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Blufstein A, Pejcic N, Spettel K, Hausmann B, Seki D, Ertekin T, Hinrichs-Priller J, Altner S, Nehr M, Bekes K, Makristathis A, Andrukhov O. Salivary microbiome and MRP-8/14 levels in children with gingivitis, healthy children, and their mothers. J Periodontol 2024. [PMID: 38696461 DOI: 10.1002/jper.23-0632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/21/2024] [Accepted: 03/29/2024] [Indexed: 05/04/2024]
Abstract
BACKGROUND Gingivitis is the most common form of periodontal disease among children and adolescents and is associated with disrupted host-microbiome homeostasis. Family is an important factor influencing the prevalence of gingivitis. In the present study, we investigated the salivary microbiome, oral hygiene habits, and the salivary level of myeloid-related protein (MRP)-8/14 in children aged 7-12 years with gingivitis, periodontally healthy children, and their mothers. METHODS This study included 24 children with gingivitis (including four sibling pairs) and 22 periodontally healthy children (including two sibling pairs) and their mothers. The whole saliva was collected, DNA was extracted, the variable V3-V4 region of the eubacterial 16S ribosomal RNA gene was amplified, and sample library preparation was performed according to the Illumina protocol. The salivary levels of MRP-8/14 were analyzed by ELISA. RESULTS Alpha diversity of the salivary microbiome was considerably higher in gingivitis children and mothers of gingivitis children compared to healthy children and their mothers, respectively. Significant differences in beta diversity between healthy and gingivitis children, healthy children and their mothers, and gingivitis children and their mothers were detected. Overall, the number of common core amplicon sequence variants between children and their own mothers was significantly higher than between children and other mothers. The salivary MRP-8/14 levels in children with gingivitis were significantly higher compared to healthy children; a similar tendency was also mentioned for mothers. CONCLUSION Our study underlines the importance of family as an essential factor influencing oral health.
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Affiliation(s)
- Alice Blufstein
- Competence Center for Periodontal Research, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria
- Division of Conservative Dentistry and Periodontology, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria
| | - Natasa Pejcic
- Competence Center for Periodontal Research, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria
- Department of Preventive and Pediatric Dentistry, Faculty of Dental Medicine, University of Belgrade, Belgrade, Serbia
| | - Kathrin Spettel
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - David Seki
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Tugba Ertekin
- Competence Center for Periodontal Research, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria
| | - Julia Hinrichs-Priller
- Division of Pediatric Dentistry, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria
| | - Sarra Altner
- Division of Pediatric Dentistry, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria
| | - Marion Nehr
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Katrin Bekes
- Division of Pediatric Dentistry, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria
| | - Athanasios Makristathis
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Oleh Andrukhov
- Competence Center for Periodontal Research, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria
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Kang J, Wang Q, Wang S, Pan Y, Niu S, Li X, Liu L, Liu X. Characteristics of Gut Microbiota in Patients with Erectile Dysfunction: A Chinese Pilot Study. World J Mens Health 2024; 42:363-372. [PMID: 37382280 PMCID: PMC10949016 DOI: 10.5534/wjmh.220278] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/14/2023] [Accepted: 03/30/2023] [Indexed: 06/30/2023] Open
Abstract
PURPOSE Little is known about the role of gut microbiota in the pathogenesis of erectile dysfunction (ED). We performed a study to compare taxonomic profiles of gut microbiota of ED and healthy males. MATERIALS AND METHODS A total of 43 ED patients and 16 healthy controls were enrolled in the study. The 5-item version of the International Index of Erectile Function (IIEF-5) with a cutoff value of 21 was used to evaluate erectile function. All participants underwent nocturnal penile tumescence and rigidity test. Samples of stool were sequenced to determine the gut microbiota. RESULTS We identified a distinct beta diversity of gut microbiome in ED patients by unweighted UniFrac analysis (R²=0.026, p=0.036). Linear discriminant analysis effect size (LEfse) analysis showed Actinomyces was significantly enriched, whereas Coprococcus_1, Lachnospiraceae_FCS020_group, Lactococcus, Ruminiclostridium_5, and Ruminococcaceae_UCG_002 were depleted in ED patients. Actinomyces showed a significant negative correlation with the duration of qualified erection, average maximum rigidity of tip, average maximum rigidity of base, tip tumescence activated unit (TAU), and base TAU. Coprococcus_1, Lachnospiraceae_FCS020_group, Ruminiclostridium_5, and Ruminococcaceae_UCG_002 were significantly correlated with the IIEF-5 score. Ruminiclostridium_5 and Ruminococcaceae_UCG_002 were positively related with average maximum rigidity of tip, average maximum rigidity of base, ΔTumescence of tip, and Tip TAU. Further, a random forest classifier based on the relative abundance of taxa showed good diagnostic efficacy with an area under curve of 0.72. CONCLUSIONS This pilot study identified evident alterations in the gut microbiome composition of ED patients and found Actinomyces was negatively correlated with erectile function, which may be a key pathogenic bacteria.
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Affiliation(s)
- Jiaqi Kang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Qihua Wang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Shangren Wang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yang Pan
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Shuai Niu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xia Li
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Li Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China.
| | - Xiaoqiang Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China.
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Wenlin C, Fang L, Yuncheng Z, Jinzhen LV, Daguo Y. Effects of Zhenggan Huayu decoction combined with entecavir on gut microbiota in patients with chronic hepatitis B fibrosis. J TRADIT CHIN MED 2023; 43:559-567. [PMID: 37147758 PMCID: PMC10133949 DOI: 10.19852/j.cnki.jtcm.20230208.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
OBJECTIVE To evaluate the effects of Zhenggan Huayu decoction (, ZGHY) combined with entecavir (ETV) on the gut microbiota in patients with chronic hepatitis B (CHB) fibrosis. METHODS A total of 59 CHB-related fibrosis patients were enrolled and treated with ZGHY combined with ETV (ZGHY + ETV) and ETV alone. Fecal samples were collected from patients at weeks 0, 12, and 24 after treatment and gut microbiota were analyzed by 16S rRNA gene sequencing. RESULTS Compared to the ETV group, microbiota diversity in the ZGHY + ETV group was increased after 24 weeks. Some potentially pathogenic bacteria, including spp., spp., and spp. were reduced in the ZGHY + ETV group, while spp., spp., and several other beneficial bacteria were increased. CONCLUSION Decreases in pathogenic bacteria and increases in probiotics were not always observed in the Traditional Chinese Medicine (TCM) group (e.g., was abundant). As an adjuvant TCM formulation for ETV, ZGHY had a positive role in the treatment of CHB patients.
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Affiliation(s)
- Chen Wenlin
- Department of Liver Diseases, Shenzhen Hospital, Beijing University of Chinese Medicine, Shenzhen 518172, China
| | - Liang Fang
- Department of Liver Diseases, Shenzhen Hospital, Beijing University of Chinese Medicine, Shenzhen 518172, China
| | - Zhang Yuncheng
- Department of Liver Diseases, Shenzhen Hospital, Beijing University of Chinese Medicine, Shenzhen 518172, China
| | - L V Jinzhen
- Department of Liver Diseases, Shenzhen Hospital, Beijing University of Chinese Medicine, Shenzhen 518172, China
| | - Yang Daguo
- Department of Liver Diseases, Shenzhen Third People's Hospital, Guangdong 518112, China
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Yanan W, Li Y, Li W, Zhiyuan XU, Hua R, Xiangdong C, Changwu D. Microbial community structure of different tongue fur types in patients with chronic gastritis. J TRADIT CHIN MED 2023; 43:365-373. [PMID: 36994526 PMCID: PMC10012201 DOI: 10.19852/j.cnki.jtcm.20221206.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
OBJECTIVE To explore the correlation between tongue and oral microbiota, we studied the microbial community structure of different tongue coating types in patients with chronic gastritis. METHODS 16S rDNA gene sequencing and bioinformatics analysis were used to study the dynamic changes and correlation of microbial flora in patients with chronic gastritis, healthy people, and patients with different tongue fur. In addition, it was also discussed between the severity of gastritis and the microflora of tongue fur. RESULTS The microbial diversity of tongue fur in patients with chronic gastritis was significantly different from healthy controls. There were significant changes in bacterial communities' diversity and relative abundance between extra tongue fur in patients but not in healthy people. Oral bacteria with relative abundance > 1% and < 0.05 among different tongue fur flora were dominant bacteria, including 12 phyla such as and , and 256 genera such as and . CONCLUSIONS The changes in oral flora in patients with chronic gastritis were related to tongue fur. Therefore, the significant microbiota might enlighten further study on the correlation between tongue inspection and oral microbiota in patients with chronic gastritis.
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Affiliation(s)
- Wang Yanan
- College of Traditional Chinese Medicine, Anhui University of Traditional Chinese Medicine, Hefei, Anhui 230000, China
| | - Yuan Li
- Department of Surgery, Cancer Hospital Affiliated to the University of Chinese Academy of Sciences, Hangzhou 310022, China
| | - Wang Li
- College of Traditional Chinese Medicine, Anhui University of Traditional Chinese Medicine, Hefei, Anhui 230000, China
| | - X U Zhiyuan
- Department of Surgery, Cancer Hospital Affiliated to the University of Chinese Academy of Sciences, Hangzhou 310022, China
| | - Ruan Hua
- Department of Surgery, Yuhang Hospital of Traditional Chinese Medicine, Hangzhou 310022, China
| | - Cheng Xiangdong
- Department of Surgery, Cancer Hospital Affiliated to the University of Chinese Academy of Sciences, Hangzhou 310022, China
| | - Dong Changwu
- College of Traditional Chinese Medicine, Anhui University of Traditional Chinese Medicine, Hefei, Anhui 230000, China
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5
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Bao WH, Tang W. [Changes of gut microflora in newly diagnosed IgA nephropathy patients and its correlation with clinical risk factors]. Beijing Da Xue Xue Bao Yi Xue Ban 2023; 55:124-32. [PMID: 36718700 DOI: 10.19723/j.issn.1671-167X.2023.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OBJECTIVE To investigate the gut microbiota in newly diagnosed IgA nephropathy patients with chronic kidney disease (CKD) stages 1-2 and the association between the gut microbiota and the clinical risk factors of IgA nephropathy. METHODS Fresh fecal samples were collected from nineteen newly diagnosed IgA nephropathy patients with CKD stages 1-2 and fifteen age- and sex-matched healthy controls. Fecal bacterial DNA was extracted and microbiota composition were characterized using 16S ribosomal RNA (16S rRNA) high-throughput sequencing for the V3-V4 region. The Illumina Miseq platform was used to analyze the results of 16S rRNA high-throughput sequencing of fecal flora. At the same time, the clinical risk factors of IgA nephropathy patients were collected to investigate the association between the gut microbiota and the clinical risk factors. RESULTS (1) At the phylum level, the abundance of Bacteroidetes was significantly reduced (P=0.046), and the abundance of Actinobacteria was significantly increased (P=0.001). At the genus level, the abundance of Escherichia-Shigella, Bifidobacte-rium, Dorea and others were significantly increased (P < 0.05). The abundance of Lachnospira, Coprococcus_2 and Sutterella was significantly reduced (P < 0.05). (2) There was no significant difference in the abundance of gut microbiota between the newly diagnosed IgA nephropathy patients and the healthy control group (P>0.05), but there were differences in the structure of the gut microbiota between the two groups. The results of LEfSe analysis showed that there were 16 differential bacteria in the newly diagnosed IgA nephropathy patients and healthy controls. Among them, the abundance of the newly diagnosed IgA nephropathy patients was increased in Enterobacteriales, Actinobacteria, Escherichia-Shigella, etc. The healthy control group was increased in Bacteroidetes and Lachnospira. (3) The result of redundancy analysis (RDA) showed that Bifidobacterium was positively correlated with serum IgA levels, 24-hour urinary protein levels and the presence of hypertension. Lachnoclostridium was positively correlated with the presence of hypertension. Escherichia-Shigella was positively correlated with urine red blood cells account. Bifidobacterium was positively correlated with the proliferation of capillaries. Faecalibacterium was positively correlated with cell/fibrocytic crescents. Ruminococcus_2 was positively correlated with mesangial cell proliferation, glomerular segmental sclerosis and renal tubular atrophy/interstitial fibrosis. CONCLUSION The gut microbiota in the newly diagnosed IgA nephropathy patients with CKD stages 1-2 is different from that of the healthy controls. Most importantly, some gut bacteria are related to the clinical risk factors of IgA nephropathy. Further research is needed to understand the potential role of these bacteria in IgA nephropathy.
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Papadopoulos VE, Patas K, Tountopoulou A, Velonakis G, Boufidou F, Chatzipanagiotou S, Vassilopoulou S. Seronegative neurobrucellosis-do we need new neurobrucellosis criteria? Int J Infect Dis 2021; 111:124-6. [PMID: 34419580 DOI: 10.1016/j.ijid.2021.08.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/02/2021] [Accepted: 08/15/2021] [Indexed: 11/22/2022] Open
Abstract
Neurobrucellosis presents in various clinical forms and should always be considered in neurological patients in highly endemic areas such as the Mediterranean basin. Establishing a diagnosis can be challenging since serological testing can sometimes yield negative results. We present a rare case of a seronegative relapse of neurobrucellosis in a patient who had been successfully treated for systemic brucellosis. Oligoclonal bands, an agglutination test, and 16S rRNA sequencing of cerebrospinal fluid proved essential in unmasking a confined central nervous system relapse. This case reinforces the need for establishing diagnostic criteria for neurobrucellosis, which could potentially include oligoclonal bands and an agglutination test on the cerebrospinal fluid.
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Bendiks ZA, Knudsen KEB, Keenan MJ, Marco ML. Conserved and variable responses of the gut microbiome to resistant starch type 2. Nutr Res 2020; 77:12-28. [PMID: 32251948 DOI: 10.1016/j.nutres.2020.02.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/31/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022]
Abstract
Resistant starch type 2 (RS2), a dietary fiber comprised solely of glucose, has been extensively studied in clinical trials and animal models for its capacity to improve metabolic and systemic health. Because the health modulatory effects of RS2 and other dietary fibers are thought to occur through modification of the gut microbiome, those studies frequently include assessments of RS2-mediated changes to intestinal microbial composition and function. In this review, we identify the conserved responses of the gut microbiome among 13 human and 35 animal RS2 intervention studies. Consistent outcomes of RS2 interventions include reductions in bacterial α-diversity; increased production of lumenal short-chain fatty acids; and enrichment of Ruminococcus bromii, Bifidobacterium adolescentis, and other gut taxa. Different taxa are usually responsive in animal models, and many RS2-mediated changes to the gut microbiome vary within and between studies. The root causes for this variation are examined with regard to methodological and analytical differences, host genetics and age, species differences (eg, human, animal), health status, intervention dose and duration, and baseline microbial composition. The significant variation found for this single dietary compound highlights the challenges in targeting the gut microbiome to improve health with dietary interventions. This knowledge on RS2 also provides opportunities to improve the design of nutrition studies targeting the gut microbiome and to ultimately identify the precise mechanisms via which dietary fiber benefits human health.
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Affiliation(s)
- Zachary A Bendiks
- Department of Food Science & Technology, University of California-Davis, Davis, CA.
| | - Knud E B Knudsen
- Department of Animal Science, Aarhus University, 8830, Tjele, Denmark.
| | - Michael J Keenan
- School of Nutrition and Food Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA.
| | - Maria L Marco
- Department of Food Science & Technology, University of California-Davis, Davis, CA.
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Pragman AA, Knutson KA, Gould TJ, Isaacson RE, Reilly CS, Wendt CH. Chronic obstructive pulmonary disease upper airway microbiota alpha diversity is associated with exacerbation phenotype: a case-control observational study. Respir Res 2019; 20:114. [PMID: 31174538 PMCID: PMC6555967 DOI: 10.1186/s12931-019-1080-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/21/2019] [Indexed: 12/25/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) frequent exacerbators (FE) suffer increased morbidity and mortality compared to infrequent exacerbators (IE). The association between the oral and sputum microbiota and exacerbation phenotype is not well defined. The objective of this study was to determine key features that differentiate the oral and sputum microbiota of FEs from the microbiota of IEs during periods of clinical stability. Methods We recruited 11 FE and 11 IE who had not used antibiotics or systemic corticosteroids in the last 1 month. Subjects provided oral wash and sputum samples, which underwent 16S V4 MiSeq sequencing and qPCR of 16S rRNA. Data were analyzed using Dada2 and R. Results FE and IE were similar in terms of age, FEV1 percent predicted (FEV1pp), pack-years of tobacco exposure, and St. George’s Respiratory Questionnaire score. 16S copy numbers were significantly greater in sputum vs. oral wash (p = 0.01), but phenotype was not associated with copy number. Shannon diversity was significantly greater in oral samples compared to sputum (p = 0.001), and IE samples were more diverse than FE samples (p < 0.001). Sputum samples from FE had more Haemophilus and Moraxella compared to IE sputum samples, due to dominance of these COPD-associated taxa in three FE sputum samples. Amplicon sequencing variant (ASV)-level analysis of sputum samples revealed one ASV (Actinomyces) was significantly more abundant in IE vs. FE sputum (padj = 0.048, Wilcoxon rank-sum test), and this persisted after controlling for FEV1pp. Principal coordinate analysis using Bray-Curtis distance with PERMANOVA analyses demonstrated clustering by anatomic site, phenotype, inhaled corticosteroid use, current tobacco use, COPD severity, and last professional dental cleaning. Conclusions FE have less diverse oral and sputum microbiota than IE. Actinomyces was significantly more abundant in IE sputum than FE sputum. The oral and sputum microbiota of COPD subjects cluster based on multiple clinical factors, including exacerbation phenotype. Even during periods of clinical stability, the frequent exacerbator phenotype is associated with decreased alpha diversity, beta-diversity clustering, and changes in taxonomic abundance. Electronic supplementary material The online version of this article (10.1186/s12931-019-1080-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexa A Pragman
- Department of Medicine, University of Minnesota and Minneapolis Veterans Affairs Medical Center, 1 Veterans Dr, Minneapolis, MN, 55417, USA. .,Minneapolis VA Health Care System, Attn: Dr. Alexa Pragman, Research Service (151), 1 Veterans Drive, Minneapolis, MN, 55417, USA.
| | - Katherine A Knutson
- Division of Biostatistics, University of Minnesota School of Public Health, University Office Plaza, 2221 University Ave. SE - Suite 200, Minneapolis, MN, 55414, USA
| | - Trevor J Gould
- University of Minnesota Informatics Institute, Biological Science Dean's Office, Room 123 SnH, 6174A, 1475 Gortner Ave, St. Paul, MN, 55108, USA
| | - Richard E Isaacson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Room 205G VetS, 6187A, 1971 Commonwealth Ave, St. Paul, MN, 55108, USA
| | - Cavan S Reilly
- Division of Biostatistics, University of Minnesota School of Public Health, University Office Plaza, 2221 University Ave. SE - Suite 200, Minneapolis, MN, 55414, USA
| | - Chris H Wendt
- Department of Medicine, University of Minnesota and Minneapolis Veterans Affairs Medical Center, 1 Veterans Dr, Minneapolis, MN, 55417, USA
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Song GQ, Cao Y, Li H, Ma K, Zhao XY, Zou KN, Zhou HG. Progress in the 16S rRNA Gene Sequencing in Forensic Science. Fa Yi Xue Za Zhi 2018; 34:542-548. [PMID: 30468060 DOI: 10.12116/j.issn.1004-5619.2018.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Indexed: 11/30/2022]
Abstract
Forensic microorganism is one of the hotspots of forensic science research. Due to its conservatism and specificity, the 16S rRNA gene is found to be an ideal marker for forensic identification. With the rapid development of high throughput sequencing technology, the research on microorganisms has been gradually applied to many fields such as environment and health care. In the field of forensic science, the results of forensic microbiology research, represented by 16S rRNA gene sequencing, are also gradually applied to forensic practice, such as biological samples identification, individual identification, postmortem interval estimation, and regional inference, which not only provide clues for the investigation of cases but also complement and assist traditional methods. This paper describes the research methods and related sequencing technologies of 16S rRNA gene sequencing, summarizes its research progress, and discusses the application value and potential of 16S rRNA in forensic science.
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Affiliation(s)
- G Q Song
- Department of Forensic Medicine, School of Basic Medical Science, Fudan University, Shanghai 200032, China.,Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China.,Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
| | - Y Cao
- Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China.,Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
| | - H Li
- Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China.,Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
| | - K Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China.,Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
| | - X Y Zhao
- Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China.,Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
| | - K N Zou
- Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China.,Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
| | - H G Zhou
- Department of Forensic Medicine, School of Basic Medical Science, Fudan University, Shanghai 200032, China.,Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China.,Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
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Kook SY, Kim Y, Kang B, Choe YH, Kim YH, Kim S. Characterization of the fecal microbiota differs between age groups in Koreans. Intest Res 2018; 16:246-254. [PMID: 29743837 PMCID: PMC5934597 DOI: 10.5217/ir.2018.16.2.246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 02/06/2023] Open
Abstract
Background/Aims Tens of trillions of microorganisms constitute the gut microbiota of the human body. The microbiota plays a critical role in maintaining host immunity and metabolism. Analyses of the gut microbial composition in Korea are limited to a few studies consisting of small sample sizes. To investigate the gut microbial community in a large sample of healthy Koreans, we analyzed the 16S ribosomal RNA of 4 representative bacterial genera Lactobacillus, Bifidobacterium, Bacteroides, and Clostridium. Methods A total of 378 DNA samples extracted from 164 infants and 214 adults were analyzed using quantitative real-time polymerase chain reaction. Results Analysis of 16S ribosomal RNA of 4 representative bacterial genera Lactobacillus, Bifidobacterium, Bacteroides, and Clostridium showed that the gut microbiota in infants had higher relative abundances of Bifidobacterium and Lactobacillus than that in adults, which was dominated by Bacteroides and Clostridium. Conclusions To the best of our knowledge, this was the first study evaluating the distinct characteristics of the microbial community of Korean infants and adults. The differences between the 2 populations suggest that external factors such as age, diet, and the environment are important contributing factors to the change in gut microbial composition during development.
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Affiliation(s)
- Sun-Young Kook
- Probioticslab R&D Institute, Bioeleven Co., Seoul, Korea
| | - Yunjeong Kim
- Probioticslab R&D Institute, Bioeleven Co., Seoul, Korea
| | - Ben Kang
- Department of Pediatric, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yon Ho Choe
- Department of Pediatric, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young-Ho Kim
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seokjin Kim
- Probioticslab R&D Institute, Bioeleven Co., Seoul, Korea
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Villamil SI, Huerlimann R, Morianos C, Sarnyai Z, Maes GE. Adverse effect of early-life high-fat/high-carbohydrate ("Western") diet on bacterial community in the distal bowel of mice. Nutr Res 2017. [PMID: 29540269 DOI: 10.1016/j.nutres.2017.11.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Obesity and other lifestyle diseases in modern society can be related to historical dietary changes from diets balanced in omega-6 and omega-3 to the unbalanced "Western-type" diet. It is recognized that diet influences the murine and human gut microbiome, and most research indicates that microbial diversity and composition are altered by high-fat diets (HFDs). However, good knowledge about the effects of early exposure to HFD on the maturation and structure of the bacterial community is limited. Using mice as model, we hypothesized that an HFD alters the early dynamic of the gut bacterial community toward an unstable/unhealthy state. By sequencing the V3 and V4 regions of the 16S ribosomal ribonucleic acid gene, we investigated the bacterial community in fecal samples of mice fed a control diet and an HFD at weaning (sampling time 1) and after 8 weeks of dietary intervention (11weeks of age; sampling time 2). Natural temporal microbiome maturation was evidenced by a general increase in microbial diversity and shifts in microbial community between sampling times 1 and 2 toward a mature community. However, the HFD led to significant structural segregation of the microbiome compared with controls; the HFD diet repressed health-enhancing bacteria (eg, Bifidobacterium and Akkermansia) and promoted health-detracting bacteria (ie, those associated with gut disorders, eg, Dorea). We suggest that early-life consumption of HFD negatively impacts the natural gut bacterial community maturation leading toward a potentially persistent unhealthy stage.
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Affiliation(s)
- Sandra Infante Villamil
- College of Sciences and Engineering, Comparative Genomics Centre, James Cook University, Townsville, 4811, Queensland, Australia
| | - Roger Huerlimann
- College of Sciences and Engineering, Comparative Genomics Centre, James Cook University, Townsville, 4811, Queensland, Australia
| | - Christina Morianos
- Laboratory of Psychiatric Neuroscience, and Comparative Genomics Centre, Australian Institute of Tropical Health and Medicine; College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Zoltan Sarnyai
- Laboratory of Psychiatric Neuroscience, and Comparative Genomics Centre, Australian Institute of Tropical Health and Medicine; College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.
| | - Gregory E Maes
- College of Sciences and Engineering, Comparative Genomics Centre, James Cook University, Townsville, 4811, Queensland, Australia; Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), B-3000 Leuven, Belgium.; Center for Human Genetics, UZ Leuven-Genomics Core, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
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12
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Frayman KB, Armstrong DS, Grimwood K, Ranganathan SC. The airway microbiota in early cystic fibrosis lung disease. Pediatr Pulmonol 2017; 52:1384-1404. [PMID: 28815937 DOI: 10.1002/ppul.23782] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/17/2017] [Indexed: 12/12/2022]
Abstract
Infection plays a critical role in the pathogenesis of cystic fibrosis (CF) lung disease. Over the past two decades, the application of molecular and extended culture-based techniques to microbial analysis has changed our understanding of the lungs in both health and disease. CF lung disease is a polymicrobial disorder, with obligate and facultative anaerobes recovered alongside traditional pathogens in varying proportions, with some differences observed to correlate with disease stage. While healthy lungs are not sterile, differences between the lower airway microbiota of individuals with CF and disease-controls are already apparent in childhood. Understanding the evolution of the CF airway microbiota, and its relationship with clinical treatments and outcome at each disease stage, will improve our understanding of the pathogenesis of CF lung disease and potentially inform clinical management. This review summarizes current knowledge of the early development of the respiratory microbiota in healthy children and then discusses what is known about the airway microbiota in individuals with CF, including how it evolves over time and where future research priorities lie.
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Affiliation(s)
- Katherine B Frayman
- Department of Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, Victoria, Australia.,Respiratory Diseases Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David S Armstrong
- Department of Respiratory Medicine, Monash Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia.,Departments of Paediatrics and Infectious Diseases, Gold Coast Health, Gold Coast, Queensland, Australia
| | - Sarath C Ranganathan
- Department of Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, Victoria, Australia.,Respiratory Diseases Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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13
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Queiroz LA, Casarin RCV, Dabdoub SM, Tatakis DN, Sallum EA, Kumar PS. Furcation Therapy With Enamel Matrix Derivative: Effects on the Subgingival Microbiome. J Periodontol 2017; 88:617-625. [PMID: 28304211 DOI: 10.1902/jop.2017.160542] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Although enamel matrix derivative (EMD) has been used to promote periodontal regeneration, little is known of its effect on the microbiome. Therefore, this investigation aims to identify changes in periodontal microbiome after treatment with EMD using a deep-sequencing approach. METHODS Thirty-nine patients with mandibular Class II buccal furcation defects were randomized to beta-tricalcium-phosphate/hydroxyapatite graft (BONE group), EMD+BONE, or EMD alone. Plaque was collected from furcation defects at baseline and 3 and 6 months post-treatment. Bacterial DNA was analyzed using terminal restriction fragment length polymorphism and 16S pyrotag sequencing, resulting in 169,000 classifiable sequences being compared with the Human Oral Microbiome Database. Statistical comparisons were made using parametric tests. RESULTS At baseline, a total of 422 species were identified from the 39 defects, belonging to Fusobacterium, Pseudomonas, Streptococcus, Filifactor, and Parvimonas. All three regenerative procedures predictably altered the disease-associated microbiome, with a restitution of health-compatible species. However, EMD and BONE+EMD groups demonstrated more long-term reductions in a higher number of species than the BONE group (P <0.05), especially disease-associated species, e.g., Selenomonas noxia, F. alocis, and Fusobacterium. CONCLUSIONS EMD treatment predictably alters a dysbiotic subgingival microbiome, decreasing pathogen richness and increasing commensal abundance. Further investigations are needed to investigate how this impacts regenerative outcomes.
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Affiliation(s)
- Lucas A Queiroz
- Department of Prosthodontics and Periodontics, Division of Periodontics, School of Dentistry at Piracicaba, State University of Campinas, Piracicaba, São Paulo, Brazil
| | - Renato C V Casarin
- Department of Prosthodontics and Periodontics, Division of Periodontics, School of Dentistry at Piracicaba, State University of Campinas, Piracicaba, São Paulo, Brazil
| | - Shareef M Dabdoub
- Division of Periodontology, College of Dentistry, The Ohio State University, Columbus, OH
| | - Dimitris N Tatakis
- Division of Periodontology, College of Dentistry, The Ohio State University, Columbus, OH
| | - Enilson A Sallum
- Department of Prosthodontics and Periodontics, Division of Periodontics, School of Dentistry at Piracicaba, State University of Campinas, Piracicaba, São Paulo, Brazil
| | - Purnima S Kumar
- Division of Periodontology, College of Dentistry, The Ohio State University, Columbus, OH
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