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Balczon R, Lin MT, Voth S, Nelson AR, Schupp JC, Wagener BM, Pittet JF, Stevens T. Lung endothelium, tau, and amyloids in health and disease. Physiol Rev 2024; 104:533-587. [PMID: 37561137 DOI: 10.1152/physrev.00006.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/26/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023] Open
Abstract
Lung endothelia in the arteries, capillaries, and veins are heterogeneous in structure and function. Lung capillaries in particular represent a unique vascular niche, with a thin yet highly restrictive alveolar-capillary barrier that optimizes gas exchange. Capillary endothelium surveys the blood while simultaneously interpreting cues initiated within the alveolus and communicated via immediately adjacent type I and type II epithelial cells, fibroblasts, and pericytes. This cell-cell communication is necessary to coordinate the immune response to lower respiratory tract infection. Recent discoveries identify an important role for the microtubule-associated protein tau that is expressed in lung capillary endothelia in the host-pathogen interaction. This endothelial tau stabilizes microtubules necessary for barrier integrity, yet infection drives production of cytotoxic tau variants that are released into the airways and circulation, where they contribute to end-organ dysfunction. Similarly, beta-amyloid is produced during infection. Beta-amyloid has antimicrobial activity, but during infection it can acquire cytotoxic activity that is deleterious to the host. The production and function of these cytotoxic tau and amyloid variants are the subject of this review. Lung-derived cytotoxic tau and amyloid variants are a recently discovered mechanism of end-organ dysfunction, including neurocognitive dysfunction, during and in the aftermath of infection.
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Affiliation(s)
- Ron Balczon
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
| | - Mike T Lin
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
| | - Sarah Voth
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, United States
| | - Amy R Nelson
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
| | - Jonas C Schupp
- Pulmonary and Critical Care Medicine, Department of Internal Medicine, Yale University, New Haven, Connecticut, United States
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- German Center for Lung Research (DZL), Hannover, Germany
| | - Brant M Wagener
- Department of Anesthesiology and Perioperative Medicine, University of Alabama-Birmingham, Birmingham, Alabama, United States
| | - Jean-Francois Pittet
- Department of Anesthesiology and Perioperative Medicine, University of Alabama-Birmingham, Birmingham, Alabama, United States
| | - Troy Stevens
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama, United States
- Department of Internal Medicine, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
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Tseng YH, Pan SW, Feng JY, Su WJ, Huang CYF, Chen YM. Detecting circulating microbial cell-free DNA by next-generation sequencing in patients with Mycobacterium avium complex-lung disease: A pilot study. Tzu Chi Med J 2024; 36:67-75. [PMID: 38406566 PMCID: PMC10887338 DOI: 10.4103/tcmj.tcmj_191_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/22/2023] [Accepted: 09/20/2023] [Indexed: 02/27/2024] Open
Abstract
Objectives Determining a diagnosis for non-Tuberculous mycobacterium (NTM)-lung disease (LD) remains difficult. The value of circulating cell-free DNA (cfDNA) secreted from microbes has been established in the detection of pathogens in septic patients. However, it is unknown whether NTM-derived cfDNA is detectable in plasma from patients with NTM-LD and whether this is associated with the disease status of NTM-LD, especially in patients with Mycobacterium avium complex (MAC)-LD. Materials and Methods In this pilot study, from 2018 to 2019, we enrolled adult patients with MAC-LD at Taipei Veterans General Hospital in Taiwan for the detection of circulating cfDNA. We performed cfDNA extraction from plasma, next-generation sequencing (NGS) for nonhuman cfDNA, and sequence matching to a microbial database and then assessed the association between pathogen cfDNA and MAC-LD. Results Two (40%) plasma samples from MAC-LD patients had detectable MAC-specific cfDNA, namely one instance of DNA polymerase III alpha subunit and one instance of ATP-binding cassette transporters permease. The plasma samples from the three other MAC-LD cases and the one tuberculosis control were negative for either NTM-derived cfDNA or tuberculosis-related cfDNA. In addition to MAC-specific cfDNA, Ralstonia solanacearum, Staphylococcus aureus, and Pasteurella multocida were the most observed bacteria in our patients. The two patients with MAC-cfDNA positivity yielded higher radiographic scores (P = 0.076) and presented a higher number of nonhuman reads than those without MAC-cfDNA positivity (P = 0.083). Conclusion Using NGS method, we demonstrated MAC-cfDNA was detectable in patients with MAC-LD. Further large-scale research is warranted to assess the clinical value of detecting MAC-specific cfDNA in MAC-LD patients.
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Affiliation(s)
- Yen-Han Tseng
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Program in Molecular Medicine, School of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Sheng-Wei Pan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jia-Yih Feng
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wei-Juin Su
- Division of Chest Medicine, Department of Internal Medicine, China Medical University Hospital, Taipei Branch, Taipei, Taiwan
| | - Chi-Ying F Huang
- Program in Molecular Medicine, School of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Biopharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yuh-Min Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
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Kang JI, Seo JH, Park CI, Kim ST, Kim YK, Jang JK, Kwon CO, Jeon S, Kim HW, Kim SJ. Microbiome analysis of circulating bacterial extracellular vesicles in obsessive-compulsive disorder. Psychiatry Clin Neurosci 2023; 77:646-652. [PMID: 37646189 DOI: 10.1111/pcn.13593] [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] [Received: 04/16/2023] [Revised: 08/07/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
AIM The present study examined the microbiome abundance and composition of drug-naive or drug-free patients with obsessive-compulsive disorder (OCD) compared with healthy controls. In addition, in the OCD group, the microbiome composition was compared between early-onset and late-onset OCD. METHODS Serum samples were collected from 89 patients with OCD and 107 age- and sex-matched healthy controls. Bacterial DNA was isolated from bacteria-derived extracellular vesicles in serum and then amplified and quantified using primers specific to the V3-V4 hypervariable region of the 16S ribosomal RNA gene. The 16S ribosomal DNA gene amplicon sequencing was performed. RESULTS The pooled estimate showed that α-diversity was significantly reduced in patients with OCD compared with that in healthy controls (PShannon = 0.00015). In addition, a statistically significant difference was observed in β-diversity between patients with OCD and healthy controls at the order (P = 0.012), family (P = 0.003), genus (P < 0.001), and species (P = 0.005) levels. In the microbiome composition, Pseudomonas, Caulobacteraceae (f), Streptococcus, Novosphingobium, and Enhydrobacter at the genus level were significantly less prevalent in patients with OCD than in controls. In addition, among patients with OCD, the microbial composition in the early-onset versus late-onset types was significantly different with respect to the genera Corynebacterium and Pelomonas. CONCLUSION The present study showed an aberrant microbiome in patients with OCD, suggesting a role of the microbiota-brain interaction in the pathophysiology of OCD. Further longitudinal studies with larger sample sizes adjusting for various confounders are warranted.
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Affiliation(s)
- Jee In Kang
- Department of Psychiatry, Yonsei University College of Medicine, Seoul, Republic of Korea
- Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jun Ho Seo
- Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Psychiatry, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Chun Il Park
- Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Psychiatry, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Shin Tae Kim
- Department of Psychiatry, Yonsei University College of Medicine, Seoul, Republic of Korea
- Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | | | | | - Sumoa Jeon
- Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hae Won Kim
- Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Medical Education, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Se Joo Kim
- Department of Psychiatry, Yonsei University College of Medicine, Seoul, Republic of Korea
- Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
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Banerjee A, Roychoudhury A. Bio-priming with a Novel Plant Growth-Promoting Acinetobacter indicus Strain Alleviates Arsenic-Fluoride Co-toxicity in Rice by Modulating the Physiome and Micronutrient Homeostasis. Appl Biochem Biotechnol 2023; 195:6441-6464. [PMID: 36870026 DOI: 10.1007/s12010-023-04410-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/05/2023]
Abstract
Sustainable remediation of arsenic-fluoride from rice fields through efficient bio-extraction is the need of the hour, since these toxicants severely challenge safe cultivation of rice and food biosafety. In the present study, we screened an arsenic-fluoride tolerant strain AB-ARC of Acinetobacter indicus from the soil of a severely polluted region of West Bengal, India, which was capable of efficiently removing extremely high doses of arsenate and fluoride from the media. The strain also behaved as a plant growth-promoting rhizobacterium, since it could produce indole-3-acetic acid and solubilize phosphate, zinc, and starch. Due to these properties of the identified strain, it was used for bio-priming the seeds of the arsenic-fluoride susceptible rice cultivar, Khitish for testing the efficacy of the AB-ARC strain to promote combined arsenic-fluoride tolerance in the rice genotype. Bio-priming with AB-ARC led to accelerated uptake of crucial elements like iron, copper, and nickel which behave as co-factors of physiological and antioxidative enzymes. Thus, the activation of superoxide dismutase, catalase, guaiacol peroxidase, glutathione peroxidase, and glutathione-S-transferase enabled detoxification of reactive oxygen species (ROS) and reduction of the oxidative injuries like malondialdehyde and methylglyoxal generation. Overall, due to ameliorated molecular damages and low uptake of the toxic xenobiotics, the plants were able to maintain improved growth vigor and photosynthesis, as evident from the elevated levels of Hill activity and chlorophyll content. Hence, bio-priming with the A. indicus AB-ARC strain may be advocated for sustainable rice cultivation in arsenic-fluoride co-polluted fields.
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Affiliation(s)
- Aditya Banerjee
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, West Bengal, 700016, India
| | - Aryadeep Roychoudhury
- Discipline of Life Sciences, School of Sciences, Indira Gandhi National Open University, Maidan Garhi, New Delhi, India.
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Guo X, Wang Z, Qu M, Guo Y, Yu M, Hong W, Zhang C, Fan X, Song J, Xu R, Zhang J, Huang H, Linghu E, Wang FS, Sun L, Jiao YM. Abnormal blood microbiota profiles are associated with inflammation and immune restoration in HIV/AIDS individuals. mSystems 2023; 8:e0046723. [PMID: 37698407 PMCID: PMC10654078 DOI: 10.1128/msystems.00467-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/22/2023] [Indexed: 09/13/2023] Open
Abstract
IMPORTANCE The characteristics of blood microbiota in HIV-infected individuals and their relevance to disease progression are still unknown, despite alterations in gut microbiota diversity and composition in HIV-infected individuals. Here, we present evidence of increased blood microbiota diversity in HIV-infected individuals, which may result from gut microbiota translocation. Also, we identify a group of microbes, Porphyromonas gingivalis, Prevotella sp. CAG:5226, Eubacterium sp. CAG:251, Phascolarctobacterium succinatutens, Anaerobutyricum hallii, Prevotella sp. AM34-19LB, and Phocaeicola plebeius, which are linked to poor immunological recovery. This work provides a scientific foundation toward therapeutic strategies targeting blood microbiota for immune recovery of HIV infection.
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Affiliation(s)
- Xiaoyan Guo
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Zerui Wang
- Department of Gastroenterology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Mengmeng Qu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Yuntian Guo
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Minrui Yu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Weiguo Hong
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Chao Zhang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xing Fan
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jinwen Song
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ruonan Xu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jiyuan Zhang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Huihuang Huang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Enqiang Linghu
- Department of Gastroenterology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fu-Sheng Wang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Lijun Sun
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yan-Mei Jiao
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
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Hou D, Lian T, Guo G, Gong H, Wu C, Han P, Weng S, He J. Integration of microbiome and Koch's postulates to reveal multiple bacterial pathogens of whitish muscle syndrome in mud crab, Scylla paramamosain. MICROBIOME 2023; 11:155. [PMID: 37475003 PMCID: PMC10357871 DOI: 10.1186/s40168-023-01570-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/12/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND For more than a century, the Koch's postulates have been the golden rule for determining the causative agents in diseases. However, in cases of multiple pathogens-one disease, in which different pathogens can cause the same disease, the selection of microorganisms that regress infection is hard when Koch's postulates are applied. Microbiome approaches can obtain relatively complete information about disease-related microorganisms and can guide the selection of target microorganisms for regression infection. In the present study, whitish muscle syndrome (WMS) of Scylla paramamosain, which has typical symptoms with whitish muscle and blackened hemolymph was used as an example to establish a new research strategy that integrates microbiome approaches and Koch's postulates to determinate causative agents of multiple pathogens-one disease. RESULTS Microbiome results revealed that Aeromonas, Acinetobacter, Shewanella, Chryseomicrobium, Exiguobacterium, Vibrio and Flavobacterium, and Kurtzmaniella in hemolymph were bacterial and fungal indicators for WMS. A total of 23 bacteria and 14 fungi were isolated from hemolymph and muscle tissues, and among the bacteria, Shewanella chilikensis, S. xiamenensis, Vibrio alginolyticus, S. putrefaciens, V. fluvialis, and V. parahaemolyticus were present in hemolymph and/or muscle tissues in each WMS crab, and the last three species were also present in three Healthy crabs. The target bacteria and fungi were further screened to regression infections based on two criteria: whether they belonged to the indicator genera for WMS, whether they were isolated from both hemolymph and muscle tissues in most WMS crabs. Only S. chilikensis, S. putrefaciens, S. xiamenensis, V. alginolyticus, V. fluvialis, and V. parahaemolyticus met both two criteria. The six bacteria that met both two criteria and six fungi and another bacterium that unmatched any of two criteria were used to perform regression infection experiments based on Koch's postulates. S. chilikensis, S. putrefaciens, S. xiamenensis, V. alginolyticus, V. fluvialis, and V. parahaemolyticus met both two criteria, and the results indicate that they cause WMS in crabs independently. CONCLUSIONS This study fully demonstrated that our research strategy that integrates the microbiome and Koch's postulates can maximize the ability to catch pathogens in one net for the situation of multiple pathogens-one disease. Video Abstract.
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Affiliation(s)
- Dongwei Hou
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Taixin Lian
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Guangyu Guo
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Han Gong
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Chengcheng Wu
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Peiyun Han
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, People's Republic of China
| | - Jianguo He
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, People's Republic of China.
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Wohlfahrt D, Tan-Torres AL, Green R, Brim K, Bradley N, Brand A, Abshier E, Nogales F, Babcock K, Brooks J, Seashols-Williams S, Singh B. A bacterial signature-based method for the identification of seven forensically relevant human body fluids. Forensic Sci Int Genet 2023; 65:102865. [PMID: 37004371 DOI: 10.1016/j.fsigen.2023.102865] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023]
Abstract
Detection and identification of body fluids plays a crucial role in criminal investigation, as it provides information on the source of the DNA as well as corroborative evidence regarding the crime committed, scene, and/or association with persons of interest. Historically, forensic serological methods have been chemical, immunological, catalytic, spectroscopic, and/or microscopic in nature. However, most of these methods are presumptive, with few robust confirmatory exceptions. In recent years several new molecular methods (mRNA, miRNA, DNA methylation, etc.) have been proposed; although promising, these methods require high quality human DNA or RNA. Additional steps are required in RNA based methods. Additionally, RNA based methods cannot be used for old cases where only DNA extracts remain to sample from. In this study, a novel non-human DNA (microbiome) based method was developed for the identification of the majority of forensically relevant human biological samples. Eight hundred and twelve (n = 812) biological samples (semen, vaginal fluid, menstrual blood, saliva, feces, urine, and blood) were collected and preserved using methods commonly used in forensic laboratories for evidence collection. Variable region four (V4) of 16 S ribosomal DNA (16 S rDNA) was amplified using a dual-indexing strategy and then sequenced on the MiSeq FGx sequencing platform using the MiSeq Reagent Kit v2 (500 cycles) and following the manufacturer's protocol. Machine learning prediction models were used to assess the classification accuracy of the newly developed method. As there was no significant difference in bacterial communities between vaginal fluid, menstrual blood, and female urine, these were combined as female intimate samples. Except in urine, the bacterial structures associated with male and female body fluid samples were not significantly different from one another. The newly developed method accurately identified human body fluid samples with an overall accuracy of more than 88%. This newly developed bacterial signature-based method is fast (no additional steps are needed as the same DNA can be used for both body fluid identification and STR typing), efficient (consume less sample as a single test can identify all major body fluids), sensitive (needs only 5 pg of bacterial DNA), accurate, and can be easily added into a forensic high throughput sequencing (HTS) panel.
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Sciarra F, Franceschini E, Campolo F, Venneri MA. The Diagnostic Potential of the Human Blood Microbiome: Are We Dreaming or Awake? Int J Mol Sci 2023; 24:10422. [PMID: 37445600 DOI: 10.3390/ijms241310422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/01/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Human blood has historically been considered a sterile environment. Recently, a thriving microbiome dominated by Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes phyla was detected in healthy blood. The localization of these microbes is restricted to some blood cell populations, particularly the peripheral blood mononuclear cells and erythrocytes. It was hypothesized that the blood microbiome originates from the skin-oral-gut axis. In addition, many studies have evaluated the potential of blood microbiome dysbiosis as a prognostic marker in cardiovascular diseases, cirrhosis, severe liver fibrosis, severe acute pancreatitis, type 2 diabetes, and chronic kidney diseases. The present review aims to summarize current findings and most recent evidence in the field.
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Affiliation(s)
- Francesca Sciarra
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Edoardo Franceschini
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Federica Campolo
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Mary Anna Venneri
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
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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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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: 5] [Impact Index Per Article: 2.5] [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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11
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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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12
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Sumida K, Han Z, Chiu CY, Mims TS, Bajwa A, Demmer RT, Datta S, Kovesdy CP, Pierre JF. Circulating Microbiota in Cardiometabolic Disease. Front Cell Infect Microbiol 2022; 12:892232. [PMID: 35592652 PMCID: PMC9110890 DOI: 10.3389/fcimb.2022.892232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/11/2022] [Indexed: 12/14/2022] Open
Abstract
The rapid expansion of microbiota research has significantly advanced our understanding of the complex interactions between gut microbiota and cardiovascular, metabolic, and renal system regulation. Low-grade chronic inflammation has long been implicated as one of the key mechanisms underlying cardiometabolic disease risk and progression, even before the insights provided by gut microbiota research in the past decade. Microbial translocation into the bloodstream can occur via different routes, including through the oral and/or intestinal mucosa, and may contribute to chronic inflammation in cardiometabolic disease. Among several gut-derived products identifiable in the systemic circulation, bacterial endotoxins and metabolites have been extensively studied, however recent advances in microbial DNA sequencing have further allowed us to identify highly diverse communities of microorganisms in the bloodstream from an -omics standpoint, which is termed "circulating microbiota." While detecting microorganisms in the bloodstream was historically considered as an indication of infection, evidence on the circulating microbiota is continually accumulating in various patient populations without clinical signs of infection and even in otherwise healthy individuals. Moreover, both quantitative and compositional alterations of the circulating microbiota have recently been implicated in the pathogenesis of chronic inflammatory conditions, potentially through their immunostimulatory, atherogenic, and cardiotoxic properties. In this mini review, we aim to provide recent evidence on the characteristics and roles of circulating microbiota in several cardiometabolic diseases, such as type 2 diabetes, cardiovascular disease, and chronic kidney disease, with highlights of our emerging findings on circulating microbiota in patients with end-stage kidney disease undergoing hemodialysis.
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Affiliation(s)
- Keiichi Sumida
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States,*Correspondence: Keiichi Sumida,
| | - Zhongji Han
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Chi-Yang Chiu
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Tahliyah S. Mims
- Department of Nutritional Sciences, College of Agriculture and Life Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Amandeep Bajwa
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Ryan T. Demmer
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, United States,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Susmita Datta
- Department of Biostatistics, University of Florida, Gainesville, FL, United States
| | - Csaba P. Kovesdy
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States,Nephrology Section, Memphis Veterans Affairs (VA) Medical Center, Memphis, TN, United States
| | - Joseph F. Pierre
- Department of Nutritional Sciences, College of Agriculture and Life Science, University of Wisconsin-Madison, Madison, WI, United States
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13
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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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14
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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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15
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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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16
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Endurance Training in Humans Modulates the Bacterial DNA Signature of Skeletal Muscle. Biomedicines 2021; 10:biomedicines10010064. [PMID: 35052744 PMCID: PMC8773292 DOI: 10.3390/biomedicines10010064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
Accumulating evidence supports the existence of a tissue microbiota, which may regulate the physiological function of tissues in normal and pathological states. To gain insight into the regulation of tissue-borne bacteria in physiological conditions, we quantified and sequenced the 16S rRNA gene in aseptically collected skeletal muscle and blood samples from eight healthy male individuals subjected to six weeks of endurance training. Potential contamination bias was evaluated and the taxa profiles of each tissue were established. We detected bacterial DNA in skeletal muscle and blood, with background noise levels of detected bacterial DNA considerably lower in control versus tissue samples. In both muscle and blood, Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes were the most prominent phyla. Endurance training changed the content of resident bacterial DNA in skeletal muscle but not in blood, with Pseudomonas being less abundant, and both Staphylococcus and Acinetobacter being more abundant in muscle after exercise. Our results provide evidence that endurance training specifically remodels the bacterial DNA profile of skeletal muscle in healthy young men. Future investigations may shed light on the physiological impact, if any, of training-induced changes in bacterial DNA in skeletal muscle.
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17
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Sedghi LM, Bacino M, Kapila YL. Periodontal Disease: The Good, The Bad, and The Unknown. Front Cell Infect Microbiol 2021; 11:766944. [PMID: 34950607 PMCID: PMC8688827 DOI: 10.3389/fcimb.2021.766944] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/11/2021] [Indexed: 01/08/2023] Open
Abstract
Periodontal disease is classically characterized by progressive destruction of the soft and hard tissues of the periodontal complex, mediated by an interplay between dysbiotic microbial communities and aberrant immune responses within gingival and periodontal tissues. Putative periodontal pathogens are enriched as the resident oral microbiota becomes dysbiotic and inflammatory responses evoke tissue destruction, thus inducing an unremitting positive feedback loop of proteolysis, inflammation, and enrichment for periodontal pathogens. Keystone microbial pathogens and sustained gingival inflammation are critical to periodontal disease progression. However, recent studies have revealed the importance of previously unidentified microbes involved in disease progression, including various viruses, phages and bacterial species. Moreover, newly identified immunological and genetic mechanisms, as well as environmental host factors, including diet and lifestyle, have been discerned in recent years as further contributory factors in periodontitis. These factors have collectively expanded the established narrative of periodontal disease progression. In line with this, new ideologies related to maintaining periodontal health and treating existing disease have been explored, such as the application of oral probiotics, to limit and attenuate disease progression. The role of systemic host pathologies, such as autoimmune disorders and diabetes, in periodontal disease pathogenesis has been well noted. Recent studies have additionally identified the reciprocated importance of periodontal disease in potentiating systemic disease states at distal sites, such as in Alzheimer's disease, inflammatory bowel diseases, and oral cancer, further highlighting the importance of the oral cavity in systemic health. Here we review long-standing knowledge of periodontal disease progression while integrating novel research concepts that have broadened our understanding of periodontal health and disease. Further, we delve into innovative hypotheses that may evolve to address significant gaps in the foundational knowledge of periodontal disease.
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Affiliation(s)
- Lea M. Sedghi
- School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
| | - Margot Bacino
- School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
| | - Yvonne Lorraine Kapila
- School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Periodontology, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
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18
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Sumida K, Pierre JF, Han Z, Mims TS, Potukuchi PK, Yuzefpolskaya M, Colombo PC, Demmer RT, Datta S, Kovesdy CP. Circulating Microbial Signatures and Cardiovascular Death in Patients With ESRD. Kidney Int Rep 2021; 6:2617-2628. [PMID: 34622101 PMCID: PMC8484116 DOI: 10.1016/j.ekir.2021.07.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Patients with end-stage renal disease (ESRD) experience disproportionately high cardiovascular morbidity and mortality. Accumulating evidence suggests a role for the circulating microbiome in the pathogenesis of cardiovascular disease; however, little is known about its association with premature cardiovascular mortality in ESRD. METHODS In a pilot case-control study of 17 hemodialysis patients who died of a cardiovascular event and 17 matched hemodialysis controls who remained alive during a median follow-up of 2.0 years, we compared the levels and composition of circulating microbiome, including Bacteria, Archaea, and Fungi, in serum samples by quantitative polymerase chain reaction and 16S or Internal Transcribed Spacer (ITS) ribosomal RNA (rRNA) sequencing, respectively. Associations of the circulating cell-free microbial signatures with clinical parameters and cardiovascular death were examined using the Spearman rank correlation and multivariable conditional logistic regression, respectively. RESULTS Both 16S and ITS rRNA were detectable in all (except 3 for ITS) examined patients' serum samples. Despite no significant difference in 16S rRNA levels and α diversity between cases and controls, taxonomic analysis demonstrated differential community membership between groups, with significantly greater Actinobacteria and less Proteobacteria observed in cases than in controls at the phylum level. Proportions of Actinobacteria and Proteobacteria phyla were significantly correlated with plasma nuclear factor erythroid 2-related factor 2 (Nrf2) levels (rho = -0.41 and 0.42, P = 0.015 and 0.013, respectively) and marginally associated with risk of cardiovascular death (adjusted odds ratios [95% confidence intervals] = 1.12 [0.98-1.29] and 0.88 [0.76-1.02] for 1% increase, respectively). CONCLUSION Alterations of the circulating cell-free microbial signatures may be associated with higher premature cardiovascular mortality in ESRD.
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Affiliation(s)
- Keiichi Sumida
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Joseph F. Pierre
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Zhongji Han
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Tahliyah S. Mims
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Praveen Kumar Potukuchi
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Melana Yuzefpolskaya
- Division of Cardiology, Department of Medicine, New York Presbyterian Hospital, Columbia University, New York, New York, USA
| | - Paolo C. Colombo
- Division of Cardiology, Department of Medicine, New York Presbyterian Hospital, Columbia University, New York, New York, USA
| | - Ryan T. Demmer
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
- Division of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Susmita Datta
- Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Csaba P. Kovesdy
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Nephrology Section, Memphis VA Medical Center, Memphis, Tennessee, USA
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19
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Chen H, Ma Y, Liu Z, Li J, Li X, Yang F, Qiu M. Circulating microbiome DNA: An emerging paradigm for cancer liquid biopsy. Cancer Lett 2021; 521:82-87. [PMID: 34461180 DOI: 10.1016/j.canlet.2021.08.036] [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: 07/08/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 02/08/2023]
Abstract
Dysbiosis of the human microbiome has long been reported to be closely associated with various cancers. Accumulating studies have shown that microbial dysbiosis can accelerate tumorigenesis through tumor-promoting inflammation, DNA damage, and inducing immune evasion. Differential composition of microbiome could be novel biomarkers for cancer detection or biomarkers of successful immunotherapy. More importantly, emerging evidence demonstrates that alterations of circulating microbiome DNA (cmDNA) could serve as promising noninvasive biomarkers for cancer detection. It has been reported that distinct circulating bacterial DNA could distinguish prostate cancer, lung cancer, and melanoma patients from healthy populations. Therefore, in this review, we summarized current literature on microbial biomarkers for cancer detection and unraveled the potential of cmDNA as a promising cancer detection tool.
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Affiliation(s)
- Haiming Chen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Yi Ma
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Zheng Liu
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Jiawei Li
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Xiao Li
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
| | - Mantang Qiu
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
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20
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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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21
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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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22
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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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23
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Abstract
Numerous studies have identified microbial sequences or epitopes in pathological and non-pathological human brain samples. It has not been resolved if these observations are artifactual, or truly represent population of the brain by microbes. Given the tempting speculation that resident microbes could play a role in the many neuropsychiatric and neurodegenerative diseases that currently lack clear etiologies, there is a strong motivation to determine the “ground truth” of microbial existence in living brains. Here I argue that the evidence for the presence of microbes in diseased brains is quite strong, but a compelling demonstration of resident microbes in the healthy human brain remains to be done. Dedicated animal models studies may be required to determine if there is indeed a “brain microbiome.”
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Affiliation(s)
- Christopher D Link
- Department of Integrative Physiology/Institute for Behavioral Genetics, University of Colorado, Boulder, Boulder, CO, USA
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24
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Cheng R, Guo J, Zhang Y, Cheng G, Qian W, Wan C, Li M, Marotta F, Shen X, He F. Impacts of ceftriaxone exposure during pregnancy on maternal gut and placental microbiota and its influence on maternal and offspring immunity in mice. Exp Anim 2021; 70:203-217. [PMID: 33268669 PMCID: PMC8150239 DOI: 10.1538/expanim.20-0114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
This study aimed to investigate the association between microbiota found in the maternal gut and placenta, and whether ceftriaxone exposure during pregnancy could alter these microbiota, and consequently affect the immunity of the mothers and their offspring. The microbiota in the feces and placenta of the dams were comprehensively analyzed using16S rRNA sequencing. Furthermore, viable bacteria in the placentas and blood of pups were also isolated by plate cultivation then taxonomically identified in detail by clone sequencing. Serum cytokines collected from dams and pups were quantitatively profiled using Luminex. The spleen organ index of dams was significantly lower and the offspring serum interleukin-6 levels were significantly higher in ceftriaxone-treated mice compared with the control group. The maternal fecal microbiota community was drastically altered in ceftriaxone-treated mice with significantly decreased diversity, depletion of Bacteroidetes and the blooming of Tenericutes. However, the placenta microbiota was dominated by Proteobacteria especially characteristically by Ralstonia, which was distinct from the maternal gut microbiota, regardless of whether ceftriaxone treatment or not. Viable bacteria have been found in placenta and blood cultures. These results indicated that ceftriaxone exposure in pregnancy could dramatically alter maternal intestinal microbiota, which affected the immunity of the mothers and their offspring at least partly, characteristically by enhanced pro-inflammatory responses. This study also indicated that the placenta might harbor its own microbes and the microbes were distinct from maternal gut microbiota, which may not be affected by oral administration of ceftriaxone during pregnancy.
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Affiliation(s)
- Ruyue Cheng
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, and Healthy Food Evaluation Research Center, Sichuan University, No. 16, 3rd section, South Renmin Road, Wuhou District, Chengdu 610041, Sichuan, P.R. China
| | - Jiawen Guo
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, and Healthy Food Evaluation Research Center, Sichuan University, No. 16, 3rd section, South Renmin Road, Wuhou District, Chengdu 610041, Sichuan, P.R. China
| | - Yujie Zhang
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, and Healthy Food Evaluation Research Center, Sichuan University, No. 16, 3rd section, South Renmin Road, Wuhou District, Chengdu 610041, Sichuan, P.R. China
| | - Guo Cheng
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, and Healthy Food Evaluation Research Center, Sichuan University, No. 16, 3rd section, South Renmin Road, Wuhou District, Chengdu 610041, Sichuan, P.R. China
| | - Wei Qian
- By-health Co. Ltd., No. 3 Kehui 3rd Street, No.99 Kexue Avenue Central, Huangpu District, 510663 Guangzhou, P.R. China
| | - ChaoMin Wan
- Department of Pediatrics of Western China Second Hospital of Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children, 610041, Chengdu, Sichuan, P.R. China
| | - Ming Li
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, and Healthy Food Evaluation Research Center, Sichuan University, No. 16, 3rd section, South Renmin Road, Wuhou District, Chengdu 610041, Sichuan, P.R. China
| | - Francesco Marotta
- ReGenera Research Group for and Gender Healthy Aging Unit, Montenapoleone Medical Center, Aging Intervention Corso Matteotti, 1/A, 20121 Milan, Italy
| | - Xi Shen
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, and Healthy Food Evaluation Research Center, Sichuan University, No. 16, 3rd section, South Renmin Road, Wuhou District, Chengdu 610041, Sichuan, P.R. China
| | - Fang He
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, and Healthy Food Evaluation Research Center, Sichuan University, No. 16, 3rd section, South Renmin Road, Wuhou District, Chengdu 610041, Sichuan, P.R. China
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25
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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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26
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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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27
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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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28
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Kirzhner V, Toledano-Kitai D, Volkovich Z. Evaluating the number of different genomes in a metagenome by means of the compositional spectra approach. PLoS One 2020; 15:e0237205. [PMID: 33156862 PMCID: PMC7647110 DOI: 10.1371/journal.pone.0237205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/22/2020] [Indexed: 01/02/2023] Open
Abstract
Determination of metagenome composition is still one of the most interesting problems of bioinformatics. It involves a wide range of mathematical methods, from probabilistic models of combinatorics to cluster analysis and pattern recognition techniques. The successful advance of rapid sequencing methods and fast and precise metagenome analysis will increase the diagnostic value of healthy or pathological human metagenomes. The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study. The approach is based on analysis of the compositional spectra of subsequently sequenced samples of the medium. Its essential feature is using random fluctuations in the bacteria number in different samples of the same metagenome. The possibility of effective implementation of the algorithm in the presence of data errors is also discussed. In the work, the algorithm of a metagenome evaluation is described, including the estimation of the genome number and the identification of the genomes with known compositional spectra. It should be emphasized that evaluating the genome number in a metagenome can be always helpful, regardless of the metagenome separation techniques, such as clustering the sequencing results or marker analysis.
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Affiliation(s)
- Valery Kirzhner
- Institute of Evolution, University of Haifa, Haifa, Israel
- * E-mail:
| | - Dvora Toledano-Kitai
- Software Engineering Department, ORT Braude College of Engineering, Karmiel, Israel
| | - Zeev Volkovich
- Software Engineering Department, ORT Braude College of Engineering, Karmiel, Israel
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29
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Velmurugan G, Dinakaran V, Rajendhran J, Swaminathan K. Blood Microbiota and Circulating Microbial Metabolites in Diabetes and Cardiovascular Disease. Trends Endocrinol Metab 2020; 31:835-847. [PMID: 33086076 DOI: 10.1016/j.tem.2020.01.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/16/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
Diabetes and cardiovascular disease (CVD) have evolved as the leading cause of mortality and morbidity worldwide. In addition to traditional risk factors, recent studies have established that the human microbiota, particularly gut bacteria, plays a role in the development of diabetes and CVD. Although the presence of microbes in blood has been known for centuries, mounting evidence in this metagenomic era provides new insights into the role of the blood microbiota in the pathogenesis of non-infectious diseases such as diabetes and CVD. We highlight the origin and physiology of the blood microbiota and circulating microbial metabolites in relation to the etiology and progression of diabetes and CVD. We also discuss translational perspectives targeting the blood microbiota in the diagnosis and treatment of diabetes and CVD.
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Affiliation(s)
- Ganesan Velmurugan
- Chemomicrobiomics Laboratory, KMCH Research Foundation, Kovai Medical Center and Hospital, Coimbatore 641 014, Tamil Nadu, India.
| | - Vasudevan Dinakaran
- Chemomicrobiomics Laboratory, KMCH Research Foundation, Kovai Medical Center and Hospital, Coimbatore 641 014, Tamil Nadu, India
| | - Jeyaprakash Rajendhran
- Pathogenomics Laboratory, Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, Tamil Nadu, India
| | - Krishnan Swaminathan
- Chemomicrobiomics Laboratory, KMCH Research Foundation, Kovai Medical Center and Hospital, Coimbatore 641 014, Tamil Nadu, India
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30
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Yang J, McDowell A, Seo H, Kim S, Min TK, Jee YK, Choi Y, Park HS, Pyun BY, Kim YK. Diagnostic Models for Atopic Dermatitis Based on Serum Microbial Extracellular Vesicle Metagenomic Analysis: A Pilot Study. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2020; 12:792-805. [PMID: 32638560 PMCID: PMC7346989 DOI: 10.4168/aair.2020.12.5.792] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 12/19/2022]
Abstract
PURPOSE Associations between a wide variety of diseases and the microbiome have been extensively verified. Recently, there has been a rising interest in the role the microbiome plays in atopic dermatitis (AD). Furthermore, metagenomic analysis of microbe-derived extracellular vesicles (EVs) has revealed the importance and relevance of microbial EVs in human health. METHODS We compared the diversity and proportion of microbial EVs in the sera of 24 AD patients and 49 healthy controls, and developed a diagnostic model. After separating microbial EVs from serum, we specifically targeted the V3-V4 hypervariable regions of the 16S rDNA gene for amplification and subsequent sequencing. RESULTS Alpha and beta diversity between controls and AD patients both differed, but only the difference in beta diversity was significant. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla in healthy controls and AD patients, accounting for over 85% of the total serum bacterial EVs. Also, Proteobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, and Cyanobacteria relative abundances were significantly different between the AD and control groups. At the genus level, the proportions of Escherichia-Shigella, Acinetobacter, Pseudomonas, and Enterococcus were drastically altered between the AD and control groups. AD diagnostic models developed using biomarkers selected on the basis of linear discriminant analysis effect size from the class to genus levels all yielded area under the receiver operating characteristic curve, sensitivity, specificity, and accuracy of value 1.00. CONCLUSIONS In summary, microbial EVs demonstrated the potential in their use as novel biomarkers for AD diagnosis. Therefore, future work should investigate larger case and control groups with cross-sectional or longitudinal clinical data to explore the utility and validity of serum microbiota EV-based AD diagnosis.
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Affiliation(s)
- Jinho Yang
- Institute of MD Healthcare Inc., Seoul, Korea
- Department of Health and Safety Convergence Science, Graduate School of Korea University, Seoul, Korea
| | | | - Hochan Seo
- Institute of MD Healthcare Inc., Seoul, Korea
| | - Sungwon Kim
- Institute of MD Healthcare Inc., Seoul, Korea
| | - Taek Ki Min
- Department of Pediatrics, Soonchunhyang University College of Medicine, Seoul, Korea
| | - Young Koo Jee
- Department of Internal Medicine, Dankook University College of Medicine, Cheonan, Korea
| | - Youngwoo Choi
- Department of Allergy and Clinical Immunology, Ajou University Medical Center, Suwon, Korea
| | - Hae Sim Park
- Department of Allergy and Clinical Immunology, Ajou University Medical Center, Suwon, Korea
| | - Bok Yang Pyun
- Department of Pediatrics, Soonchunhyang University College of Medicine, Seoul, Korea.
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31
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Microbiome and Schizophrenia: Current Evidence and Future Challenges. Curr Behav Neurosci Rep 2020. [DOI: 10.1007/s40473-020-00206-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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32
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Chakaroun RM, Massier L, Kovacs P. Gut Microbiome, Intestinal Permeability, and Tissue Bacteria in Metabolic Disease: Perpetrators or Bystanders? Nutrients 2020; 12:E1082. [PMID: 32295104 PMCID: PMC7230435 DOI: 10.3390/nu12041082] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023] Open
Abstract
The emerging evidence on the interconnectedness between the gut microbiome and host metabolism has led to a paradigm shift in the study of metabolic diseases such as obesity and type 2 diabetes with implications on both underlying pathophysiology and potential treatment. Mounting preclinical and clinical evidence of gut microbiota shifts, increased intestinal permeability in metabolic disease, and the critical positioning of the intestinal barrier at the interface between environment and internal milieu have led to the rekindling of the "leaky gut" concept. Although increased circulation of surrogate markers and directly measurable intestinal permeability have been linked to increased systemic inflammation in metabolic disease, mechanistic models behind this phenomenon are underdeveloped. Given repeated observations of microorganisms in several tissues with congruent phylogenetic findings, we review current evidence on these unanticipated niches, focusing specifically on the interaction between gut permeability and intestinal as well as extra-intestinal bacteria and their joint contributions to systemic inflammation and metabolism. We further address limitations of current studies and suggest strategies drawing on standard techniques for permeability measurement, recent advancements in microbial culture independent techniques and computational methodologies to robustly develop these concepts, which may be of considerable value for the development of prevention and treatment strategies.
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Affiliation(s)
- Rima M. Chakaroun
- Medical Department III—Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103 Leipzig, Germany; (L.M.); (P.K.)
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Ali Alharbi S. Isolation of ultrasmall (filterable) bacteria from patients suffering from ME, and patients and staff of a paediatric hospital. Saudi J Biol Sci 2020; 27:1566-1568. [PMID: 32489295 PMCID: PMC7253900 DOI: 10.1016/j.sjbs.2020.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 11/26/2022] Open
Abstract
A total of 108 blood samples obtained from 28 male and 80 female patients diagnosed with ME were diluted in sterile, Ringer’s Solution and forced (by suction) through 0.2 µm filters. Of the 28 male samples, 4 yielded filterable bacteria and of the 80 female samples, 18 gave filterable bacteria; as a result, of the total of 124 samples, 22 yielded FB. Filterable (0.4 and 0.2, but not 0.1micron filterable) bacteria were also isolated from the nose throat and skin of paediatric patients and from the throat and skin of staff at an emergency paediatric hospital. The highest percentage of bacterial passage occurred through the largest (0.4 µm) pores. The results show that ultrasmall bacteria occur in ME patients and in paediatric patients and nurses. The potential pathogenic role of such filterable bacteria is briefly discussed.
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Affiliation(s)
- Sulaiman Ali Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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34
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Simões-Silva L, Araujo R, Pestana M, Soares-Silva I, Sampaio-Maia B. Peritoneal Microbiome in End-Stage Renal Disease Patients and the Impact of Peritoneal Dialysis Therapy. Microorganisms 2020; 8:E173. [PMID: 31991821 PMCID: PMC7074711 DOI: 10.3390/microorganisms8020173] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/09/2020] [Accepted: 01/18/2020] [Indexed: 12/12/2022] Open
Abstract
Factors influencing the occurrence of peritoneal dialysis (PD)-related infections are still far from fully understood. Recent studies described the existence of specific microbiomes in body sites previously considered microbiome-free, unravelling new microbial pathways in the human body. In the present study, we analyzed the peritoneum of end-stage kidney disease (ESKD) patients to determine if they harbored a specific microbiome and if it is altered in patients on PD therapy. We conducted a cross-sectional study where the peritoneal microbiomes from ESKD patients with intact peritoneal cavities (ESKD non-PD, n = 11) and ESKD patients undergoing PD therapy (ESKD PD, n = 9) were analyzed with a 16S rRNA approach. Peritoneal tissue of ESKD patients contained characteristically low-abundance microbiomes dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Patients undergoing PD therapy presented lower species richness, with dominance by the Pseudomonadaceae and Prevotelaceae families. This study provides the first characterization of the peritoneal microbiome in ESKD patients, bringing new insight to the human microbiome. Additionally, PD therapy may induce changes in this unique microbiome. The clinical relevance of these observations should be further explored to uncover the role of the peritoneal microbiome as a key element in the onset or aggravation of infection in ESKD patients, especially those undergoing PD.
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Affiliation(s)
- Liliana Simões-Silva
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-180 Porto, Portugal; (L.S.-S.); (R.A.); (M.P.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200-180 Porto, Portugal
- Escola Superior de Saúde Dr. Lopes Dias, Instituto Politécnico de Castelo Branco, 6000-767 Castelo Branco, Portugal
| | - Ricardo Araujo
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-180 Porto, Portugal; (L.S.-S.); (R.A.); (M.P.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200-180 Porto, Portugal
- Medical Biotechnology, Flinders University of South Australia, Bedford Park SA 5042, Australia
| | - Manuel Pestana
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-180 Porto, Portugal; (L.S.-S.); (R.A.); (M.P.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200-180 Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Department of Nephrology, Centro Hospitalar Universitário de São João, EPE, 4200-319 Porto, Portugal
| | - Isabel Soares-Silva
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-180 Porto, Portugal; (L.S.-S.); (R.A.); (M.P.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200-180 Porto, Portugal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Benedita Sampaio-Maia
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-180 Porto, Portugal; (L.S.-S.); (R.A.); (M.P.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200-180 Porto, Portugal
- Faculdade de Medicina Dentária, Universidade do Porto, 4200-393 Porto, Portugal
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Abstract
Microbiome dysbiosis is strongly associated with alcoholic liver disease (ALD). Recent studies on comprehensive analyses of microbiome compositional and functional changes have begun to uncover the mechanistic relation between microbiome and the pathogenesis of ALD. Importantly, targeting the microbiome has become a potential strategy for the prevention and treatment of ALD. In this review, we summarize the clinical evidence of microbiome dysbiosis in ALD patients, and experimental advances in microbiome and metabolomic functional changes in animals with different species and genetic backgrounds in ALD. We also summarize the studies in humanized intestinal microbiome and fecal microbiota transplantation in mice. We introduce new developments in the studies on the role of the circulating bacterial microbiome, oral bacterial microbiome and fungal microbiome in the development of ALD. We highlight the potential mechanisms by which microbiome dysbiosis contributes to ALD, including short chain fatty acid changes, bile acid metabolism, intestinal barrier function, release of bacterial and fungal products, and inflammation. In addition, we summarize the recent developments targeting the microbiome in prevention and treatment of ALD, including dietary nutrient interference, herbal medicine, antibiotics, anti-fungal agents, probiotics, engineered bacterial therapy, fecal transplantation and oral hygiene. Although recent preclinical studies have advanced our understanding of the microbiome and ALD, clinical studies, especially prospective studies with large samples, are needed to better understand the cause-effect of microbiome dysbiosis in ALD. Identifying new precision-based strategies targeting the microbiome are expected to be developed as more effective therapies in ALD.
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36
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Dysbiotic microbiota in autistic children and their mothers: persistence of fungal and bacterial wall-deficient L-form variants in blood. Sci Rep 2019; 9:13401. [PMID: 31527606 PMCID: PMC6746791 DOI: 10.1038/s41598-019-49768-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/31/2019] [Indexed: 01/01/2023] Open
Abstract
Based on our hypothesis for existing microbiota of wall-deficient variants (L-forms) in human blood, we created an innovative methodology, which allowed for the development of L-form populations from blood of all investigated people. In contrast to healthy controls, blood L-forms from autistic children and their mothers converted under appropriate conditions of cultivation into detectable opportunistic bacteria and fungi, а process demonstrated by light and transmission electron microscopy. It can be distinguished into two types of states – “eubiotic” blood microbiota in healthy individuals, and “dysbiotic” in autistic children and their mothers. Remarkably, the unifying finding for autistic children and their mothers was the presence in blood of wall-free variants from life-cycle of filamentous fungi. Increased specific IgG, IgM and IgA, together with typical mold growth were a decisive argument for proven presence of Aspergillus fumigatus in almost all of the autistic children. As it was demonstrated in our previous study, filterable L-forms can be transmitted by vertical pathway from mother to child before birth. Thus, it can be suggested that autistic children may be born already colonized with fungi, while a “silent aspergillosis” could contribute or even be a leading cause for neurodevelopmental disorders in the early childhood.
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37
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Hosainzadegan H, Khalilov R, Gholizadeh P. The necessity to revise Koch's postulates and its application to infectious and non-infectious diseases: a mini-review. Eur J Clin Microbiol Infect Dis 2019; 39:215-218. [PMID: 31440916 DOI: 10.1007/s10096-019-03681-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/12/2019] [Indexed: 01/15/2023]
Abstract
Advances in the science have promoted all aspects of human's life; these, in turn, have changed many principles and scientific postulates. Koch's postulates, since the beginning of their implementation, have been one of the important subjects involving complications and misinterpretations regarding the causal relationship of microbe-hosts. These postulates have been shown not to be correct in some cases including the inability of some microbes to grow in the culture medium, viruses, or anaerobic bacteria. Today, due to some new scientific facts like the social behaviors of bacteria, such as quorum sensing, there are serious problems regarding the definition of whole microbial effects; these include microbiomes and viromes, as well as their interaction with the existing eukaryotics, the complicated relations between bacteria, L-forms, and cell wall-deficient bacteria, and the important role of microbes in the development of non-infectious diseases. So, the application of Koch's postulates to explain the causal relationships between host-microbes could be difficult. Therefore, nowadays, even the molecular Koch's postulates are not accountable. Also, according to the new scientific discoveries, various criteria such as changes in the immune system, pathology, and clinical findings, along with the results of daily laboratory tests, should be used to apply Koch's postulates in the etiologic studies. Otherwise, the possible etiologic relationships between the host-microbes cannot be verified due to numerous complications; certainly, the relationship between the doctor and the lab is ultimately weakened. Therefore, public health, prevention, and much of the antimicrobial treatments will also remain in a state of ambiguity.
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Affiliation(s)
- Hasan Hosainzadegan
- Department of Microbiology, Faculty of Medicine, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Rovshan Khalilov
- Institute of Radiation Problems, Azerbaijan National Academy of Sciences, Baku, Azerbaijan
| | - Pourya Gholizadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.
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38
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Chiu KP, Yu AL. Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions. PeerJ 2019; 7:e7426. [PMID: 31404440 PMCID: PMC6688590 DOI: 10.7717/peerj.7426] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/07/2019] [Indexed: 12/29/2022] Open
Abstract
It is an important issue whether microorganisms can live harmoniously with normal cells in the cardiovascular system. The answer to the question will have enormous impact on medical microbiology. To address the issue, it is essential to identify and characterize the bloodborne microbes in an efficient and comprehensive manner. Due to microbial sequence complexity and the composition of significant number of unknown microbial species in the circulatory system, traditional approaches using cell culture, PCR, or microarray are not suitable for the purpose. Recent reports indicate that cell-free DNA (cfDNA) sequencing using next-generation sequencing (NGS) or single-molecule sequencing (SMS), together with bioinformatics approaches, possesses a strong potential enabling us to distinguish microbial species at the nucleotide level. Multiple studies using microbial cfDNA sequencing to identify microbes for septic patients have shown strong agreement with cell culture. Similar approaches have also been applied to reveal previously unidentified microorganisms or to demonstrate the feasibility of comprehensive assessment of bloodborne microorganisms for healthy and/or diseased individuals. SMS using either SMRT (single-molecule real-time) sequencing or Nanopore sequencing are providing new momentum to reinforce this line of investigation. Taken together, microbial cfDNA sequencing provides a novel opportunity allowing us to further understand the involvement of bloodborne microbes in development of diseases. Similar approaches should also be applicable to the study of metagenomics for sufficient and comprehensive analysis of microbial species living in various environments. This article reviews this line of research and discuss the methodological approaches that have been developed, or are likely to be developed in the future, which may have strong potential to facilitate cfDNA- and cfRNA-based studies of cancer and acute/chronic diseases, in the hope that a better understanding of the hidden microbes in the circulatory system will improve diagnosis, prevention and treatment of problematic diseases.
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Affiliation(s)
- Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Departent of Life Sciences, National Taiwan University, Taipei, Taiwan
| | - Alice L Yu
- Department of Pediatrics, University of California, San Diego, San Diego, United States of America.,Institute of Stem Cell and Translational Cancer Research, Chang Gung University, Taipei, Taiwan
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39
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Castillo DJ, Rifkin RF, Cowan DA, Potgieter M. The Healthy Human Blood Microbiome: Fact or Fiction? Front Cell Infect Microbiol 2019; 9:148. [PMID: 31139578 PMCID: PMC6519389 DOI: 10.3389/fcimb.2019.00148] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
The blood that flows perpetually through our veins and arteries performs numerous functions essential to our survival. Besides distributing oxygen, this vast circulatory system facilitates nutrient transport, deters infection and dispenses heat throughout our bodies. Since human blood has traditionally been considered to be an entirely sterile environment, comprising only blood-cells, platelets and plasma, the detection of microbes in blood was consistently interpreted as an indication of infection. However, although a contentious concept, evidence for the existence of a healthy human blood-microbiome is steadily accumulating. While the origins, identities and functions of these unanticipated micro-organisms remain to be elucidated, information on blood-borne microbial phylogeny is gradually increasing. Given recent advances in microbial-hematology, we review current literature concerning the composition and origin of the human blood-microbiome, focusing on bacteria and their role in the configuration of both the diseased and healthy human blood-microbiomes. Specifically, we explore the ways in which dysbiosis in the supposedly innocuous blood-borne bacterial microbiome may stimulate pathogenesis. In addition to exploring the relationship between blood-borne bacteria and the development of complex disorders, we also address the matter of contamination, citing the influence of contaminants on the interpretation of blood-derived microbial datasets and urging the routine analysis of laboratory controls to ascertain the taxonomic and metabolic characteristics of environmentally-derived contaminant-taxa.
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Affiliation(s)
- Diego J Castillo
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Riaan F Rifkin
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa.,Human Origins and Palaeo Environmental Research Group, Department of Anthropology and Geography, Oxford Brookes University, Oxford, United Kingdom
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Marnie Potgieter
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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40
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Shah NB, Allegretti AS, Nigwekar SU, Kalim S, Zhao S, Lelouvier B, Servant F, Serena G, Thadhani RI, Raj DS, Fasano A. Blood Microbiome Profile in CKD : A Pilot Study. Clin J Am Soc Nephrol 2019; 14:692-701. [PMID: 30962186 PMCID: PMC6500932 DOI: 10.2215/cjn.12161018] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/01/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND OBJECTIVES The association between gut dysbiosis, high intestinal permeability, and endotoxemia-mediated inflammation is well established in CKD. However, changes in the circulating microbiome in patients with CKD have not been studied. In this pilot study, we compare the blood microbiome profile between patients with CKD and healthy controls using 16S ribosomal DNA sequencing. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Blood bacterial DNA was studied in buffy coat samples quantitatively by 16S PCR and qualitatively by 16S targeted metagenomic sequencing using a molecular pipeline specifically optimized for blood samples in a cross-sectional study comparing 20 nondiabetic patients with CKD and 20 healthy controls. RESULTS There were 22 operational taxonomic units significantly different between the two groups. 16S metagenomic sequencing revealed a significant reduction in α diversity (Chao1 index) in the CKD group compared with healthy controls (127±18 versus 145±31; P=0.04). Proteobacteria phylum, Gammaproteobacteria class, and Enterobacteriaceae and Pseudomonadaceae families were more abundant in the CKD group compared with healthy controls. Median 16S ribosomal DNA levels did not significantly differ between CKD and healthy groups (117 versus 122 copies/ng DNA; P=0.38). GFR correlated inversely with the proportion of Proteobacteria (r=-0.54; P≤0.01). CONCLUSIONS Our pilot study demonstrates qualitative differences in the circulating microbiome profile with lower α diversity and significant taxonomic variations in the blood microbiome in patients with CKD compared with healthy controls.
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Affiliation(s)
- Neal B Shah
- 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
| | - 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
| | - Sophia Zhao
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Benjamin Lelouvier
- Vaiomer, Department of Research and Development, Bioinformatics Division, Labège, France
| | - Florence Servant
- Vaiomer, Department of Research and Development, Bioinformatics Division, Labège, France
| | - Gloria Serena
- Division of Pediatric Gastroenterology and Nutrition, Center for Celiac Research, Massachusetts General Hospital for Children, Boston, Massachusetts
| | - Ravi Ishwar Thadhani
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California; and
| | - Dominic S Raj
- Division of Renal Diseases and Hypertension, The George Washington University, Washington, DC
| | - Alessio Fasano
- Division of Pediatric Gastroenterology and Nutrition, Center for Celiac Research, Massachusetts General Hospital for Children, Boston, Massachusetts
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41
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Whittle E, Leonard MO, Harrison R, Gant TW, Tonge DP. Multi-Method Characterization of the Human Circulating Microbiome. Front Microbiol 2019; 9:3266. [PMID: 30705670 PMCID: PMC6345098 DOI: 10.3389/fmicb.2018.03266] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/17/2018] [Indexed: 01/14/2023] Open
Abstract
The term microbiome describes the genetic material encoding the various microbial populations that inhabit our body. Whilst colonization of various body niches (e.g., the gut) by dynamic communities of microorganisms is now universally accepted, the existence of microbial populations in other "classically sterile" locations, including the blood, is a relatively new concept. The presence of bacteria-specific DNA in the blood has been reported in the literature for some time, yet the true origin of this is still the subject of much deliberation. The aim of this study was to investigate the phenomenon of a "blood microbiome" by providing a comprehensive description of bacterially derived nucleic acids using a range of complementary molecular and classical microbiological techniques. For this purpose we utilized a set of plasma samples from healthy subjects (n = 5) and asthmatic subjects (n = 5). DNA-level analyses involved the amplification and sequencing of the 16S rRNA gene. RNA-level analyses were based upon the de novo assembly of unmapped mRNA reads and subsequent taxonomic identification. Molecular studies were complemented by viability data from classical aerobic and anaerobic microbial culture experiments. At the phylum level, the blood microbiome was predominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key phyla detected were consistent irrespective of molecular method (DNA vs. RNA), and consistent with the results of other published studies. In silico comparison of our data with that of the Human Microbiome Project revealed that members of the blood microbiome were most likely to have originated from the oral or skin communities. To our surprise, aerobic and anaerobic cultures were positive in eight of out the ten donor samples investigated, and we reflect upon their source. Our data provide further evidence of a core blood microbiome, and provide insight into the potential source of the bacterial DNA/RNA detected in the blood. Further, data reveal the importance of robust experimental procedures, and identify areas for future consideration.
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Affiliation(s)
- Emma Whittle
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, United Kingdom
| | - Martin O. Leonard
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, United Kingdom
| | - Rebecca Harrison
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, United Kingdom
| | - Timothy W. Gant
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, United Kingdom
| | - Daniel Paul Tonge
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, United Kingdom
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42
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Bonartsev AP, Voinova VV, Bonartseva GA. Poly(3-hydroxybutyrate) and Human Microbiota (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818060066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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43
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Olde Loohuis LM, Mangul S, Ori APS, Jospin G, Koslicki D, Yang HT, Wu T, Boks MP, Lomen-Hoerth C, Wiedau-Pazos M, Cantor RM, de Vos WM, Kahn RS, Eskin E, Ophoff RA. Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia. Transl Psychiatry 2018; 8:96. [PMID: 29743478 PMCID: PMC5943399 DOI: 10.1038/s41398-018-0107-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 01/31/2018] [Indexed: 12/26/2022] Open
Abstract
The role of the human microbiome in health and disease is increasingly appreciated. We studied the composition of microbial communities present in blood across 192 individuals, including healthy controls and patients with three disorders affecting the brain: schizophrenia, amyotrophic lateral sclerosis, and bipolar disorder. By using high-quality unmapped RNA sequencing reads as candidate microbial reads, we performed profiling of microbial transcripts detected in whole blood. We were able to detect a wide range of bacterial and archaeal phyla in blood. Interestingly, we observed an increased microbial diversity in schizophrenia patients compared to the three other groups. We replicated this finding in an independent schizophrenia case-control cohort. This increased diversity is inversely correlated with estimated cell abundance of a subpopulation of CD8+ memory T cells in healthy controls, supporting a link between microbial products found in blood, immunity and schizophrenia.
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Affiliation(s)
- Loes M Olde Loohuis
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA
| | - Serghei Mangul
- Department of Computer, Science University of California Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
| | - Anil P S Ori
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA
| | | | - David Koslicki
- Mathematics Department, Oregon State University, Corvallis, OR, USA
| | - Harry Taegyun Yang
- Department of Computer, Science University of California Los Angeles, Los Angeles, CA, USA
| | - Timothy Wu
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA
| | - Marco P Boks
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Martina Wiedau-Pazos
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Rita M Cantor
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Bacteriology and Immunology, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
| | - René S Kahn
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eleazar Eskin
- Department of Computer, Science University of California Los Angeles, Los Angeles, CA, USA
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA.
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands.
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA.
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44
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The microbiome in chronic kidney disease patients undergoing hemodialysis and peritoneal dialysis. Pharmacol Res 2018; 130:143-151. [DOI: 10.1016/j.phrs.2018.02.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 12/19/2022]
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Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females. BMC Med Genomics 2018; 11:16. [PMID: 29504912 PMCID: PMC5836824 DOI: 10.1186/s12920-018-0329-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Cell-free circulating DNA (cfDNA) is becoming a useful biopsy for noninvasive diagnosis of diseases. Microbial sequences in plasma cfDNA may provide important information to improve prognosis and treatment. We have developed a stringent method to identify microbial species via microbial cfDNA in the blood plasma of early-onset breast cancer (EOBC) patients and healthy females. Empirically, microbe-originated sequence reads were identified by mapping non-human PE reads in cfDNA libraries to microbial databases. Those mapped concordantly to unique microbial species were assembled into contigs, which were subsequently aligned to the same databases. Microbial species uniquely aligned were identified and compared across all individuals on MCRPM (Microbial CfDNA Reads Per Million quality PE reads) basis. Results The predominant microbial cfDNAs in all plasma samples examined are originated from bacteria and these bacteria were limited to only a few genera. Among those, Acinetobacter johnsonii XBB1 and low levels of Mycobacterium spp. were commonly found in all healthy females, but also present in an EOBC patient. Compared to those in healthy counterparts, bacterial species in EOBC patients are more diverse and more likely to present at high levels. Among these three EOBC patients tested, a patient who has record high titer (2,724 MCRPM) of Pseudomonas mendocina together with 8.82 MCRPM of Pannonibacter phragmitetus has passed away; another patient infected by multiple Sphingomonas species remains alive; while the third patient who has similar microbial species (Acinetobacter johnsonii XBB1) commonly seen in normal controls is having a normal life. Conclusions Our preliminary data on the profiles of microbial cfDNA sequences suggested that it may have some prognostic value in cancer patients. Validation in larger number of patients is warranted.
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Martel J, Wu CY, Huang PR, Cheng WY, Young JD. Pleomorphic bacteria-like structures in human blood represent non-living membrane vesicles and protein particles. Sci Rep 2017; 7:10650. [PMID: 28878382 PMCID: PMC5587737 DOI: 10.1038/s41598-017-10479-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/10/2017] [Indexed: 01/01/2023] Open
Abstract
Although human blood is believed to be a sterile environment, recent studies suggest that pleomorphic bacteria exist in the blood of healthy humans. These studies have led to the development of “live-blood analysis,” a technique used by alternative medicine practitioners to diagnose various human conditions, including allergies, cancer, cardiovascular disease and septicemia. We show here that bacteria-like vesicles and refringent particles form in healthy human blood observed under dark-field microscopy. These structures gradually increase in number during incubation and show morphologies reminiscent of cells undergoing division. Based on lipid analysis and Western blotting, we show that the bacteria-like entities consist of membrane vesicles containing serum and exosome proteins, including albumin, fetuin-A, apolipoprotein-A1, alkaline phosphatase, TNFR1 and CD63. In contrast, the refringent particles represent protein aggregates that contain several blood proteins. 16S rDNA PCR analysis reveals the presence of bacterial DNA in incubated blood samples but also in negative controls, indicating that the amplified sequences represent contaminants. These results suggest that the bacteria-like vesicles and refringent particles observed in human blood represent non-living membrane vesicles and protein aggregates derived from blood. The phenomena observed during live-blood analysis are therefore consistent with time-dependent decay of cells and body fluids during incubation ex vivo.
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Affiliation(s)
- Jan Martel
- Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan, Taiwan.,Laboratory of Nanomaterials, Chang Gung University, Taoyuan, Taiwan.,Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng-Yeu Wu
- Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan, Taiwan.,Laboratory of Nanomaterials, Chang Gung University, Taoyuan, Taiwan.,Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Research Center of Bacterial Pathogenesis, Chang Gung University, Taoyuan, Taiwan
| | - Pei-Rong Huang
- Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan, Taiwan.,Laboratory of Nanomaterials, Chang Gung University, Taoyuan, Taiwan.,Department of Molecular and Cellular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Yun Cheng
- Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan, Taiwan.,Laboratory of Nanomaterials, Chang Gung University, Taoyuan, Taiwan.,Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - John D Young
- Center for Molecular and Clinical Immunology, Chang Gung University, Taoyuan, Taiwan. .,Laboratory of Nanomaterials, Chang Gung University, Taoyuan, Taiwan. .,Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan. .,Laboratory of Cellular Physiology and Immunology, Rockefeller University, New York, NY, USA. .,Biochemical Engineering Research Center, Ming Chi University of Technology, Taipei, Taiwan.
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Waugh L, Ramachandran A, Talent S, Cole G, D'Agostino J. Survey of Aerobic and Anaerobic Blood Cultures in Free-Ranging Western Ratsnakes (Pantherophis obsoletus). ACTA ACUST UNITED AC 2017. [DOI: 10.5818/1529-9651-27.1-2.44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Lynnette Waugh
- 1. Oklahoma City Zoo, 2101 NE 50th, Oklahoma City, OK 73111, USA
| | - Akhilesh Ramachandran
- 2. Oklahoma Animal Disease Diagnostic Laboratory, W Farm Road, Stillwater, OK 74078, USA
| | - Scott Talent
- 2. Oklahoma Animal Disease Diagnostic Laboratory, W Farm Road, Stillwater, OK 74078, USA
| | - Gretchen Cole
- 1. Oklahoma City Zoo, 2101 NE 50th, Oklahoma City, OK 73111, USA
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Mitchell AJ, Gray WD, Schroeder M, Yi H, Taylor JV, Dillard RS, Ke Z, Wright ER, Stephens D, Roback JD, Searles CD. Pleomorphic Structures in Human Blood Are Red Blood Cell-Derived Microparticles, Not Bacteria. PLoS One 2016; 11:e0163582. [PMID: 27760197 PMCID: PMC5070825 DOI: 10.1371/journal.pone.0163582] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 09/12/2016] [Indexed: 12/01/2022] Open
Abstract
Background Red blood cell (RBC) transfusions are a common, life-saving therapy for many patients, but they have also been associated with poor clinical outcomes. We identified unusual, pleomorphic structures in human RBC transfusion units by negative-stain electron microscopy that appeared identical to those previously reported to be bacteria in healthy human blood samples. The presence of viable, replicating bacteria in stored blood could explain poor outcomes in transfusion recipients and have major implications for transfusion medicine. Here, we investigated the possibility that these structures were bacteria. Results Flow cytometry, miRNA analysis, protein analysis, and additional electron microscopy studies strongly indicated that the pleomorphic structures in the supernatant of stored RBCs were RBC-derived microparticles (RMPs). Bacterial 16S rDNA PCR amplified from these samples were sequenced and was found to be highly similar to species that are known to commonly contaminate laboratory reagents. Conclusions These studies suggest that pleomorphic structures identified in human blood are RMPs and not bacteria, and they provide an example in which laboratory contaminants may can mislead investigators.
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Affiliation(s)
- Adam J. Mitchell
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Warren D. Gray
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Max Schroeder
- Division of Infectious Disease, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Hong Yi
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, Georgia, United States of America
| | - Jeannette V. Taylor
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, Georgia, United States of America
| | - Rebecca S. Dillard
- Division of Infectious Disease, Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Zunlong Ke
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Elizabeth R. Wright
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, Georgia, United States of America
- Division of Infectious Disease, Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - David Stephens
- Division of Infectious Disease, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - John D. Roback
- Center for Transfusion and Cellular Therapy, Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Charles D. Searles
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
- Section of Cardiology, Atlanta VA Medical Center, Decatur, Georgia, United States of America
- * E-mail:
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Kell DB, Pretorius E. On the translocation of bacteria and their lipopolysaccharides between blood and peripheral locations in chronic, inflammatory diseases: the central roles of LPS and LPS-induced cell death. Integr Biol (Camb) 2016; 7:1339-77. [PMID: 26345428 DOI: 10.1039/c5ib00158g] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have recently highlighted (and added to) the considerable evidence that blood can contain dormant bacteria. By definition, such bacteria may be resuscitated (and thus proliferate). This may occur under conditions that lead to or exacerbate chronic, inflammatory diseases that are normally considered to lack a microbial component. Bacterial cell wall components, such as the endotoxin lipopolysaccharide (LPS) of Gram-negative strains, are well known as potent inflammatory agents, but should normally be cleared. Thus, their continuing production and replenishment from dormant bacterial reservoirs provides an easy explanation for the continuing, low-grade inflammation (and inflammatory cytokine production) that is characteristic of many such diseases. Although experimental conditions and determinants have varied considerably between investigators, we summarise the evidence that in a great many circumstances LPS can play a central role in all of these processes, including in particular cell death processes that permit translocation between the gut, blood and other tissues. Such localised cell death processes might also contribute strongly to the specific diseases of interest. The bacterial requirement for free iron explains the strong co-existence in these diseases of iron dysregulation, LPS production, and inflammation. Overall this analysis provides an integrative picture, with significant predictive power, that is able to link these processes via the centrality of a dormant blood microbiome that can resuscitate and shed cell wall components.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and The Manchester Institute of Biotechnology, The University of Manchester, 131, Princess St, Manchester M1 7DN, Lancs, UK.
| | - Etheresia Pretorius
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia 0007, South Africa.
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Campylobacter jejuni Fatal Sepsis in a Patient with Non-Hodgkin's Lymphoma: Case Report and Literature Review of a Difficult Diagnosis. Int J Mol Sci 2016; 17:544. [PMID: 27077849 PMCID: PMC4849000 DOI: 10.3390/ijms17040544] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/02/2016] [Accepted: 04/07/2016] [Indexed: 02/06/2023] Open
Abstract
Campylobacter jejuni (C. jejuni) bacteremia is difficult to diagnose in individuals with hematological disorders undergoing chemotherapy. The cause can be attributed to the rarity of this infection, to the variable clinical presentation, and to the partial overlapping symptoms underlying the disease. Here, we report a case of a fatal sepsis caused by C. jejuni in a 76-year-old Caucasian man with non-Hodgkin’s lymphoma. After chemotherapeutic treatment, the patient experienced fever associated with severe neutropenia and thrombocytopenia without hemodynamic instability, abdominal pain, and diarrhea. The slow growth of C. jejuni in the blood culture systems and the difficulty in identifying it with conventional biochemical phenotyping methods contributed to the delay of administering a targeted antimicrobial treatment, leading to a fatal outcome. Early recognition and timely intervention are critical for the successful management of C. jejuni infection. Symptoms may be difficult to recognize in immunocompromised patients undergoing chemotherapy. Thus, it is important to increase physician awareness regarding the clinical manifestations of C. jejuni to improve therapeutic efficacy. Moreover, the use of more aggressive empirical antimicrobial treatments with aminoglycosides and/or carbapenems should be considered in immunosuppressed patients, in comparison to those currently indicated in the guidelines for cancer-related infections supporting the use of cephalosporins as monotherapy.
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