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Rashidi A, Gem H, McLean JS, Kerns K, Dean DR, Dey N, Minot S. Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults. Sci Data 2024; 11:75. [PMID: 38228614 PMCID: PMC10792082 DOI: 10.1038/s41597-024-02916-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
The multitude of barriers between the mouth and colon may eliminate swallowed oral bacteria. Ascertaining the presence of the same bacteria in the mouth and colon is methodologically challenging partly because 16S rRNA gene sequencing - the most commonly used method to characterize the human microbiota - has low confidence in taxonomic assignments deeper than genus for most bacteria. As different species of the same genus can have low-level variation across the same 16S rRNA gene region, shotgun sequencing is needed to identify a true overlap. We analyzed a curated, multi-cohort, shotgun metagenomic database with species-level taxonomy and clade-specific marker genes to fill this knowledge gap. Using 500 paired fecal/oral (4 oral sites) samples from 4 healthy adult cohorts, we found a minute overlap between the two niches. Comparing marker genes between paired oral and fecal samples with species-level overlap, the pattern of overlap in only 7 individuals was consistent with same-strain colonization. These findings argue against ectopic colonization of oral bacteria in the distal gut in healthy adults.
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Affiliation(s)
- Armin Rashidi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Division of Oncology, Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Hakan Gem
- School of Dentistry, University of Washington, Seattle, WA, USA
| | | | | | - David R Dean
- School of Dentistry, University of Washington, Seattle, WA, USA
| | - Neelendu Dey
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Samuel Minot
- Microbiome Research Initiative, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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Rashidi A, Ebadi M, Rehman TU, Elhusseini H, Kazadi D, Halaweish H, Khan MH, Hoeschen A, Cao Q, Luo X, Kabage AJ, Lopez S, Holtan SG, Weisdorf DJ, Khoruts A, Staley C. Randomized Double-Blind Phase II Trial of Fecal Microbiota Transplantation Versus Placebo in Allogeneic Hematopoietic Cell Transplantation and AML. J Clin Oncol 2023; 41:5306-5319. [PMID: 37235836 PMCID: PMC10691796 DOI: 10.1200/jco.22.02366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 04/03/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
PURPOSE Gut microbiota injury in allogeneic hematopoietic cell transplantation (HCT) recipients and patients with AML has been associated with adverse clinical outcomes. Previous studies in these patients have shown improvements in various microbiome indices after fecal microbiota transplantation (FMT). However, whether microbiome improvements translate into improved clinical outcomes remains unclear. We examined this question in a randomized, double-blind, placebo-controlled phase II trial. METHODS Two independent cohorts of allogeneic HCT recipients and patients with AML receiving induction chemotherapy were randomly assigned in a 2:1 ratio to receive standardized oral encapsulated FMT versus placebo upon neutrophil recovery. After each course of antibacterial antibiotics, patients received a study treatment. Up to three treatments were administered within 3 months. The primary end point was 4-month all-cause infection rate. Patients were followed for 9 months. RESULTS In the HCT cohort (74 patients), 4-month infection density was 0.74 and 0.91 events per 100 patient-days in FMT and placebo arms, respectively (infection rate ratio, 0.83; 95% CI, 0.48 to 1.42; P = .49). In the AML cohort (26 patients), 4-month infection density was 0.93 in the FMT arm and 1.25 in the placebo arm, with an infection rate ratio of 0.74 (95% CI, 0.32 to 1.71; P = .48). Unique donor bacterial sequences comprised 25%-30% of the fecal microbiota after FMT. FMT improved postantibiotic recovery of microbiota diversity, restored several depleted obligate anaerobic commensals, and reduced the abundance of expanded genera Enterococcus, Streptococcus, Veillonella, and Dialister. CONCLUSION In allogeneic HCT recipients and patients with AML, third-party FMT was safe and ameliorated intestinal dysbiosis, but did not decrease infections. Novel findings from this trial will inform future development of FMT trials.
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Affiliation(s)
- Armin Rashidi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN
- Clinical Research Division, Fred Hutchinson Cancer Center; and Division of Oncology, University of Washington, Seattle, WA
| | - Maryam Ebadi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN
- Department of Radiation Oncology, University of Washington, Seattle, WA
| | - Tauseef Ur Rehman
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Heba Elhusseini
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN
| | - David Kazadi
- Department of Medicine, University of Minnesota, Minneapolis, MN
| | | | | | - Andrea Hoeschen
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Qing Cao
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Xianghua Luo
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN
| | | | - Sharon Lopez
- Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Shernan G. Holtan
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Daniel J. Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Alexander Khoruts
- Center for Immunology, University of Minnesota, Minneapolis, MN
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, MN
- Biotechnology Institute, University of Minnesota, St Paul, MN
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Taş E, Ülgen KO. Understanding the ADHD-Gut Axis by Metabolic Network Analysis. Metabolites 2023; 13:metabo13050592. [PMID: 37233633 DOI: 10.3390/metabo13050592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder diagnosed with hyperactivity, impulsivity, and a lack of attention inconsistent with the patient's development level. The fact that people with ADHD frequently experience gastrointestinal (GI) dysfunction highlights the possibility that the gut microbiome may play a role in this condition. The proposed research aims to determine a biomarker for ADHD by reconstructing a model of the gut-microbial community. Genome-scale metabolic models (GEM) considering the relationship between gene-protein-reaction associations are used to simulate metabolic activities in organisms of gut. The production rates of dopamine and serotonin precursors and the key short chain fatty acids which affect the health status are determined under three diets (Western, Atkins', Vegan) and compared with those of healthy people. Elasticities are calculated to understand the sensitivity of exchange fluxes to changes in diet and bacterial abundance at the species level. The presence of Bacillota (genus Coprococcus and Subdoligranulum), Actinobacteria (genus Collinsella), Bacteroidetes (genus Bacteroides), and Bacteroidota (genus Alistipes) may be possible gut microbiota indicators of ADHD. This type of modeling approach taking microbial genome-environment interactions into account helps us understand the gastrointestinal mechanisms behind ADHD, and establish a path to improve the quality of life of ADHD patients.
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Affiliation(s)
- Ezgi Taş
- Department of Chemical Engineering, Bogazici University, Istanbul 34342, Turkey
| | - Kutlu O Ülgen
- Department of Chemical Engineering, Bogazici University, Istanbul 34342, Turkey
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Li J, Zhu S, Wang Y, Fan M, Dai J, Zhu C, Xu K, Cui M, Suo C, Jin L, Jiang Y, Chen X. Metagenomic association analysis of cognitive impairment in community-dwelling older adults. Neurobiol Dis 2023; 180:106081. [PMID: 36931530 DOI: 10.1016/j.nbd.2023.106081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/25/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The gut microbiota is reportedly involved in neurodegenerative disorders, and exploration of differences in the gut microbiota in different cognitive status could provide clues for early detection and intervention in cognitive impairment. Here, we used data from the Taizhou Imaging Study (N = 516), a community-based cohort, to compare the overall structure of the gut microbiota at the species level through metagenomic sequencing, and to explore associations with cognition. Interestingly, bacteria capable of producing short-chain fatty acids (SCFAs), such as Bacteroides massiliensis, Bifidobacterium pseudocatenulatum, Fusicatenibacter saccharivorans and Eggerthella lenta, that can biotransform polyphenols, were positively associated with better cognitive performance (p < 0.05). Although Diallister invisus and Streptococcus gordonii were not obviously related to cognition, the former was dominant in individuals with mild cognitive impairment (MCI), while the later was more abundant in cognitively normal (CN) than MCI groups, and positively associated with cognitive performance (p < 0.05). Functional analysis further supported a potential role of SCFAs and lactic acid in the association between the gut microbiota and cognition. The significant associations persisted after accounting for dietary patterns. Collectively, our results demonstrate an association between the gut microbiota and cognition in the general population, indicating a potential role in cognitive impairment. The findings provide clues for microbiome biomarkers of dementia, and insight for the prevention and treatment of dementia.
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Affiliation(s)
- Jincheng Li
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China
| | - Yingzhe Wang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Min Fan
- Taixing Disease Control and Prevention Center, Taizhou, Jiangsu, China
| | - Jiacheng Dai
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China
| | - Chengkai Zhu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Kelin Xu
- Fudan University Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China; Ministry of Education Key Laboratory of Public Health Safety, Department of Biostatistics, School of Public Health, Fudan University, Shanghai, China
| | - Mei Cui
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chen Suo
- Fudan University Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China; Ministry of Education Key Laboratory of Public Health Safety, Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China
| | - Yanfeng Jiang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China; International Human Phenome Institute (Shanghai), Shanghai, China.
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China; Yiwu Research Institute of Fudan University, Yiwu, Zhejiang, China.
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McLeod A, Penalver Bernabe B, Xia Y, Sanchez-Flack J, Lamar M, Schiffer L, Castellanos K, Fantuzzi G, Maki P, Fitzgibbon M, Tussing-Humphreys L. Comparing the gut microbiome of obese, African American, older adults with and without mild cognitive impairment. PLoS One 2023; 18:e0280211. [PMID: 36827280 PMCID: PMC9955629 DOI: 10.1371/journal.pone.0280211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 12/08/2022] [Indexed: 02/25/2023] Open
Abstract
Those with mild cognitive impairment (MCI), a precursor to dementia, have a gut microbiome distinct from healthy individuals, but this has only been shown in healthy individuals, not in those exhibiting several risk factors for dementia. Using amplicon 16S rRNA gene sequencing in a case-control study of 60 older (ages 55-76), obese, predominately female, African American adults, those with MCI (cases) had different gut microbiota profiles than controls. While microbial community diversity was similar between cases and controls, the abundances of specific microbial taxa weren't, such as Parabacteroides distasonis (lower in cases) and Dialister invisus (higher in cases). These differences disappeared after adjusting for markers of oxidative stress and systemic inflammation. Cognitive scores were positively correlated with levels of Akkermansia muciniphila, a bacterium associated with reduced inflammation. Our study shows that gut microbial composition may be associated with inflammation, oxidative stress, and MCI in those at high risk for dementia.
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Affiliation(s)
- Andrew McLeod
- Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, Illinois, United States of America
- Institute for Health Research and Policy, University of Illinois Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Beatriz Penalver Bernabe
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Yinglin Xia
- Department of Medicine, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Jennifer Sanchez-Flack
- Institute for Health Research and Policy, University of Illinois Chicago, Chicago, Illinois, United States of America
- Department of Pediatrics, University of Illinois Chicago, Chicago, Illinois, United States of America
- University of Illinois Cancer Center, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Melissa Lamar
- Rush Alzheimer’s Disease Center, Rush University, Chicago, Illinois, United States of America
| | - Linda Schiffer
- Institute for Health Research and Policy, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Karla Castellanos
- Department of Medicine, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Giamila Fantuzzi
- Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Pauline Maki
- Departments of Psychology and Psychiatry, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Marian Fitzgibbon
- Institute for Health Research and Policy, University of Illinois Chicago, Chicago, Illinois, United States of America
- Department of Pediatrics, University of Illinois Chicago, Chicago, Illinois, United States of America
- University of Illinois Cancer Center, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Lisa Tussing-Humphreys
- Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, Illinois, United States of America
- Institute for Health Research and Policy, University of Illinois Chicago, Chicago, Illinois, United States of America
- University of Illinois Cancer Center, University of Illinois Chicago, Chicago, Illinois, United States of America
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6
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Liang S, Sin ZY, Yu J, Zhao S, Xi Z, Bruzzone R, Tun HM. Multi-cohort analysis of depression-associated gut bacteria sheds insight on bacterial biomarkers across populations. Cell Mol Life Sci 2022; 80:9. [PMID: 36495344 PMCID: PMC11072413 DOI: 10.1007/s00018-022-04650-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/15/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022]
Abstract
Gut microbes are associated with the development of depression based on extensive evidence. However, previous studies have led to conflicting reports on this association, posing challenges to the application of gut bacteria in the diagnostics and treatment of depression. To minimise heterogenicity in data analysis, the present meta-analysis adopted a standardised bioinformatics and statistical pipeline to analyse 16S rRNA sequences of 1827 samples from eight different cohorts. Although changes in the overall bacterial community were identified by our meta-analysis, depressive-correlated changes in alpha-diversity were absent. Enrichment of Bacteroidetes, Parabacteroides, Barnesiella, Bacteroides, and Bacteroides vulgatus, along with depletion in Firmicutes, Dialister, Oscillospiraceae UCG 003 and UCG 002, and Bacteroides plebeius, were observed in depressive-associated bacteria. By contrast, elevated L-glutamine degradation, and reduced L-glutamate and L-isoleucine biosynthesis were identified in depressive-associated microbiomes. After systemically reviewing the data of these collected cohorts, we have established a bacterial classifier to identify depressive symptoms with AUC 0.834 and 0.685 in the training and external validation dataset, respectively. Moreover, a low-risk bacterial cluster for depressive symptoms was identified, which was represented by a lower abundance of Escherichia-Shigella, and a higher abundance of Faecalibacterium, Oscillospiraceae UCG 002, Ruminococcus, and Christensenellaceae R.7 group.
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Affiliation(s)
- Suisha Liang
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zhen Ye Sin
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Juelei Yu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shilin Zhao
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhang Xi
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Hein M Tun
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Microbiota I-Center (MagIC), Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Huh JW, Kim MJ, Kim J, Lee HG, Ryoo SB, Ku JL, Jeong SY, Park KJ, Kim D, Kim JF, Park JW. Enterotypical Prevotella and three novel bacterial biomarkers in preoperative stool predict the clinical outcome of colorectal cancer. MICROBIOME 2022; 10:203. [PMID: 36443754 PMCID: PMC9703702 DOI: 10.1186/s40168-022-01388-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND A significant proportion of colorectal cancer (CRC) patients suffer from early recurrence and progression after surgical treatment. Although the gut microbiota is considered as a key player in the initiation and progression of CRC, most prospective studies have been focused on a particular pathobionts such as Fusobacterium nucleatum. Here, we aimed to identify novel prognostic bacteria for CRC by examining the preoperative gut microbiota through 16S ribosomal RNA gene sequencing. RESULTS We collected stool samples from 333 patients with primary CRC within 2 weeks before surgery and followed up the patients for a median of 27.6 months for progression and 43.6 months for survival. The sequence and prognosis data were assessed using the log-rank test and multivariate Cox proportional hazard analysis. The gut microbiota was associated with the clinical outcomes of CRC patients (Pprogress = 0.011, Pdecease = 0.007). In particular, the high abundance of Prevotella, a representative genus of human enterotypes, indicated lower risks of CRC progression (P = 0.026) and decease (P = 0.0056), while the occurrence of Alistipes assigned to Bacteroides sp., Pyramidobacter piscolens, Dialister invisus, and Fusobacterium nucleatum indicated a high risk of progression. A microbiota-derived hazard score considering the five prognostic bacteria accurately predicted CRC progression in 1000 random subsamples; it outperformed widely accepted clinical biomarkers such as carcinoembryonic antigen and lymphatic invasion, after adjustment for the clinicopathological stage (adjusted HR 2.07 [95% CI, 1.61-2.64], P = 7.8e-9, C-index = 0.78). PICRUSt2 suggested that microbial pathways pertaining to thiamine salvage and L-histidine degradation underlie the different prognoses. CONCLUSIONS The enterotypical genus Prevotella was demonstrated to be useful in improving CRC prognosis, and combined with the four pathobionts, our hazard score based on the gut microbiota should provide an important asset in predicting medical outcomes for CRC patients. Video Abstract.
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Affiliation(s)
- Ji-Won Huh
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Min Jung Kim
- Division of Colorectal Surgery, Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Jaesik Kim
- Department of Computer Engineering, Ajou University, Suwon, Republic of Korea
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Hyeon Gwon Lee
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Seung-Bum Ryoo
- Division of Colorectal Surgery, Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ja-Lok Ku
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung-Yong Jeong
- Division of Colorectal Surgery, Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Kyu Joo Park
- Division of Colorectal Surgery, Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, USA
| | - Jihyun F Kim
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea.
- Microbiome Initiative, Yonsei University, Seoul, Republic of Korea.
| | - Ji Won Park
- Division of Colorectal Surgery, Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
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Widhani A, Djauzi S, Suyatna FD, Dewi BE. Changes in Gut Microbiota and Systemic Inflammation after Synbiotic Supplementation in Patients with Systemic Lupus Erythematosus: A Randomized, Double-Blind, Placebo-Controlled Trial. Cells 2022; 11:3419. [PMID: 36359816 PMCID: PMC9658918 DOI: 10.3390/cells11213419] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 08/04/2023] Open
Abstract
Gut dysbiosis has a role in the pathogenesis of lupus. Synbiotic supplementation may restore the balance of gut microbiota. This study investigated whether synbiotics could improve gut microbiota and systemic inflammation in lupus patients. This randomized, double-blind, placebo-controlled trial was conducted in adult systemic lupus erythematosus (SLE) patients. Subjects were randomized to receive either synbiotics or a placebo. Fecal microbiota, hs-CRP, IL-6, and IL-17 were measured at baseline and after 60 days. Patients who fulfilled the inclusion criteria were randomized into synbiotic (n = 23) and placebo groups (n = 23). In the synbiotic group, hs-CRP was not significantly increased (1.8 [0.9; 4.85] vs. 2.1 [0.9; 4.25] mg/L; pre vs. post; p = 0.23), whereas in the placebo group hs-CRP was increased significantly (1.75 [0.4; 4.45] vs. 3.75 [0.58; 7.05] mg/L; pre vs. post; p = 0.005). In the synbiotic group, IL-6 decreased significantly (8.76 [6.62; 11.39] vs. 6.59 [4.96; 8.01]; pre vs. post; p = 0.02), while there was no significant change in IL-17 level. In the placebo group, there was no significant change in IL-6 and IL-17. Synbiotic supplementation increased the Firmicutes:Bacteroidetes ratio (0.05 ± 0.60 vs. -0.08 ± 0.63, synbiotic vs. placebo p = 0.48) and butyrate metabolism (p = 0.037) and decreased amino sugar and nucleotide sugar metabolism (p = 0.040). There was improvement in the SLE disease activity index 2K (SLEDAI-2K) score in the synbiotic group (14 [9; 16] vs. 8 [2; 12]; pre vs. post; p < 0.001), while no change in the placebo group (9 [8; 18.25] vs. 9 [5.5; 15]; pre vs. post; p = 0.31). Synbiotic supplementation could reduce systemic inflammation and SLE disease activity and alter the composition and functions of gut microbiota.
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Affiliation(s)
- Alvina Widhani
- Allergy and Clinical Immunology Division, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Dr. Cipto Mangunkusumo Hospital, Jakarta 10430, Indonesia
- Doctoral Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Samsuridjal Djauzi
- Allergy and Clinical Immunology Division, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Dr. Cipto Mangunkusumo Hospital, Jakarta 10430, Indonesia
| | | | - Beti Ernawati Dewi
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
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Cao J, Xu C, Zhou R, Duan G, Lin A, Yang X, You S, Zhou Y, Yang G. Potato peel waste for fermentative biohydrogen production using different pretreated culture. BIORESOURCE TECHNOLOGY 2022; 362:127866. [PMID: 36049714 DOI: 10.1016/j.biortech.2022.127866] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
How to manage potato peel waste sustainably has been an issue faced by the potato industry. This work explored the feasibility of potato peel waste for biohydrogen production via dark fermentation, and investigated the effects of various inoculum enrichment methods (acid, aeration, heat-shock and base) on the process efficiency. It was observed that the hydrogen production showed a great variation when using various inoculum enrichment methods, and the aeration enriched inoculum obtained the maximum hydrogen yield of 71.0 mL/g-VSadded and VS removal of 28.9 %. Different enriched cultures also exhibited huge variations in the bacterial community structure and metabolic pathway. The highest abundance of Clostridium sensu stricto fundamentally contributed to the highest process efficiency for the fermenter inoculated with aeration treated culture. This work puts forward a promising strategy for recycling potato peel waste, and fills a gap in the optimal inoculum preparation method for biohydrogen fermentation of potato peel waste.
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Affiliation(s)
- Jinman Cao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chonglin Xu
- College of Resources and Environment, Key Laboratory of Agricultural Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Rui Zhou
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guilan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aijun Lin
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiao Yang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Siming You
- James Watt School of Engineering, University of Glasgow G12 8QQ, UK
| | - Yaoyu Zhou
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Guang Yang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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10
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Gao Y, O’Hely M, Quinn TP, Ponsonby AL, Harrison LC, Frøkiær H, Tang MLK, Brix S, Kristiansen K, Burgner D, Saffery R, Ranganathan S, Collier F, Vuillermin P. Maternal gut microbiota during pregnancy and the composition of immune cells in infancy. Front Immunol 2022; 13:986340. [PMID: 36211431 PMCID: PMC9535361 DOI: 10.3389/fimmu.2022.986340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Background Preclinical studies have shown that maternal gut microbiota during pregnancy play a key role in prenatal immune development but the relevance of these findings to humans is unknown. The aim of this prebirth cohort study was to investigate the association between the maternal gut microbiota in pregnancy and the composition of the infant’s cord and peripheral blood immune cells over the first year of life. Methods The Barwon Infant Study cohort (n=1074 infants) was recruited using an unselected sampling frame. Maternal fecal samples were collected at 36 weeks of pregnancy and flow cytometry was conducted on cord/peripheral blood collected at birth, 6 and 12 months of age. Among a randomly selected sub-cohort with available samples (n=293), maternal gut microbiota was characterized by sequencing the 16S rRNA V4 region. Operational taxonomic units (OTUs) were clustered based on their abundance. Associations between maternal fecal microbiota clusters and infant granulocyte, monocyte and lymphocyte subsets were explored using compositional data analysis. Partial least squares (PLS) and regression models were used to investigate the relationships/associations between environmental, maternal and infant factors, and OTU clusters. Results We identified six clusters of co-occurring OTUs. The first two components in the PLS regression explained 39% and 33% of the covariance between the maternal prenatal OTU clusters and immune cell populations in offspring at birth. A cluster in which Dialister, Escherichia, and Ruminococcus were predominant was associated with a lower proportion of granulocytes (p=0.002), and higher proportions of both central naïve CD4+ T cells (CD4+/CD45RA+/CD31−) (p<0.001) and naïve regulatory T cells (Treg) (CD4+/CD45RA+/FoxP3low) (p=0.02) in cord blood. The association with central naïve CD4+ T cells persisted to 12 months of age. Conclusion This birth cohort study provides evidence consistent with past preclinical models that the maternal gut microbiota during pregnancy plays a role in shaping the composition of innate and adaptive elements of the infant’s immune system following birth.
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Affiliation(s)
- Yuan Gao
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Child Health Research Unit, Barwon Health, Geelong, VIC, Australia
- Faculty of Science, Copenhagen University, København, Denmark
| | - Martin O’Hely
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC, Australia
| | | | - Anne-Louise Ponsonby
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC, Australia
- The Early Brain Science Department, Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia
| | - Leonard C. Harrison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Hanne Frøkiær
- Faculty of Science, Copenhagen University, København, Denmark
| | - Mimi L. K. Tang
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dave Burgner
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC, Australia
| | - Richard Saffery
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Sarath Ranganathan
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Fiona Collier
- School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Peter Vuillermin
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Child Health Research Unit, Barwon Health, Geelong, VIC, Australia
- *Correspondence: Peter Vuillermin,
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11
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Dash S, Syed YA, Khan MR. Understanding the Role of the Gut Microbiome in Brain Development and Its Association With Neurodevelopmental Psychiatric Disorders. Front Cell Dev Biol 2022; 10:880544. [PMID: 35493075 PMCID: PMC9048050 DOI: 10.3389/fcell.2022.880544] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome has a tremendous influence on human physiology, including the nervous system. During fetal development, the initial colonization of the microbiome coincides with the development of the nervous system in a timely, coordinated manner. Emerging studies suggest an active involvement of the microbiome and its metabolic by-products in regulating early brain development. However, any disruption during this early developmental process can negatively impact brain functionality, leading to a range of neurodevelopment and neuropsychiatric disorders (NPD). In this review, we summarize recent evidence as to how the gut microbiome can influence the process of early human brain development and its association with major neurodevelopmental psychiatric disorders such as autism spectrum disorders, attention-deficit hyperactivity disorder, and schizophrenia. Further, we discuss how gut microbiome alterations can also play a role in inducing drug resistance in the affected individuals. We propose a model that establishes a direct link of microbiome dysbiosis with the exacerbated inflammatory state, leading to functional brain deficits associated with NPD. Based on the existing research, we discuss a framework whereby early diet intervention can boost mental wellness in the affected subjects and call for further research for a better understanding of mechanisms that govern the gut-brain axis may lead to novel approaches to the study of the pathophysiology and treatment of neuropsychiatric disorders.
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Affiliation(s)
- Somarani Dash
- Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Yasir Ahmed Syed
- School of Biosciences and Neuroscience and Mental Health Research Institute, Cardiff University, Hadyn Ellis Building, Cardiff, United Kingdom
| | - Mojibur R. Khan
- Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, India
- *Correspondence: Mojibur R. Khan,
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12
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Shi H, Ter Horst R, Nielen S, Bloemendaal M, Jaeger M, Joosten I, Koenen H, Joosten LAB, Schweren LJS, Vasquez AA, Netea MG, Buitelaar J. The gut microbiome as mediator between diet and its impact on immune function. Sci Rep 2022; 12:5149. [PMID: 35338162 PMCID: PMC8956630 DOI: 10.1038/s41598-022-08544-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/18/2022] [Indexed: 12/22/2022] Open
Abstract
Dietary habits may affect inflammatory status in humans. Here we explore this interaction as well as the potential mediating role of the gut microbiome (GM), given that the GM is both involved in processing of dietary components and influences the immune system. A cross-sectional analysis of a sample of 482 healthy participants (207 males and 275 females) was performed. Dietary intake was assessed by a semiquantitative food questionnaire. Adipokines and soluble inflammatory mediators were assayed with multiple immunoassays and ELISA. Microbial DNA was extracted from frozen stool samples of 471 participants. Polychoric correlation analysis was used to establish dietary patterns, and joint multivariate associations between these dietary patterns and immune biomarkers were studied using regression analyses with adjustment for sex, age, BMI, smoking, education levels and physical exercise and other dietary patterns. Non-parametric entropy mediation was applied to investigate whether diet-immune relationships are mediated by abundance of microbial species. In this cohort, we identified three dietary patterns, characterized as “high-meat” (meat and sweetened drink), “prudent diet” (fish, fruit, legumes and vegetables) and “high alcohol” (higher alcohol consumption). Higher adherence to prudent diet was associated with a higher adiponectin level. The high alcohol pattern was associated with high concentrations of circulating concentrations of pro-inflammatory markers (CRP, IL-6, VEGF). Dialister invisus was found to mediate the relationship between a prudent dietary pattern and adiponectin, AAT, CRP, IL-6, and VEGF. In conclusion, a meat-based diet and a diet with high alcohol consumption were associated with high concentrations of biomarkers of chronic low-grade inflammation, and conversely, a prudent diet was associated with anti-inflammatory biomarkers. Diet-inflammation regulation may differ between sexes. Mediation analyses revealed that the association between prudent diet and immune function was partially mediated by the GM. The study adds to our understanding of the associations between diet, the immune system and the GM in a healthy population.
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Affiliation(s)
- Huiqing Shi
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Radboudumc, Kapittelweg 29, 6525 EN, Nijmegen, Gelderland, The Netherlands.
| | - Rob Ter Horst
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboudumc, 6500 HB, Nijmegen, Gelderland, The Netherlands
| | - Suzanne Nielen
- Department of Psychiatry, and Department of Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, 6525 EN, Nijmegen, Gelderland, The Netherlands
| | - Mirjam Bloemendaal
- Department of Psychiatry, and Department of Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, 6525 EN, Nijmegen, Gelderland, The Netherlands
| | - Martin Jaeger
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboudumc, 6500 HB, Nijmegen, Gelderland, The Netherlands
| | - Irma Joosten
- Department of Laboratory Medicine, Radboudumc, 6500 HB, Nijmegen, Gelderland, The Netherlands
| | - Hans Koenen
- Department of Laboratory Medicine, Radboudumc, 6500 HB, Nijmegen, Gelderland, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboudumc, 6500 HB, Nijmegen, Gelderland, The Netherlands
| | - Lizanne J S Schweren
- Interdisciplinary Center Psychopathology and Emotion Regulation, University Medical Center Groningen, University of Groningen, 9700 RB, Hanzeplein 1, Groningen, The Netherlands
| | - Alejandro Arias Vasquez
- Department of Psychiatry, and Department of Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, 6525 EN, Nijmegen, Gelderland, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboudumc, 6500 HB, Nijmegen, Gelderland, The Netherlands.,Department of Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Jan Buitelaar
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Radboudumc, Kapittelweg 29, 6525 EN, Nijmegen, Gelderland, The Netherlands.,Karakter Child and Adolescent Psychiatry University Centre, 6525 GC, Nijmegen, Gelderland, The Netherlands
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13
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No evidence for colonization of oral bacteria in the distal gut in healthy adults. Proc Natl Acad Sci U S A 2021; 118:2114152118. [PMID: 34610963 PMCID: PMC8594488 DOI: 10.1073/pnas.2114152118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
The microbial communities in the mouth and colon are anatomically connected via the saliva. However, the extent to which oral microbes reach and successfully colonize the distal gut has been debated. To resolve this long-standing controversy, we used exact amplicon sequence variants generated from concurrently collected saliva/stool microbiota in 66 healthy adults from two countries to show that, with one exception (Dialister invisus), the two niches are completely distinct. Thus, there is no evidence for colonization of oral bacteria in the distal gut. This defines the healthy state to which pathological states could be compared. Finding the same bacteria in the mouth and stool may warrant clinical investigation for an underlying pathology.
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14
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Baldewijns S, Sillen M, Palmans I, Vandecruys P, Van Dijck P, Demuyser L. The Role of Fatty Acid Metabolites in Vaginal Health and Disease: Application to Candidiasis. Front Microbiol 2021; 12:705779. [PMID: 34276639 PMCID: PMC8282898 DOI: 10.3389/fmicb.2021.705779] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022] Open
Abstract
Although the vast majority of women encounters at least one vaginal infection during their life, the amount of microbiome-related research performed in this area lags behind compared to alternative niches such as the intestinal tract. As a result, effective means of diagnosis and treatment, especially of recurrent infections, are limited. The role of the metabolome in vaginal health is largely elusive. It has been shown that lactate produced by the numerous lactobacilli present promotes health by limiting the chance of infection. Short chain fatty acids (SCFA) have been mainly linked to dysbiosis, although the causality of this relationship is still under debate. In this review, we aim to bring together information on the role of the vaginal metabolome and microbiome in infections caused by Candida. Vulvovaginal candidiasis affects near to 70% of all women at least once in their life with a significant proportion of women suffering from the recurrent variant. We assess the role of fatty acid metabolites, mainly SCFA and lactate, in onset of infection and virulence of the fungal pathogen. In addition, we pinpoint where lack of research limits our understanding of the molecular processes involved and restricts the possibility of developing novel treatment strategies.
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Affiliation(s)
- Silke Baldewijns
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Mart Sillen
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Ilse Palmans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Paul Vandecruys
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Liesbeth Demuyser
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
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15
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Singh P, Rawat A, Al-Jarrah B, Saraswathi S, Gad H, Elawad M, Hussain K, Hendaus MA, Al-Masri W, Malik RA, Al Khodor S, Akobeng AK. Distinctive Microbial Signatures and Gut-Brain Crosstalk in Pediatric Patients with Coeliac Disease and Type 1 Diabetes Mellitus. Int J Mol Sci 2021; 22:ijms22041511. [PMID: 33546364 PMCID: PMC7913584 DOI: 10.3390/ijms22041511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023] Open
Abstract
Coeliac disease (CD) and Type 1 diabetes mellitus (T1DM) are immune-mediated diseases. Emerging evidence suggests that dysbiosis in the gut microbiome plays a role in the pathogenesis of both diseases and may also be associated with the development of neuropathy. The primary goal in this cross-sectional pilot study was to identify whether there are distinct gut microbiota alterations in children with CD (n = 19), T1DM (n = 18) and both CD and T1DM (n = 9) compared to healthy controls (n = 12). Our second goal was to explore the relationship between neuropathy (corneal nerve fiber damage) and the gut microbiome composition. Microbiota composition was determined by 16S rRNA gene sequencing. Corneal confocal microscopy was used to determine nerve fiber damage. There was a significant difference in the overall microbial diversity between the four groups with healthy controls having a greater microbial diversity as compared to the patients. The abundance of pathogenic proteobacteria Shigella and E. coli were significantly higher in CD patients. Differential abundance analysis showed that several bacterial amplicon sequence variants (ASVs) distinguished CD from T1DM. The tissue transglutaminase antibody correlated significantly with a decrease in gut microbial diversity. Furthermore, the Bacteroidetes phylum, specifically the genus Parabacteroides was significantly correlated with corneal nerve fiber loss in the subjects with neuropathic damage belonging to the diseased groups. We conclude that disease-specific gut microbial features traceable down to the ASV level distinguish children with CD from T1DM and specific gut microbial signatures may be associated with small fiber neuropathy. Further research on the mechanisms linking altered microbial diversity with neuropathy are warranted.
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Affiliation(s)
- Parul Singh
- Research Department, Sidra Medicine, Doha 26999, Qatar or (P.S.); (A.R.); (B.A.-J.)
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha 24404, Qatar
| | - Arun Rawat
- Research Department, Sidra Medicine, Doha 26999, Qatar or (P.S.); (A.R.); (B.A.-J.)
| | - Bara Al-Jarrah
- Research Department, Sidra Medicine, Doha 26999, Qatar or (P.S.); (A.R.); (B.A.-J.)
| | - Saras Saraswathi
- Division of Gastroenterology, Hepatology, and Nutrition, Sidra Medicine, Doha 26999, Qatar; (S.S.); (M.E.); (W.A.-M.); (A.K.A.)
| | - Hoda Gad
- Department Medicine, Weill Cornell Medicine-Qatar, Doha 24144, Qatar; (H.G.); (R.A.M.)
| | - Mamoun Elawad
- Division of Gastroenterology, Hepatology, and Nutrition, Sidra Medicine, Doha 26999, Qatar; (S.S.); (M.E.); (W.A.-M.); (A.K.A.)
| | - Khalid Hussain
- Division of Endocrinology, Sidra Medicine, Doha 26999, Qatar;
| | | | - Wesam Al-Masri
- Division of Gastroenterology, Hepatology, and Nutrition, Sidra Medicine, Doha 26999, Qatar; (S.S.); (M.E.); (W.A.-M.); (A.K.A.)
| | - Rayaz A. Malik
- Department Medicine, Weill Cornell Medicine-Qatar, Doha 24144, Qatar; (H.G.); (R.A.M.)
| | - Souhaila Al Khodor
- Research Department, Sidra Medicine, Doha 26999, Qatar or (P.S.); (A.R.); (B.A.-J.)
- Correspondence:
| | - Anthony K. Akobeng
- Division of Gastroenterology, Hepatology, and Nutrition, Sidra Medicine, Doha 26999, Qatar; (S.S.); (M.E.); (W.A.-M.); (A.K.A.)
- Department Medicine, Weill Cornell Medicine-Qatar, Doha 24144, Qatar; (H.G.); (R.A.M.)
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16
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Murugkar PP, Collins AJ, Chen T, Dewhirst FE. Isolation and cultivation of candidate phyla radiation Saccharibacteria (TM7) bacteria in coculture with bacterial hosts. J Oral Microbiol 2020; 12:1814666. [PMID: 33209205 PMCID: PMC7651992 DOI: 10.1080/20002297.2020.1814666] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background The vast majority of bacteria on earth have not yet been cultivated. There are many bacterial phyla with no cultivated examples including most members of the Candidate Phylum Radiation with the exception of human oral isolates from the phylum Saccharibacteria. Aims The aims of this research were to develop reproducible methods and validate approaches for the cultivation of human oral Saccharibacteria and to identify the conceptual pitfalls that delayed isolation of these bacteria for 20 years after their discovery. Methods Oral samples were dispersed and passed through 0.2 µm membrane filters. The ultrasmall saccharibacterial cells in the filtrate were pelleted, inoculated into broth cultures of potential bacterial host cells and passaged into fresh medium every 2–3 days. Results Thirty-two isolates representing four species of Saccharibacteria were isolated in stable coculture with three species of host bacteria from the phylum Actinobacteria. Complete genome sequences were obtained for 16 isolates. Conclusions Human oral Saccharibacteria are obligate bacterial parasites that can be stably passaged in coculture with specific species of host bacteria. Isolating these important members of the human oral microbiome, and many natural environments, requires abandoning many of Koch’s concepts and methods and embracing novel microbiological approaches.
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Affiliation(s)
- Pallavi P Murugkar
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Andrew J Collins
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Tsute Chen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Floyd E Dewhirst
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
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17
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Ferrer MD, López-López A, Nicolescu T, Perez-Vilaplana S, Boix-Amorós A, Dzidic M, Garcia S, Artacho A, Llena C, Mira A. Topic Application of the Probiotic Streptococcus dentisani Improves Clinical and Microbiological Parameters Associated With Oral Health. Front Cell Infect Microbiol 2020; 10:465. [PMID: 32984080 PMCID: PMC7488176 DOI: 10.3389/fcimb.2020.00465] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/28/2020] [Indexed: 01/04/2023] Open
Abstract
Streptococcus dentisani 7746, isolated from dental plaque of caries-free individuals, has been shown to have several beneficial effects in vitro which could contribute to promote oral health, including an antimicrobial activity against oral pathogens by the production of bacteriocins and a pH buffering capacity through ammonia production. Previous work has shown that S. dentisani was able to colonize the oral cavity for 2–4 weeks after application. The aim of the present work was to evaluate its clinical efficacy by a randomized, double-blind, placebo-controlled parallel group study. Fifty nine volunteers were enrolled in the study and randomly assigned to a treatment or placebo group. The treatment consisted of a bucco-adhesive gel application (2.5 109 cfu/dose) with a dental splint for 5 min every 48 h, for a period of 1 month (i.e., 14 doses). Dental plaque and saliva samples were collected at baseline, 15 and 30 days after first application, and 15 days after the end of treatment. At baseline, there was a significant correlation between S. dentisani levels and frequency of toothbrushing. Salivary flow, a major factor influencing oral health, was significantly higher in the probiotic group at day 15 compared with the placebo (4.4 and 3.4 ml/5 min, respectively). In the probiotic group, there was a decrease in the amount of dental plaque and in gingival inflammation, but no differences were observed in the placebo group. The probiotic group showed a significant increase in the levels of salivary ammonia and calcium. Finally, Illumina sequencing of plaque samples showed a beneficial shift in bacterial composition at day 30 relative to baseline, with a reduction of several cariogenic organisms and the key players in plaque formation, probably as a result of bacteriocins production. Only 58% of the participants in the probiotic group showed increased plaque levels of S. dentisani at day 30 and 71% by day 45, indicating that the benefits of S. dentisani application could be augmented by improving colonization efficiency. In conclusion, the application of S. dentisani 7746 improved several clinical and microbiological parameters associated with oral health, supporting its use as a probiotic to prevent tooth decay.
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Affiliation(s)
- María D Ferrer
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia, Spain
| | - Aranzazu López-López
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia, Spain
| | - Teodora Nicolescu
- Clínica Odontológica, Fundació Lluís Alcanyis, Universitat de València, Valencia, Spain
| | | | - Alba Boix-Amorós
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia, Spain
| | - Majda Dzidic
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia, Spain
| | - Sandra Garcia
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia, Spain
| | - Alejandro Artacho
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia, Spain
| | - Carmen Llena
- Clínica Odontológica, Fundació Lluís Alcanyis, Universitat de València, Valencia, Spain
| | - Alex Mira
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia, Spain
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Sakamoto M, Ikeyama N, Toyoda A, Murakami T, Mori H, Iino T, Ohkuma M. Dialister hominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2020; 70:589-595. [DOI: 10.1099/ijsem.0.003797] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takumi Murakami
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Mori
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Pruski P, Lewis HV, Lee YS, Marchesi JR, Bennett PR, Takats Z, MacIntyre DA. Assessment of microbiota:host interactions at the vaginal mucosa interface. Methods 2018; 149:74-84. [PMID: 29705211 DOI: 10.1016/j.ymeth.2018.04.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/10/2018] [Accepted: 04/22/2018] [Indexed: 12/12/2022] Open
Abstract
There is increasing appreciation of the role that vaginal microbiota play in health and disease throughout a woman's lifespan. This has been driven partly by molecular techniques that enable detailed identification and characterisation of microbial community structures. However, these methods do not enable assessment of the biochemical and immunological interactions between host and vaginal microbiota involved in pathophysiology. This review examines our current knowledge of the relationships that exist between vaginal microbiota and the host at the level of the vaginal mucosal interface. We also consider methodological approaches to microbiomic, immunologic and metabolic profiling that permit assessment of these interactions. Integration of information derived from these platforms brings the potential for biomarker discovery, disease risk stratification and improved understanding of the mechanisms regulating vaginal microbial community dynamics in health and disease.
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Affiliation(s)
- Pamela Pruski
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Holly V Lewis
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK; Queen Charlotte's Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London W12 0HS, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Julian R Marchesi
- Department of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Centre for Digestive and Gut Health, Surgery and Cancer, Imperial College London, London W2 1NY, UK
| | - Phillip R Bennett
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK; Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Zoltan Takats
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK.
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20
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Insights into the human oral microbiome. Arch Microbiol 2018; 200:525-540. [PMID: 29572583 DOI: 10.1007/s00203-018-1505-3] [Citation(s) in RCA: 258] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/19/2018] [Accepted: 03/20/2018] [Indexed: 12/20/2022]
Abstract
Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host's metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.
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Abstract
BACKGROUND Nasal microbiota may influence asthma pathobiology. OBJECTIVE We sought to characterize the nasal microbiome of subjects with exacerbated asthma, nonexacerbated asthma, and healthy controls to identify nasal microbiota associated with asthma activity. METHODS We performed 16S ribosomal RNA sequencing on nasal swabs obtained from 72 primarily adult subjects with exacerbated asthma (n = 20), nonexacerbated asthma (n = 31), and healthy controls (n = 21). Analyses were performed using Quantitative Insights into Microbial (QIIME); linear discriminant analysis effect size (LEfSe); Phylogenetic Investigation of Communities by Reconstruction of Unobserved States; and Statistical Analysis of Metagenomic Profiles (PICRUSt); and Statistical Analysis of Metagenomic Profiles (STAMP). Species found to be associated with asthma activity were validated using quantitative PCR. Metabolic pathways associated with differentially abundant nasal taxa were inferred through metagenomic functional prediction. RESULTS Nasal bacterial composition significantly differed among subjects with exacerbated asthma, nonexacerbated asthma, and healthy controls (permutational multivariate ANOVA, P = 2.2 × 10-2). Relative to controls, the nasal microbiota of subjects with asthma were enriched with taxa from Bacteroidetes (Wilcoxon-Mann-Whitney, r = 0.33, P = 5.1 × 10-3) and Proteobacteria (r = 0.29, P = 1.4 × 10-2). Four species were differentially abundant based on asthma status after correction for multiple comparisons: Prevotella buccalis, Padj = 1.0 × 10-2; Dialister invisus, Padj = 9.1 × 10-3; Gardnerella vaginalis, Padj = 2.8 × 10-3; Alkanindiges hongkongensis, Padj = 2.6 × 10-3. These phyla and species were also differentially abundant based on asthma activity (exacerbated asthma vs nonexacerbated asthma vs controls). Quantitative PCR confirmed species overrepresentation in asthma relative to controls for Prevotella buccalis (fold change = 130, P = 2.1 × 10-4) and Gardnerella vaginalis (fold change = 160, P = 6.8 × 10-4). Metagenomic inference revealed differential glycerolipid metabolism (Kruskal-Wallis, P = 1.9 × 10-4) based on asthma activity. CONCLUSIONS Nasal microbiome composition differs in subjects with exacerbated asthma, nonexacerbated asthma, and healthy controls. The identified nasal taxa could be further investigated for potential mechanistic roles in asthma and as possible biomarkers of asthma activity.
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22
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Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol 2018; 3:337-346. [PMID: 29311644 PMCID: PMC6131705 DOI: 10.1038/s41564-017-0089-z] [Citation(s) in RCA: 303] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract affecting millions of people worldwide. Genetic, environmental and microbial factors have been implicated in onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project (iHMP) seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of more than 100 individuals sampled over a one year period. Here, we present the first results based on 78 paired fecal metagenomes/metatranscriptomes and 222 additional metagenomes from 59 Crohn’s disease (CD), 34 ulcerative colitis (UC), and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, while many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microbes per host (e.g. by Faecalibacterium prausnitzii). Therefore, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Further, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (e.g. Dialister invisus). Lastly, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways predominantly expressed by different organisms in IBD patients (e.g. Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypic changes complementary to those linked to metagenomic abundances. The study’s results highlight the strength of analyzing both the activity and presence of gut microbes to provide insight into the role of the microbiome in IBD.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric A Franzosa
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jason Lloyd-Price
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Lauren J McIver
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Randall Schwager
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tiffany W Poon
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashwin N Ananthakrishnan
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth Andrews
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Gildardo Barron
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kathleen Lake
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mahadev Prasad
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jenny Sauk
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA.,Vatche and Tamar Manoukian Division of Digestive Disease, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Betsy Stevens
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Robin G Wilson
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Jonathan Braun
- Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA.,Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Dermot P B McGovern
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA. .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA. .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Curtis Huttenhower
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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23
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Wang Y, Zhang J, Chen X, Jiang W, Wang S, Xu L, Tu Y, Zheng P, Wang Y, Lin X, Chen H. Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing. Front Microbiol 2017; 8:2244. [PMID: 29187843 PMCID: PMC5694851 DOI: 10.3389/fmicb.2017.02244] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/31/2017] [Indexed: 01/03/2023] Open
Abstract
Background: Alterations of oral microbiota are the main cause of the progression of caries. The goal of this study was to characterize the oral microbiota in childhood caries based on single-molecule real-time sequencing. Methods: A total of 21 preschoolers, aged 3-5 years old with severe early childhood caries, and 20 age-matched, caries-free children as controls were recruited. Saliva samples were collected, followed by DNA extraction, Pacbio sequencing, and phylogenetic analyses of the oral microbial communities. Results: Eight hundred and seventy six species derived from 13 known bacterial phyla and 110 genera were detected from 41 children using Pacbio sequencing. At the species level, 38 species, including Veillonella spp., Streptococcus spp., Prevotella spp., and Lactobacillus spp., showed higher abundance in the caries group compared to the caries-free group (p < 0.05). The core microbiota at the genus and species levels was more stable in the caries-free micro-ecological niche. At follow-up, oral examinations 6 months after sample collection, development of new dental caries was observed in 5 children (the transitional group) among the 21 caries free children. Compared with the caries-free children, in the transitional and caries groups, 6 species, which were more abundant in the caries-free group, exhibited a relatively low abundance in both the caries group and the transitional group (p < 0.05). We conclude that Abiotrophia spp., Neisseria spp., and Veillonella spp., might be associated with healthy oral microbial ecosystem. Prevotella spp., Lactobacillus spp., Dialister spp., and Filifactor spp. may be related to the pathogenesis and progression of dental caries.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Hui Chen
- Department of Conservative Dentistry and Periodontics, Affiliated Hospital of Stomatology, College of Medicine, Zhejiang University, Hangzhou, China
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24
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Kugaji MS, Bhat KG, Joshi VM, Pujar M, Mavani PT. Simplified Method of Detection of Dialister invisus and Olsenella uli in Oral Cavity Samples by Polymerase Chain Reaction. JOURNAL OF ADVANCED ORAL RESEARCH 2017. [DOI: 10.1177/2229411217729105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Aims and Objectives: The oral microbial flora is highly complex and diverse with obligate anaerobic bacteria as the predominant component. Most of these are not yet cultivated/difficult to cultivate due to technical limitations. In this study, we aim to detect two novel oral bacterial species Dialister invisus and Olsenella uli by simplified and economical procedure of polymerase chain reaction (PCR) and study their association with primary and persistent endodontic infections. Material and Methods: The study involved 60 patients that included 30 patients of primary endodontic infections and 30 with persistent endodontic infections. The sample collection from the root canal was performed by universally accepted protocol by using sterile paper points. The deoxyribonucleic acid (DNA) extraction was done, followed by PCR with species specific primers. We made several changes to the protocol mentioned by original authors. We adopted a one-step protocol for amplification of bacterial DNA, omitting the 16SrDNA amplification step with universal primers. Results: It was seen that 7 (23.3 %) samples in primary endodontic infection group and 24 (80 %) samples in persistent endodontic infection group were positive for D. invisus. On the other hand, 11 (36.6 %) patients of primary endodontic infection showed positivity for O. uli in comparison to 9 (30 %) of persistent endodontic infection. Conclusion: The results from the present study showed efficient amplification of both O. uli and D. invisus in a single-step PCR. Hence, we conclude that the modified protocol used here with taq polymerase enzyme offers a faster and cheaper alternative to nested PCR without compromising the quality of amplification process.
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Affiliation(s)
- Manohar S. Kugaji
- Maratha Mandal’s Central Research Laboratory, Maratha Mandal’s NGH Institute of Dental Sciences & Research Centre, Belagavi, Karnataka, India
| | - Kishore G. Bhat
- Maratha Mandal’s Central Research Laboratory, Maratha Mandal’s NGH Institute of Dental Sciences & Research Centre, Belagavi, Karnataka, India
| | - Vinayak M. Joshi
- Maratha Mandal’s Central Research Laboratory, Maratha Mandal’s NGH Institute of Dental Sciences & Research Centre, Belagavi, Karnataka, India
| | - Madhu Pujar
- Department of Conservative Dentistry and Endodontics, Maratha Mandal’s NGH Institute of Dental Sciences & Research Centre, Belagavi, Karnataka, India
| | - Pratik T. Mavani
- Department of Conservative Dentistry and Endodontics, Maratha Mandal’s NGH Institute of Dental Sciences & Research Centre, Belagavi, Karnataka, India
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25
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Nagao-Kitamoto H, Kamada N. Host-microbial Cross-talk in Inflammatory Bowel Disease. Immune Netw 2017; 17:1-12. [PMID: 28261015 PMCID: PMC5334117 DOI: 10.4110/in.2017.17.1.1] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/19/2017] [Accepted: 01/27/2017] [Indexed: 02/06/2023] Open
Abstract
A vast community of commensal microorganisms, commonly referred to as the gut microbiota, colonizes the gastrointestinal tract (GI). The involvement of the gut microbiota in the maintenance of the gut ecosystem is two-fold: it educates host immune cells and protects the host from pathogens. However, when healthy microbial composition and function are disrupted (dysbiosis), the dysbiotic gut microbiota can trigger the initiation and development of various GI diseases, including inflammatory bowel disease (IBD). IBD, primarily includes ulcerative colitis (UC) and Crohn's disease (CD), is a major global public health problem affecting over 1 million patients in the United States alone. Accumulating evidence suggests that various environmental and genetic factors contribute to the pathogenesis of IBD. In particular, the gut microbiota is a key factor associated with the triggering and presentation of disease. Gut dysbiosis in patients with IBD is defined as a reduction of beneficial commensal bacteria and an enrichment of potentially harmful commensal bacteria (pathobionts). However, as of now it is largely unknown whether gut dysbiosis is a cause or a consequence of IBD. Recent technological advances have made it possible to address this question and investigate the functional impact of dysbiotic microbiota on IBD. In this review, we will discuss the recent advances in the field, focusing on host-microbial cross-talk in IBD.
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Affiliation(s)
- Hiroko Nagao-Kitamoto
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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26
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Smeda-Pienaar K, Kaambo E, Africa CWJ. Bacterial morphotype grading for periodontal disease assessment. BDJ Open 2017; 3:16011. [PMID: 29607072 PMCID: PMC5842865 DOI: 10.1038/bdjopen.2016.11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 11/22/2022] Open
Abstract
Background: Listgarten and Hellden (1978) used darkfield microscopy of wet mounts to differentiate between healthy and periodontally diseased sites in the mouth by expressing the different bacterial morphotypes observed as a percentage of the total number of bacteria counted. This method of periodontal disease assessment gained favour as a diagnostic tool but presented with the limitation of immediate examination to determine the number of motile rods present and an inability to distinguish between gingivitis and periodontitis. Grading of bacterial morphotypes into several distinct categories of health or disease (Ison and Hay, 2002), simplified the scoring system of Gram-stained smears for the diagnosis of bacterial vaginosis (Nugent et al. 1991). The application of a similar grading system using stained smears rather than wet mounts could be advantageous to the diagnosis of periodontal disease. Objectives/aims: This study tested the hypothesis that stained smears of dental plaque collected from the gingival crevice of individuals with varying probing pocket depths (PD) may provide a grading system for periodontal disease assessment. Materials and methods: Subgingival plaque samples were collected from 49 patients, stained with a silver stain and the proportions of each bacterial morphotype graded relative to their respective PD measurements. Results: This technique allowed for a grading system of I–IV, with grade I indicating health and grade IV indicating severe periodontal disease. Discussion: Stained smear examination eliminates the time restriction for motile rod enumeration and allows for storage of smears for future reference. Conclusion: Standardization of the microscopic areas to be evaluated or examined will facilitate the agreement of cut-off values for the diagnosis of periodontal disease.
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Affiliation(s)
- Kim Smeda-Pienaar
- Microbial Endogenous Infections Studies (MEnIS) Research Laboratories, Department of Medical Biosciences, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Eveline Kaambo
- Microbial Endogenous Infections Studies (MEnIS) Research Laboratories, Department of Medical Biosciences, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Charlene W J Africa
- Microbial Endogenous Infections Studies (MEnIS) Research Laboratories, Department of Medical Biosciences, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
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27
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Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota. PLoS One 2015; 10:e0144042. [PMID: 26629816 PMCID: PMC4667893 DOI: 10.1371/journal.pone.0144042] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 11/12/2015] [Indexed: 12/28/2022] Open
Abstract
The role of dietary fiber in supporting healthy gut microbiota and overall well-being of the host has been revealed in several studies. Here, we show the effect of a bacterial polyfructan levan on the growth dynamics and metabolism of fecal microbiota in vitro by using isothermal microcalorimetry. Eleven fecal samples from healthy donors were incubated in phosphate-buffered defined medium with or without levan supplementation and varying presence of amino acids. The generation of heat, changes in pH and microbiota composition, concentrations of produced and consumed metabolites during the growth were determined. The composition of fecal microbiota and profile of metabolites changed in response to substrate (levan and amino acids) availability. The main products of levan metabolism were acetic, lactic, butyric, propionic and succinic acids and carbon dioxide. Associated growth of levan-degrading (e.g. Bacteroides) and butyric acid-producing (e.g. Faecalibacterium) taxa was observed in levan-supplemented media. The study shows that the capacity of levan and possibly also other dietary fibers/prebiotics to modulate the composition and function of colon microbiota can be predicted by using isothermal microcalorimetry of fecal samples linked to metabolite and consortia analyses.
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28
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Lactulose increases bacterial diversity and modulates the swine faecal microbiome as revealed by 454-pyrosequencing. Anim Feed Sci Technol 2015. [DOI: 10.1016/j.anifeedsci.2015.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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29
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Abstract
The oral bacterial microbiome encompasses approximately 700 commonly occurring phylotypes, approximately half of which can be present at any time in any individual. These bacteria are largely indigenous to the oral cavity; this limited habitat range suggests that interactions between the various phylotypes, and between the phylotypes and their environment, are crucial for their existence. Molecular cataloging has confirmed many basic observations on the composition of the oral microbiome that were formulated well before ribosomal RNA-based systematics, but the power and the scope of molecular taxonomy have resulted in the discovery of new phylotypes and, more importantly, have made possible a level of bacterial community analysis that was unachievable with classical methods. Bacterial community structure varies with location within the mouth, and changes in community structure are related to disease initiation and disease progression. Factors that influence the formation and the evolution of communities include selective adherence to epithelial or tooth surfaces, specific cell-to-cell binding as a driver of early community composition, and interorganismal interaction leading to alteration of the local environment, which represents the first step on the road to oral disease. A comprehensive understanding of how these factors interact to drive changes in the composition of the oral microbial community can lead to new strategies for the inhibition of periodontal diseases and dental caries.
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30
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Aldunate M, Srbinovski D, Hearps AC, Latham CF, Ramsland PA, Gugasyan R, Cone RA, Tachedjian G. Antimicrobial and immune modulatory effects of lactic acid and short chain fatty acids produced by vaginal microbiota associated with eubiosis and bacterial vaginosis. Front Physiol 2015; 6:164. [PMID: 26082720 PMCID: PMC4451362 DOI: 10.3389/fphys.2015.00164] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/12/2015] [Indexed: 12/14/2022] Open
Abstract
Lactic acid and short chain fatty acids (SCFAs) produced by vaginal microbiota have reported antimicrobial and immune modulatory activities indicating their potential as biomarkers of disease and/or disease susceptibility. In asymptomatic women of reproductive-age the vaginal microbiota is comprised of lactic acid-producing bacteria that are primarily responsible for the production of lactic acid present at ~110 mM and acidifying the vaginal milieu to pH ~3.5. In contrast, bacterial vaginosis (BV), a dysbiosis of the vaginal microbiota, is characterized by decreased lactic acid-producing microbiota and increased diverse anaerobic bacteria accompanied by an elevated pH>4.5. BV is also characterized by a dramatic loss of lactic acid and greater concentrations of mixed SCFAs including acetate, propionate, butyrate, and succinate. Notably women with lactic acid-producing microbiota have more favorable reproductive and sexual health outcomes compared to women with BV. Regarding the latter, BV is associated with increased susceptibility to sexually transmitted infections (STIs) including HIV. In vitro studies demonstrate that lactic acid produced by vaginal microbiota has microbicidal and virucidal activities that may protect against STIs and endogenous opportunistic bacteria as well as immune modulatory properties that require further characterization with regard to their effects on the vaginal mucosa. In contrast, BV-associated SCFAs have far less antimicrobial activity with the potential to contribute to a pro-inflammatory vaginal environment. Here we review the composition of lactic acid and SCFAs in respective states of eubiosis (non-BV) or dysbiosis (BV), their effects on susceptibility to bacterial/viral STIs and whether they have inherent microbicidal/virucidal and immune modulatory properties. We also explore their potential as biomarkers for the presence and/or increased susceptibility to STIs.
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Affiliation(s)
- Muriel Aldunate
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Microbiology, Nursing and Health, Faculty of Medicine, Monash University Clayton, VIC, Australia
| | - Daniela Srbinovski
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Microbiology, Nursing and Health, Faculty of Medicine, Monash University Clayton, VIC, Australia
| | - Anna C Hearps
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Infectious Disease, Monash University Melbourne, VIC, Australia
| | - Catherine F Latham
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Immunology, Monash University Melbourne, VIC, Australia ; Department of Surgery Austin Health, The University of Melbourne Heidelberg, VIC, Australia ; School of Biomedical Sciences, CHIRI Biosciences, Curtin University Perth, WA, Australia
| | - Raffi Gugasyan
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Immunology, Monash University Melbourne, VIC, Australia
| | - Richard A Cone
- Department of Biophysics, Johns Hopkins University Baltimore, MD, USA
| | - Gilda Tachedjian
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Microbiology, Nursing and Health, Faculty of Medicine, Monash University Clayton, VIC, Australia ; Department of Infectious Disease, Monash University Melbourne, VIC, Australia ; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity Parkville, VIC, Australia
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Alexeev D, Bibikova T, Kovarsky B, Melnikov D, Tyakht A, Govorun V. Bacterial rose garden for metagenomic SNP-based phylogeny visualization. BioData Min 2015; 8:10. [PMID: 25815061 PMCID: PMC4374582 DOI: 10.1186/s13040-015-0045-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 03/02/2015] [Indexed: 01/27/2023] Open
Abstract
Background One of the most challenging tasks in genomic analysis nowadays is metagenomics. Biomedical applications of metagenomics give rise to datasets containing hundreds and thousands of samples from various body sites for hundreds of patients. Inherently metagenome is by far more complex than a single genome as it varies in time by the amount of bacteria comprising it. Other levels of data complexity include geography of the samples and phylogenetic distance between the genomes of the same operational taxonomic unit (OTU). We have developed the visualization concept for the representation of multilayer metagenomics data – the bacterial rose garden. The approach allows to display the taxonomic distance between the representatives of the same OTU in different samples and use variety of the metadata for display. Results We have developed the principle of visualization allowing for multilayer information representation. We have incorporated data on OTU diversity across metagenomes and origin of the samples. The visual representation we have called “rose” is focused on the phylogenetic distance between the representatives of the same OTU. The visual representation is realized as interactive data chart which allows user to interact with data and explore variables. It is known that classical representation of the taxonomic tree is a reduction of information from original pairwise distance matrix. The visualization presented is a way to save all the information available through projection of distance matrix into single dimensional space of one sample. It could serve as a basis for further more complex information representation. We have used the principle proposed for visualization of 101 bacterial OTUs phylogenetic distances, finally we provide open code for the web page generation. Conclusions Bacterial rose garden is a versatile visualization principle coping with the major difficulties of metagenomic big-data visualization without loss of data. The method proposed is showing the interconnectedness of variables and is realized as user-friendly web page allowing for dynamic data exploration. The concept provided serves as one of the original approaches for metagenomic data representation and sharing. Full functional prototype could be found at http://rosegarden.datalaboratory.ru Electronic supplementary material The online version of this article (doi:10.1186/s13040-015-0045-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dmitry Alexeev
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia.,Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region Dolgoprudny, 141700 Russia
| | | | - Boris Kovarsky
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | | | - Alexander Tyakht
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Vadim Govorun
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
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Pajarillo EAB, Chae JP, Balolong MP, Kim HB, Park CS, Kang DK. Effects of probiotic Enterococcus faecium NCIMB 11181 administration on swine fecal microbiota diversity and composition using barcoded pyrosequencing. Anim Feed Sci Technol 2015. [DOI: 10.1016/j.anifeedsci.2015.01.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Association between tobacco use and the upper gastrointestinal microbiome among Chinese men. Cancer Causes Control 2015; 26:581-8. [PMID: 25701246 DOI: 10.1007/s10552-015-0535-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 02/10/2015] [Indexed: 01/14/2023]
Abstract
PURPOSE Tobacco causes many adverse health conditions and may alter the upper gastrointestinal (UGI) microbiome. However, the few studies that studied the association between tobacco use and the microbiome were small and underpowered. Therefore, we investigated the association between tobacco use and the UGI microbiome in Chinese men. METHODS We included 278 men who underwent esophageal cancer screening in Henan Province, China. Men were categorized as current, former, or never smokers from questionnaire data. UGI tract bacterial cells were characterized using the Human Oral Microbial Identification Microarray. Counts of unique bacterial species and genera estimated alpha diversity. For beta diversity, principal coordinate (PCoA) vectors were generated from an unweighted UniFrac distance matrix. Polytomous logistic regression models were used for most analyses. RESULTS Of the 278 men in this study, 46.8% were current smokers and 12.6% were former smokers. Current smokers tended to have increased alpha diversity (mean 42.3 species) compared to never smokers (mean 38.9 species). For a 10 species increase, the odds ratio (OR) for current smoking was 1.29 (95% CI 1.04-1.62). Beta diversity was also associated with current smoking. The first two PCoA vectors were strongly associated with current smoking (PCoA1 OR 0.66; 95% CI 0.51-0.87; PCoA2 OR 0.73; 95% CI 0.56-0.95). Furthermore, Dialister invisus and Megasphaera micronuciformis were more commonly detected in current smokers than in never smokers. CONCLUSIONS Current smoking was associated with both alpha and beta diversity in the UGI tract. Future work should consider how the UGI microbiome is associated with smoking-related diseases.
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Abstract
BACKGROUND Anaerobic culture has been critical in our understanding of the oral microbiotas. HIGHLIGHT Studies in advanced periodontitis in the 1970's revealed microbial complexes that associated with different clinical presentations. Taxonomy studies identified species newly-observed in periodontitis as Aggregatibacter (Actinobacillus) actinomycetemcomitans, Campylobacter (Wolinella) rectus and other Campylobacter species, and Tannerella (Bacteroides) forsythia. Anaerobic culture of initial periodontitis showed overlap in the microbiota with gingivitis, and added Selenomonas noxia and Filifactor alocis as putative periodontal pathogens. Porphyromonas gingivalis and T. forsythia were found to be associated with initial periodontitis in adults. The dominant microbiota of dental caries differs from that of periodontitis. The major cariogenic species are acidogenic and acid tolerant species particularly Streptococcus mutans, and Lactobacillus and Bifidobacterium species. Anaerobic culture of severe early childhood caries revealed a widely diverse microbiota, comparable to that observed using cloning and sequencing. The PCR-based cloning approach, however, underestimated Actinobacteria compared with culture. Only a subset of the caries-associated microbiota was acid tolerant, with different segments of the microbiota cultured on blood agar compared to a low pH acid agar. While the major caries-associated species was S. mutans, a new species, Scardovia wiggsiae, was significantly associated with early childhood caries. Higher counts of S. wiggsiae were also observed in initial white spot carious lesions in adolescents. CONCLUSION In periodontitis and dental caries, anaerobic culture studies of advanced disease provided a comprehensive analysis of the microbiota of these infections. Anaerobic culture highlighted the limitation of PCR with standard primers that underestimate detection of Actinobacteria.
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Affiliation(s)
- Anne C R Tanner
- Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts 02142, USA ; Department of Oral Medicine, Infection and Immunity, Harvard School Dental Medicine, Boston MA 02115, USA
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Axenic culture of a candidate division TM7 bacterium from the human oral cavity and biofilm interactions with other oral bacteria. Appl Environ Microbiol 2014; 80:6480-9. [PMID: 25107981 DOI: 10.1128/aem.01827-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The diversity of bacterial species in the human oral cavity is well recognized, but a high proportion of them are presently uncultivable. Candidate division TM7 bacteria are almost always detected in metagenomic studies but have not yet been cultivated. In this paper, we identified candidate division TM7 bacterial phylotypes in mature plaque samples from around orthodontic bonds in subjects undergoing orthodontic treatment. Successive rounds of enrichment in laboratory media led to the isolation of a pure culture of one of these candidate division TM7 phylotypes. The bacteria formed filaments of 20 to 200 μm in length within agar plate colonies and in monospecies biofilms on salivary pellicle and exhibited some unusual morphological characteristics by transmission electron microscopy, including a trilaminated cell surface layer and dense cytoplasmic deposits. Proteomic analyses of cell wall protein extracts identified abundant polypeptides predicted from the TM7 partial genomic sequence. Pleiomorphic phenotypes were observed when the candidate division TM7 bacterium was grown in dual-species biofilms with representatives of six different oral bacterial genera. The TM7 bacterium formed long filaments in dual-species biofilm communities with Actinomyces oris or Fusobacterium nucleatum. However, the TM7 isolate grew as short rods or cocci in dual-species biofilms with Porphyromonas gingivalis, Prevotella intermedia, Parvimonas micra, or Streptococcus gordonii, forming notably robust biofilms with the latter two species. The ability to cultivate TM7 axenically should majorly advance understanding of the physiology, genetics, and virulence properties of this novel candidate division oral bacterium.
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Abstract
Although the composition of the human microbiome is now well-studied, the microbiota's >8 million genes and their regulation remain largely uncharacterized. This knowledge gap is in part because of the difficulty of acquiring large numbers of samples amenable to functional studies of the microbiota. We conducted what is, to our knowledge, one of the first human microbiome studies in a well-phenotyped prospective cohort incorporating taxonomic, metagenomic, and metatranscriptomic profiling at multiple body sites using self-collected samples. Stool and saliva were provided by eight healthy subjects, with the former preserved by three different methods (freezing, ethanol, and RNAlater) to validate self-collection. Within-subject microbial species, gene, and transcript abundances were highly concordant across sampling methods, with only a small fraction of transcripts (<5%) displaying between-method variation. Next, we investigated relationships between the oral and gut microbial communities, identifying a subset of abundant oral microbes that routinely survive transit to the gut, but with minimal transcriptional activity there. Finally, systematic comparison of the gut metagenome and metatranscriptome revealed that a substantial fraction (41%) of microbial transcripts were not differentially regulated relative to their genomic abundances. Of the remainder, consistently underexpressed pathways included sporulation and amino acid biosynthesis, whereas up-regulated pathways included ribosome biogenesis and methanogenesis. Across subjects, metatranscriptional profiles were significantly more individualized than DNA-level functional profiles, but less variable than microbial composition, indicative of subject-specific whole-community regulation. The results thus detail relationships between community genomic potential and gene expression in the gut, and establish the feasibility of metatranscriptomic investigations in subject-collected and shipped samples.
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Seon J, Lee T, Lee SC, Pham HD, Woo HC, Song M. Bacterial community structure in maximum volatile fatty acids production from alginate in acidogenesis. BIORESOURCE TECHNOLOGY 2014; 157:22-27. [PMID: 24530946 DOI: 10.1016/j.biortech.2014.01.072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 01/15/2014] [Accepted: 01/19/2014] [Indexed: 06/03/2023]
Abstract
Alginate as biomass feedstock for bioconversion into volatile fatty acids (VFAs) is limited primarily by the low solubility in water or little utilization as microbial substrate and yet unknown about the microbial community structure for acidogenesis. The bacterial community structure was demonstrated the reflected changes in VFAs profiles in the maximized acidogenic process from alginate. Bacteroides- and Clostridium-related microorganisms were suggested to be mainly responsible for the hydrolysis of alginate and VFAs production, respectively. And the bacterial community shifted corresponded to VFAs producing was statistically demonstrated. A number of features discussed in this research can stimulate further interests on bioconversion of alginate into anaerobic biofuels production.
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Affiliation(s)
- Jiyun Seon
- The Institute of Cleaner Production, Pukyong National University, 365 Sinseon-ro, Nam-gu, Busan 608-739, Republic of Korea; Department of Civil and Environmental Engineering, Pusan National University, 63 Busandaehak-ro, Geumjeong-gu, Busan 609-735, Republic of Korea
| | - Taeho Lee
- Department of Civil and Environmental Engineering, Pusan National University, 63 Busandaehak-ro, Geumjeong-gu, Busan 609-735, Republic of Korea
| | - Seong Chan Lee
- Department of Chemical Engineering, Pukyong National University, 365 Sinseon-ro, Nam-gu, Busan 608-739, Republic of Korea
| | - Hong Duc Pham
- Department of Chemical Engineering, Pukyong National University, 365 Sinseon-ro, Nam-gu, Busan 608-739, Republic of Korea
| | - Hee Chul Woo
- Department of Chemical Engineering, Pukyong National University, 365 Sinseon-ro, Nam-gu, Busan 608-739, Republic of Korea.
| | - Minkyung Song
- The Institute of Cleaner Production, Pukyong National University, 365 Sinseon-ro, Nam-gu, Busan 608-739, Republic of Korea.
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Kaakoush NO, Castaño-Rodríguez N, Day AS, Lemberg DA, Leach ST, Mitchell HM. Campylobacter concisus and exotoxin 9 levels in paediatric patients with Crohn’s disease and their association with the intestinal microbiota. J Med Microbiol 2014; 63:99-105. [DOI: 10.1099/jmm.0.067231-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
There is mounting evidence for a possible role for Campylobacter concisus in Crohn’s disease (CD). However, the pathogenic potential of C. concisus remains disputed due to its presence in healthy subjects. It is documented that genetic diversity exists within this species, with some strains possessing putative virulence determinants such as exotoxin 9/DnaI that may enable them to persist intracellularly in host cells. In order to clarify this, we employed real-time PCR to determine C. concisus and exotoxin 9 levels within faecal samples of CD patients and healthy controls, and correlated these levels with abundances of microbial taxa identified in a subset of subjects. Both C. concisus and exotoxin 9 levels were found to be higher in CD patients than healthy controls, suggesting not only that CD patients had a greater abundance of C. concisus but also that their strains were likely to be more virulent. Moreover, C. concisus levels correlated with the exotoxin 9 levels in CD patients but not in healthy controls, indicating that healthy controls were colonized by non-virulent C. concisus strains. Correlations with the intestinal microbiota found C. concisus levels to correlate with Eubacterium, Subdoligranulum and Blautia, while exotoxin 9 levels correlated with Dialister, Oscillospira, Lachnospira and Prevotella. This suggests that either the composition of the intestinal microbial flora has the ability to influence levels of both virulent and non-virulent C. concisus strains, or infection with C. concisus may modulate the levels of specific bacterial taxa within the gastrointestinal tract.
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Affiliation(s)
- Nadeem O. Kaakoush
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Natalia Castaño-Rodríguez
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Andrew S. Day
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
- Department of Paediatrics, University of Otago, Christchurch, New Zealand
- Department of Gastroenterology, Sydney Children's Hospital, Sydney, Australia
| | - Daniel A. Lemberg
- Department of Gastroenterology, Sydney Children's Hospital, Sydney, Australia
| | - Steven T. Leach
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Hazel M. Mitchell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Siqueira JF, Rôças IN. As-yet-uncultivated oral bacteria: breadth and association with oral and extra-oral diseases. J Oral Microbiol 2013; 5:21077. [PMID: 23717756 PMCID: PMC3664057 DOI: 10.3402/jom.v5i0.21077] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 05/01/2013] [Accepted: 05/02/2013] [Indexed: 12/19/2022] Open
Abstract
It has been shown that 40–60% of the bacteria found in different healthy and diseased oral sites still remain to be grown in vitro, phenotypically characterized, and formally named as species. The possibility exists that these as-yet-uncultivated bacteria play important ecological roles in oral bacterial communities and may participate in the pathogenesis of several oral infectious diseases. There is also a potential for these as-yet-uncultivated oral bacteria to take part in extra-oral infections. For a comprehensive characterization of physiological and pathogenic properties as well as antimicrobial susceptibility of individual bacterial species, strains need to be grown in pure culture. Advances in culturing techniques have allowed the cultivation of several oral bacterial taxa only previously known by a 16S rRNA gene sequence signature, and novel species have been proposed. There is a growing need for developing improved methods to cultivate and characterize the as-yet-uncultivated portion of the oral microbiome so as to unravel its role in health and disease.
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Affiliation(s)
- José F Siqueira
- Department of Endodontics and Molecular Microbiology Laboratory, Estácio de Sá University, Rio de Janeiro, Brazil
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40
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Yeoman CJ, Thomas SM, Miller MEB, Ulanov AV, Torralba M, Lucas S, Gillis M, Cregger M, Gomez A, Ho M, Leigh SR, Stumpf R, Creedon DJ, Smith MA, Weisbaum JS, Nelson KE, Wilson BA, White BA. A multi-omic systems-based approach reveals metabolic markers of bacterial vaginosis and insight into the disease. PLoS One 2013; 8:e56111. [PMID: 23405259 PMCID: PMC3566083 DOI: 10.1371/journal.pone.0056111] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 01/09/2013] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) is the most common vaginal disorder of reproductive-age women. Yet the cause of BV has not been established. To uncover key determinants of BV, we employed a multi-omic, systems-biology approach, including both deep 16S rRNA gene-based sequencing and metabolomics of lavage samples from 36 women. These women varied demographically, behaviorally, and in terms of health status and symptoms. PRINCIPAL FINDINGS 16S rRNA gene-based community composition profiles reflected Nugent scores, but not Amsel criteria. In contrast, metabolomic profiles were markedly more concordant with Amsel criteria. Metabolomic profiles revealed two distinct symptomatic BV types (SBVI and SBVII) with similar characteristics that indicated disruption of epithelial integrity, but each type was correlated to the presence of different microbial taxa and metabolites, as well as to different host behaviors. The characteristic odor associated with BV was linked to increases in putrescine and cadaverine, which were both linked to Dialister spp. Additional correlations were seen with the presence of discharge, 2-methyl-2-hydroxybutanoic acid, and Mobiluncus spp., and with pain, diethylene glycol and Gardnerella spp. CONCLUSIONS The results not only provide useful diagnostic biomarkers, but also may ultimately provide much needed insight into the determinants of BV.
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Affiliation(s)
- Carl J. Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, United States of America
- The Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Susan M. Thomas
- The Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Margret E. Berg Miller
- The Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Alexander V. Ulanov
- Biotechnology Center, University of Illinois, Urbana, Illinois, United States of America
| | - Manolito Torralba
- J. Craig Venter Institute, Maryland Campus, Rockville, Maryland, United States of America
| | - Sarah Lucas
- J. Craig Venter Institute, Maryland Campus, Rockville, Maryland, United States of America
| | - Marcus Gillis
- J. Craig Venter Institute, Maryland Campus, Rockville, Maryland, United States of America
| | - Melissa Cregger
- The Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Andres Gomez
- The Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Mengfei Ho
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Steven R. Leigh
- Department of Anthropology, University of Illinois, Urbana, Illinois, United States of America
| | - Rebecca Stumpf
- Department of Anthropology, University of Illinois, Urbana, Illinois, United States of America
| | - Douglas J. Creedon
- The Department of Obstetrics and Gynecology, The Mayo Clinic, Rochester, Minnesota, United States of America
| | - Michael A. Smith
- Department of Obstetrics and Gynecology, Christie Clinic, Urbana, Illinois, United States of America
| | - Jon S. Weisbaum
- Department of Obstetrics and Gynecology, Carle Clinic, Urbana, Illinois, United States of America
| | - Karen E. Nelson
- J. Craig Venter Institute, Maryland Campus, Rockville, Maryland, United States of America
| | - Brenda A. Wilson
- The Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Bryan A. White
- The Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
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Parahitiyawa NB, Scully C, Leung WK, Yam WC, Jin LJ, Samaranayake LP. Exploring the oral bacterial flora: current status and future directions. Oral Dis 2009; 16:136-45. [PMID: 19627515 DOI: 10.1111/j.1601-0825.2009.01607.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE The oral cavity forms an indispensable part of the human microbiome, for its unique and diverse microflora distributed within various niches. While majority of these organisms exhibit commensalism, shifts in bacterial community dynamics cause pathological changes within oral cavity and distant sites. The aim of this review was to appraise the current and emerging methods of detecting bacteria of the oral cavity paying particular attention to the cultivation independent methods. DESIGN Literature pertaining to cultivation based and cultivation independent methods of oral bacterial identification was reviewed. METHODS The specific advantages and disadvantages of cultivation based, microscopic, immunological and metagenomic identification methods were appraised. RESULTS Because of their fastidious and exacting growth requirements, cultivation based studies grossly underestimate the extent of bacterial diversity in these polymicrobial infections. Culture independent methods deemed more sensitive in identifying difficult to culture and novel bacterial species. CONCLUSION Apart from characterizing potentially novel bacterial species, the nucleic acid sequence data analyzed using various bioinformatics protocols have revealed that there are in excess of 700 bacterial species inhabiting the mouth. Moreover, the latest pyrosequencing based methods have further broadened the extent of bacterial diversity in oral niches.
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Affiliation(s)
- N B Parahitiyawa
- Oral Biosciences, Faculty of Dentistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
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Downes J, Vartoukian SR, Dewhirst FE, Izard J, Chen T, Yu WH, Sutcliffe IC, Wade WG. Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum 'Synergistetes' isolated from the human oral cavity. Int J Syst Evol Microbiol 2009; 59:972-80. [PMID: 19406777 DOI: 10.1099/ijs.0.000364-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Four strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group distinct from any species with validly published names. 16S rRNA and 23S rRNA gene sequence analyses and DNA-DNA reassociation data revealed that the strains constituted a novel group within the phylum 'Synergistetes' and were most closely related to Jonquetella anthropi. Two libraries of randomly cloned DNA were prepared from strain W5455(T) and were sequenced to provide a genome survey as a resource for metagenomic studies. A new genus and novel species, Pyramidobacter piscolens gen. nov., sp. nov., is proposed to accommodate these strains. The genus Pyramidobacter comprises strains that are anaerobic, non-motile, asaccharolytic bacilli that produce acetic and isovaleric acids and minor to trace amounts of propionic, isobutyric, succinic and phenylacetic acids as end products of metabolism. P. piscolens gen. nov., sp. nov. produced hydrogen sulphide but was otherwise largely biochemically unreactive. Growth was stimulated by the addition of glycine to broth media. The G+C content of the DNA of the type strain was 59 mol%. The type strain of Pyramidobacter piscolens sp. nov. is W5455(T) (=DSM 21147(T)=CCUG 55836(T)).
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Affiliation(s)
- Julia Downes
- King's College London Dental Institute, Infection Research Group, London SE1 9RT, UK
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García-Sánchez JE, José Fresnadillo M, García-Sánchez E. [New anaerobic bacterial species in human infections]. Enferm Infecc Microbiol Clin 2009; 28:173-84. [PMID: 19477040 DOI: 10.1016/j.eimc.2008.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 09/18/2008] [Accepted: 09/19/2008] [Indexed: 10/20/2022]
Abstract
This review offers succinct, precise, and complete information based on the available data concerning new anaerobic bacterial species involved in infectious diseases in humans. All hitherto undescribed species, those not previously implicated in clinical conditions, those with confirmed implication in human disease that have not been characterized, and those that have undergone taxonomic changes are considered to be "new".
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44
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Morotomi M, Nagai F, Sakon H, Tanaka R. Dialister succinatiphilus sp. nov. and Barnesiella intestinihominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2009; 58:2716-20. [PMID: 19060046 DOI: 10.1099/ijs.0.2008/000810-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Two anaerobic, non-spore-forming, bacteria (YIT 11850(T) and YIT 11860(T)) that stained Gram-negative, were isolated from human faeces. Cells of strain YIT 11850(T) were coccobacilli, asaccharolytic and largely unreactive, with only traces of lactate and propionate as metabolic end products; however, strain YIT 11850(T) was able to decarboxylate succinate to propionate. The DNA G+C content of strain YIT 11850(T) was 51.9 mol%. Following 16S rRNA gene sequence analysis, this strain was found to be most closely related to Dialister propionicifaciens, with 95.1 % sequence similarity between the two taxa. Biochemical data supported the affiliation of strain YIT 11850(T) to the genus Dialister. Strain YIT 11850(T) therefore represents a novel species for which the name Dialister succinatiphilus sp. nov. is proposed; the type strain is YIT 11850(T) (=DSM 21274(T)=JCM 15077(T)). Cells of the other isolate, strain YIT 11860(T), were non-motile, rod-shaped, positive for aesculin hydrolysis, negative for indole production, produced succinic and acetic acids as end products of glucose metabolism and possessed a DNA G+C content of 45.5 mol%. On the basis of 16S rRNA gene sequence similarity values, this strain was shown to belong to the family 'Porphyromonadaceae' related to Barnesiella viscericola (96.0 %); similarity values with species within the family 'Porphyromonadaceae' with validly published names were less than 86 %. Biochemical data supported the affiliation of strain YIT 11860(T) to the genus Barnesiella. Strain YIT 11860(T) therefore represents a novel species for which the name Barnesiella intestinihominis sp. nov. is proposed; the type strain is YIT 11860(T) (=DSM 21032(T)=JCM 15079(T)).
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Affiliation(s)
- Masami Morotomi
- Yakult Central Institute for Microbiological Research, Kunitachi, Tokyo, Japan.
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Kalmokoff ML, Austin JW, Cyr TD, Hefford MA, Teather RM, Selinger LB. Physical and genetic characterization of an outer-membrane protein (OmpM1) containing an N-terminal S-layer-like homology domain from the phylogenetically Gram-positive gut anaerobe Mitsuokella multacida. Anaerobe 2009; 15:74-81. [PMID: 19344649 DOI: 10.1016/j.anaerobe.2009.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 06/17/2008] [Accepted: 01/09/2009] [Indexed: 12/12/2022]
Abstract
Thin sectioning and freeze-fracture-etch of the ovine ruminal isolate Mitsuokella multacida strain 46/5(2) revealed a Gram-negative envelope ultra-structure consisting of a peptidoglycan wall overlaid by an outer membrane. Sodium-dodecyl-sulfate-polyacrylamide gel electrophoretic (SDS-PAGE) analysis of whole cells, cell envelopes and Triton X-100 extracted envelopes in combination with thin-section and N-terminal sequence analyses demonstrated that the outer membrane contained two major proteins (45 and 43 kDa) sharing identical N-termini (A-A-N-P-F-S-D-V-P-A-D-H-W-A-Y-D). A gene encoding a protein with a predicted N-terminus identical to those of the 43 and 45 kDa outer-membrane proteins was cloned. The 1290 bp open reading frame encoded a 430 amino acid polypeptide with a predicted molecular mass of 47,492 Da. Cleavage of a predicted 23 amino acid leader sequence would yield a protein with a molecular mass of 45,232 Da. Mass spectroscopic analysis confirmed that the cloned gene (ompM1) encoded the 45 kDa outer-membrane protein. The N-terminus of the mature OmpM1 protein (residues 24-70) shared homology with surface-layer homology (SLH) domains found in a wide variety of regularly structured surface-layers (S-layers). However, the outer-membrane locale, resistance to denaturation by SDS and high temperatures and the finding that the C-terminal residue was a phenylalanine suggested that ompM1 encoded a porin. Threading analysis in combination with the identification of membrane spanning domains indicated that the C-terminal region of OmpM1 (residues 250-430) likely forms a 16-strand beta-barrel and appears to be related to the unusual N-terminal SLH-domain-containing beta-barrel-porins previously described in the cyanobacterium Synechococcus PCC6301.
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Affiliation(s)
- M L Kalmokoff
- Atlantic Food and Horticulture Research Centre, Agriculture and Agri-Food Canada, Kentville, NS, Canada
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Woo P, Lau S, Teng J, Tse H, Yuen KY. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect 2008; 14:908-34. [DOI: 10.1111/j.1469-0691.2008.02070.x] [Citation(s) in RCA: 524] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Jacinto RC, Gomes BPFA, Desai M, Rajendram D, Shah HN. Bacterial examination of endodontic infections by clonal analysis in concert with denaturing high-performance liquid chromatography. ACTA ACUST UNITED AC 2007; 22:403-10. [PMID: 17949344 DOI: 10.1111/j.1399-302x.2007.00378.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND/AIMS The aim of this study was to examine the diversity of bacterial species in the infected root canals of teeth associated with endodontic abscesses by cloning and sequencing techniques in concert with denaturing high-performance liquid chromatography. METHODS Samples collected from five infected root canals were subjected to polymerase chain reaction (PCR) with universal 16S ribosomal DNA primers. Products of these PCRs were cloned and sequenced. Denaturing high-performance liquid chromatography (DHPLC) was used as a screening method to reduce the number of clones necessary for DNA sequencing. RESULTS All samples were positive for the presence of bacteria and a range of 7-13 different bacteria were found per root canal sample. In total, 48 different oral clones were detected among the five root canal samples. Olsenella profusa was the only species present in all samples. Porphyromonas gingivalis, Dialister pneumosintes, Dialister invisus, Lachnospiraceae oral clone, Staphylococcus aureus, Pseudoramibacter alactolyticus, Peptostreptococcus micros and Enterococcus faecalis were found in two of the five samples. The majority of the taxa were present in only one sample, for example Tannerella forsythia, Shuttleworthia satelles and Filifactor alocis. Some facultative anaerobes that are frequently isolated from endodontic infections such as E. faecalis, Streptococcus anginosus and Lactobacillus spp. were also found in this study. CONCLUSION Clonal analysis of the microflora associated with endodontic infections revealed a wide diversity of oral species.
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Affiliation(s)
- R C Jacinto
- Department of Restorative Dentistry, Endodontic Area, Piracicaba Dental School, State University of Campinas-UNICAMP, Piracicaba, SP, Brazil
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Rajilić-Stojanović M, Smidt H, de Vos WM. Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 2007; 9:2125-36. [PMID: 17686012 DOI: 10.1111/j.1462-2920.2007.01369.x] [Citation(s) in RCA: 412] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.
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Affiliation(s)
- Mirjana Rajilić-Stojanović
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands.
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Antimicrobial susceptibilities and clinical sources of Dialister species. Antimicrob Agents Chemother 2007; 51:4498-501. [PMID: 17923492 DOI: 10.1128/aac.00538-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seventy-four strains representing the four species of the genus Dialister were isolated from various clinical samples. Dialister pneumosintes and Dialister micraerophilus were the two mainly encountered species. Fifty-five isolates were tested against 14 antimicrobial agents. Decreased susceptibilities to piperacillin, metronidazole, macrolides, fluoroquinolones, and rifampin were demonstrated. The clinical impact of these decreased susceptibilities remains to be investigated but should prompt microbiologists to perform antimicrobial susceptibility testing for clinically important Dialister spp.
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Siqueira JF, Rôças IN, Paiva SSM, Magalhães KM, Guimarães-Pinto T. Cultivable bacteria in infected root canals as identified by 16S rRNA gene sequencing. ACTA ACUST UNITED AC 2007; 22:266-71. [PMID: 17600539 DOI: 10.1111/j.1399-302x.2007.00355.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Traditionally, cultivable bacteria isolated from infected root canals have been identified by phenotype-based methods. Because 16S ribosomal RNA (rRNA) gene sequencing has emerged as a more accurate and reliable tool for bacterial identification, the present study applied this approach to identify bacterial isolates recovered from the root canals of teeth with chronic apical periodontitis. METHODS Anaerobic techniques were used for culturing; identification of the isolates was carried out by polymerase chain reaction amplification and sequencing of the V5-V8 region of the 16S rRNA gene. Bacteria were found in all samples. The mean number of taxa per canal was 3.1, ranging from 2 to 8. The median number of cultivable bacterial cells in the root canals was 4.2 x 10(5), ranging from 2.8 x 10(3) to 3.3 x 10(7). Eighty-seven strains belonging to 52 bacterial taxa were identified. The most prevalent taxa were Fusobacterium nucleatum, Porphyromonas gingivalis, Pseudoramibacter alactolyticus, Micromonas micros and streptococci. The following bacterial phyla were represented in this study: Firmicutes (22 taxa, 46% of the identified isolates), Actinobacteria (14 taxa, 25.3% of the isolates), Bacteroidetes (eight taxa, 13.8% of the isolates), Fusobacteria (three taxa, 9.2% of the isolates) and Proteobacteria (five taxa, 5.7% of the isolates). Some of the isolates represented unnamed species not previously cultivated and characterized. In conclusion, our findings using a combined anaerobic culture-molecular identification approach confirmed the polymicrobial nature of primary endodontic infections with dominance of anaerobic bacteria. Notably several bacteria that are difficult or impossible to identify by phenotypic means were identified, including previously uncultivated taxa, cultivated-but-not-yet-characterized taxa and newly named species.
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Affiliation(s)
- J F Siqueira
- Department of Endodontics, Estácio de Sá University, Rio de Janeiro, RJ, Brazil
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