected in periodontal health and, little changed at 66.7% in periodontitis. Compared to studies using total DNA Proteobacteria were found here at relatively low levels in blood at 13.3% in periodontitis and 17.6% in health. This study reveals significant phylogenetic differences in blood bacterial population profiles when comparing periodontal health to periodontal disease cohorts.
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Affiliation(s)
- David C Emery
- Bristol Medical School, Translational Health Sciences, Learning & Research, Southmead Hospital, Bristol, United Kingdom
| | - Tanya L Cerajewska
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Joon Seong
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Maria Davies
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Alex Paterson
- University of Bristol Genomics Facility, School of Biological Sciences, Bristol, United Kingdom
| | - Shelley J Allen-Birt
- Bristol Medical School, Translational Health Sciences, Learning & Research, Southmead Hospital, Bristol, United Kingdom
| | - Nicola X West
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
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50
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Yegin Z, Avsar C, Sarisoy G. Frequency of retrotransposon human endogenous retrovirus-K113 and a preliminary analysis of some microbial clues in bipolar disorder. Future Microbiol 2020; 15:1621-1629. [PMID: 33215524 DOI: 10.2217/fmb-2020-0166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: The aim of our study was to investigate whether the retrotransposon human endogenous retrovirus (HERV)-K113 could be related with bipolar disorder or not. As a second and a preliminary aim, we also conducted bacterial screening in whole blood in a limited number of samples. Patients & methods: Three separate PCR reactions including the preintegration sites and sites within the viral sequences were performed for HERV-K113 detection. Bacterial screening was performed with SSCP/sequencing analysis. Results & conclusion: No difference was observed in terms of the frequency of retrotransposon HERV-K113 in Turkish bipolar disorder patients and healthy controls. SSCP/sequencing and alignment analysis for bacterial screening reflected the possible presence of different bacteria. We strongly recommend the broadened retrotransposon and microbial diversity analyses in bipolar disorder for future studies.
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Affiliation(s)
- Zeynep Yegin
- Medical Laboratory Techniques Program, Vocational School of Health Services, Sinop University, Sinop, Turkey
| | - Cumhur Avsar
- Department of Biology, Faculty of Arts & Sciences, Sinop University, Sinop, Turkey
| | - Gokhan Sarisoy
- Department of Psychiatry, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
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