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Laumen JGE, Abdellati S, Van Dijck C, Martiny D, De Baetselier I, Manoharan-Basil SS, Van den Bossche D, Kenyon C. A Novel Method to Assess Antimicrobial Susceptibility in Commensal Oropharyngeal Neisseria-A Pilot Study. Antibiotics (Basel) 2022; 11:100. [PMID: 35052976 PMCID: PMC8772996 DOI: 10.3390/antibiotics11010100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
Commensal Neisseria provide a reservoir of resistance genes that can be transferred to the pathogens Neisseria gonorrhoeae and N. meningitidis in the human oropharynx. Surveillance programs are thus needed to monitor resistance in oropharyngeal commensal Neisseria, but currently the isolation and antimicrobial susceptibility testing of these commensals is laborious, complex and expensive. In addition, the posterior oropharyngeal/tonsillar swab, which is commonly used to sample oropharyngeal Neisseria, is poorly tolerated by many individuals. We evaluated an alternative non-invasive method to isolate oropharyngeal commensal Neisseria and to detect decreased susceptibility to azithromycin using selective media (LBVT.SNR) with and without azithromycin (2 µg/mL). In this pilot study, we compared paired posterior oropharyngeal/tonsillar swabs and oral rinse-and-gargle samples from 10 participants and demonstrated that a similar Neisseria species diversity and number of colonies were isolated from both sample types. Moreover, the proportion of Neisseria colonies that had a decreased susceptibility to azithromycin was similar in the rinse samples compared to the swabs. This pilot study has produced encouraging data that a simple protocol of oral rinse-and-gargle and culture on plates selective for commensal Neisseria with and without a target antimicrobial can be used as a surveillance tool to monitor antimicrobial susceptibility in commensal oropharyngeal Neisseria. Larger studies are required to validate these findings.
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Affiliation(s)
- Jolein Gyonne Elise Laumen
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (C.V.D.); (S.S.M.-B.); (C.K.)
- Laboratory of Medical Microbiology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Saïd Abdellati
- Clinical and Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (I.D.B.); (D.V.d.B.)
| | - Christophe Van Dijck
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (C.V.D.); (S.S.M.-B.); (C.K.)
- Laboratory of Medical Microbiology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles-Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles, 1000 Brussels, Belgium;
- Faculté de Médecine et Pharmacie, Université de Mons, 7000 Mons, Belgium
| | - Irith De Baetselier
- Clinical and Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (I.D.B.); (D.V.d.B.)
| | - Sheeba Santhini Manoharan-Basil
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (C.V.D.); (S.S.M.-B.); (C.K.)
| | - Dorien Van den Bossche
- Clinical and Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (I.D.B.); (D.V.d.B.)
| | - Chris Kenyon
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (C.V.D.); (S.S.M.-B.); (C.K.)
- Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town 7700, South Africa
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The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial. Microbiol Spectr 2022; 10:e0175721. [PMID: 35019769 PMCID: PMC8754113 DOI: 10.1128/spectrum.01757-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mouthwash is a commonly used product and has been proposed as an alternative intervention to prevent gonorrhea transmission. However, the long-term effects of mouthwash on the oral microbiota are largely unknown. We investigated the impact of 12 weeks of daily mouthwash use on the oropharyngeal microbiota in a subset of men who have sex with men who participated in a randomized trial comparing the efficacy of two alcohol-free mouthwashes for the prevention of gonorrhea. We characterized the oropharyngeal microbiota using 16S rRNA gene sequencing of tonsillar fossae samples collected before and after 12 weeks of daily use of Listerine mouthwash or Biotène dry mouth oral rinse. Permutational multivariate analysis of variance (PERMANOVA) was used to assess differences in oropharyngeal microbiota composition following mouthwash use. Differential abundance testing was performed using ALDEx2, with false-discovery rate correction. A total of 306 samples from 153 men were analyzed (Listerine, n = 78 and Biotène, n = 75). There was no difference in the overall structure of the oropharyngeal microbiota following Listerine or Biotène use (PERMANOVA P = 0.413 and P = 0.331, respectively). Although no bacterial taxa were significantly differentially abundant following Listerine use, we observed a small but significant decrease in the abundance of both Streptococcus and Leptotrichia following Biotène use. Overall, our findings suggest that daily use of antiseptic mouthwash has minimal long-term effects on the composition of the oropharyngeal microbiota. IMPORTANCE Given the role of the oral microbiota in human health, it is important to understand if and how external factors influence its composition. Mouthwash use is common in some populations, and the use of antiseptic mouthwash has been proposed as an alternative intervention to prevent gonorrhea transmission. However, the long-term effect of mouthwash use on the oral microbiota composition is largely unknown. We found that daily use of two different commercially available mouthwashes had limited long-term effects on the composition of the oropharyngeal microbiota over a 12-week period. The results from our study and prior studies highlight that different mouthwashes may differentially affect the oral microbiome composition and that further studies are needed to determine if mouthwash use induces short-term changes to the oral microbiota that may have detrimental effects.
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Jacob KM, Reguera G. Competitive advantage of oral streptococci for colonization of the middle ear mucosa. Biofilm 2022; 4:100067. [PMID: 35146417 PMCID: PMC8818537 DOI: 10.1016/j.bioflm.2022.100067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/17/2021] [Accepted: 01/10/2022] [Indexed: 10/29/2022] Open
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Investigation of Sources, Diversity, and Variability of Bacterial Aerosols in Athens, Greece: A Pilot Study. ATMOSPHERE 2021. [DOI: 10.3390/atmos13010045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We characterized the composition, diversity, and potential bacterial aerosol sources in Athens’ urban air by DNA barcoding (analysis of 16S rRNA genes) during three seasons in 2019. Air samples were collected using the recently developed Rutgers Electrostatic Passive Sampler (REPS). It is the first field application of REPS to study bacterial aerosol diversity. REPS samplers captured a sufficient amount of biological material to demonstrate the diversity of airborne bacteria and their variability over time. Overall, in the air of Athens, we detected 793 operational taxonomic units (OTUs), which were fully classified into the six distinct taxonomic categories (Phylum, Class, Order, etc.). These OTUs belonged to Phyla Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Fusobacteria. We found a complex community of bacterial aerosols with several opportunistic or potential pathogens in Athens’ urban air. Referring to the available literature, we discuss the likely sources of observed airborne bacteria, including soil, plants, animals, and humans. Our results on bacterial diversity are comparable to earlier studies, even though the sampling sites are different or geographically distant. However, the exact functional and ecological role of bioaerosols and, even more importantly, their impact on public health and the ecosystem requires further air monitoring and analysis.
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Evaluation of Changes to the Oral Microbiome Based on 16S rRNA Sequencing among Children Treated for Cancer. Cancers (Basel) 2021; 14:cancers14010007. [PMID: 35008173 PMCID: PMC8750156 DOI: 10.3390/cancers14010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Childhood cancer survivors suffer from many oral complications during and after primary therapy. Our study focuses on changes in the oral microbiome of cancer survivors. Using 16S rRNA sequencing, we observed global and distinct changes in oral microbiome associated with a patient’s age and therapy duration, but not antibiotic therapy or cancer type. Observed changes in the oral microbiome could differentiate patients at higher risk of long-term oral complications. Abstract A child’s mouth is the gateway to many species of bacteria. Changes in the oral microbiome may affect the health of the entire body. The aim of the study was to evaluate the changes in the oral microbiome of childhood cancer survivors. Saliva samples before and after anti-cancer treatment were collected from 20 patients aged 6–18 years, diagnosed de novo with cancer in 2018–2019 (7 girls and 13 boys, 7.5–19 years old at the second time point). Bacterial DNA was extracted, and the microbial community profiles were assessed by 16S rRNA sequencing. The relative abundances of Cellulosilyticum and Tannerella genera were found to significantly change throughout therapy (p = 0.043 and p = 0.036, respectively). However, no differences in the alpha-diversity were observed (p = 0.817). The unsupervised classification revealed two clusters of patients: the first with significant changes in Campylobacter and Fusobacterium abundance, and the other with change in Neisseria. These two groups of patients differed in median age (10.25 vs. 16.16 years; p = 0.004) and the length of anti-cancer therapy (19 vs. 4 months; p = 0.003), but not cancer type or antibiotic treatment.
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Biogeography of Bacterial Communities and Specialized Metabolism in Human Aerodigestive Tract Microbiomes. Microbiol Spectr 2021; 9:e0166921. [PMID: 34704787 PMCID: PMC8549736 DOI: 10.1128/spectrum.01669-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The aerodigestive tract (ADT) is the primary portal through which pathogens and other invading microbes enter the body. As the direct interface with the environment, we hypothesize that the ADT microbiota possess biosynthetic gene clusters (BGCs) for antibiotics and other specialized metabolites to compete with both endogenous and exogenous microbes. From 1,214 bacterial genomes, representing 136 genera and 387 species that colonize the ADT, we identified 3,895 BGCs. To determine the distribution of BGCs and bacteria in different ADT sites, we aligned 1,424 metagenomes, from nine different ADT sites, onto the predicted BGCs. We show that alpha diversity varies across the ADT and that each site is associated with distinct bacterial communities and BGCs. We identify specific BGC families enriched in the buccal mucosa, external naris, gingiva, and tongue dorsum despite these sites harboring closely related bacteria. We reveal BGC enrichment patterns indicative of the ecology at each site. For instance, aryl polyene and resorcinol BGCs are enriched in the gingiva and tongue, which are colonized by many anaerobes. In addition, we find that streptococci colonizing the tongue and cheek possess different ribosomally synthesized and posttranslationally modified peptide BGCs. Finally, we highlight bacterial genera with BGCs but are underexplored for specialized metabolism and demonstrate the bioactivity of Actinomyces against other bacteria, including human pathogens. Together, our results demonstrate that specialized metabolism in the ADT is extensive and that by exploring these microbiomes further, we will better understand the ecology and biogeography of this system and identify new bioactive natural products. IMPORTANCE Bacteria produce specialized metabolites to compete with other microbes. Though the biological activities of many specialized metabolites have been determined, our understanding of their ecology is limited, particularly within the human microbiome. As the aerodigestive tract (ADT) faces the external environment, bacteria colonizing this tract must compete both among themselves and with invading microbes, including human pathogens. We analyzed the genomes of ADT bacteria to identify biosynthetic gene clusters (BGCs) for specialized metabolites. We found that the majority of ADT BGCs are uncharacterized and the metabolites they encode are unknown. We mapped the distribution of BGCs across the ADT and determined that each site is associated with its own distinct bacterial community and BGCs. By further characterizing these BGCs, we will inform our understanding of ecology and biogeography across the ADT, and we may uncover new specialized metabolites, including antibiotics.
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Mullally CA, Mikucki A, Wise MJ, Kahler CM. Modelling evolutionary pathways for commensalism and hypervirulence in Neisseria meningitidis. Microb Genom 2021; 7. [PMID: 34704920 PMCID: PMC8627216 DOI: 10.1099/mgen.0.000662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Neisseria meningitidis, the meningococcus, resides exclusively in humans and causes invasive meningococcal disease (IMD). The population of N. meningitidis is structured into stable clonal complexes by limited horizontal recombination in this naturally transformable species. N. meningitidis is an opportunistic pathogen, with some clonal complexes, such as cc53, effectively acting as commensal colonizers, while other genetic lineages, such as cc11, are rarely colonizers but are over-represented in IMD and are termed hypervirulent. This study examined theoretical evolutionary pathways for pathogenic and commensal lineages by examining the prevalence of horizontally acquired genomic islands (GIs) and loss-of-function (LOF) mutations. Using a collection of 4850 genomes from the BIGSdb database, we identified 82 GIs in the pan-genome of 11 lineages (10 hypervirulent and one commensal lineage). A new computational tool, Phaser, was used to identify frameshift mutations, which were examined for statistically significant association with genetic lineage. Phaser identified a total of 144 frameshift loci of which 105 were shown to have a statistically significant non-random distribution in phase status. The 82 GIs, but not the LOF loci, were associated with genetic lineage and invasiveness using the disease carriage ratio metric. These observations have been integrated into a new model that infers the early events of the evolution of the human adapted meningococcus. These pathways are enriched for GIs that are involved in modulating attachment to the host, growth rate, iron uptake and toxin expression which are proposed to increase competition within the meningococcal population for the limited environmental niche of the human nasopharynx. We surmise that competition for the host mucosal surface with the nasopharyngeal microbiome has led to the selection of isolates with traits that enable access to cell types (non-phagocytic and phagocytic) in the submucosal tissues leading to an increased risk for IMD.
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Affiliation(s)
- Christopher A. Mullally
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - August Mikucki
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - Michael J. Wise
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia
| | - Charlene M. Kahler
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
- Telethon Kids Institute, Perth Children’s Hospital, Perth, Australia
- *Correspondence: Charlene M. Kahler,
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de Castilhos J, Zamir E, Hippchen T, Rohrbach R, Schmidt S, Hengler S, Schumacher H, Neubauer M, Kunz S, Müller-Esch T, Hiergeist A, Gessner A, Khalid D, Gaiser R, Cullin N, Papagiannarou SM, Beuthien-Baumann B, Krämer A, Bartenschlager R, Jäger D, Müller M, Herth F, Duerschmied D, Schneider J, Schmid RM, Eberhardt JF, Khodamoradi Y, Vehreschild MJGT, Teufel A, Ebert MP, Hau P, Salzberger B, Schnitzler P, Poeck H, Elinav E, Merle U, Stein-Thoeringer CK. Severe Dysbiosis and Specific Haemophilus and Neisseria Signatures as Hallmarks of the Oropharyngeal Microbiome in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients. Clin Infect Dis 2021; 75:e1063-e1071. [PMID: 34694375 PMCID: PMC8586732 DOI: 10.1093/cid/ciab902] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND At the entry site of respiratory virus infections, the oropharyngeal microbiome has been proposed as a major hub integrating viral and host immune signals. Early studies suggested that infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are associated with changes of the upper and lower airway microbiome, and that specific microbial signatures may predict coronavirus disease 2019 (COVID-19) illness. However, the results are not conclusive, as critical illness can drastically alter a patient's microbiome through multiple confounders. METHODS To study oropharyngeal microbiome profiles in SARS-CoV-2 infection, clinical confounders, and prediction models in COVID-19, we performed a multicenter, cross-sectional clinical study analyzing oropharyngeal microbial metagenomes in healthy adults, patients with non-SARS-CoV-2 infections, or with mild, moderate, and severe COVID-19 (n = 322 participants). RESULTS In contrast to mild infections, patients admitted to a hospital with moderate or severe COVID-19 showed dysbiotic microbial configurations, which were significantly pronounced in patients treated with broad-spectrum antibiotics, receiving invasive mechanical ventilation, or when sampling was performed during prolonged hospitalization. In contrast, specimens collected early after admission allowed us to segregate microbiome features predictive of hospital COVID-19 mortality utilizing machine learning models. Taxonomic signatures were found to perform better than models utilizing clinical variables with Neisseria and Haemophilus species abundances as most important features. CONCLUSIONS In addition to the infection per se, several factors shape the oropharyngeal microbiome of severely affected COVID-19 patients and deserve consideration in the interpretation of the role of the microbiome in severe COVID-19. Nevertheless, we were able to extract microbial features that can help to predict clinical outcomes.
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Affiliation(s)
- Juliana de Castilhos
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,Vale do Rio dos Sinos University (UNISINOS), Sao Leopoldo, Brazil
| | - Eli Zamir
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Theresa Hippchen
- Department of Gastroenterology and Infectious Diseases, University Clinic Heidelberg, Heidelberg, Germany
| | - Roman Rohrbach
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Sabine Schmidt
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Silvana Hengler
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Hanna Schumacher
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Melanie Neubauer
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Sabrina Kunz
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - Tonia Müller-Esch
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Clinic Regensburg, Regensburg, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Clinic Regensburg, Regensburg, Germany
| | - Dina Khalid
- Department of Virology, University Clinic Heidelberg, Heidelberg, Germany
| | - Rogier Gaiser
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Nyssa Cullin
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Stamatia M Papagiannarou
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | | | - Alwin Krämer
- German Cancer Research Center (DKFZ), Research Division Molecular Hematology/Oncology, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany,German Cancer Research Center (DKFZ), Research Division Virus-associated Carcinogenesis, Heidelberg
| | - Dirk Jäger
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Michael Müller
- Thoraxklinik and Translational Lung Research Center, Heidelberg University, Heidelberg, Germany
| | - Felix Herth
- Thoraxklinik and Translational Lung Research Center, Heidelberg University, Heidelberg, Germany
| | - Daniel Duerschmied
- Department of Internal Medicine III, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jochen Schneider
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Roland M Schmid
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Johann F Eberhardt
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Andreas Teufel
- Department of Medicine II, Section of Hepatology, University Medical Center Mannheim, University of Heidelberg, Mannheim, and Center for Preventive Medicine and Digital Health Baden-Württemberg, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, Section of Hepatology, University Medical Center Mannheim, University of Heidelberg, Mannheim, and Center for Preventive Medicine and Digital Health Baden-Württemberg, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Peter Hau
- Wilhelm Sander-NeuroOncology Unit and Department of Neurology, University Clinic Regensburg, Regensburg, Germany
| | - Bernd Salzberger
- Department of Infectious Disease, University Clinic Regensburg, Regensburg, Germany
| | - Paul Schnitzler
- Department of Virology, University Clinic Heidelberg, Heidelberg, Germany
| | - Hendrik Poeck
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany,National Center for Tumor Diseases (NCT) WERA
| | - Eran Elinav
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,Weizmann Institute of Science, Rehovot, Israel
| | - Uta Merle
- Department of Gastroenterology and Infectious Diseases, University Clinic Heidelberg, Heidelberg, Germany
| | - Christoph K Stein-Thoeringer
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany,Corresponding author: Christoph K. Stein-Thoeringer, MD, Microbiome and Cancer Research Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany,
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Gunathilake M, Lee J, Choi IJ, Kim YI, Kim J. Association between bacteria other than Helicobacter pylori and the risk of gastric cancer. Helicobacter 2021; 26:e12836. [PMID: 34268831 DOI: 10.1111/hel.12836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND The gastric microbiota, including Helicobacter pylori (HP), has a remarkable role in gastric cancer (GC) occurrence. Evidence for the role of non-HP bacteria in GC risk is limited. We aimed to observe the association between bacteria other than HP and risk of GC in a Korean population. METHODS In this study, 268 GC cases and 288 healthy controls were included. Demographic data and total energy intake data were collected using a general questionnaire and a semiquantitative food frequency questionnaire, respectively. 16S rRNA gene sequencing was performed using DNA extracted from gastric biopsy samples. RESULTS Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and non-HP Proteobacteria were the five main phyla in the gastric environment. The five phyla were negatively related to the relative abundance of Helicobacter species (all p < 0.001). The Shannon index, richness, and Pilou-evenness were negatively correlated with Helicobacter species (all p < 0.001), while the microbial dysbiosis index was positively correlated with Helicobacter species (p < 0.001). Participants with a higher relative abundance of Actinobacteria species showed a significantly increased risk of GC (OR: 3.16, 95% CI = 1.92-5.19, p-trend<0.001). The non-HP microbiota composition among the four groups (HP+cases, HP- cases, HP+controls, and HP- controls) was significantly different (ANOSIM R = 0.10, p = 0.001). CONCLUSION Other than HP, several bacterial species might be associated with GC risk. HP status and GC status could determine the differences in microbial compositions. Further large prospective studies are warranted to confirm our findings.
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Affiliation(s)
- Madhawa Gunathilake
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, Goyang-si, South Korea
| | - Jeonghee Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, Goyang-si, South Korea
| | - Il Ju Choi
- Center for Gastric Cancer, National Cancer Center Hospital, National Cancer Center, Goyang-si, South Korea
| | - Young-Il Kim
- Center for Gastric Cancer, National Cancer Center Hospital, National Cancer Center, Goyang-si, South Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, Goyang-si, South Korea
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Lee BG, Yang JI, Kim E, Geum SW, Park JH, Yeo MK. Investigation of bacterial and fungal communities in indoor and outdoor air of elementary school classrooms by 16S rRNA gene and ITS region sequencing. INDOOR AIR 2021; 31:1553-1562. [PMID: 33780050 DOI: 10.1111/ina.12825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 05/23/2023]
Abstract
The advent of high-throughput sequencing methods allowed researchers to fully characterize microbial community in environmental samples, which is crucial to better understand their health effects upon exposures. In our study, we investigated bacterial and fungal community in indoor and outdoor air of nine classrooms in three elementary schools in Seoul, Korea. The extracted bacterial 16S rRNA gene and fungal ITS regions were sequenced, and their taxa were identified. Quantitative polymerase chain reaction for total bacteria DNA was also performed. The bacterial community was richer in outdoor air than classroom air, whereas fungal diversity was similar indoors and outdoors. Bacteria such as Enhydrobacter, Micrococcus, and Staphylococcus that are generally found in human skin, mucous membrane, and intestine were found in great abundance. For fungi, Cladosporium, Clitocybe, and Daedaleopsis were the most abundant genera in classroom air and mostly related to outdoor plants. Bacterial community composition in classroom air was similar among all classrooms but differed from that in outdoor air. However, indoor and outdoor fungal community compositions were similar for the same school but different among schools. Our study indicated the main source of airborne bacteria in classrooms was likely human occupants; however, classroom airborne fungi most likely originated from outdoors.
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Affiliation(s)
- Bong Gu Lee
- Department of Applied Environmental Science, Graduate School Kyung Hee University, Yongin-si, Korea
| | - Jun Il Yang
- Department of Applied Environmental Science, Graduate School Kyung Hee University, Yongin-si, Korea
| | - Euna Kim
- Department of Applied Environmental Science, Graduate School Kyung Hee University, Yongin-si, Korea
| | - Sun Woo Geum
- Department of Applied Environmental Science, Graduate School Kyung Hee University, Yongin-si, Korea
| | - Ju-Hyeong Park
- Respiratory Health Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Min-Kyeong Yeo
- Department of Applied Environmental Science, Graduate School Kyung Hee University, Yongin-si, Korea
- Department of Environmental Science and Engineering, College of Engineering, Kyung Hee University, Yongin-si, Korea
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Abstract
Abstract
Neisseria sp. is a Gram-negative diplococcus bacterium usually present on the mucosal surfaces of animals without causing an obvious pathology. The objective of this study was to report the isolation of Neisseria sp. from severe cases of pyogranulomatous pneumonia with the formation of a Splendore-Hoeppli structure in two cats treated at a veterinary hospital. This paper suggests that the Neisseria genus members may be involved in lower respiratory tract infections in cats, with the molecular diagnosis being a necessary method for the correct identification of this bacteria in animals.
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Vimal J, Himal I, Kannan S. Role of microbial dysbiosis in carcinogenesis & cancer therapies. Indian J Med Res 2021; 152:553-561. [PMID: 34145094 PMCID: PMC8224166 DOI: 10.4103/ijmr.ijmr_1026_18] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human body supports a heterogeneous population of microorganisms. Every microorganism has the ability to contribute to the unique microenvironment around it. The aim of this review is to discuss the changes in the microbial population and their relative abundance across different ecosystems of the human body, the interactions within the microbial communities, metabolites they secrete to their external environment, their immunomodulatory functions, their signal transduction pathways and how these respond to environmental stimuli such as various diets, alcohol and drug consumption, smoking and finally suggest new therapeutic approaches. The microbiota may leads to cancer through inflammation mediated mechanisms which modulate immune responses, or produce carcinogenic metabolites and genotoxins, or deregulate cell proliferative signalling pathways. The identification of these molecular mechanisms in carcinogenesis may lead to better treatment strategies. In this review we have tried to explore the changes in microbial composition between cancer and normal tissues and what molecular mechanisms provide a connecting link between microbial dysbiosis and cancer.
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Affiliation(s)
- Joseph Vimal
- Laboratory of Cell Cycle Regulation & Molecular Oncology, Division of Cancer Research, Regional Cancer Centre (Research Centre, University of Kerala), Thiruvananthapuram, Kerala, India
| | - Iris Himal
- Laboratory of Cell Cycle Regulation & Molecular Oncology, Division of Cancer Research, Regional Cancer Centre (Research Centre, University of Kerala), Thiruvananthapuram, Kerala, India
| | - S Kannan
- Laboratory of Cell Cycle Regulation & Molecular Oncology, Division of Cancer Research, Regional Cancer Centre (Research Centre, University of Kerala), Thiruvananthapuram, Kerala, India
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63
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Roode GJ, Bütow KW, Naidoo S. Microbial contamination profile change over a 4-year period in nonoperated cleft soft palate. J Appl Microbiol 2021; 132:665-674. [PMID: 34180558 DOI: 10.1111/jam.15193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/16/2021] [Accepted: 06/10/2021] [Indexed: 11/29/2022]
Abstract
AIMS Surgical site infection is a major concern in cleft soft palate. Knowledge of the type, number and antimicrobial resistance of pathogens present preoperatively contribute to treatment success. The aim of this study is to determine whether or not the microbial contamination (diversity) preoperatively has changed since 2015. METHODS AND RESULTS Swabs were taken from the surgical site in 103 consecutive patients who presented for primary repair of the soft palate cleft. These were sent for microscopy, culture and sensitivity testing. Swabs were taken before disinfecting the site. Results were tabled and compared with two previous studies from the same facility. Out of 103 patients, 100 patients showed positive cultures with 42 different pathogenic micro-organisms identified. Most dominant pathogen was Klebsiella pneumoniae, 45.6%, increased by 28% from the previous two studies, with 93.6% of these pathogens resistant to one or more antimicrobials. Most of the other identified pathogens showed an alarming increase in occurrence, with a wide resistance to antimicrobials. CONCLUSIONS The increase in number and diversity of microbial contamination as well as their resistance to antimicrobials is a real concern. Ways of preventing postoperative infection in a natural way need to be explored. SIGNIFICANCE Surgeons need to be aware of constant changes in micro-organisms.
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Affiliation(s)
| | - Kurt-Wilhelm Bütow
- Maxillo-Facial and Oral Surgical Practice, Life-Wilgers Hospital, Lynnwood Ridge, South Africa
| | - Sharan Naidoo
- Maxillo-Facial and Oral Surgical Practice, Mediclinic Midstream Hospital, Lyttelton, South Africa.,Department of Maxillofacial and Oral surgery, Facial Deformity Clinic, University of Pretoria, Pretoria, South Africa
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64
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Clark SA, Gray S, Finn A, Borrow R. Colistin Sensitivity and Factor H-Binding Protein Expression among Commensal Neisseria Species. mSphere 2021; 6:e0017521. [PMID: 34133203 PMCID: PMC8265630 DOI: 10.1128/msphere.00175-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/28/2021] [Indexed: 11/20/2022] Open
Abstract
Many bacterial carriage studies utilize colistin-containing media to select for Neisseria meningitidis among the diverse human pharyngeal milieu. These studies commonly report the isolation of Neisseria commensal species, with carriage rates of around 1% or less typically observed. Here, we describe the isolation of N. cinerea and N. polysaccharea from pharyngeal swabs using nonselective agar and confirm they are unable to grow on colistin-containing media. We also demonstrated colistin sensitivity among archived Neisseria commensal strains, including N. cinerea, N. polysaccharea, N. mucosa, and N. subflava. The distribution of lptA among these strains indicated that, while the phosphoethanolamine (PEA) transferase encoded by this gene confers colistin resistance, other mechanisms may lead to reduced susceptibility in some lptA-deficient strains. The majority of the N. cinerea and N. polysaccharea isolates expressed medium to very high levels of factor H-binding protein (fHbp), an important meningococcal vaccine antigen. Sequence analysis showed that the commensal fHbp peptide variants were similar in sequence to fHbp variants typically observed among invasive meningococci. Altogether, these results not only suggest that Neisseria commensal strains could be carried at much higher rates than previously reported but also raise questions about the impact of protein-based meningococcal vaccines on these unencapsulated commensals. IMPORTANCE This study highlights the need for further work to accurately determine the pharyngeal carriage prevalence of Neisseria commensal bacteria (e.g., N. cinerea and N. polysaccharea) among the general population. Previous studies have clearly demonstrated the suppressive effect these commensal species can have on meningococcal colonization, and so the carriage prevalence of these species could be an important factor in the spread of meningococci through the population. Furthermore, the surface expression of the meningococcal vaccine antigen factor H-binding protein by many of these commensal strains could have important implications for the use of fHbp-containing vaccines. Carriage of these commensal species may influence the immune response to these vaccines, or conversely, the immune response elicited by vaccination may induce clearance of these potentially important members of the pharyngeal niche.
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Affiliation(s)
- Stephen A. Clark
- Meningococcal Reference Unit (MRU), Public Health England (PHE), Manchester, United Kingdom
| | - Steve Gray
- Meningococcal Reference Unit (MRU), Public Health England (PHE), Manchester, United Kingdom
| | - Adam Finn
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Ray Borrow
- Meningococcal Reference Unit (MRU), Public Health England (PHE), Manchester, United Kingdom
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65
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Risk factors, clinical features and outcomes of Neisseria keratitis. Int Ophthalmol 2021; 41:3361-3369. [PMID: 34047910 DOI: 10.1007/s10792-021-01898-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVE To describe the clinical features, risk factors and outcomes of Neisseria keratitis. METHODS This is a retrospective observational study wherein medical records of cases with microbiologically proven Neisseria keratitis were reviewed. Data pertaining to the underlying predisposing factors, clinical characteristics of the corneal ulcer, antibiotic susceptibility of the Neisseria species isolate from the corneal scraping, the treatment given, and outcomes were collected and analyzed. RESULTS Medical records of 60 patients (60 eyes) with Neisseria keratitis were reviewed. Among the causes of poor ocular surface as predisposing factor, vernal keratoconjunctivitis (n = 6 eyes), along with use of topical corticosteroids (n = 18 eyes) was the most common. The ulcer was characterized by a central infiltrate (31/60, 51.7%) involving up to the mid-stroma (43/60, 71.7%). Of the forty-four (73.3%) eyes with pure Neisseria keratitis, 31 eyes (72.1%) resolved with medical therapy alone while five eyes (11.6%) underwent therapeutic penetrating keratoplasty and in two (4.6%) eyes evisceration was performed. The other 5/44 (11.6%) patients were lost to follow-up. Resolution with medical therapy was found to be similar in cases with pure infection and mixed infection (p = 0.58). CONCLUSIONS Neisseria keratitis most commonly causes a mild form of keratitis and is often associated with the poor ocular surface or prior steroid use. In most cases medical therapy is sufficient for complete resolution of the keratitis.
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66
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Ahmad F, Farooq A, Khan MUG. Deep Learning Model for Pathogen Classification Using Feature Fusion and Data Augmentation. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200707143535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Bacterial pathogens are deadly for animals and humans. The ease of their dissemination, coupled
with their high capacity for ailment and death in infected individuals, makes them a threat to society.
Objective:
Due to high similarity among genera and species of pathogens, it is sometimes difficult for microbiologists to
differentiate between them. Their automatic classification using deep-learning models can help in reliable, and accurate
outcomes.
Method:
Deep-learning models, namely; AlexNet, GoogleNet, ResNet101, and InceptionV3 are used with numerous
variations including training model from scratch, fine-tuning without pre-trained weights, fine-tuning along with freezing
weights of initial layers, fine-tuning along with adjusting weights of all layers and augmenting the dataset by random
translation and reflection. Moreover, as the dataset is small, fine-tuning and data augmentation strategies are applied to
avoid overfitting and produce a generalized model. A merged feature vector is produced using two best-performing models
and accuracy is calculated by xgboost algorithm on the feature vector by applying cross-validation.
Results:
Fine-tuned models where augmentation is applied produces the best results. Out of these, two-best-performing
deep models i.e. (ResNet101, and InceptionV3) selected for feature fusion, produced a similar validation accuracy of 95.83
with a loss of 0.0213 and 0.1066, and a testing accuracy of 97.92 and 93.75, respectively. The proposed model used xgboost
to attained a classification accuracy of 98.17% by using 35-folds cross-validation.
Conclusion:
The automatic classification using these models can help experts in the correct identification of pathogens.
Consequently, they can help in controlling epidemics and thereby minimizing the socio-economic impact on the community.
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Affiliation(s)
- Fareed Ahmad
- Department of Computer Science and Engineering, Faculty of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Amjad Farooq
- Department of Computer Science and Engineering, Faculty of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Muhammad Usman Ghani Khan
- Department of Computer Science and Engineering, Faculty of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
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Mujica-Alarcon JF, Thornton SF, Rolfe SA. Long-term dynamic changes in attached and planktonic microbial communities in a contaminated aquifer. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 277:116765. [PMID: 33647805 DOI: 10.1016/j.envpol.2021.116765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
Biodegradation is responsible for most contaminant removal in plumes of organic compounds and is fastest at the plume fringe where microbial cell numbers and activity are highest. As the plume migrates from the source, groundwater containing the contaminants and planktonic microbial community encounters uncontaminated substrata on which an attached community subsequently develops. While attached microbial communities are important for biodegradation, the time needed for their establishment, their relationship with the planktonic community and the processes controlling their development are not well understood. We compare the dynamics of development of attached microbial communities on sterile substrata in the field and laboratory microcosms, sampled simultaneously at intervals over two years. We show that attached microbial cell numbers increased rapidly and stabilised after similar periods of incubation (∼100 days) in both field and microcosm experiments. These timescales were similar even though variation in the contaminant source evident in the field was absent in microcosm studies, implying that this period was an emergent property of the attached microbial community. 16S rRNA gene sequencing showed that attached and planktonic communities differed markedly, with many attached organisms strongly preferring attachment. Successional processes were evident, both in community diversity indices and from community network analysis. Community development was governed by both deterministic and stochastic processes and was related to the predilection of community members for different lifestyles and the geochemical environment.
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Affiliation(s)
- Juan F Mujica-Alarcon
- Groundwater Protection and Restoration Group, Department of Civil and Structural Engineering, University of Sheffield, Sheffield, United Kingdom; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Steven F Thornton
- Groundwater Protection and Restoration Group, Department of Civil and Structural Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Stephen A Rolfe
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.
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68
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McNally KL, Mott CR, Guertin JR, Bowen JL. Microbial communities of wild-captured Kemp’s ridley (Lepidochelys kempii) and green sea turtles (Chelonia mydas). ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Conservation efforts for endangered sea turtle species, such as Kemp’s ridley turtles Lepidochelys kempii and green turtles Chelonia mydas, may benefit from information on the microbial communities that contribute to host health. Previous studies examining host-associated microbiomes of these species have been limited in geographic region, life stage, and/or health. Here, we characterized the microbiome of the oral cavity and cloaca from wild-captured Kemp’s ridley and green turtles off the west coast of Florida, USA, by using Illumina sequencing to analyze the 16S rRNA gene. Microbial communities were distinct between body sites as well as between turtle species, suggesting that the turtle species is more important than the local environment in determining the microbiome of sea turtles. We identified the core microbiome for each species at each body site and determined that there were very few bacteria shared among the oral samples of both species, and no taxa co-occurred in the cloaca samples among both species. The core microbiome of the green turtle cloaca was primarily from the order Clostridiales, which plays an important role in digestion for other herbivorous species. Due to high prevalence of fibropapillomatosis in the green turtles (90%), we also investigated the correlation between the microbiome and the severity of fibropapillomatosis, and we identified changes in beta diversity associated with the total number of tumors. This study provides the first glimpse of the microbiome in 2 sympatric species of sea turtle and sheds an important species-specific light on the microbiome of these endangered species.
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Affiliation(s)
- KL McNally
- Animal Health Department, New England Aquarium, Boston, Massachusetts 02110, USA
- University of Massachusetts, Boston, Massachusetts 20125, USA
| | - CR Mott
- Inwater Research Group, Inc., Jensen Beach, Florida 34957, USA
| | - JR Guertin
- Inwater Research Group, Inc., Jensen Beach, Florida 34957, USA
| | - JL Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts 01908, USA
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Antimicrobial Resistance Profiles of Human Commensal Neisseria Species. Antibiotics (Basel) 2021; 10:antibiotics10050538. [PMID: 34066576 PMCID: PMC8148603 DOI: 10.3390/antibiotics10050538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/17/2022] Open
Abstract
Pathogenic Neisseria gonorrhoeae causes the sexually transmitted infection gonorrhea. N. gonorrhoeae has evolved high levels of antimicrobial resistance (AR) leading to therapeutic failures even in dual-therapy treatment with azithromycin and ceftriaxone. AR mechanisms can be acquired by genetic transfer from closely related species, such as naturally competent commensal Neisseria species. At present, little is known about the antimicrobial resistance profiles of commensal Neisseria. Here, we characterized the phenotypic resistance profile of four commensal Neisseria species (N. lactamica, N. cinerea, N. mucosa, and N. elongata) against 10 commonly used antibiotics, and compared their profiles to 4 N. gonorrhoeae strains, using disk diffusion and minimal inhibitory concentration assays. Overall, we observed that 3 of the 4 commensals were more resistant to several antibiotics than pathogenic N. gonorrhoeae strains. Next, we compared publicly available protein sequences of known AR genes, including penicillin-binding-protein 2 (PBP2) from commensals and N. gonorrhoeae strains. We found mutations in PBP2 known to confer resistance in N. gonorrhoeae also present in commensal Neisseria sequences. Our results suggest that commensal Neisseria have unexplored antibiotic resistance gene pools that may be exchanged with pathogenic N. gonorrhoeae, possibly impairing drug development and clinical treatment.
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70
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Altdorfer A, Pirotte BF, Gaspard L, Gregoire E, Firre E, Moerman F, Moonen M, Sanoussi A, Van Esbroeck M, Mori M. Infective endocarditis caused by Neisseria mucosa on a prosthetic pulmonary valve with false positive serology for Coxiella burnetii - The first described case. IDCases 2021; 24:e01146. [PMID: 34026536 PMCID: PMC8122163 DOI: 10.1016/j.idcr.2021.e01146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/30/2022] Open
Abstract
We present a case of infective endocarditis (IE) on a prosthetic pulmonary valve in a 36-year-old patient with tetralogy of Fallot (TOF). The patient underwent valve replacement surgery and active antibiotic treatment against Gram-negative cocci (Piperacillin Tazobactam then Ceftriaxone) for a total duration of 42 days with a favourable outcome. The causative agent was Neisseria mucosa which was identified on the infected valve by sequencing of 16S ribosomal RNA. To our knowledge, this is the first described case of a N. mucosa infective endocarditis on a pulmonary valve. Initially, serologies performed in clinical settings by immunofluorescence for Coxiella burnetii antibodies showed a major increase in phase I IgG titers at 1024 (normal values <16) corresponding with the diagnostic criteria for Q fever endocarditis. However, this diagnosis could not be confirmed by the National Reference Center, making it the first reported case of a false positive serology for C. burnetii during an infection due to Neisseria spp.
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Affiliation(s)
- Antoine Altdorfer
- Department of Infectious Diseases and Internal Medicine, CHR de la Citadelle, Liège, Belgium
| | - Benoit F Pirotte
- Department of Infectious Diseases and Internal Medicine, CHR de la Citadelle, Liège, Belgium
| | - Laura Gaspard
- Department of Infectious Diseases and Internal Medicine, CHR de la Citadelle, Liège, Belgium
| | - Emilien Gregoire
- Department of Infectious Diseases and Internal Medicine, CHR de la Citadelle, Liège, Belgium
| | - Eric Firre
- Department of Infectious Diseases and Internal Medicine, CHR de la Citadelle, Liège, Belgium
| | - Filip Moerman
- Department of Infectious Diseases and Internal Medicine, CHR de la Citadelle, Liège, Belgium
| | - Martial Moonen
- Department of Infectious Diseases and Internal Medicine, CHR de la Citadelle, Liège, Belgium
| | - Ahmed Sanoussi
- Department of Cardiothoracic Surgery, CHR de la Citadelle, Liège, Belgium
| | - Marjan Van Esbroeck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Marcella Mori
- Bacterial Zoonoses of Animals Unit, Veterinary Bacteriology, Sciensano, Brussels, Belgium
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Ciocan D, Cassard AM, Becquemont L, Verstuyft C, Voican CS, El Asmar K, Colle R, David D, Trabado S, Feve B, Chanson P, Perlemuter G, Corruble E. Blood microbiota and metabolomic signature of major depression before and after antidepressant treatment: a prospective case-control study. J Psychiatry Neurosci 2021; 46:E358-E368. [PMID: 34008933 PMCID: PMC8327971 DOI: 10.1503/jpn.200159] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The microbiota interacts with the brain through the gut-brain axis, and a distinct dysbiosis may lead to major depressive episodes. Bacteria can pass through the gut barrier and be found in the blood. Using a multiomic approach, we investigated whether a distinct blood microbiome and metabolome was associated with major depressive episodes, and how it was modulated by treatment. METHODS In this case-control multiomic study, we analyzed the blood microbiome composition, inferred bacterial functions and metabolomic profile of 56 patients experiencing a current major depressive episode and 56 matched healthy controls, before and after treatment, using 16S rDNA sequencing and liquid chromatography coupled to tandem mass spectrometry. RESULTS The baseline blood microbiome in patients with a major depressive episode was distinct from that of healthy controls (patients with a major depressive episode had a higher proportion of Janthinobacterium and lower levels of Neisseria) and changed after antidepressant treatment. Predicted microbiome functions confirmed by metabolomic profiling showed that patients who were experiencing a major depressive episode had alterations in the cyanoamino acid pathway at baseline. High baseline levels of Firmicutes and low proportions of Bosea and Tetrasphaera were associated with response to antidepressant treatment. Based on inferred baseline metagenomic profiles, bacterial pathways that were significantly associated with treatment response were related to xenobiotics, amino acids, and lipid and carbohydrate metabolism, including tryptophan and drug metabolism. Metabolomic analyses showed that plasma tryptophan levels are independently associated with response to antidepressant treatment. LIMITATIONS Our study has some limitations, including a lack of information on blood microbiome origin and the lack of a validation cohort to confirm our results. CONCLUSION Patients with depression have a distinct blood microbiome and metabolomic signature that changes after treatment. Dysbiosis could be a new therapeutic target and prognostic tool for the treatment of patients who are experiencing a major depressive episode.
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Affiliation(s)
- Dragos Ciocan
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Anne-Marie Cassard
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Laurent Becquemont
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Céline Verstuyft
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Cosmin Sebastian Voican
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Khalil El Asmar
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Romain Colle
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Denis David
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Séverine Trabado
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Bruno Feve
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Philippe Chanson
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Gabriel Perlemuter
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
| | - Emmanuelle Corruble
- From the INSERM UMRS 996 - Intestinal Microbiota, Macrophages and Liver Inflammation, DHU Hepatinov, Clamart, France (Ciocan, Cassard, Voican, Perlemuter); the University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, France (Ciocan, Cassard, Becquemont, Verstuyft, Voican, El Asmar, Colle, Trabado, Chanson, Perlemuter, Corruble); the APHP, Hepato-Gastroenterology and Nutrition, Antoine-Béclère Hospital, Clamart, France (Ciocan, Voican, Perlemuter); the Centre for Clinical Research (CRC), Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, France (Becquemont); the INSERM UMR-1178, CESP, "MOODS" Team, Le Kremlin-Bicêtre, France (Becquemont, Verstuyft, El Asmar, David, Corruble); the Department of Molecular Genetics, Pharmacogenetics and Hormones, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Becquemont, Verstuyft, Trabado); the Psychiatry Department, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Colle, Corruble); the University Paris-Saclay, University Paris-Sud, Faculty of Pharmacy, Chatenay-Malabry, 92 296, France (David); the INSERM 1185, University Paris-Saclay, University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicêtre, 94276, France (Trabado, Chanson); the Department of Endocrinology, Saint-Antoine Hospital, AP-HP, Sorbonne University, University Paris 6, Paris, France (Feve); the INSERM UMR S_938, Saint-Antoine Research Centre, Paris, France (Feve); and the Department of Endocrinology and Reproductive Diseases, Kremlin-Bicêtre Hospital, AP-HP, Le Kremlin-Bicêtre, 94275, France (Chanson)
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Lopez Leyva L, Gonzalez E, Li C, Ajeeb T, Solomons NW, Agellon LB, Scott ME, Koski KG. Human Milk Microbiota in an Indigenous Population Is Associated with Maternal Factors, Stage of Lactation, and Breastfeeding Practices. Curr Dev Nutr 2021; 5:nzab013. [PMID: 33898919 PMCID: PMC8053399 DOI: 10.1093/cdn/nzab013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/29/2021] [Accepted: 02/17/2021] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Human milk contains a diverse community of bacteria that are modified by maternal factors, but whether these or other factors are similar in developing countries has not been explored. Our objective was to determine whether the milk microbiota was modified by maternal age, BMI, parity, lactation stage, subclinical mastitis (SCM), and breastfeeding practices in the first 6 mo of lactation in an indigenous population from Guatemala. METHODS For this cross-sectional study, Mam-Mayan indigenous mothers nursing infants aged <6 mo were recruited. Unilateral human milk samples were collected (n = 86) and processed for 16S rRNA sequencing at the genus level. Microbial diversity and relative abundance were compared with maternal factors [age, BMI, parity, stage of lactation, SCM, and 3 breastfeeding practices (exclusive, predominant, mixed)] obtained through questionnaires. RESULTS Streptococcus was the most abundant genus (33.8%), followed by Pseudomonas (18.7%) and Sphingobium (10.7%) but relative abundance was associated with maternal factors. First, Lactobacillus and Streptococcus were more abundant in early lactation whereas the common oral (Leptotrichia) and environmental (Comamonas) bacteria were more abundant in established lactation. Second, Streptococcus,Lactobacillus,Lactococcus,Leuconostoc, and Micrococcus had a higher abundance in multiparous mothers compared with primiparous mothers. Third, a more diverse microbiota characterized by a higher abundance of lactic acid bacteria (Lactobacillus,Leuconostoc, and Lactococcus), Leucobacter, and Micrococcus was found in mothers with a healthy BMI. Finally, distinct microbial communities differed by stage of lactation and by exclusive, predominant, or mixed breastfeeding practices. CONCLUSION Milk bacterial communities in an indigenous community were associated with maternal factors. Higher microbial diversity was supported by having a healthy BMI, the absence of SCM, and by breastfeeding. Interestingly, breastfeeding practices when assessed by lactation stage were associated with distinct microbiota profiles.
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Affiliation(s)
- Lilian Lopez Leyva
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics (C3G), Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
- Microbiome Research Platform, McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montréal, QC, Canada
| | - Chen Li
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Tamara Ajeeb
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Noel W Solomons
- Center for Studies of Sensory Impairment, Aging and Metabolism (CeSSIAM), Guatemala City, Guatemala
| | - Luis B Agellon
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Marilyn E Scott
- Institute of Parasitology, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Kristine G Koski
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, QC, Canada
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Yang CY, Li SW, Chin CY, Hsu CW, Lee CC, Yeh YM, Wu KA. Association of exacerbation phenotype with the sputum microbiome in chronic obstructive pulmonary disease patients during the clinically stable state. J Transl Med 2021; 19:121. [PMID: 33757530 PMCID: PMC7988976 DOI: 10.1186/s12967-021-02788-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 03/15/2021] [Indexed: 01/04/2023] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a progressive, life-threatening lung disease with increasing prevalence and incidence worldwide. Increasing evidence suggests that lung microbiomes might play a physiological role in acute exacerbations of COPD. The objective of this study was to characterize the association of the microbiota and exacerbation risk or airflow limitation in stable COPD patients. Methods The sputum microbiota from 78 COPD outpatients during periods of clinical stability was investigated using 16S rRNA V3-V4 amplicon sequencing. The microbiome profiles were compared between patients with different risks of exacerbation, i.e., the low risk exacerbator (LRE) or high risk exacerbator (HRE) groups, and with different airflow limitation severity, i.e., mild to moderate (FEV1 ≥ 50; PFT I) or severe to very severe (FEV1 < 50; PFT II). Results The bacterial diversity (Chao1 and observed OTUs) was significantly decreased in the HRE group compared to that in the LRE group. The top 3 dominant phyla in sputum were Firmicutes, Actinobacteria, and Proteobacteria, which were similar in the HRE and LRE groups. At the genus level, compared to that in the LRE group (41.24%), the proportion of Streptococcus was slightly decreased in the HRE group (28.68%) (p = 0.007). However, the bacterial diversity and the proportion of dominant bacteria at the phylum and genus levels were similar between the PFT I and PFT II groups. Furthermore, the relative abundances of Gemella morbillorum, Prevotella histicola, and Streptococcus gordonii were decreased in the HRE group compared to those in the LRE group according to linear discriminant analysis effect size (LEfSe). Microbiome network analysis suggested altered bacterial cooperative regulation in different exacerbation phenotypes. The proportions of Proteobacteria and Neisseria were negatively correlated with the FEV1/FVC value. According to functional prediction of sputum bacterial communities through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis, genes involved in lipopolysaccharide biosynthesis and energy metabolism were enriched in the HRE group. Conclusion The present study revealed that the sputum microbiome changed in COPD patients with different risks of exacerbation. Additionally, the bacterial cooperative networks were altered in the HRE patients and may contribute to disease exacerbation. Our results provide evidence that sputum microbiome community dysbiosis is associated with different COPD phenotypes, and we hope that by understanding the lung microbiome, a potentially modifiable clinical factor, further targets for improved COPD therapies during the clinically stable state may be elucidated. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02788-4.
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Affiliation(s)
- Chia-Yu Yang
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Yin Chin
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Wei Hsu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Ching Lee
- Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Kuo-An Wu
- Department of Internal Medicine, Taoyuan Armed Forces General Hospital, No. 168, Zhongxing Rd., Longtan District, Taoyuan, 32551, Taiwan (R.O.C.). .,School of Medicine, Fu Jen Catholic University, New Taipei City, 24205, Taiwan.
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Pacífico C, Petri RM, Ricci S, Mickdam E, Wetzels SU, Neubauer V, Zebeli Q. Unveiling the Bovine Epimural Microbiota Composition and Putative Function. Microorganisms 2021; 9:microorganisms9020342. [PMID: 33572291 PMCID: PMC7915655 DOI: 10.3390/microorganisms9020342] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 01/31/2023] Open
Abstract
Numerous studies have used the 16S rRNA gene target in an attempt to characterize the structure and composition of the epimural microbiota in cattle. However, comparisons between studies are challenging, as the results show large variations associated with experimental protocols and bioinformatics methodologies. Here, we present a meta-analysis of the rumen epimural microbiota from 11 publicly available amplicon studies to assess key technical and biological sources of variation between experiments. Using the QIIME2 pipeline, 332 rumen epithelial microbiota samples were analyzed to investigate community structure, composition, and functional potential. Despite having a significant impact on microbial abundance, country of origin, farm, hypervariable region, primer set, animal variability, and biopsy location did not obscure the identification of a core microbiota. The bacterial genera Campylobacter, Christensenellaceae R-7 group, Defluviitaleaceae UCG-011, Lachnospiraceae UCG-010, Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-014, Succiniclasticum, Desulfobulbus, and Comamonas spp. were found in nearly all epithelium samples (>90%). Predictive analysis (PICRUSt) was used to assess the potential functions of the epithelial microbiota. Regularized canonical correlation analysis identified several pathways associated with the biosynthesis of precursor metabolites in Campylobacter, Comamonas, Desulfobulbus, and Ruminococcaceae NK4A214, highlighting key metabolic functions of these microbes within the epithelium.
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Affiliation(s)
- Cátia Pacífico
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria; (S.R.); (Q.Z.)
- Correspondence:
| | - Renée Maxine Petri
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M1Z7, Canada;
| | - Sara Ricci
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria; (S.R.); (Q.Z.)
| | - Elsayed Mickdam
- Nutrition and Clinical Nutrition Department, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt;
| | - Stefanie Urimare Wetzels
- Unit for Food Microbiology, Department for Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria; (S.U.W.); (V.N.)
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, 3430 Tulln, Austria
| | - Viktoria Neubauer
- Unit for Food Microbiology, Department for Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria; (S.U.W.); (V.N.)
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, 3430 Tulln, Austria
| | - Qendrim Zebeli
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria; (S.R.); (Q.Z.)
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75
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Lee JY, Jacob KM, Kashefi K, Reguera G. Oral seeding and niche-adaptation of middle ear biofilms in health. Biofilm 2021; 3:100041. [PMID: 33665609 PMCID: PMC7822943 DOI: 10.1016/j.bioflm.2020.100041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
The entrenched dogma of a sterile middle ear mucosa in health is incongruent with its periodic aeration and seeding with saliva aerosols. To test this, we sequenced 16S rRNA-V4 amplicons from otic secretions collected at the nasopharyngeal orifice of the tympanic tube and, as controls, oropharyngeal and buccal samples. The otic samples harbored a rich diversity of oral keystone genera and similar functional traits but were enriched in anaerobic genera in the Bacteroidetes (Prevotella and Alloprevotella), Fusobacteria (Fusobacterium and Leptotrichia) and Firmicutes (Veillonella) phyla. Facultative anaerobes in the Streptococcus genus were also abundant in the otic and oral samples but corresponded to distinct, and sometimes novel, cultivars, consistent with the ecological diversification of the oral migrants once in the middle ear microenvironment. Neutral community models also predicted a large contribution of oral dispersal to the otic communities and the positive selection of taxa better adapted to growth and reproduction under limited aeration. These results challenge the traditional view of a sterile middle ear in health and highlight hitherto unknown roles for oral dispersal and episodic ventilation in seeding and diversifying otic biofilms. The middle ear mucosa harbors a rich bacterial community in health. Oral migration is the primary mechanism for seeding otic biofilms. Periodic aeration of the middle ear enriches for anaerobic taxa and promotes the ecological diversification of oral migrants. Our study challenges the entrenched dogma of a sterile middle ear in health.
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Affiliation(s)
- Joo-Young Lee
- Department of Microbiology and Molecular Genetics, Michigan State University, MI, USA
| | - Kristin M Jacob
- Department of Microbiology and Molecular Genetics, Michigan State University, MI, USA
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, MI, USA
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, MI, USA
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76
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Kahler CM. Neisseria species and their complicated relationships with human health. MICROBIOLOGY AUSTRALIA 2021. [DOI: 10.1071/ma21024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Neisseria spp. are a transient low abundance member of the human microbiome. This species contains the very well described pathogens, Neisseria gonorrhoeae and N. meningitidis. Recent advances in molecular typing have revealed that this genus is more diverse than previously thought and that commensal species may have important roles in inhibiting the growth the pathogens. This short review summates these new findings and examines the evidence that the relatively under-reported Neisseria commensal species maybe beneficial to human health.
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77
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Aho EL, Ogle JM, Finck AM. The Human Microbiome as a Focus of Antibiotic Discovery: Neisseria mucosa Displays Activity Against Neisseria gonorrhoeae. Front Microbiol 2020; 11:577762. [PMID: 33343520 PMCID: PMC7744932 DOI: 10.3389/fmicb.2020.577762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023] Open
Abstract
Neisseria gonorrhoeae infections are a serious global health problem. This organism has developed disturbing levels of antibiotic resistance, resulting in the need for new approaches to prevent and treat gonorrhea. The genus Neisseria also includes several members of the human microbiome that live in close association with an array of microbial partners in a variety of niches. We designed an undergraduate antibiotic discovery project to examine a panel of nonpathogenic Neisseria species for their ability to produce antimicrobial secondary metabolites. Five strains belonging to the N. mucosa species group displayed activity against other Neisseria in delayed antagonism assays; three of these were active against N. gonorrhoeae. The antimicrobial compound secreted by N. mucosa NRL 9300 remained active in the presence of catalase, trypsin, and HEPES buffer, and effectively inhibited a DNA uptake mutant of N. gonorrhoeae. Antimicrobial activity was also retained in an ethyl acetate extract of plate grown N. mucosa NRL 9300. These data suggest N. mucosa produces an antimicrobial secondary metabolite that is distinct from previously described antigonococcal agents. This work also serves as a demonstration project that could easily be adapted to studying other members of the human microbiome in undergraduate settings. We offer the perspective that both introductory and more advanced course-based and apprentice-style antibiotic discovery projects focused on the microbiome have the potential to enrich undergraduate curricula and we describe transferrable techniques and strategies to facilitate project design.
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Affiliation(s)
- Ellen L Aho
- Department of Biology, Concordia College, Moorhead, MN, United States
| | - Jenie M Ogle
- Department of Biology, Concordia College, Moorhead, MN, United States
| | - Anna M Finck
- Department of Biology, Concordia College, Moorhead, MN, United States
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78
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Characterization of Oral Microbiome and Exploration of Potential Biomarkers in Patients with Pancreatic Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4712498. [PMID: 33204698 PMCID: PMC7652608 DOI: 10.1155/2020/4712498] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/08/2020] [Accepted: 09/29/2020] [Indexed: 02/08/2023]
Abstract
Pancreatic cancer (PC) is highly malignant and lacks an effective therapeutic schedule, hence that early diagnosis is of great importance to achieve a good prognosis. Oral bacteria have been proved to be associated with pancreatic cancer, but the specific mechanism has not been comprehensively illustrated. In our study, thirty-seven saliva samples in total were collected with ten from PC patients, seventeen from benign pancreatic disease (BPD) patients, and ten from healthy controls (HC). The oral bacterial community of HC, PC, and BPD groups was profiled by 16S rDNA high-throughput sequencing and bioinformatic methods. As shown by Simpson, Inverse Simpson, Shannon and Heip, oral microbiome diversity of HC, BPD and PC groups is in increasing order with the BPD and PC groups significantly higher than the HC group. Principal coordinate analysis (PCoA) suggested that grouping by PC, BPD and HC was statistically significant. The linear discriminant analysis effect size (LEfSe) identified high concentrations of Fusobacterium periodonticum and low concentrations of Neisseria mucosa as specific risk factors for PC. Furthermore, predicted functions showed changes such as RNA processing and modification as well as the pathway of NOD-like receptor signaling occurred in both PC and HC groups. Conclusively, our findings have confirmed the destruction of oral bacterial community balance among patients with PC and BPD and indicated the potential of Fusobacterium periodonticum and Neisseria mucosa as diagnostic biomarkers of PC.
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79
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Li S, Yang Z, Hu D, Cao L, He Q. Understanding building-occupant-microbiome interactions toward healthy built environments: A review. FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING 2020; 15:65. [PMID: 33145119 PMCID: PMC7596174 DOI: 10.1007/s11783-020-1357-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/30/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Built environments, occupants, and microbiomes constitute a system of ecosystems with extensive interactions that impact one another. Understanding the interactions between these systems is essential to develop strategies for effective management of the built environment and its inhabitants to enhance public health and well-being. Numerous studies have been conducted to characterize the microbiomes of the built environment. This review summarizes current progress in understanding the interactions between attributes of built environments and occupant behaviors that shape the structure and dynamics of indoor microbial communities. In addition, this review also discusses the challenges and future research needs in the field of microbiomes of the built environment that necessitate research beyond the basic characterization of microbiomes in order to gain an understanding of the causal mechanisms between the built environment, occupants, and microbiomes, which will provide a knowledge base for the development of transformative intervention strategies toward healthy built environments. The pressing need to control the transmission of SARS-CoV-2 in indoor environments highlights the urgency and significance of understanding the complex interactions between the built environment, occupants, and microbiomes, which is the focus of this review.
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Affiliation(s)
- Shuai Li
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Zhiyao Yang
- Lyles School of Civil Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - Da Hu
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Liu Cao
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Institute for a Secure & Sustainable Environment, University of Tennessee, Knoxville, TN 37996 USA
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80
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Banerji R, Kanojiya P, Patil A, Saroj SD. Polyamines in the virulence of bacterial pathogens of respiratory tract. Mol Oral Microbiol 2020; 36:1-11. [PMID: 32979241 DOI: 10.1111/omi.12315] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/24/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022]
Abstract
Polyamines are positively charged hydrocarbons that are essential for the growth and cellular maintenance in prokaryotes and eukaryotes. Polyamines have been demonstrated to play a role in bacterial pathogenicity and biofilm formation. However, the role of extracellular polyamines as a signaling molecule in the regulation of virulence is not investigated in detail. The bacterial pathogens residing in the respiratory tract remain asymptomatic for an extended period; however, the factors that lead to symptomatic behavior are poorly understood. Further investigation to understand the relation between the host-secreted factors and virulence of pathogenic bacteria in the respiratory tract may provide insights into the pathogenesis of respiratory tract infections. Polyamines produced within the bacterial cell are generally sequestered. Therefore, the pool of extracellular polyamines formed by secretion of the commensals and the host may be one of the signaling molecules that might contribute toward the alterations in the expression of virulence factors in bacterial pathogens. Besides, convergent mechanisms of polyamine biosynthesis do exist across the border of species and genus level. Also, several novel polyamine transporters in the host and bacteria remain yet to be identified. The review focuses on the role of polyamines in the expression of virulence phenotypes and biofilm formation of the respiratory tract pathogens.
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Affiliation(s)
- Rajashri Banerji
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Poonam Kanojiya
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Amrita Patil
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Sunil D Saroj
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
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81
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Wang N, Anonsen JH, Hadjineophytou C, Reinar WB, Børud B, Vik Å, Koomey M. Allelic polymorphisms in a glycosyltransferase gene shape glycan repertoire in the O-linked protein glycosylation system of Neisseria. Glycobiology 2020; 31:477-491. [PMID: 32776107 PMCID: PMC8091471 DOI: 10.1093/glycob/cwaa073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/11/2022] Open
Abstract
Glycosylation of multiple proteins via O-linkage is well documented in bacterial species of Neisseria of import to human disease. Recent studies of protein glycosylation (pgl) gene distribution established that related protein glycosylation systems occur throughout the genus including nonpathogenic species. However, there are inconsistencies between pgl gene status and observed glycan structures. One of these relates to the widespread distribution of pglG, encoding a glycosyltransferase that in Neisseria elongata subsp. glycolytica is responsible for the addition of di-N-acetyl glucuronic acid at the third position of a tetrasaccharide. Despite pglG residing in strains of N. gonorrhoeae, N. meningitidis and N. lactamica, no glycan structures have been correlated with its presence in these backgrounds. Moreover, PglG function in N. elongata subsp. glycolytica minimally requires UDP-glucuronic acid (GlcNAcA), and yet N. gonorrhoeae, N. meningitidis and N. lactamica lack pglJ, the gene whose product is essential for UDP-GlcNAcA synthesis. We examined the functionality of pglG alleles from species spanning the Neisseria genus by genetic complementation in N. elongata subsp. glycolytica. The results indicate that select pglG alleles from N. meningitidis and N. lactamica are associated with incorporation of an N-acetyl-hexosamine at the third position and reveal the potential for an expanded glycan repertoire in those species. Similar experiments using pglG from N. gonorrhoeae failed to find any evidence of function suggesting that those alleles are missense pseudogenes. Taken together, the results are emblematic of how allelic polymorphisms can shape bacterial glycosyltransferase function and demonstrate that such alterations may be constrained to distinct phylogenetic lineages.
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Affiliation(s)
- Nelson Wang
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, 0371 Oslo, Norway.,Department of Biosciences, Centre for Integrative Microbial Evolution, University of Oslo, 0371 Oslo, Norway
| | - Jan Haug Anonsen
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, 0371 Oslo, Norway.,Norwegian Research Centre AS, 4072 Randaberg, Norway
| | - Chris Hadjineophytou
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, 0371 Oslo, Norway.,Department of Biosciences, Centre for Integrative Microbial Evolution, University of Oslo, 0371 Oslo, Norway
| | - William Brynildsen Reinar
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 1066 Oslo, Norway
| | - Bente Børud
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, 0403 Oslo, Norway
| | - Åshild Vik
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, 0371 Oslo, Norway.,Research Council of Norway, 0283 Oslo, Norway
| | - Michael Koomey
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, 0371 Oslo, Norway.,Department of Biosciences, Centre for Integrative Microbial Evolution, University of Oslo, 0371 Oslo, Norway.,Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 1066 Oslo, Norway
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82
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A case of infective endocarditis caused by "Neisseria skkuensis". J Infect Chemother 2020; 27:83-85. [PMID: 32861578 DOI: 10.1016/j.jiac.2020.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/12/2020] [Accepted: 08/15/2020] [Indexed: 11/20/2022]
Abstract
"Neisseria skkuensis" is a gram-negative coccus that is endemic in the human oral cavity, with only few reports of infection in humans. Herein, we report a case of a male patient in his sixties presenting with infective endocarditis (IE) caused by "N. skkuensis". To our knowledge, this is the second case of IE confirmed using 16S rRNA gene to have been caused by "N. skkuensis". The accurate diagnosis of rare or difficult-to-identify pathogens is a major challenge for clinical microbiological laboratories. Although Neisseria spp. are common in the oral cavity and are often seen in routine tests, identification of their biochemical properties and mass spectrometric analysis are difficult. In this case report, we describe the accurate identification of "N. skkuensis" by 16S rRNA gene sequencing analysis compared to other identification methods. Further cases of "N. skkuensis" are needed to fully evaluate the clinical approach of this detection method.
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83
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Takei H, Takeuchi N, Hoshino T, Ohkusu M, Segawa S, Murata S, Ishiwada N. Bacteriological analysis of Neisseria lactamica isolated from the respiratory tract in Japanese children. J Infect Chemother 2020; 27:65-69. [PMID: 32873462 DOI: 10.1016/j.jiac.2020.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/07/2020] [Accepted: 08/14/2020] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Neisseria lactamica is a commensal bacterium of the upper respiratory tract in humans and is closely related to Neisseria meningitidis. N. lactamica colonization may contribute to preventing N. meningitidis colonization and invasive meningococcal disease. However, the transference of antimicrobial resistance genes from N. lactamica to N. meningitidis has been reported. METHODS In this study, we aimed to identify N. lactamica using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and performed multilocus sequence typing of seven N. lactamica strains isolated from Japanese children. We also analyzed the antimicrobial susceptibility of these strains and the mutations in their antimicrobial resistance genes (penA, gyrA, and parC). RESULTS All the N. lactamica strains could be identified using MALDI-TOF MS. All strains were of different sequence types (STs), including five new STs. Five strains had intermediate susceptibility, two were resistant to ampicillin, and all had five out of the five known PBP2 mutations. Six strains were resistant to levofloxacin. Among the quinolone-resistant strains, three had GyrA mutations, and three had both ParC and GyrA mutations. CONCLUSIONS N. lactamica STs may vary in Japanese children, and penicillin- and quinolone-resistant strains may be prevalent. We should pay attention not only to the drug resistance of N. meningitidis but also to the drug susceptibility of N. lactamica whose drug-resistance genes may transfer to N. meningitidis.
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Affiliation(s)
- Haruka Takei
- Department of Infectious, Immune and Allergic Diseases, Saitama Children's Medical Center, Japan; Department of Pediatrics, Chiba University Graduate School of Medicine, Japan
| | - Noriko Takeuchi
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Japan.
| | - Tadashi Hoshino
- Division of Infectious Diseases, Chiba Children's Hospital, Japan
| | - Misako Ohkusu
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Japan
| | - Shunsuke Segawa
- Division of Clinical Laboratory, Chiba University Hospital, Japan
| | - Shota Murata
- Division of Clinical Laboratory, Chiba University Hospital, Japan
| | - Naruhiko Ishiwada
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Japan
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84
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Calder A, Menkiti CJ, Çağdaş A, Lisboa Santos J, Streich R, Wong A, Avini AH, Bojang E, Yogamanoharan K, Sivanesan N, Ali B, Ashrafi M, Issa A, Kaur T, Latif A, Mohamed HAS, Maqsood A, Tamang L, Swager E, Stringer AJ, Snyder LAS. Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire. Microb Genom 2020; 6. [PMID: 32845827 PMCID: PMC7643975 DOI: 10.1099/mgen.0.000423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Commensal non-pathogenic Neisseria spp. live within the human host alongside the pathogenic Neisseria meningitidis and Neisseria gonorrhoeae and due to natural competence, horizontal gene transfer within the genus is possible and has been observed. Four distinct Neisseria spp. isolates taken from the throats of two human volunteers have been assessed here using a combination of microbiological and bioinformatics techniques. Three of the isolates have been identified as Neisseria subflava biovar perflava and one as Neisseria cinerea. Specific gene clusters have been identified within these commensal isolate genome sequences that are believed to encode a Type VI Secretion System, a newly identified CRISPR system, a Type IV Secretion System unlike that in other Neisseria spp., a hemin transporter, and a haem acquisition and utilization system. This investigation is the first to investigate these systems in either the non-pathogenic or pathogenic Neisseria spp. In addition, the N. subflava biovar perflava possess previously unreported capsule loci and sequences have been identified in all four isolates that are similar to genes seen within the pathogens that are associated with virulence. These data from the four commensal isolates provide further evidence for a Neisseria spp. gene pool and highlight the presence of systems within the commensals with functions still to be explored.
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Affiliation(s)
- Alan Calder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Chukwuma Jude Menkiti
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Aylin Çağdaş
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Jefferson Lisboa Santos
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Ricarda Streich
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Alice Wong
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Amir H Avini
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Ebrima Bojang
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Karththeepan Yogamanoharan
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Nivetha Sivanesan
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Besma Ali
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Mariam Ashrafi
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Abdirizak Issa
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Tajinder Kaur
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Aisha Latif
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Hani A Sheik Mohamed
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Atifa Maqsood
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Laxmi Tamang
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Emily Swager
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Alex J Stringer
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Lori A S Snyder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
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85
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Microbiota composition in bilateral healthy breast tissue and breast tumors. Cancer Causes Control 2020; 31:1027-1038. [PMID: 32844256 DOI: 10.1007/s10552-020-01338-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 08/13/2020] [Indexed: 12/15/2022]
Abstract
PURPOSE Previous reports suggest that a complex microbiome exists within the female human breast that might contribute to breast cancer etiology. The purpose of this pilot study was to assess the variation in microbiota composition by breast side (left versus right) within individual women and compare the microbiota of normal and breast tumor tissue between women. We aimed to determine whether microbiota composition differs between these groups and whether certain bacterial taxa may be associated with breast tumors. METHODS Bilateral normal breast tissue samples (n = 36) were collected from ten women who received routine mammoplasty procedures. Archived breast tumor samples (n = 10) were obtained from a biorepository. DNA was extracted, amplified, and sequenced. Microbiota data were analyzed using QIIME and RStudio. RESULTS The most abundant phyla in both tumor and normal tissues were Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. There were statistically significant differences in the relative abundance of various bacterial taxa between groups. Alpha diversity (Simpson's index) was significantly higher in normal compared to tumor samples (0.968 vs. 0.957, p = 0.022). Based on unweighted UniFrac measures, breast tumor samples clustered distinctly from normal samples (R2 = 0.130; p = 0.01). Microbiota composition in normal samples clustered within women (R2 = 0.394; p = 0.01) and by breast side (left or right) within a woman (R2 = 0.189; p = 0.03). CONCLUSION Significant differences in diversity between tumor and normal tissue and in composition between women and between breasts of the same woman were identified. These results warrant further research to investigate the relationship between microbiota and breast cancer.
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Radaic A, Ye C, Parks B, Gao L, Kuraji R, Malone E, Kamarajan P, Zhan L, Kapila YL. Modulation of pathogenic oral biofilms towards health with nisin probiotic. J Oral Microbiol 2020; 12:1809302. [PMID: 32944159 PMCID: PMC7482728 DOI: 10.1080/20002297.2020.1809302] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Background Oral dysbiosis is an imbalance in the oral microbiome and is associated with a variety of oral and systemic diseases, including periodontal disease, caries, and head and neck/oral cancer. Although antibiotics can be used to control this dysbiosis, they can lead to adverse side effects and superinfections. Thus, novel strategies have been proposed to address these shortcomings. One strategy is the use of probiotics as antimicrobial agents, since they are considered safe for humans and the environment. Specifically, the Gram-positive Lactococcus lactis, a species present in the oral and gut microbiota, is able to produce nisin, which has been used worldwide for food preservation. Objective The objective of this study was to test whether a nisin probiotic can promote a healthier oral microbiome in pathogen-spiked oral biofilms. Results We found that L. lactis can prevent oral biofilm formation and disrupt 24-h and 48-h pre-formed biofilms. Finally, we demonstrate that both treatments, a nisin-producing L. lactis probiotic and nisin can decrease the levels of pathogens in the biofilms and return the diversity levels back to control or ‘healthy’ levels. Conclusion A nisin-producing probiotic, can be used to treat ‘disease-altered’ biofilms and promote healthier oral biofilms, which may be useful for improving patient oral health.
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Affiliation(s)
- Allan Radaic
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, CA, USA
| | - Changchang Ye
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, CA, USA.,State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Periodontology, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Brett Parks
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, CA, USA
| | - Li Gao
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, CA, USA.,Department of Periodontology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Ryutaro Kuraji
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, CA, USA.,Department of Life Science Dentistry, The Nippon Dental University, Tokyo, Japan.,Department of Periodontology, The Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan
| | - Erin Malone
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, CA, USA
| | - Pachiyappan Kamarajan
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, CA, USA
| | - Ling Zhan
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, CA, USA
| | - Yvonne L Kapila
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, CA, USA
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Onyango SO, De Clercq N, Beerens K, Van Camp J, Desmet T, Van de Wiele T. Oral Microbiota Display Profound Differential Metabolic Kinetics and Community Shifts upon Incubation with Sucrose, Trehalose, Kojibiose, and Xylitol. Appl Environ Microbiol 2020; 86:e01170-20. [PMID: 32561577 PMCID: PMC7414948 DOI: 10.1128/aem.01170-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/05/2020] [Indexed: 01/19/2023] Open
Abstract
This study compares the metabolic properties of kojibiose, trehalose, sucrose, and xylitol upon incubation with representative oral bacteria as monocultures or synthetic communities or with human salivary bacteria in a defined medium. Compared to sucrose and trehalose, kojibiose resisted metabolism during a 48-h incubation with monocultures, except for Actinomyces viscosus Incubations with Lactobacillus-based communities, as well as salivary bacteria, displayed kojibiose metabolism, yet to a lesser extent than sucrose and trehalose. Concurring with our in vitro findings, screening for carbohydrate-active enzymes revealed that only Lactobacillus spp. and A. viscosus possess enzymes from glycohydrolase (GH) families GH65 and GH15, respectively, which are associated with kojibiose metabolism. Donor-dependent differences in salivary microbiome composition were noted, and differences in pH drop during incubation indicated different rates of sugar metabolism. However, functional analysis indicated that lactate, acetate, and formate evenly dominated the metabolic profile for all sugars except for xylitol. 16S rRNA gene sequencing analysis and α-diversity markers revealed that a significant shift of the microbiome community by sugars was more pronounced in sucrose and trehalose than in kojibiose and xylitol. In Streptococcus spp., a taxon linked to cariogenesis dominated in sucrose (mean ± standard deviation, 91.8 ± 6.4%) and trehalose (55.9 ± 38.6%), representing a high diversity loss. In contrast, Streptococcus (5.1 ± 3.7%) was less abundant in kojibiose, which instead was dominated by Veillonella (26.8 ± 19.6%), while for xylitol, Neisseria (29.4 ± 19.1%) was most abundant. Overall, kojibiose and xylitol incubations stimulated cariogenic species less yet closely maintained an abundance of key phyla and genera of the salivary microbiome, suggesting that kojibiose has low cariogenic properties.IMPORTANCE This study provides a detailed scientific insight on the metabolism of a rare disaccharide, kojibiose, whose mass production has recently been made possible. While the resistance of kojibiose was established with monocultures, delayed utilization of kojibiose was observed with communities containing lactobacilli and A. viscosus as well as with complex communities of bacteria from human saliva. Kojibiose is, therefore, less metabolizable than sucrose and trehalose. Moreover, although conventional sugars cause distinct shifts in salivary microbial communities, our study has revealed that kojibiose is able to closely maintain the salivary microbiome composition, suggesting its low cariogenic properties. This study furthermore underscores the importance and relevance of microbial culture and ex vivo mixed cultures to study cariogenicity and substrate utilization; this is in sharp contrast with tests that solely rely on monocultures such as Streptococcus mutans, which clearly fail to capture complex interactions between oral microbiota.
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Affiliation(s)
- Stanley O Onyango
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - Nele De Clercq
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - Koen Beerens
- Center for Synthetic Biology, Department of Biochemical and Microbial Technology, Ghent University, Ghent, Belgium
| | - John Van Camp
- Laboratory of Nutrition and Food Chemistry, Ghent University, Ghent, Belgium
| | - Tom Desmet
- Center for Synthetic Biology, Department of Biochemical and Microbial Technology, Ghent University, Ghent, Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
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Bacterial Composition, Community Structure, and Diversity in Apis nigrocincta Gut. Int J Microbiol 2020; 2020:6906921. [PMID: 32802072 PMCID: PMC7414324 DOI: 10.1155/2020/6906921] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 07/08/2020] [Indexed: 02/06/2023] Open
Abstract
Understanding the honeybee gut bacteria is an essential aspect as honeybees are the primary pollinators of many crops. In this study, the honeybee-associated gut bacteria were investigated by targeting the V3-V4 region of 16S rRNA genes using the Illumina MiSeq. The adult worker was captured in an urban area in a dense settlement. In total, 83,018 reads were obtained, revealing six phyla from 749 bacterial operational taxonomic units (OTUs). The gut was dominated by Proteobacteria (58% of the total reads, including Enterobacteriaceae 28.2%, Erwinia 6.43%, and Klebsiella 4.90%), Firmicutes (29% of the total reads, including Lactococcus garvieae 13.45%, Lactobacillus spp. 8.19%, and Enterococcus spp. 4.47%), and Actinobacteria (8% of the total reads, including Bifidobacterium spp. 7.96%). Many of these bacteria belong to the group of lactic acid bacteria (LAB), which was claimed to be composed of beneficial bacteria involved in maintaining a healthy host. The honeybee was identified as Apis nigrocincta based on an identity BLAST search of its COI region. This study is the first report on the gut microbial community structure and composition of A. nigrocincta from Indonesia.
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Abstract
PURPOSE OF REVIEW Nonpathogenic commensal Neisseria are rarely considered in the clinical setting despite evidence that they can cause invasive opportunistic infections. In contrast, they may offer protection against pathogenic Neisseria, and such relationships are being actively explored in experimental studies. RECENT FINDINGS Recent case reports are presented of invasive infection caused by nonpathogenic Neisseria in patients on novel biologic therapies. On the other hand, Neisseria lactamica, a nonpathogenic commensal, has been shown in human challenge studies to inhibit colonization by Neisseria meningitidis. Experimental mouse models have also explored the inhibitory effects of nonpathogenic Neisseria on Neisseria gonnhoreae infection. Cutting-edge advances in metagenomics and microbiomics are being used to understand the mechanisms underpinning these effects. SUMMARY Clinicians should have increased awareness of nonpathogenic Neisseria. First, as new immunomodulating therapies become licenced, the interactions that maintain balance between commensals and their human hosts may be altered. Second, these bacteria are showing promise in their capacity to exclude pathogenic Neisseria species from their anatomical niches.
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Thapa E, Knauss HM, Colvin BA, Fischer BA, Weyand NJ. Persistence Dynamics of Antimicrobial-Resistant Neisseria in the Pharynx of Rhesus Macaques. Antimicrob Agents Chemother 2020; 64:e02232-19. [PMID: 32423958 PMCID: PMC7526842 DOI: 10.1128/aac.02232-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/13/2020] [Indexed: 11/20/2022] Open
Abstract
Pharyngeal infections by Neisseria gonorrhoeae are often asymptomatic, making them difficult to treat. However, in vivo animal modeling of human pharyngeal infections by pathogenic Neisseria species is challenging due to numerous host tropism barriers. We have relied on rhesus macaques to investigate pharyngeal persistence of naturally occurring Neisseria species in response to antibiotics. These species include Neisseria mucosa, Neisseria oralis, and a species unique to macaques. Four animals previously treated intramuscularly with the fluoroquinolone enrofloxacin for 2 weeks were monitored for persistence of their preexisting Neisseria populations for a period of 10 weeks. Enrofloxacin exposure did not eliminate preexisting flora from two of the four animals. Characterization of a collection of macaque Neisseria isolates supported the hypothesis that pharyngeal persistence was linked to reduced enrofloxacin susceptibility conferred by mutations in either gyrA or parC Interestingly, we observed a change in neisserial population dynamics for several weeks following enrofloxacin exposure. Enrofloxacin appeared to promote competition between strains for dominance in the pharyngeal niche. Specifically, following enrofloxacin treatment, strains bearing single gyrA mutations and low MICs persisted long-term. In contrast, strains with both gyrA and parC mutations and high MICs became culturally undetectable, consistent with the hypothesis that they were less fit. Our study has provided insight into pharyngeal persistence dynamics of Neisseria species bearing fluoroquinolone resistance determinants. The rhesus macaque provides a valuable host animal that may be used in the future to simulate treatment failures associated with the presence of antimicrobial-resistant Neisseria spp. in the human pharynx.
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Affiliation(s)
- Eliza Thapa
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Hanna M Knauss
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Benjamin A Colvin
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | | | - Nathan J Weyand
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
- The Infectious and Tropical Disease Institute, Ohio University, Athens, Ohio, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, Ohio, USA
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91
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Characteristics of Neisseria Species Colonized in the Human’s Nasopharynx. Jundishapur J Microbiol 2020. [DOI: 10.5812/jjm.99915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Context: Neisseria meningitidis is the causative agent of a life-threatening infection with high mortality and morbidity worldwide. The most common types of this bacterium are serogroups A, B, C, W135, X, and Y. Although in some countries, such as Iran, the meningococcal meningitis has been well monitored and controlled by the use of divalent and quadrivalent vaccines, other fatal infections caused by these bacteria are still an important threat. For the above reason, this review focused on the differences of Neisseria characteristics, particularly in capsular composition, pathogenic and commensal stages to a better understanding of how to manage Neisseria infections. Evidence Acquisition: In this review, PubMed, EMBASE, ScienceDirect, Scopus, and Google Scholar were searched for English-language publications on pathogenic or commensal strains of Neisseria, meningococcal disease, Neisseria biology, genetic diversity, molecular typing, serogroups, diagnostic, and epidemiology around the world up to July 2019. All articles and academic reports in the defined area of this research were considered too. The data were extracted and descriptively discussed. Results: We included 85 studies in the survey. The data analysis revealed that the distribution of meningococcal serogroups was different regionally. For example, the serogroups C and W-135 accounted for Africa and Latin America regions, serogroup B in the European countries, and rarely in the Western Pacific, and serogroups A and C were dominant in Asian countries. Although data set for laboratory-based diagnosis of N. meningitidis are available for all countries, only 30% of the countries rely on reference laboratories for serogroup determination, and more than half of the countries lack the ability of surveillance system. Nevertheless, molecular detection procedure is also available for all countries. The use of the meningococcal vaccine is a variable country by country, but most countries have applied the meningococcal vaccine, either divalent or quadrivalent, for the protection of high-risk groups. Conclusions: Owing to the geographical distribution of N. meningitidis serogroups in circulating, each country has to monitor for changes in serogroups diversity and its control management. Furthermore, laboratories should scale up the epidemiology and disease burden. It should be mentioned that quadrivalent meningococcal vaccines reduce the meningococcal disease burden sharply.
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Next-Generation Sequencing of the Ocular Surface Microbiome: In Health, Contact Lens Wear, Diabetes, Trachoma, and Dry Eye. Eye Contact Lens 2020; 46:254-261. [DOI: 10.1097/icl.0000000000000697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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93
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Zhao P, Xu L, Zhang A, Zhu B, Shao Z. Evolutionary analysis of gyrA gene from Neisseria meningitidis bacterial strains of clonal complex 4821 collected in China between 1978 and 2016. BMC Microbiol 2020; 20:71. [PMID: 32228482 PMCID: PMC7106703 DOI: 10.1186/s12866-020-01751-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 03/12/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Neisseria meningitidis (N.meningitidis) bacteria belonging to clonal complex 4821 (CC4821) have been mainly reported in China and have been characterized by a high resistance rate to ciprofloxacin (CIP). The aim of this study was to assess the evolution of the DNA gyrase A (gyrA) gene from N.meningitidis CC4821 strains collected in China between 1978 and 2016. The complete sequence of gyrA gene from 77 strains are reported in this study and analyzed in the context of publicly available sequences from N. meningitidis of other CCs as well as other Neisseria species. RESULTS The phylogenetic analysis of CC4821 gyrA gene reveals at least 5 distinct genetic clusters. These clusters are not CC4821-specific showing that gyrA evolution is independent of CC4821 evolution. Some clusters contain sequences from other Neisseria species. Recombination within N.meningitidis strains and between Neisseria species was identified in SimPlot analysis. Finally, amino acid substitutions within GyrA protein were analyzed. Only one position, 91 (83 in E.coli gyrA gene), was linked to CIP resistance. Thirty-one additional putative resistance markers were identified, as amino acid substitutions were only found in resistant strains. CONCLUSIONS The evolution of gyrA gene of CC4821 N.meningitidis strains is not dependent on CC4821 evolution or on CIP resistance phenotype. Only amino acid 91 is linked to CIP resistance phenotype. Finally, recombination inter- and intra-species is likely to result in the acquisition of various resistance markers, 31 of them being putatively mapped in the present study. Analyzing the evolution of gyrA gene within CC4821 strains is critical to monitor the CIP resistance phenotype and the acquisition of new resistance markers. Such studies are necessary for the control of the meningococcal disease and the development of new drugs targeting DNA gyrase.
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Affiliation(s)
- Pan Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing, China
| | - Li Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing, China
| | - Aiyu Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing, China
| | - Bingqing Zhu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing, China
| | - Zhujun Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing, China.
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Infant respiratory syncytial virus prophylaxis and nasopharyngeal microbiota until 6 years of life: a subanalysis of the MAKI randomised controlled trial. THE LANCET RESPIRATORY MEDICINE 2020; 8:1022-1031. [PMID: 32203712 DOI: 10.1016/s2213-2600(19)30470-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/02/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) infection during infancy is suggested to cause long-term wheeze. In turn, wheeze has been associated with bacterial dysbiosis of the respiratory tract. We investigated the effects of RSV prophylaxis with palivizumab in otherwise healthy preterm infants on respiratory microbiota composition at 1 year and 6 years of age. METHODS In a multicentre, single-blind, randomised, placebo-controlled trial (the MAKI trial), infants born between 32-35 weeks of gestation, in one university and in 15 regional hospitals in the the Netherlands, were randomly assigned (1:1) to receive palivizumab or placebo during the RSV season of their first year of life. Intramuscular injections of palivizumab 15 mg/kg or placebo were given during one RSV season: either from Oct 1, or from discharge from the neonatal unit until March 10 (minimun of 2 and maximum of 5 injections were given). Children were 6 months old or younger at the start of the RSV season; exclusion criteria included congenital heart disease, bronchopulmonary dysplasia, Down's syndrome, or other serious congenital disorders, use of mechanical ventilation at birth, treatment with surfactant, or physician-diagnosed wheeze before the start of the RSV season. Children were followed up for clinical symptoms until 6 years of age. For this subanalysis, we obtained nasopharyngeal swabs from children aged 1 year and 6 years and analysed them using 16S-rRNA sequencing. At 6 years we also measured reversible airway obstruction. The primary outcome was the effect of palivizumab during infancy on the respiratory microbiota composition at age 1 year and 6 years (intention-to-treat analysis). The trial is registered in the ISRCTN registry, number ISRCTN73641710. FINDINGS From April 1, 2008, to Dec 31, 2010, 429 infants were enrolled in the MAKI trial (n=214 to the palivizumab group; n=215 to the placebo group). At 1 year, we collected swabs and sequenced DNA from 170 (40%) of 429 children, of which 145 (85%) samples had high-quality DNA. The overall microbiota composition was significantly different (R2 1·3%; p=0·0185) between the palivizumab group and the placebo group at 1 year of life; children in the palivizumab group had a significantly lower abundance of the Staphylococcus-dominated cluster (odds ratio 0·28 [95% CI 0·11-0·68]; p=0·00394), an increased abundance of biomarker species, such as Klebsiella, and a more diverse set of oral taxa, including Streptococcus spp, compared with children in the placebo group. At 6 years, we collected swabs and sequenced DNA from 349 (88%) of 395 children who completed follow-up, of which 342 (98%) samples had high-quality DNA. The overall microbiota composition was not significantly different between groups at 6 years (R2 0·6%; p=0·0575); however, children in the palivizumab group had a significantly increased abundance of Haemophilus spp and lower abundance of Moraxella and Neisseriaceae spp compared with children in the placebo group. Absence of PCR-confirmed RSV infection at 1 year was significantly associated with a higher abundance of Haemophilus spp at age 6 years and a significantly lower abundance of Moraxella and Neisseriaceae than children with RSV infection at 1 year. Reversible airway obstruction at 6 years was also positively associated with Haemophilus abundance and negatively associated with the abundance of health-associated taxa, such as Moraxella, Corynebacterium, Dolosigranulum, and Staphylococcus, even after correction for RSV immunoprophylaxis (all: p<0·05). Additionally, reversible airway instruction was associated with significantly higher Streptococcus pneumoniae abundance. INTERPRETATION Palivizumab in infancy in otherwise healthy preterm infants is associated with persistent effects on the abundance of specific, potentially pathogenic, microbial taxa in the respiratory tract. Several of the palivizumab-associated biomarker species were associated with reversible airway obstruction at age 6 years. These results warrant further studies to establish the long-term ecological effects and health consequences of palivizumab in infancy. FUNDING MedImmune.
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95
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Custodio R, Johnson E, Liu G, Tang CM, Exley RM. Commensal Neisseria cinerea impairs Neisseria meningitidis microcolony development and reduces pathogen colonisation of epithelial cells. PLoS Pathog 2020; 16:e1008372. [PMID: 32208456 PMCID: PMC7092958 DOI: 10.1371/journal.ppat.1008372] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/31/2020] [Indexed: 12/16/2022] Open
Abstract
It is increasingly being recognised that the interplay between commensal and pathogenic bacteria can dictate the outcome of infection. Consequently, there is a need to understand how commensals interact with their human host and influence pathogen behaviour at epithelial surfaces. Neisseria meningitidis, a leading cause of sepsis and meningitis, exclusively colonises the human nasopharynx and shares this niche with several other Neisseria species, including the commensal Neisseria cinerea. Here, we demonstrate that during adhesion to human epithelial cells N. cinerea co-localises with molecules that are also recruited by the meningococcus, and show that, similar to N. meningitidis, N. cinerea forms dynamic microcolonies on the cell surface in a Type four pilus (Tfp) dependent manner. Finally, we demonstrate that N. cinerea colocalises with N. meningitidis on the epithelial cell surface, limits the size and motility of meningococcal microcolonies, and impairs the effective colonisation of epithelial cells by the pathogen. Our data establish that commensal Neisseria can mimic and affect the behaviour of a pathogen on epithelial cell surfaces.
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Affiliation(s)
- Rafael Custodio
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Errin Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Christoph M. Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Rachel M. Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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Agany DDM, Potts R, Gonzalez Hernandez JL, Gnimpieba EZ, Pietri JE. Microbiome Differences between Human Head and Body Lice Ecotypes Revealed by 16S rRNA Gene Amplicon Sequencing. J Parasitol 2020. [DOI: 10.1645/19-132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Diing D. M. Agany
- University of South Dakota, Biomedical Engineering Program, Sioux Falls, South Dakota 57107
| | - Rashaun Potts
- University of South Dakota, Sanford School of Medicine, Division of Basic Biomedical Sciences, Vermillion, South Dakota 57069
| | | | - Etienne Z. Gnimpieba
- University of South Dakota, Biomedical Engineering Program, Sioux Falls, South Dakota 57107
| | - Jose E. Pietri
- University of South Dakota, Sanford School of Medicine, Division of Basic Biomedical Sciences, Vermillion, South Dakota 57069
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Katagiri S, Shiba T, Tohara H, Yamaguchi K, Hara K, Nakagawa K, Komatsu K, Watanabe K, Ohsugi Y, Maekawa S, Iwata T. Re-initiation of Oral Food Intake Following Enteral Nutrition Alters Oral and Gut Microbiota Communities. Front Cell Infect Microbiol 2019; 9:434. [PMID: 31956606 PMCID: PMC6951430 DOI: 10.3389/fcimb.2019.00434] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/05/2019] [Indexed: 11/22/2022] Open
Abstract
Stroke is associated with multiple forms of disability, including dysphagia. Post-stroke dysphagia increases the risks of pneumonia and mortality and often results in cessation of oral feeding. However, appropriate rehabilitation methods can eventually lead to resumption of oral food intake. This study tried to clarify that re-initiating oral food intake could modify the composition of oral/gut microbial communities in patients with dysphagia. From 78 patients with sub-acute stage of stroke, 11 complete tube feeding subjects without taking antibiotics were enrolled and received rehabilitation for re-initiation of oral food intake, and 8 subjects were brought back to complete oral feeding. Oral and gut microbiota community profiles were evaluated using 16S rRNA sequencing of the saliva and feces samples before and after re-initiation of oral food intake in patients recovering from enteral nutrition under the same nutrient condition. Standard nutrition in the hospital was 1,840 kcal, including protein = 75 g, fat = 45 g, and carbohydrates = 280 g both for tube and oral feeding subjects. Oral food intake increased oral and gut microbiome diversity and altered the composition of the microbiome. Oral and gut microbiome compositions were drastically different; however, the abundance of family Carnobacteriaceae and genus Granulicatella was increased in both the oral and gut microbiome after re-initiation of oral food intake. Although oral microbiota showed more significant changes than the gut microbiota, metagenome prediction revealed the presence of more differentially enriched pathways in the gut. In addition, simpler co-occurrence networks of oral and gut microbiomes, indicating improved dysbiosis of the microbiome, were observed during oral feeding as compared to that during tube feeding. Oral food intake affects oral and gut microbiomes in patients recovering from enteral nutrition. Rehabilitation for dysphagia can modify systemic health by increasing the diversity and altering the composition and co-occurrence network structure of oral and gut microbial communities.
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Affiliation(s)
- Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Haruka Tohara
- Gerodontology and Oral Rehabilitation, Department of Gerontology and Gerodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kohei Yamaguchi
- Gerodontology and Oral Rehabilitation, Department of Gerontology and Gerodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Koji Hara
- Gerodontology and Oral Rehabilitation, Department of Gerontology and Gerodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuharu Nakagawa
- Gerodontology and Oral Rehabilitation, Department of Gerontology and Gerodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keiji Komatsu
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuki Watanabe
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shogo Maekawa
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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Humbert MV, Christodoulides M. Atypical, Yet Not Infrequent, Infections with Neisseria Species. Pathogens 2019; 9:E10. [PMID: 31861867 PMCID: PMC7168603 DOI: 10.3390/pathogens9010010] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/24/2022] Open
Abstract
Neisseria species are extremely well-adapted to their mammalian hosts and they display unique phenotypes that account for their ability to thrive within niche-specific conditions. The closely related species N. gonorrhoeae and N. meningitidis are the only two species of the genus recognized as strict human pathogens, causing the sexually transmitted disease gonorrhea and meningitis and sepsis, respectively. Gonococci colonize the mucosal epithelium of the male urethra and female endo/ectocervix, whereas meningococci colonize the mucosal epithelium of the human nasopharynx. The pathophysiological host responses to gonococcal and meningococcal infection are distinct. However, medical evidence dating back to the early 1900s demonstrates that these two species can cross-colonize anatomical niches, with patients often presenting with clinically-indistinguishable infections. The remaining Neisseria species are not commonly associated with disease and are considered as commensals within the normal microbiota of the human and animal nasopharynx. Nonetheless, clinical case reports suggest that they can behave as opportunistic pathogens. In this review, we describe the diversity of the genus Neisseria in the clinical context and raise the attention of microbiologists and clinicians for more cautious approaches in the diagnosis and treatment of the many pathologies these species may cause.
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Affiliation(s)
- Maria Victoria Humbert
- Molecular Microbiology, School of Clinical and Experimental Sciences, University of Southampton, Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UK;
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99
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Shimuta K, Nakayama SI, Takahashi H, Ohnishi M. A Loop-Mediated Isothermal Amplification Assay Targeting Neisseria gonorrhoeae penA-60.001. Antimicrob Agents Chemother 2019; 64:e01663-19. [PMID: 31658968 PMCID: PMC7187580 DOI: 10.1128/aac.01663-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/19/2019] [Indexed: 11/20/2022] Open
Abstract
Ceftriaxone (CRO) is widely used as the first-line treatment for gonococcal infections. However, CRO-resistant Neisseria gonorrhoeae strains carrying mosaic penA-60.001 have emerged recently and disseminated worldwide. To meet the urgent need to detect these strains, we report here a loop-mediated isothermal amplification (LAMP) assay system that targets N. gonorrhoeaepenA-60.001. This assay system can differentiate N. gonorrhoeae strains carrying mosaic penA-60.001 from strains carrying other penA alleles.
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Affiliation(s)
- Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shu-Ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideyuki Takahashi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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100
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Ozga AT, Gilby I, Nockerts RS, Wilson ML, Pusey A, Stone AC. Oral microbiome diversity in chimpanzees from Gombe National Park. Sci Rep 2019; 9:17354. [PMID: 31758037 PMCID: PMC6874655 DOI: 10.1038/s41598-019-53802-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/28/2019] [Indexed: 12/27/2022] Open
Abstract
Historic calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies.
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Affiliation(s)
- Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA. .,Institute of Human Origins, Arizona State University, Tempe, Arizona, USA. .,Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida, USA.
| | - Ian Gilby
- Institute of Human Origins, Arizona State University, Tempe, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Rebecca S Nockerts
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael L Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, Minnesota, USA
| | - Anne Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.,Institute of Human Origins, Arizona State University, Tempe, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
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